title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2018-06 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Resveratrol reduces the inflammatory response in adipose tissue and improves adipose insulin signaling in high-fat diet-fed mice link: https://peerj.com/articles/5173 last-modified: 2018-06-29 description: BackgroundObesity-induced glucose metabolism disorder is associated with chronic, low-grade, systemic inflammation and is considered a risk factor for diabetes and metabolic syndrome. Resveratrol (RES), a natural anti-inflammatory compound, is observed to improve glucose tolerance and insulin sensitivity in obese rodents and humans. This study aimed to test the effects of RES administration on insulin signaling and the inflammatory response in visceral white adipose tissue (WAT) caused by a high-fat diet (HFD) in mice.MethodsA total of 40 wild-type C57BL/6 male mice were divided into four groups (10 in each group): the standard chow diet (STD) group was fed a STD; the HFD group was fed a HFD; and the HFD-RES/L and HFD-RES/H groups were fed a HFD plus RES (200 and 400 mg/kg/day, respectively). The L and H in RES/L and RES/H stand for low and high, respectively. Glucose tolerance, insulin sensitivity, circulating inflammatory biomarkers and lipid profile were determined. Quantitative PCR and Western blot were used to determine the expression of CC-chemokine receptor 2 (CCR2), other inflammation markers, glucose transporter 4 (GLUT4), insulin receptor substrate 1 (IRS-1) and pAkt/Akt and to assess targets of interest involving glucose metabolism and inflammation in visceral WAT.ResultsHFD increased the levels of total cholesterol, triglycerides, low-density lipoprotein cholesterol and proinflammatory cytokines in serum, decreased the high-density lipoprotein cholesterol level in serum, and induced insulin resistance and WAT inflammation in mice. However, RES treatment alleviated insulin resistance, increased the expressions of pAkt, GLUT4 and IRS-1 in WAT, and decreased serum proinflammatory cytokine levels, macrophage infiltration and CCR2 expression in WAT.ConclusionOur results indicated that WAT CCR2 may play a vital role in macrophage infiltration and the inflammatory response during the development of insulin resistance in HFD-induced obesity. These data suggested that administration of RES offers protection against abnormal glucose metabolism and inflammatory adaptations in visceral WAT in mice with HFD-induced obesity. creator: Shibin Ding creator: Jinjin Jiang creator: Zhe Wang creator: Guofu Zhang creator: Jianli Yin creator: Xiaoya Wang creator: Sui Wang creator: Zengli Yu uri: https://doi.org/10.7717/peerj.5173 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Ding et al. title: Impact of extreme drought and incentive programs on flooded agriculture and wetlands in California’s Central Valley link: https://peerj.com/articles/5147 last-modified: 2018-06-29 description: BackgroundBetween 2013 and 2015, a large part of the western United States, including the Central Valley of California, sustained an extreme drought. The Central Valley is recognized as a region of hemispheric importance for waterbirds, which use flooded agriculture and wetlands as habitat. Thus, the impact of drought on the distribution of surface water needed to be assessed to understand the effects on waterbird habitat availability.MethodsWe used remote sensing data to quantify the impact of the recent extreme drought on the timing and extent of waterbird habitat during the non-breeding season (July–May) by examining open water in agriculture (rice, corn, and other crops) and managed wetlands across the Central Valley. We assessed the influence of habitat incentive programs, particularly The Nature Conservancy’s BirdReturns and The Natural Resources Conservation Service’s Waterbird Habitat Enhancement Program (WHEP), at offsetting habitat loss related to drought.ResultsOverall, we found statistically significant declines in open water in post-harvest agriculture (45–80% declines) and in managed wetlands (39–60% declines) during the 2013–2015 drought compared to non-drought years during the period of 2000–2011. Crops associated with the San Joaquin Basin, specifically corn, as well as wetlands in that part of the Central Valley exhibited larger reductions in open water than rice and wetlands in the Sacramento Valley. Semi-permanent wetlands on protected lands had significantly lower (39–49%) open water in the drought years than those on non-protected lands while seasonal wetlands on protected lands had higher amounts of open water. A large fraction of the daily open water in rice during certain times of the year, particularly in the fall for BirdReturns (61%) and the winter for WHEP (100%), may have been provided through incentive programs which underscores the contribution of these programs. However, further assessment is needed to know how much the incentive programs directly offset the impact of drought in post-harvest rice by influencing water management or simply supplemented funding for activities that might have been done regardless.DiscussionOur landscape analysis documents the significant impacts of the recent extreme drought on freshwater wetland habitats in the Central Valley, the benefits of incentive programs, and the value of using satellite data to track surface water and waterbird habitats. More research is needed to understand subsequent impacts on the freshwater dependent species that rely on these systems and how incentive programs can most strategically support vulnerable species during future extreme drought. creator: Matthew E. Reiter creator: Nathan K. Elliott creator: Dennis Jongsomjit creator: Gregory H. Golet creator: Mark D. Reynolds uri: https://doi.org/10.7717/peerj.5147 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Reiter et al. title: Homologous alignment cloning: a rapid, flexible and highly efficient general molecular cloning method link: https://peerj.com/articles/5146 last-modified: 2018-06-29 description: Homologous alignment cloning (HAC) is a rapid method of molecular cloning that facilitates low-cost, highly efficient cloning of polymerase chain reaction products into any plasmid vector in approximately 2 min. HAC facilitates insert integration due to a sequence alignment strategy, by way of short, vector-specific homology tails appended to insert during amplification. Simultaneous exposure of single-stranded fragment ends, utilising the 3′→5′ exonuclease activity of T4 DNA polymerase, creates overlapping homologous DNA on each molecule. The exonuclease activity of T4 polymerase is quenched simply by the addition of EDTA and a simple annealing step ensures high yield and high fidelity vector formation. The resultant recombinant plasmids are transformed into standard E. coli cloning strains and screened via established methods as necessary. HAC exploits reagents commonly found in molecular research laboratories and achieves efficiencies that exceed conventional cloning methods, including another ligation-independent method we tested. HAC is also suitable for combining multiple fragments in a single reaction, thus extending its flexibility. creator: Lendl Tan creator: Emily J. Strong creator: Kyra Woods creator: Nicholas P. West uri: https://doi.org/10.7717/peerj.5146 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Tan et al. title: Achilles and tail tendons of perlecan exon 3 null heparan sulphate deficient mice display surprising improvement in tendon tensile properties and altered collagen fibril organisation compared to C57BL/6 wild type mice link: https://peerj.com/articles/5120 last-modified: 2018-06-29 description: The aim of this study was to determine the role of the perlecan (Hspg2) heparan sulphate (HS) side chains on cell and matrix homeostasis in tail and Achilles tendons in 3 and 12 week old Hspg2 exon 3 null HS deficient (Hspg2Δ3 − ∕Δ3 −) and C57 BL/6 Wild Type (WT) mice. Perlecan has important cell regulatory and matrix organizational properties through HS mediated interactions with a range of growth factors and morphogens and with structural extracellular matrix glycoproteins which define tissue function and allow the resident cells to regulate tissue homeostasis. It was expected that ablation of the HS chains on perlecan would severely disrupt normal tendon organization and functional properties and it was envisaged that this study would better define the role of HS in normal tendon function and in tendon repair processes. Tail and Achilles tendons from each genotype were biomechanically tested (ultimate tensile stress (UTS), tensile modulus (TM)) and glycosaminoglycan (GAG) and collagen (hydroxyproline) compositional analyses were undertaken. Tenocytes were isolated from tail tendons from each mouse genotype and grown in monolayer culture. These cultures were undertaken in the presence of FGF-2 to assess the cell signaling properties of each genotype. Total RNA was isolated from 3–12 week old tail and Achilles tendons and qRT-PCR was undertaken to assess the expression of the following genes Vcan, Bgn, Dcn, Lum, Hspg2, Ltbp1, Ltbp2, Eln and Fbn1. Type VI collagen and perlecan were immunolocalised in tail tendon and collagen fibrils were imaged using transmission electron microscopy (TEM). FGF-2 stimulated tenocyte monolayers displayed elevated Adamts4, Mmp2, 3, 13 mRNA levels compared to WT mice. Non-stimulated tendon Col1A1, Vcan, Bgn, Dcn, Lum, Hspg2, Ltbp1, Ltbp2, Eln and Fbn1 mRNA levels showed no major differences between the two genotypes other than a decline with ageing while LTBP2 expression increased. Eln expression also declined to a greater extent in the perlecan exon 3 null mice (P < 0.05). Type VI collagen and perlecan were immunolocalised in tail tendon and collagen fibrils imaged using transmission electron microscopy (TEM). This indicated a more compact form of collagen localization in the perlecan exon 3 null mice. Collagen fibrils were also smaller by TEM, which may facilitate a more condensed fibril packing accounting for the superior UTS displayed by the perlecan exon 3 null mice. The amplified catabolic phenotype of Hspg2Δ3 − ∕Δ3 − mice may account for the age-dependent decline in GAG observed in tail tendon over 3 to 12 weeks. After Achilles tenotomy Hspg2Δ3 − ∕Δ3 − and WT mice had similar rates of recovery of UTS and TM over 12 weeks post operatively indicating that a deficiency of HS was not detrimental to tendon repair. creator: Cindy C. Shu creator: Margaret M. Smith creator: Richard C. Appleyard creator: Christopher B. Little creator: James Melrose uri: https://doi.org/10.7717/peerj.5120 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Shu et al. title: Water environmental stress, rebound effect, and economic growth of China’s textile industry link: https://peerj.com/articles/5112 last-modified: 2018-06-29 description: The rapid development of China’s textile industry (TI) has led to severe water environmental stress. Water environmental stress of China’s TI mainly comes from large quantities of discharged wastewater and chemical oxygen demand (COD). The sustainable development of the TI is realized to achieve the decoupling between economic growth and water environmental stress. This study analyzes the decoupling elasticity results from wastewater discharge and COD discharge, respectively. Decoupling results show that TI’s wastewater has strong decoupling from economic growth for three years (2002, 2013–2014) while COD has strong decoupling for six years (2002–2003, 2008, 2010, 2013–2014). The paper further calculates the decoupling elasticity results of the TI’s three sub-sectors (manufacture of textile sector, manufacture of textile wearing and apparel sector, and manufacture of chemical fibers (MCF) sector), and calculates the factors that affect wastewater discharge. The decrement and rebound effects of wastewater discharge are analyzed based on calculated results. Decomposition results show that the scale factor is the most significant contributor to wastewater discharge, the intensity factor inhibits wastewater discharge, and the effect of the structure factor is not evident. The decrement effect of TI increases yearly, but the rebound effect shows that the absolute amount of wastewater discharge also increases. The rebound effect has declined since 2012. In the three sub-sectors, MCF’s decrement effect is the strongest, and its rebound effect is the weakest, which indicate that MCF is the biggest contributor to the discharge reduction of China’s TI. creator: Yi Li creator: Jie Shen creator: Linyi Lu creator: Yan Luo creator: Laili Wang creator: Manhong Shen uri: https://doi.org/10.7717/peerj.5112 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Li et al. title: Attentional demands associated with augmented visual feedback during quiet standing link: https://peerj.com/articles/5101 last-modified: 2018-06-29 description: To investigate how additional visual feedback (VFB) affects postural stability we compared 20-sec center-of-pressure (COP) recordings in two conditions: without and with the VFB. Seven healthy adult subjects performed 10 trials lasting 20 seconds in each condition. Simultaneously, during all trials the simple auditory reaction time (RT) was measured. Based on the COP data, the following sway parameters were computed: standard deviation (SD), mean speed (MV), sample entropy (SE), and mean power frequency (MPF). The RT was higher in the VFB condition (p < 0.001) indicating that this condition was attention demanding. The VFB resulted in decreased SD and increased SE in both the medial-lateral (ML) and anterior-posterior (AP) planes (p < .001). These results account for the efficacy of the VFB in stabilizing posture and in producing more irregular COP signals which may be interpreted as higher automaticity and/or larger level of noise in postural control. The MPF was higher during VFB in both planes as was the MV in the AP plane only (p < 0.001). The latter data demonstrate higher activity of postural control system that was caused by the availability of the set-point on the screen and the resulting control error which facilitated and sped up postural control. creator: Krzysztof Kręcisz creator: Michał Kuczyński uri: https://doi.org/10.7717/peerj.5101 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Kręcisz and Kuczyński title: Direct and legacy effects of plant-traits control litter decomposition in a deciduous oak forest in Mexico link: https://peerj.com/articles/5095 last-modified: 2018-06-29 description: BackgroundLitter decomposition is a key process in the functioning of forest ecosystems, because it strongly controls nutrient recycling and soil fertility maintenance. The interaction between the litter chemical composition and the metabolism of the soil microbial community has been described as the main factor of the decomposition process based on three hypotheses: substrate-matrix interaction (SMI), functional breadth (FB) and home-field advantage (HFA). The objective of the present study was to evaluate the effect of leaf litter quality (as a direct plant effect, SMI hypothesis), the metabolic capacity of the microbial community (as a legacy effect, FB hypothesis), and the coupling between the litter quality and microbial activity (HFA hypothesis) on the litter decomposition of two contiguous deciduous oak species at a local scale.MethodsTo accomplish this objective, we performed a litterbag experiment in the field for 270 days to evaluate mass loss, leaf litter quality and microbial activity in a complete factorial design for litter quality and species site.ResultsThe litter of Quercus deserticola had higher rate of decomposition independently of the site, while the site of Quercus castanea promoted a higher rate of decomposition independently of the litter quality, explained by the specialization of the soil microbial community in the use of recalcitrant organic compounds. The Home-Field Advantage Index was reduced with the decomposition date (22% and 4% for 30 and 270 days, respectively).DiscussionWe observed that the importance of the coupling of litter quality and microbial activity depends on decomposition stage. At the early decomposition stage, the home-advantage hypothesis explained the mass loss of litter; however, in the advanced decomposition stage, the litter quality and the metabolic capacity of the microbial community can be the key drivers. creator: Bruno Chávez-Vergara creator: Agustín Merino creator: Antonio González-Rodríguez creator: Ken Oyama creator: Felipe García-Oliva uri: https://doi.org/10.7717/peerj.5095 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Chávez-Vergara et al. title: Bibliometric analysis of research on the role of intestinal microbiota in obesity link: https://peerj.com/articles/5091 last-modified: 2018-06-29 description: BackgroundObesity is a key public health problem. The advancement of gut microbiota research sheds new light on this field. This article aims to present the research trends in global intestinal microbiota studies within the domain of obesity research.MethodsBibliographic information of the publications on intestinal microbiota and obesity was retrieved from the Scopus database, and then analyzed by using bibliometric approaches.ResultsA total of 3,446 references were retrieved; the data indicated a steady growth and an exponential increase in publication numbers. The references were written in 23 different languages (93.8% in English). A number of 3,056 English journal papers were included in the further analyses. Among the 940 journals, the most prolific ones were PLOS ONE, Scientific Reports, and British Journal of Nutrition. North America and Europe were the highest publication output areas. The US (995 publications) ranked first in the number of publications, followed by the China (243 publications) and France (242 publications). The publication numbers were significantly correlated with gross domestic product (GDP), human development index (HDI), and population number (PN). International collaboration analysis also shows that most of the collaborations are among developed countries.DiscussionThis comprehensive bibliometric study indicates that gut microbiota is a significant topic in the obesity research. The structured information may be helpful in understanding research trends, and locating research hot spots and gaps in this domain. creator: Haiqiang Yao creator: Jin-Yi Wan creator: Chong-Zhi Wang creator: Lingru Li creator: Ji Wang creator: Yingshuai Li creator: Wei-Hua Huang creator: Jinxiang Zeng creator: Qi Wang creator: Chun-Su Yuan uri: https://doi.org/10.7717/peerj.5091 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Yao et al. title: The impact of the Wenchuan earthquake on early puberty: a natural experiment link: https://peerj.com/articles/5085 last-modified: 2018-06-29 description: BackgroundThe factors influencing pubertal timing have gained much attention due to a secular trend toward earlier pubertal onset in many countries. However, no studies have investigated the association between the Great earthquake and early puberty. We aimed to assess whether the Wenchuan earthquake is associated with early puberty, in both boys and girls.MethodsWe used data from two circles of a survey on reproductive health in China to explore the impact of the Wenchuan earthquake on early puberty , and a total of 9,785 adolescents (4,830 boys, 49.36%) aged 12–20 years from 29 schools in eight provinces were recruited. Wenchuan earthquake exposure was defined as those Sichuan students who had not experienced oigarche/menarche before May 12, 2008. Early puberty was identified as a reported onset of oigarche/menarche at 11 years or earlier. We tested the association between the Wenchuan earthquake and early puberty in boys and girls. Then, subgroup analysis stratified by the age at earthquake exposure also was performed.ResultsIn total, 8,883 adolescents (4,543 boys, 51.14%) with a mean (SD) age of 15.13 (1.81) were included in the final sample. In general, children exposed to the earthquake had three times greater risk of early puberty (boys, RR [95% CI] = 3.18 [2.21–4.57]; girls: RR [95%CI] =3.16 [2.65–3.78]). Subgroup analysis showed that the adjusted RR was 1.90 [1.19–3.03] for boys and 2.22 [1.75–2.80] for girls. Earthquake exposure predicted almost a fourfold (RR [95%CI] = 3.91 [1.31–11.72]) increased risk of early puberty in preschool girls, whereas the increase was about twofold (RR [95%CI] = 2.09 [1.65–2.64]) in schoolgirls. Among boys, only older age at earthquake exposure was linked to early puberty (RR [95%CI] = 1.93 [1.18–3.16]).ConclusionsWenchuan earthquake exposure increased the risk of early puberty in boys and girls, and preschoolers were more at risk than schoolchildren. The implications are relevant to support policies for those survivors, especially children, to better rebuild after disasters. creator: Qiguo Lian creator: Xiayun Zuo creator: Yanyan Mao creator: Yan Zhang creator: Shan Luo creator: Shucheng Zhang creator: Chaohua Lou creator: Xiaowen Tu creator: Weijin Zhou uri: https://doi.org/10.7717/peerj.5085 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Lian et al. title: ­Morphological variations in the dorsal fin finlets of extant polypterids raise questions about their taxonomical validity link: https://peerj.com/articles/5083 last-modified: 2018-06-29 description: Fossil polypterids are mainly represented by disarticulated material, most of them pinnules. However, there is no study that proves the taxonomical validity of these structures. Here we describe the pinnules of four species of extant polypterids and report for the first time intraindividual variations in the pinnules according to their position in the dorsal fin. Nevertheless, when comparing two different specimens of one species there is little or no interindividual variation, suggesting that pinnule morphology may have taxonomical validity. As the fossil polypterid record is based mainly on the articular head of the pinnules, we suggest caution when describing new taxa, especially if different fragments corresponding to specific positions in the dorsal fin occur in the same locality. creator: Marcos Vinícius Coelho creator: Camila Cupello creator: Paulo M. Brito uri: https://doi.org/10.7717/peerj.5083 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Coelho et al. title: Perioperative management of angiotensin-converting enzyme inhibitors and/or angiotensin receptor blockers: a survey of perioperative medicine practitioners link: https://peerj.com/articles/5061 last-modified: 2018-06-29 description: BackgroundAngiotensin-converting enzyme inhibitors (ACEi) and angiotensin receptor blockers (ARB) are the most commonly prescribed antihypertensive medications in higher-risk surgical patients. However, there is no clinical consensus on their use in the perioperative period, in part, due to an inconsistent evidence-base. To help inform the design of a large multi-centre randomized controlled trial (ISRCTN17251494), we undertook a questionnaire-based survey exploring variability in ACEi/ARB prescribing in perioperative practice.MethodsThe online survey included perioperative scenarios to examine how consistent respondents were with their stated routine preoperative practice. Clinicians with an academic interest in perioperative medicine were primarily targeted between July and September 2017. STROBE guidelines for observational research and ANZCA Trials Group Survey Reporting recommendations were adhered to.Results194 responses were received, primarily from clinicians practicing in the UK. A similar minority of respondents continue ACEi (n = 57; 30%) and ARBs (n = 62; 32%) throughout the perioperative period. However, timing of preoperative cessation was highly variable, and rarely influenced by the pharmacokinetics of individual ACE-i/ARBs. Respondents’ stated routine practice was frequently misaligned with their management of common pre- and postoperative scenarios involving continuation or restarting ACE-i/ARBs.DiscussionThis survey highlights many inconsistencies amongst clinicians’ practice in perioperative ACE-i/ARB management. Studies designed to reveal an enhanced understanding of perioperative mechanisms at play, coupled with randomised controlled trials, are required to rationally inform the clinical management of ACE-i/ARBs in patients most at risk of postoperative morbidity. creator: Sophie L.M. Walker creator: Tom E.F. Abbott creator: Katherine Brown creator: Rupert M. Pearse creator: Gareth L. Ackland uri: https://doi.org/10.7717/peerj.5061 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Walker et al. title: Changes in leaf chlorophyll content associated with flowering and its role in the diversity of phytophagous insects in a tree species from a semiarid Caatinga link: https://peerj.com/articles/5059 last-modified: 2018-06-29 description: Phytophagous insects choose their feeding resources according to their own requirements, but their feeding preferences in the semiarid Caatinga have rarely been studied. Flowering trees leads to a greater diversity of flower visitors and their predators in the host plant, but little is known about why the diversity of phytophagous insects not associated with flowers is also increased. The purpose of this study was to evaluate the diversity of sap-sucking, wood-boring and leaf-chewing insects associated with leaf chlorophyll content in flowering and non-flowering plants of Poincianella pyramidalis, an endemic tree of Caatinga. We used a leaf chlorophyll index (LCI) as a surrogate for resource quality, and an entomological umbrella to collect phytophagous insects. We show that trees which bloomed demonstrated higher chlorophyll content, greater abundance and a significant difference in the composition of phytophagous insect species when compared to non-flowering trees (p < 0.05). The results suggest that not only the presence of flowers themselves, but also the higher nutritional quality of leaf tissue, can explain the differences in species diversity and abundance of phytophagous insects. Exceptional flowering trees in the Caatinga area studied may thus act as spots of high quality resources, favouring changes in the diversity of insects in this environment. creator: Leandro Sousa-Souto creator: Adriana Bocchiglieri creator: Douglas de M. Dias creator: Anthony S. Ferreira creator: José P. de L. Filho uri: https://doi.org/10.7717/peerj.5059 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Sousa-Souto et al. title: Wolf spider burrows from a modern saline sandflat in central Argentina: morphology, taphonomy and clues for recognition of fossil examples link: https://peerj.com/articles/5054 last-modified: 2018-06-29 description: Pavocosa sp. (Lycosidae) burrows found in an open sparsely vegetated area on the edge of the Gran Salitral saline lake, in central Argentina, are described. Burrows were studied by capturing the occupant and casting them with dental plaster. The hosting sediments and vegetation were also characterized. Inhabited Pavocosa sp. burrows display distinctive features as open, cylindrical, nearly vertical, silk lined shafts about 120 mm long, subcircular entrances, a gradual downward widening, and a particularly distinctive surface ornamentation in the form of sets of two linear parallel marks at a high angle to the burrow axis. Instead, casts of vacated Pavocosa sp. burrows showed some disturbances caused either by the reoccupation by another organism or by predation of the dweller. Two morphologies are related to reoccupation of burrows: those with a structure in form of an “umbrella” and another with smaller excavations at the bottom of the burrow. Predation by small mammals produces funnel-shaped burrows. Both active and abandoned Pavocosa sp. burrow casts are compared with existing ichnogenera and inorganic sedimentary structures, highlighting its distinction. It is argued that key features like the presence of a neck, a downward widening and the described surface texture will allow recognition of wolf spider burrows in the fossil record. However, the putative spider burrows described in the literature either lack the necessary preservational quality or do not show ornamentation similar to the modern wolf spider burrows. Fossil wolf spiders are recorded since the Paleogene (possibly Late Cretaceous), therefore Cenozoic continental rocks can contain wolf spider burrows awaiting recognition. In addition, the particular distribution of Pavocosa sp. in saline lakes may imply that this type of burrow is linked to saline environments. creator: Fatima Mendoza Belmontes creator: Ricardo N. Melchor creator: Luis N. Piacentini uri: https://doi.org/10.7717/peerj.5054 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Mendoza Belmontes et al. title: Gene buddies: linked balanced polymorphisms reinforce each other even in the absence of epistasis link: https://peerj.com/articles/5110 last-modified: 2018-06-28 description: The fates of genetic polymorphisms maintained by balancing selection depend on evolutionary dynamics at linked sites. While coevolution across linked, epigenetically-interacting loci has been extensively explored, such supergenes may be relatively rare. However, genes harboring adaptive variation can occur in close physical proximity while generating independent effects on fitness. Here, I present a model in which two linked loci without epistasis are both under balancing selection for unrelated reasons. Using forward-time simulations, I show that recombination rate strongly influences the retention of adaptive polymorphism, especially for intermediate selection coefficients. A locus is more likely to retain adaptive variation if it is closely linked to another locus under balancing selection, even if the two loci have no interaction. Thus, two linked polymorphisms can both be retained indefinitely even when they would both be lost to drift if unlinked. While these results may be intuitive, they have important implications for genetic architecture: clusters of mutually reinforcing genes may underlie phenotypic variation in natural populations, and such genes cannot be assumed to be functionally associated. Future studies that measure selection coefficients and recombination rates among closely linked genes will be fruitful for characterizing the extent of this phenomenon. creator: Jacob A. Tennessen uri: https://doi.org/10.7717/peerj.5110 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Tennessen title: Re-emergence of the leaf clip gesture during an alpha takeover affects variation in male chimpanzee loud calls link: https://peerj.com/articles/5079 last-modified: 2018-06-28 description: Loud calls are used by many species as long-distance signals for group defense, mate attraction, and inter- and intragroup spacing. Chimpanzee loud calls, or pant hoots, are used in a variety of contexts including group coordination and during male contests. Here, we observed an alpha male takeover in wild chimpanzees (Pan troglodytes verus) during which the leaf clipping gesture re-emerged after disappearing for almost two years in this community. Leaf clipping only occurred in males and was observed almost exclusively prior to pant hoot vocalizations, as has been observed in other chimpanzee communities of the Taï forest in Côte d’Ivoire. Consequently, we hypothesized that leaf clipping may be important for male-male competition by affecting variation in the acoustic properties of male chimpanzee loud calls. We therefore investigated whether pant hoots preceded by leaf clipping differed acoustically from those without, while also testing the influence of social context on pant hoot variation, namely male dominance rank and hierarchy instability, i.e., before, during and after the alpha takeover. We found that pant hoots preceded by leaf clipping were longer, contained more call elements and drum beats, and lower fundamental and peak frequencies. Moreover, during the alpha takeover pant hoots were shorter, contained fewer drum beats and higher fundamental frequencies. Additionally, pant hoot and aggression rates were also highest during the alpha takeover with leaf clipping more likely to occur on days when pant hooting rates were high. Overall social rank had limited effects on pant hoot variation. We suggest that elevated arousal and aggression during the alpha takeover triggered the re-emergence of leaf clipping and the associated acoustic changes in pant hoots. Further research should focus on the potential mechanisms by which leaf clipping is connected to variation in pant hoots and cross-population comparisons of the behaviour. creator: Ammie K. Kalan creator: Christophe Boesch uri: https://doi.org/10.7717/peerj.5079 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Kalan and Boesch title: Unsupervised segmentation of greenhouse plant images based on modified Latent Dirichlet Allocation link: https://peerj.com/articles/5036 last-modified: 2018-06-28 description: Agricultural greenhouse plant images with complicated scenes are difficult to precisely manually label. The appearance of leaf disease spots and mosses increases the difficulty in plant segmentation. Considering these problems, this paper proposed a statistical image segmentation algorithm MSBS-LDA (Mean-shift Bandwidths Searching Latent Dirichlet Allocation), which can perform unsupervised segmentation of greenhouse plants. The main idea of the algorithm is to take advantage of the language model LDA (Latent Dirichlet Allocation) to deal with image segmentation based on the design of spatial documents. The maximum points of probability density function in image space are mapped as documents and Mean-shift is utilized to fulfill the word-document assignment. The proportion of the first major word in word frequency statistics determines the coordinate space bandwidth, and the spatial LDA segmentation procedure iteratively searches for optimal color space bandwidth in the light of the LUV distances between classes. In view of the fruits in plant segmentation result and the ever-changing illumination condition in greenhouses, an improved leaf segmentation method based on watershed is proposed to further segment the leaves. Experiment results show that the proposed methods can segment greenhouse plants and leaves in an unsupervised way and obtain a high segmentation accuracy together with an effective extraction of the fruit part. creator: Yi Wang creator: Lihong Xu uri: https://doi.org/10.7717/peerj.5036 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Wang and Xu title: The antimicrobial action of polyaniline involves production of oxidative stress while functionalisation of polyaniline introduces additional mechanisms link: https://peerj.com/articles/5135 last-modified: 2018-06-27 description: Polyaniline (PANI) and functionalised polyanilines (fPANI) are novel antimicrobial agents whose mechanism of action was investigated. Escherichia coli single gene deletion mutants revealed that the antimicrobial mechanism of PANI likely involves production of hydrogen peroxide while homopolymer poly(3-aminobenzoic acid), P3ABA, used as an example of a fPANI, disrupts metabolic and respiratory machinery, by targeting ATP synthase and causes acid stress. PANI was more active against E. coli in aerobic, compared to anaerobic, conditions, while this was apparent for P3ABA only in rich media. Greater activity in aerobic conditions suggests involvement of reactive oxygen species. P3ABA treatment causes an increase in intracellular free iron, which is linked to perturbation of metabolic enzymes and could promote reactive oxygen species production. Addition of exogenous catalase protected E. coli from PANI antimicrobial action; however, this was not apparent for P3ABA treated cells. The results presented suggest that PANI induces production of hydrogen peroxide, which can promote formation of hydroxyl radicals causing biomolecule damage and potentially cell death. P3ABA is thought to act as an uncoupler by targeting ATP synthase resulting in a futile cycle, which precipitates dysregulation of iron homeostasis, oxidative stress, acid stress, and potentially the fatal loss of proton motive force. creator: Julia Robertson creator: Marija Gizdavic-Nikolaidis creator: Michel K. Nieuwoudt creator: Simon Swift uri: https://doi.org/10.7717/peerj.5135 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Robertson et al. title: Triple stable isotope analysis to estimate the diet of the Velvet Scoter (Melanitta fusca) in the Baltic Sea link: https://peerj.com/articles/5128 last-modified: 2018-06-27 description: This study quantifies contributions of different food sources in the winter diet of the Velvet Scoter (Melanitta fusca) in coastal waters of the Lithuanian Baltic Sea using non-lethal avian sampling. We highlight the application of stable sulphur isotope ratios as complementary to stable carbon and nitrogen isotope analysis in order to discriminate sandy bottom macrozoobenthos organisms as potential food sources for the Velvet Scoter. Selection of the most relevant trophic enrichment factors and Monte Carlo simulations in order to choose the best fitted model were undertaken. The stable isotope mixing model revealed the main contributions of a group of bivalves, Mya arenaria and Cerastoderma glaucum, to be 46–54%, and while the crustacean, Saduria entomon, comprised 26–35% of the diet. creator: Rasa Morkūnė creator: Jūratė Lesutienė creator: Julius Morkūnas creator: Rūta Barisevičiūtė uri: https://doi.org/10.7717/peerj.5128 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Morkūnė et al. title: Two sugar beet chitinase genes, BvSP2 and BvSE2, analysed with SNP Amplifluor-like markers, are highly expressed after Fusarium root rot inoculations and field susceptibility trial link: https://peerj.com/articles/5127 last-modified: 2018-06-27 description: BackgroundThe pathogens from Fusarium species can cause Fusarium root rot (RR) and other diseases in plant species including sugar beet (Beta vulgaris L.), and they have a strong negative impact on sugar beet yield and quality.MethodsA total of 22 sugar beet breeding lines were evaluated for the symptoms of RR after inoculation with Fusarium oxysporum Sch., isolate No. 5, and growth in a field trial. Two candidate genes for RR resistance, BvSP2 and BvSE2, encoding chitinases Class IV and III, respectively, were previously identified in sugar beet, and used for genotyping using modern Amplifluor-like single nucleotide polymorphism (SNP) genotyping approach. The qPCR expression analysis was used to verify responses of the candidate genes for RR infections.ResultsA strong association of two SNP markers for BvSP2 and BvSE2 with resistance to RR in sugar beet was found in our study. Very high BvSP2 expression (100-fold compared to Controls) was observed in three RR resistant accessions (2182, 2236 and KWS2320) 14 days after inoculation which returned to the control level on Day 18. RR sensitive breeding line 2210 showed a delay in mRNA level, reaching maximal expression of BvSP2 18 days after inoculation. The gene BvSE2, showed a strong expression level in leaf samples from the infected field trial only in the breeding line 2236, which showed symptoms of RR, and this may be a response to other strains of F. oxysporum. creator: Raushan Yerzhebayeva creator: Alfiya Abekova creator: Kerimkul Konysbekov creator: Sholpan Bastaubayeva creator: Aynur Kabdrakhmanova creator: Aiman Absattarova creator: Yuri Shavrukov uri: https://doi.org/10.7717/peerj.5127 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Yerzhebayeva et al. title: The effect of biochar amendments on phenanthrene sorption, desorption and mineralisation in different soils link: https://peerj.com/articles/5074 last-modified: 2018-06-27 description: The contamination of soils and waters with organic pollutants, such as polycyclic aromatic hydrocarbons (PAHs), affect a large number of sites worldwide that need remediation. In this context soils amendments can be used to immobilise PAHs while maintaining soil functioning, with biochar being a promising amendment. In this experiment, phenantrene (Phe) was used as a frequent PAH contaminating soils and we studied the effect of three biochars at 1% applications to three different substrates, two agricultural topsoils and pure sand. We evaluated the changes in soil properties, sorption-desorption of Phe, and mineralisation of Phe in all treatments. Phe in pure sand was effectively sorbed to olive pruning (OBC) and rice husk (RBC) biochars, but pine biochar (PBC) was not as effective. In the soils, OBC and RBC only increased sorption of Phe in the silty soil. Desorption was affected by biochar application, RBC and OBC decreased water soluble Phe independently of the soil, which may be useful in preventing leaching of Phe into natural waters. Contrastingly, OBC and RBC slightly decreased the mineralisation of Phe in the soils, thus indicating lower bioavailability of the contaminant. Overall, biochar effects in the two tested soils were low, most likely due to the rather high soil organic C (SOC) contents of 2.2 and 2.8% with Koc values in the same range as those of the biochars. However, OBC and RBC additions can substantially increase adsorption of Phe in soils poor in SOC. creator: Eduardo Moreno Jiménez creator: Sara Aceña-Heras creator: Vladimír Frišták creator: Stefanie Heinze creator: Bernd Marschner uri: https://doi.org/10.7717/peerj.5074 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Moreno Jiménez et al. title: Methods matter: the relationship between strength and hypertrophy depends on methods of measurement and analysis link: https://peerj.com/articles/5071 last-modified: 2018-06-27 description: PurposeThe relationship between changes in muscle size and strength may be affected by both measurement and statistical approaches, but their effects have not been fully considered or quantified. Therefore, the purpose of this investigation was to explore how different methods of measurement and analysis can affect inferences surrounding the relationship between hypertrophy and strength gain.MethodsData from a previous study—in which participants performed eight weeks of elbow flexor training, followed by an eight-week period of detraining—were reanalyzed using different statistical models, including standard between-subject correlations, analysis of covariance, and hierarchical linear modeling.ResultsThe associative relationship between strength and hypertrophy is highly dependent upon both method/site of measurement and analysis; large differences in variance accounted for (VAF) by the statistical models were observed (VAF = 0–24.1%). Different sites and measurements of muscle size showed a range of correlations coefficients with one another (r = 0.326–0.945). Finally, exploratory analyses revealed moderate-to-strong relationships between within-individual strength-hypertrophy relationships and strength gained over the training period (ρ = 0.36–0.55).ConclusionsMethods of measurement and analysis greatly influence the conclusions that may be drawn from a given dataset. Analyses that do not account for inter-individual differences may underestimate the relationship between hypertrophy and strength gain, and different methods of assessing muscle size will produce different results. It is suggested that robust experimental designs and analysis techniques, which control for different mechanistic sources of strength gain and inter-individual differences (e.g., muscle moment arms, muscle architecture, activation, and normalized muscle force), be employed in future investigations. creator: Andrew D. Vigotsky creator: Brad J. Schoenfeld creator: Christian Than creator: J. Mark Brown uri: https://doi.org/10.7717/peerj.5071 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Vigotsky et al. title: Non-linear curve adjustments widen biological interpretation of relative growth analyses of the clam Tivela mactroides (Bivalvia, Veneridae) link: https://peerj.com/articles/5070 last-modified: 2018-06-27 description: Evaluation of relative (allometric) growth provides useful information to understand the development of organisms, as well as to aid in the management of fishery-exploited species. Usually, relative growth analyses use classical models such as the linear equation or the power function (allometric equation). However, these methods do not consider discontinuities in growth and may mask important biological information. As an alternative to overcome poor results and misleading interpretations, recent studies have suggested the use of more complex models, such as non-linear regressions, in conjunction with a model selection approach. Here, we tested differences in the performance of diverse models (simple linear regression, power function, and polynomial models) to assess the relative growth of the trigonal clam Tivela mactroides, an important fishing resource along the South American coast. Regressions were employed to relate parameters of the shell (length (L), width (W), height (H) and weight (SW)) among each other and with soft parts of the organism (dry weight (DW) and ash-free dry weight (ASDW)). Then, model selection was performed using the information theory and multi-model inference approach. The power function was more suitable to describe the relationships involving shell parameters and soft parts weight parameters (i.e., L vs. SW, DW, and AFDW, and SW vs. DW). However, it failed in unveiling changes in the morphometric relationships between shell parameters (i.e., L vs. W and H; W vs. H) over time, which were better described by polynomial functions. Linear models, in turn, were not selected for any relationship. Overall, our results show that more complex models (in this study polynomial functions) can unveil changes in growth related to modifications in environmental features or physiology. Therefore, we suggest that classical and more complex models should be combined in future studies of allometric growth of molluscs. creator: Alexander Turra creator: Guilherme N. Corte creator: Antonia Cecília Z. Amaral creator: Leonardo Q. Yokoyama creator: Márcia R. Denadai uri: https://doi.org/10.7717/peerj.5070 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Turra et al. title: One-pot multicomponent nitro-Mannich reaction using a heterogeneous catalyst under solvent-free conditions link: https://peerj.com/articles/5065 last-modified: 2018-06-27 description: An environmentally-friendly, one-pot multicomponent reaction of various aldehydes, amines and nitroalkanes for the synthesis of β-nitroamines is here described. Amberlyst A-21 supported CuI was found to be a highly efficient novel heterogeneous catalyst for the three-component nitro-Mannich reaction between aldehydes, amines and nitroalkanes. The developed protocol is performed in a solvent-free medium to produce a variety of β-nitroamines in good to excellent yields within short reaction times. The catalyst can be easily prepared and recovered. It has been tested up to eight times with only a minor activity loss. creator: Giovanna Bosica creator: Ramon Zammit uri: https://doi.org/10.7717/peerj.5065 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Bosica and Zammit title: Mitochondrial diversity of Bulgarian native dogs suggests dual phylogenetic origin link: https://peerj.com/articles/5060 last-modified: 2018-06-27 description: The dog has been the first domesticated animal to have a central role in human society from ancient times to present day. Although there have been numerous investigations of dog phylogeny and origin, genetic data of dogs in the region of the Balkan Peninsula (South-Eastern Europe) are still scarce. Therefore, the aim of the present study was to perform phylogenetic analysis of three native Bulgarian dog breeds. A total of 130 samples were analyzed at HVR1 (hypervariable region, D-loop region). The samples were taken from two hunting dog breeds (Bulgarian Hound Dog: Barak, n = 34; Bulgarian Scenthound Dog: Gonche, n = 45) as well as from a Bulgarian Shepherd Dog (n = 51). The first two breeds are reared in a flat region of the country (the Northern part of Bulgaria, the Danubian Plain), while the last breed is a typical representative of the mountainous part of the country. The results have shown the presence of almost all main clades—A, B, C and D—in the three dog breeds taken together, except clades E and F, as expected. With regard to haplogroups distribution, there are clear differences among investigated breeds. While hunting breeds exhibit a prevalence of clade C, the mountainous Shepherd dog shows presence of the D2 haplogroup but absence of the C clade. In conclusion, the present study has been the first to investigate the mitochondrial DNA diversity of native dog breeds in Bulgaria. The results have revealed a clear difference of haplogroups dissemination in native hunting and shepherd dogs, which suggests a dual independent phylogenetic origin, without hybridization events between these dogs. creator: Miroslav Marinov creator: Denitsa Teofanova creator: Dimitar Gadjev creator: Georgi Radoslavov creator: Peter Hristov uri: https://doi.org/10.7717/peerj.5060 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Marinov et al. title: Seasonal dynamics of terrestrial vertebrate abundance between Amazonian flooded and unflooded forests link: https://peerj.com/articles/5058 last-modified: 2018-06-27 description: The flood pulse is the main factor structuring and differentiating the ecological communities of Amazonian unflooded (terra firme) and seasonally-flooded (várzea) forests as they require unique adaptations to survive the prolonged annual floods. Therefore, várzea and terra firme forests hammer out a spatio-temporal mosaic of resource availability, which may result in landscape scale seasonal movements of terrestrial vertebrates between adjacent forest types. Yet the lateral movements of terrestrial vertebrates between hydrologically distinct neighbouring forest types exhibiting staggered resource availability remains poorly understood, despite the important implications of this spatial dynamic for the ecology and conservation of forest wildlife. We examined the hypothesis of terrestrial fauna seasonal movements between two adjacent forest types at two contiguous sustainable-use forest reserves in Western Brazilian Amazonia. We used camera trapping data on the overall species richness, composition, and abundance of nine major vertebrate trophic guilds to infer on terrestrial vertebrate movements as a function of seasonal changes in floodplain water level. Species richness differed in neighboring terra firme forests between the high-and low-water phases of the flood pulse and terra firme forests were more species rich than várzea forests. There were clear differences in species composition between both forest types and seasons. Generalized Linear Models showed that water level was the main factor explaining aggregate abundance of all species and three trophic guilds. Our results indicate that the persistence of viable populations of large terrestrial vertebrates adjacent to major Amazonian rivers requires large, well-connected forest landscapes encompassing different forest types to ensure large-scale lateral movements by forest wildlife. creator: Hugo C.M. Costa creator: Carlos A. Peres creator: Mark I. Abrahams uri: https://doi.org/10.7717/peerj.5058 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Costa et al. title: A new, three-dimensional geometric morphometric approach to assess egg shape link: https://peerj.com/articles/5052 last-modified: 2018-06-27 description: This paper proposes a new methodology to quantify patterns of egg shape variation using geometric morphometrics of three-dimensional landmarks captured on digitally reconstructed eggshells and demonstrates its performance in capturing shape variation at multiple biological levels. This methodology offers unique benefits to complement established linear measurement or two-dimensional (2D) contour profiling techniques by (i) providing a more precise representation of eggshell curvature by accounting for variation across the entire surface of the egg; (ii) avoids the occurrence of correlations from combining multiple egg shape features; (iii) avoids error stemming from projecting a highly-curved three-dimensional (3D) object into 2D space; and (iv) enables integration into 3D workflows such as finite elements analysis. To demonstrate, we quantify patterns of egg shape variation and estimate morphological disparity at multiple biological levels, within and between clutches and among species of four passerine species of different lineages, using volumetric dataset obtained from micro computed tomography. The results indicate that species broadly have differently shaped eggs, but with extensive within-species variation so that all four-focal species occupy a range of shapes. Within-species variation is attributed to between-clutch differences in egg shape; within-clutch variation is surprisingly substantial. Recent comparative analyses that aim to explain shape variation among avian taxa have largely ignored potential biases due to within-species variation, or use methods limited to a narrow range of egg shapes. Through our approach, we suggest that there is appreciable variation in egg shape across clutches and that this variation needs to be accounted for in future research. The approach developed in this study to assess variation in shape is freely accessible and can be applied to any spherical-to-conical shaped object, including eggs of non-avian dinosaurs and reptiles through to other extant taxa such as poultry. creator: Marie R.G. Attard creator: Emma Sherratt creator: Paul McDonald creator: Iain Young creator: Marta Vidal-García creator: Stephen Wroe uri: https://doi.org/10.7717/peerj.5052 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Attard et al. title: Significance and potential of marine microbial natural bioactive compounds against biofilms/biofouling: necessity for green chemistry link: https://peerj.com/articles/5049 last-modified: 2018-06-27 description: Natural products from the unique environments of sea water and oceans represent a largely unfamiliar source for isolation of new microbes, which are potent producers of secondary bioactive metabolites. These unique life-forms from the marine ecosphere have served as an important source of drugs since ancient times and still offer a valuable resource for novel findings by providing remedial treatments. Therefore, it can be expected that many naturally bioactive marine microbial compounds with novel structures and bioactivities against those from terrestrial environments may be found among marine metabolites. Biofilms in aquatic environment possess serious problems to naval forces and oceanic industries around the globe. Current anti-biofilm or anti-biofouling technology is based on the use of toxic substances that can be harmful to their surrounding natural locales. Comprehensive research has been done to examine the bioactive potential of marine microbes. Results are remarkably varied and dynamic, but there is an urgent need for bioactive compounds with environmentally friendly or “green” chemical activities. Marine microbes have the potential as upcoming and promising source of non-toxic compounds with sustainable anti-biofouling/anti-biofilm properties as they can produce substances that can inhibit not only the chemical components required for biofilm production but also the attachment, microorganism growth, and/or cell–cell communication. creator: Mohd Adnan creator: Eyad Alshammari creator: Mitesh Patel creator: Syed Amir Ashraf creator: Saif Khan creator: Sibte Hadi uri: https://doi.org/10.7717/peerj.5049 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Adnan et al. title: Pathway analysis identifies altered mitochondrial metabolism, neurotransmission, structural pathways and complement cascade in retina/RPE/ choroid in chick model of form-deprivation myopia link: https://peerj.com/articles/5048 last-modified: 2018-06-27 description: PurposeRNA sequencing analysis has demonstrated bidirectional changes in metabolism, structural and immune pathways during early induction of defocus induced myopia. Thus, the aim of this study was to investigate whether similar gene pathways are also related to the more excessive axial growth, ultrastructural and elemental microanalytic changes seen during the induction and recovery from form-deprivation myopia (FDM) in chicks and predicted by the RIDE model of myopia.MethodsArchived genomic transcriptome data from the first three days of induction of monocularly occluded form deprived myopia (FDMI) in chicks was obtained from the GEO database (accession # GSE6543) while data from chicks monocularly occluded for 10 days and then given up to 24 h of normal visual recovery (FDMR) were collected. Gene set enrichment analysis (GSEA) software was used to determine enriched pathways during the induction (FDMI) and recovery (FDMR) from FD. Curated gene-sets were obtained from open access sources.ResultsClusters of significant changes in mitochondrial energy metabolism, neurotransmission, ion channel transport, G protein coupled receptor signalling, complement cascades and neuron structure and growth were identified during the 10 days of induction of profound myopia and were found to correlate well with change in axial dimensions. Bile acid and bile salt metabolism pathways (cholesterol/lipid metabolism and sodium channel activation) were significantly upregulated during the first 24 h of recovery from 10 days of FDM.ConclusionsThe gene pathways altered during induction of FDM are similar to those reported in defocus induced myopia and are established indicators of oxidative stress, osmoregulatory and associated structural changes. These findings are also consistent with the choroidal thinning, axial elongation and hyperosmotic ion distribution patterns across the retina and choroid previously reported in FDM and predicted by RIDE. creator: Loretta Giummarra creator: Sheila G. Crewther creator: Nina Riddell creator: Melanie J. Murphy creator: David P. Crewther uri: https://doi.org/10.7717/peerj.5048 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Giummarra et al. title: A new species of the deep-bodied actinopterygian Dapedium from the Middle Jurassic (Aalenian) of southwestern Germany link: https://peerj.com/articles/5033 last-modified: 2018-06-27 description: Dapedium is one of the most abundant and diverse genera of ganoid fishes from the Early Jurassic fossil lagerstätte of Europe. In spite of its abundance, however, its timing of extinction is poorly constrained, with the youngest described material being Early Jurassic in age. We describe new diagnostic and relatively complete material of a large species of Dapedium (standard length estimated at 50 cm) from the Middle Jurassic (earliest Aalenian) Opalinuston Formation of Baden-Württemberg, Germany. The Aalenian material represents a distinct species, D. ballei sp. nov., differing from Early Jurassic species in a unique combination of characters pertaining to the shape of the dermal skull elements, pectoral fin position, and scale shape and ornamentation. However, although D. ballei sp. nov. exhibits a unique combination of characters, there are no autapomorphies with which to distinguish it from the Toarcian species of Dapedium. Dapedium ballei represents the geologically youngest species of Dapedium, extending the range of this genus into the Middle Jurassic. The Opalinuston Formation fills an important gap in the marine vertebrate fossil record, and finds from this horizon have the potential to greatly improve our understanding of evolutionary dynamics over this period of faunal transition. creator: Erin E. Maxwell creator: Adriana López-Arbarello uri: https://doi.org/10.7717/peerj.5033 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Maxwell and López-Arbarello title: Osteohistology of Late Triassic prozostrodontian cynodonts from Brazil link: https://peerj.com/articles/5029 last-modified: 2018-06-27 description: The Prozostrodontia includes a group of Late Triassic-Early Cretaceous eucynodonts plus the clade Mammaliaformes, in which Mammalia is nested. Analysing their growth patterns is thus important for understanding the evolution of mammalian life histories. Obtaining material for osteohistological analysis is difficult due to the rare and delicate nature of most of the prozostrodontian taxa, much of which comprises mostly of crania or sometimes even only teeth. Here we present a rare opportunity to observe the osteohistology of several postcranial elements of the basal prozostrodontid Prozostrodon brasiliensis, the tritheledontid Irajatherium hernandezi, and the brasilodontids Brasilodon quadrangularis and Brasilitherium riograndensis from the Late Triassic of Brazil (Santa Maria Supersequence). Prozostrodon and Irajatherium reveal similar growth patterns of rapid early growth with annual interruptions later in ontogeny. These interruptions are associated with wide zones of slow growing bone tissue. Brasilodon and Brasilitherium exhibit a mixture of woven-fibered bone tissue and slower growing parallel-fibered and lamellar bone. The slower growing bone tissues are present even during early ontogeny. The relatively slower growth in Brasilodon and Brasilitherium may be related to their small body size compared to Prozostrodon and Irajatherium. These brasilodontids also exhibit osteohistological similarities with the Late Triassic/Early Jurassic mammaliaform Morganucodon and the Late Cretaceous multituberculate mammals Kryptobaatar and Nemegtbaatar. This may be due to similar small body sizes, but may also reflect their close phylogenetic affinities as Brasilodon and Brasilitherium are the closest relatives to Mammaliaformes. However, when compared with similar-sized extant placental mammals, they may have grown more slowly to adult size as their osteohistology shows it took more than one year for growth to attenuate. Thus, although they exhibit rapid juvenile growth, the small derived, brasilodontid prozostrodontians still exhibit an extended growth period compared to similar-sized extant mammals. creator: Jennifer Botha-Brink creator: Marina Bento Soares creator: Agustín G. Martinelli uri: https://doi.org/10.7717/peerj.5029 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Botha-Brink et al. title: Nectopsyche of Ecuador: a new species from the high Andean páramo and redescription of Nectopsyche spiloma (Ross) (Trichoptera: Leptoceridae) link: https://peerj.com/articles/4981 last-modified: 2018-06-27 description: The male and female of a new species of long-horned caddisfly, Nectopsyche paramo, are described from the high Andes of Ecuador. The new species was found above 4,000 m, representing the highest recorded elevation for a species in the genus. The larval stage of the species is also described. Only a total of 13 larvae were collected during a 17-month sampling program and 11 adults, suggesting that the species is rare. Larvae were found mainly in leaf packs. A male and female were observed in a mating swarm ca. 3 m above a stream during late afternoon. In addition, we redescribe the adult male of Nectopsyche spiloma (Ross), previously known from Ecuador from unsubstantiated literature records. creator: Ralph W. Holzenthal creator: Blanca Rios-Touma uri: https://doi.org/10.7717/peerj.4981 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Holzenthal and Rios-Touma title: Transcriptome profiling by RNA-Seq reveals differentially expressed genes related to fruit development and ripening characteristics in strawberries (Fragaria × ananassa) link: https://peerj.com/articles/4976 last-modified: 2018-06-27 description: Strawberry (Fragaria × ananassa) is an ideal plant for fruit development and ripening research due to the rapid substantial changes in fruit color, aroma, taste, and softening. To gain deeper insights into the genes that play a central regulatory role in strawberry fruit development and ripening characteristics, transcriptome profiling was performed for the large green fruit, white fruit, turning fruit, and red fruit stages of strawberry. A total of 6,608 differentially expressed genes (DEGs) with 2,643 up-regulated and 3,965 down-regulated genes were identified in the fruit development and ripening process. The DEGs related to fruit flavonoid biosynthesis, starch and sucrose biosynthesis, the citrate cycle, and cell-wall modification enzymes played important roles in the fruit development and ripening process. Particularly, some candidate genes related to the ubiquitin mediated proteolysis pathway and MADS-box were confirmed to be involved in fruit development and ripening according to their possible regulatory functions. A total of five ubiquitin-conjugating enzymes and 10 MADS-box transcription factors were differentially expressed between the four fruit ripening stages. The expression levels of DEGs relating to color, aroma, taste, and softening of fruit were confirmed by quantitative real-time polymerase chain reaction. Our study provides important insights into the complicated regulatory mechanism underlying the fruit ripening characteristics in Fragaria × ananassa. creator: Panpan Hu creator: Gang Li creator: Xia Zhao creator: Fengli Zhao creator: Liangjie Li creator: Houcheng Zhou uri: https://doi.org/10.7717/peerj.4976 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Hu et al. title: Distinctive facial features in idiopathic Moyamoya disease in Caucasians: a first systematic analysis link: https://peerj.com/articles/4740 last-modified: 2018-06-27 description: BackgroundCraniofacial dysmorphic features are morphological changes of the face and skull which are associated with syndromic conditions. Moyamoya angiopathy is a rare cerebral vasculopathy that can be divided into Moyamoya syndrome, which is associated or secondary to other diseases, and into idiopathic Moyamoya disease. Facial dysmorphism has been described in rare genetic syndromes with associated Moyamoya syndrome. However, a direct relationship between idiopathic Moyamoya disease with dysmorphic facial changes is not known yet.MethodsLandmarks were manually placed on frontal photographs of the face of 45 patients with bilateral Moyamoya disease and 50 matched controls. After procrustes alignment of landmarks a multivariate, penalized logistic regression (elastic-net) was performed on geometric features derived from landmark data to classify patients against controls. Classifiers were visualized in importance plots that colorcode importance of geometric locations for the classification decision.ResultsThe classification accuracy for discriminating the total patient group from controls was 82.3% (P-value = 6.3×10−11, binomial test, a-priori chance 50.2%) for an elastic-net classifier. Importance plots show that differences around the eyes and forehead were responsible for the discrimination. Subgroup analysis corrected for body mass index confirmed a similar result.DiscussionResults suggest that there is a resemblance in faces of Caucasian patients with idiopathic Moyamoya disease and that there is a difference to matched controls. Replication of findings is necessary as it is difficult to control all residual confounding in study designs such as ours. If our results would be replicated in a larger cohort, this would be helpful for pathophysiological interpretation and early detection of the disease. creator: Markus Kraemer creator: Quoc Bao Huynh creator: Dagmar Wieczorek creator: Brunilda Balliu creator: Barbara Mikat creator: Stefan Boehringer uri: https://doi.org/10.7717/peerj.4740 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Kraemer et al. title: Huperzine A attenuates nonalcoholic fatty liver disease by regulating hepatocyte senescence and apoptosis: an in vitro study link: https://peerj.com/articles/5145 last-modified: 2018-06-26 description: ObjectiveThis study was undertaken to detect if free fatty acids (FFA) induce hepatocyte senescence in L-02 cells and if huperzine A has an anti-aging effect in fatty liver cells.MethodsL-02 cells were treated with a FFA mixture (oleate/palmitate, at 3:0, 2:1, 1:1, 1:2 and 0:3 ratios) at different concentrations. Cell viability and fat accumulation rate were assessed by a Cell Counting Kit 8 and Nile Red staining, respectively. The mixture with the highest cell viability and fat accumulation rate was selected to continue with the following experiment. The L-02 cells were divided into five groups, including the control group, FFA group, FFA + 0.1 μmol/L huperzine A (LH) group, FFA + 1.0 μmol/L huperzine A (MH) group and FFA + 10 μmol/L huperzine A (HH) group, and were cultured for 24 h. The expression of senescence-associated β-galactosidase (SA-β-gal) was detected by an SA-β-gal staining kit. The expression levels of aging genes were measured by qRT-PCR. The expression levels of apoptosis proteins were detected by a Western blot. ELISA kits were used to detect inflammatory factors and oxidative stress products. The expression of nuclear factor (NF-κB) and IκBα were detected by immunofluorescence.ResultsThe FFA mixture (oleate/palmitate, at a 2:1 ratio) of 0.5 mmol/L had the highest cell viability and fat accumulation rate, which was preferable for establishing an in vitro fatty liver model. The expression of inflammatory factors (TNF-α and IL-6) and oxidants Malonaldehyde (MDA), 4-hydroxynonenal (HNE) and reactive oxygen species (ROS) also increased in the L-02 fatty liver cells. The expression levels of aging markers and aging genes, such as SA-β-gal, p16, p21, p53 and pRb, increased more in the L-02 fatty liver cells than in the L-02 cells. The total levels of the apoptosis-associated proteins Bcl2, Bax, Bax/Bcl-2, CyCt and cleaved caspase 9 were also upregulated in the L-02 fatty liver cells. All of the above genes and proteins were downregulated in the huperzine A and FFA co-treatment group. In the L-02 fatty liver cells, the expression of IκBα decreased, while the expression of NF-κB increased. After the huperzine A and FFA co-treatment, the expression of IκBα increased, while the expression of NF-κB decreased.ConclusionFatty liver cells showed an obvious senescence and apoptosis phenomenon. Huperzine A suppressed hepatocyte senescence, and it might exert its anti-aging effect via the NF-κB pathway. creator: Xiao-na Hu creator: Jiao-feng Wang creator: Yi-qin Huang creator: Zheng Wang creator: Fang-yuan Dong creator: Hai-fen Ma creator: Zhi-jun Bao uri: https://doi.org/10.7717/peerj.5145 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Hu et al. title: A reference cytochrome c oxidase subunit I database curated for hierarchical classification of arthropod metabarcoding data link: https://peerj.com/articles/5126 last-modified: 2018-06-26 description: Metabarcoding is a popular application which warrants continued methods optimization. To maximize barcoding inferences, hierarchy-based sequence classification methods are increasingly common. We present methods for the construction and curation of a database designed for hierarchical classification of a 157 bp barcoding region of the arthropod cytochrome c oxidase subunit I (COI) locus. We produced a comprehensive arthropod COI amplicon dataset including annotated arthropod COI sequences and COI sequences extracted from arthropod whole mitochondrion genomes, the latter of which provided the only source of representation for Zoraptera, Callipodida and Holothyrida. The database contains extracted sequences of the target amplicon from all major arthropod clades, including all insect orders, all arthropod classes and Onychophora, Tardigrada and Mollusca outgroups. During curation, we extracted the COI region of interest from approximately 81 percent of the input sequences, corresponding to 73 percent of the genus-level diversity found in the input data. Further, our analysis revealed a high degree of sequence redundancy within the NCBI nucleotide database, with a mean of approximately 11 sequence entries per species in the input data. The curated, low-redundancy database is included in the Metaxa2 sequence classification software (http://microbiology.se/software/metaxa2/). Using this database with the Metaxa2 classifier, we performed a cross-validation analysis to characterize the relationship between the Metaxa2 reliability score, an estimate of classification confidence, and classification error probability. We used this analysis to select a reliability score threshold which minimized error. We then estimated classification sensitivity, false discovery rate and overclassification, the propensity to classify sequences from taxa not represented in the reference database. Our work will help researchers design and evaluate classification databases and conduct metabarcoding on arthropods and alternate taxa. creator: Rodney T. Richardson creator: Johan Bengtsson-Palme creator: Mary M. Gardiner creator: Reed M. Johnson uri: https://doi.org/10.7717/peerj.5126 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Richardson et al. title: Single-nucleotide polymorphisms of uracil-processing genes affect the occurrence and the onset of recurrent depressive disorder link: https://peerj.com/articles/5116 last-modified: 2018-06-26 description: Depressive disorders (DD) are known to be associated with increased DNA damage, the impairment of DNA damage repair, and the presence of single-nucleotide polymorphisms (SNPs) in DNA damage repair genes. Some indirect evidence also suggests that uracil metabolism may be disrupted in depressed patients. Therefore, the current study genotypes three SNPs localized in genes encoding uracil-processing proteins: two glycosylases, i.e., UNG g.7245G>C (rs34259), SMUG1 c.-31A>G (rs3087404), and dUTPase, i.e., DUT g.48638795G>T (rs4775748). The polymorphisms were analyzed in 585 DNA samples (282 cases and 303 controls) using TaqMan probes. The G/G genotype and G allele of UNG polymorphism decreased the risk of depression, while the G/C genotype and C allele of the same SNP increased it. It was also found that G/G carriers had their first episode significantly later than the heterozygotes. Although there was no association between the occurrence of depression and the SMUG1 SNP, a significant difference was found between the homozygotes regarding the onset of DD. In conclusion, the SNPs localized in the uracil-processing genes may modulate the occurrence and the onset of depression, which further supports the hypothesis that impairment of DNA damage repair, especially base-excision repair, may play an important role in the pathogenesis of the disease. creator: Piotr Czarny creator: Paulina Wigner creator: Justyna Strycharz creator: Cezary Watala creator: Ewa Swiderska creator: Ewelina Synowiec creator: Piotr Galecki creator: Monika Talarowska creator: Janusz Szemraj creator: Kuan-Pin Su creator: Tomasz Sliwinski uri: https://doi.org/10.7717/peerj.5116 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Czarny et al. title: Association of Crohn’s disease-related chromosome 1q32 with ankylosing spondylitis is independent of bowel symptoms and faecal calprotectin link: https://peerj.com/articles/5088 last-modified: 2018-06-26 description: BackgroundGenome-wide association studies have identified a plethora of risk genes for both Crohn’s disease (CD) and ankylosing spondylitis (AS). A subset of genes found to be risk factors for CD have also been found to be risk factors for AS. The objective of our study was to assess whether CD risk genes were associated with non-invasive clinical markers of gut inflammation in patients with AS, indicating a potential subset of patients with clinical as well as genetic overlap.MethodsA total of 308 Caucasian patients who fulfilled the modified New York Criteria for AS, were assessed for bowel symptoms using the Dudley Inflammatory Bowel Symptom Questionnaire (DISQ). Of these patients, 157 also had faecal calprotectin measured. All AS patients and 568 healthy controls were genotyped for 10 CD risk loci using predesigned single nucleotide polymorphism (SNP) genotyping assays. Chi-square analysis was used to test for association between genotype and DISQ score and faecal calprotectin level.ResultsThe minor allele of two SNPs, one in chromosome region 1q32 SNP (rs11584383), and one in the gene coding for IL23R (rs11209026) conferred protection against AS. Only the association of 1q32 remained significant after Bonferroni correction for multiple testing. Stratification by DISQ score and faecal calprotectin did not influence the association of 1q32 with AS.ConclusionIn patients with AS, the association of the CD 1q32 SNP was independent of non-invasive markers of bowel inflammation. Other CD related SNPs were not found have a significant association with AS. creator: Rebecca L. Roberts creator: Mary C. Wallace creator: Andrew A. Harrison creator: Douglas White creator: Nicola Dalbeth creator: Lisa K. Stamp creator: Daniel Ching creator: John Highton creator: Tony R. Merriman creator: Philip C. Robinson creator: Matthew A. Brown creator: Simon M. Stebbings uri: https://doi.org/10.7717/peerj.5088 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Roberts et al. title: Annual plankton community metabolism in estuarine and coastal waters in Perth (Western Australia) link: https://peerj.com/articles/5081 last-modified: 2018-06-26 description: The planktonic metabolic balance that is the balance between gross primary production (GPP) and community respiration (CR) was determined in Matilda Bay (estuarine) and Woodman Point (coastal) in Perth, Western Australia. The rates of net community production (NCP = GPP – CR) and the ratio between GPP and CR (P/R) were assessed to evaluate whether the metabolic balance in the two coastal locations tends to be net autotrophic (production exceeding community respiration) or net heterotrophic (respiration exceeding production). We also analyzed environmental variability by measuring temperature, salinity, and nutrients and chlorophyll a concentration. Samples were collected biweekly from March 2014 to March 2015. During the study period the metabolic rates were three times higher in Matilda Bay than in Woodman Point. The predominant metabolism was net autotrophic at both sites with P/R ratios >1 in the majority of the sampling dates. In Matilda Bay, the metabolic rates were negatively correlated with salinity denoting river dynamics influence, and positively with chlorophyll a. In Woodman Point only the GPP was positively correlated with chlorophyll a. The positive correlation between P/R ratio and GPP in Matilda Bay and the positive correlations between the metabolic rates and chlorophyll a suggest that factors controlling autotrophic processes are modulating the planktonic metabolic balance in the coastal marine ecosystem in Perth. Significant correlations were found between CR and GPP-standardized to chlorophyll a and water temperature. The net autotrophic metabolic balance indicates that in both ecosystems planktonic communities are acting as a sink of CO2 and as a source of organic matter and oxygen to the system and are able to export organic matter to other ecosystems. creator: Susana Agusti creator: Lorena Vigoya creator: Carlos Manuel Duarte uri: https://doi.org/10.7717/peerj.5081 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Agusti et al. title: Synthesis, enzyme inhibitory kinetics mechanism and computational study of N-(4-methoxyphenethyl)-N-(substituted)-4-methylbenzenesulfonamides as novel therapeutic agents for Alzheimer’s disease link: https://peerj.com/articles/4962 last-modified: 2018-06-26 description: The present study comprises the synthesis of a new series of sulfonamides derived from 4-methoxyphenethylamine (1). The synthesis was initiated by the reaction of 1 with 4-methylbenzenesulfonyl chloride (2) in aqueous sodium carbonate solution at pH 9 to yield N-(4-methoxyphenethyl)-4-methylbenzensulfonamide (3).This parent molecule 3 was subsequently treated with various alkyl/aralkyl halides, (4a–j), using N,N-dimethylformamide (DMF) as solvent and LiH as activator to produce a series of new N-(4-methoxyphenethyl)-N-(substituted)-4-methylbenzenesulfonamides (5a–j). The structural characterization of these derivatives was carried out by spectroscopic techniques like IR, 1H-NMR, and 13C-NMR. The elemental analysis data was also coherent with spectral data of these molecules. The inhibitory effects on acetylcholinesterase and DPPH were evaluated and it was observed that N-(4-Methoxyphenethyl)-4-methyl-N-(2-propyl)benzensulfonamide (5c) showed acetylcholinesterase inhibitory activity 0.075 ± 0.001 (IC50 0.075 ± 0.001 µM) comparable to Neostigmine methylsulfate (IC50 2.038 ± 0.039 µM).The docking studies of synthesized ligands 5a–j were also carried out against acetylcholinesterase (PDBID 4PQE) to compare the binding affinities with IC50 values. The kinetic mechanism analyzed by Lineweaver-Burk plots demonstrated that compound (5c) inhibits the acetylcholinesterase competitively to form an enzyme inhibitor complex. The inhibition constants Ki calculated from Dixon plots for compound (5c) is 2.5 µM. It was also found from kinetic analysis that derivative 5c irreversible enzyme inhibitor complex. It is proposed on the basis of our investigation that title compound 5c may serve as lead structure for the design of more potent acetylcholinesterase inhibitors. creator: Muhammad Athar Abbasi creator: Mubashir Hassan creator: Aziz-ur-Rehman creator: Sabahat Zahra Siddiqui creator: Syed Adnan Ali Shah creator: Hussain Raza creator: Sung Yum Seo uri: https://doi.org/10.7717/peerj.4962 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Abbasi et al. title: A new species of Middle Miocene baleen whale from the Nupinai Group, Hikatagawa Formation of Hokkaido, Japan link: https://peerj.com/articles/4934 last-modified: 2018-06-26 description: A fossil whale from the Hikatagawa Formation (Middle Miocene, 15.2–11.5 Ma) of Hokkaido, Japan is described as a new genus and species Taikicetus inouei and its phylogenetic position is examined. Consistent with the result of Marx, Lambert & de Muizon (2017), the Cetotheriidae form a clade with the Balaenopteroidea, and “a clade comprising Isanacetus, Parietobalaena and related taxa” is located basal to the Balaenopteroidea + Cetotheriidae clade. Taikicetus inouei is placed in the clade with most of members of “Cetotheres” sensu lato comprising Isanacetus, Parietobalaena and related taxa. Taikicetus inouei can be distinguished from the other members of “Cetotheres” sensu lato in having an anteriorly swollen short zygomatic process, high triangular coronoid process, and angular process, which does not reach as far posterior as the mandibular condyle. Taikicetus inouei is only record of “Cetotheres” sensu lato from Hokkaido, Japan and the northern-most records of “Cetotheres” sensu lato in Japan. creator: Yoshihiro Tanaka creator: Tatsuro Ando creator: Hiroshi Sawamura uri: https://doi.org/10.7717/peerj.4934 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Tanaka et al. title: Hi-MC: a novel method for high-throughput mitochondrial haplogroup classification link: https://peerj.com/articles/5149 last-modified: 2018-06-25 description: Effective approaches for assessing mitochondrial DNA (mtDNA) variation are important to multiple scientific disciplines. Mitochondrial haplogroups characterize branch points in the phylogeny of mtDNA. Several tools exist for mitochondrial haplogroup classification. However, most require full or partial mtDNA sequence which is often cost prohibitive for studies with large sample sizes. The purpose of this study was to develop Hi-MC, a high-throughput method for mitochondrial haplogroup classification that is cost effective and applicable to large sample sizes making mitochondrial analysis more accessible in genetic studies. Using rigorous selection criteria, we defined and validated a custom panel of mtDNA single nucleotide polymorphisms that allows for accurate classification of European, African, and Native American mitochondrial haplogroups at broad resolution with minimal genotyping and cost. We demonstrate that Hi-MC performs well in samples of European, African, and Native American ancestries, and that Hi-MC performs comparably to a commonly used classifier. Implementation as a software package in R enables users to download and run the program locally, grants greater flexibility in the number of samples that can be run, and allows for easy expansion in future revisions. Hi-MC is available in the CRAN repository and the source code is freely available at https://github.com/vserch/himc. creator: Sandra Smieszek creator: Sabrina L. Mitchell creator: Eric H. Farber-Eger creator: Olivia J. Veatch creator: Nicholas R. Wheeler creator: Robert J. Goodloe creator: Quinn S. Wells creator: Deborah G. Murdock creator: Dana C. Crawford uri: https://doi.org/10.7717/peerj.5149 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Smieszek et al. title: Forecasting influenza epidemics by integrating internet search queries and traditional surveillance data with the support vector machine regression model in Liaoning, from 2011 to 2015 link: https://peerj.com/articles/5134 last-modified: 2018-06-25 description: BackgroundInfluenza epidemics pose significant social and economic challenges in China. Internet search query data have been identified as a valuable source for the detection of emerging influenza epidemics. However, the selection of the search queries and the adoption of prediction methods are crucial challenges when it comes to improving predictions. The purpose of this study was to explore the application of the Support Vector Machine (SVM) regression model in merging search engine query data and traditional influenza data.MethodsThe official monthly reported number of influenza cases in Liaoning province in China was acquired from the China National Scientific Data Center for Public Health from January 2011 to December 2015. Based on Baidu Index, a publicly available search engine database, search queries potentially related to influenza over the corresponding period were identified. An SVM regression model was built to be used for predictions, and the choice of three parameters (C, γ, ε) in the SVM regression model was determined by leave-one-out cross-validation (LOOCV) during the model construction process. The model’s performance was evaluated by the evaluation metrics including Root Mean Square Error, Root Mean Square Percentage Error and Mean Absolute Percentage Error.ResultsIn total, 17 search queries related to influenza were generated through the initial query selection approach and were adopted to construct the SVM regression model, including nine queries in the same month, three queries at a lag of one month, one query at a lag of two months and four queries at a lag of three months. The SVM model performed well when with the parameters (C = 2, γ = 0.005, ɛ = 0.0001), based on the ensemble data integrating the influenza surveillance data and Baidu search query data.ConclusionsThe results demonstrated the feasibility of using internet search engine query data as the complementary data source for influenza surveillance and the efficiency of SVM regression model in tracking the influenza epidemics in Liaoning. creator: Feng Liang creator: Peng Guan creator: Wei Wu creator: Desheng Huang uri: https://doi.org/10.7717/peerj.5134 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Liang et al. title: Complex characterization of oat (Avena sativa L.) lines obtained by wide crossing with maize (Zea mays L.) link: https://peerj.com/articles/5107 last-modified: 2018-06-25 description: BackgroundThe oat × maize addition (OMA) lines are used for mapping of the maize genome, the studies of centromere-specific histone (CENH3), gene expression, meiotic chromosome behavior and also for introducing maize C4 photosynthetic system to oat. The aim of our study was the identification and molecular-cytogenetic characterization of oat × maize hybrids.MethodsOat DH lines and oat × maize hybrids were obtained using the wide crossing of Avena sativa L. with Zea mays L. The plants identified as having a Grande-1 retrotransposon fragment, which produced seeds, were used for genomic in situ hybridization (GISH).ResultsA total of 138 oat lines obtained by crossing of 2,314 oat plants from 80 genotypes with maize cv. Waza were tested for the presence of maize chromosomes. The presence of maize chromatin was indicated in 66 lines by amplification of the PCR product (500 bp) generated using primers specific for the maize retrotransposon Grande-1. Genomic in situ hybridization (GISH) detected whole maize chromosomes in eight lines (40%). All of the analyzed plants possessed full complement of oat chromosomes. The number of maize chromosomes differed between the OMA lines. Four OMA lines possessed two maize chromosomes similar in size, three OMA—one maize chromosome, and one OMA—four maize chromosomes. In most of the lines, the detected chromosomes were labeled uniformly. The presence of six 45S rDNA loci was detected in oat chromosomes, but none of the added maize chromosomes in any of the lines carried 45S rDNA locus. Twenty of the analyzed lines did not possess whole maize chromosomes, but the introgression of maize chromatin in the oat chromosomes. Five of 66 hybrids were shorter in height, grassy type without panicles. Twenty-seven OMA lines were fertile and produced seeds ranging in number from 1–102 (in total 613). Sixty-three fertile DH lines, out of 72 which did not have an addition of maize chromosomes or chromatin, produced seeds in the range of 1–343 (in total 3,758). Obtained DH and OMA lines were fertile and produced seeds.DiscussionIn wide hybridization of oat with maize, the complete or incomplete chromosomes elimination of maize occur. Hybrids of oat and maize had a complete set of oat chromosomes without maize chromosomes, and a complete set of oat chromosomes with one to four retained maize chromosomes. creator: Edyta Skrzypek creator: Tomasz Warzecha creator: Angelika Noga creator: Marzena Warchoł creator: Ilona Czyczyło-Mysza creator: Kinga Dziurka creator: Izabela Marcińska creator: Kamila Kapłoniak creator: Agnieszka Sutkowska creator: Zygmunt Nita creator: Krystyna Werwińska creator: Dominika Idziak-Helmcke creator: Magdalena Rojek creator: Marta Hosiawa-Barańska uri: https://doi.org/10.7717/peerj.5107 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Skrzypek et al. title: Differing responses of red abalone (Haliotis rufescens) and white abalone (H. sorenseni) to infection with phage-associated Candidatus Xenohaliotis californiensis link: https://peerj.com/articles/5104 last-modified: 2018-06-25 description: The Rickettsiales-like prokaryote and causative agent of Withering Syndrome (WS)—Candidatus Xenohaliotis californiensis (Ca. Xc)—decimated black abalone populations along the Pacific coast of North America. White abalone—Haliotis sorenseni—are also susceptible to WS and have become nearly extinct in the wild due to overfishing in the 1970s. Candidatus Xenohaliotis californiensis proliferates within epithelial cells of the abalone gastrointestinal tract and causes clinical signs of starvation. In 2012, evidence of a putative bacteriophage associated with Ca. Xc in red abalone—Haliotis rufescens—was described. Recently, histologic examination of animals with Ca. Xc infection in California abalone populations universally appear to have the phage-containing inclusions. In this study, we investigated the current virulence of Ca. Xc in red abalone and white abalone at different environmental temperatures. Using a comparative experimental design, we observed differences over time between the two abalone species in mortality, body condition, and bacterial load by quantitative real time PCR (qPCR). By day 251, all white abalone exposed to the current variant of Ca. Xc held in the warm water (18.5 °C) treatment died, while red abalone exposed to the same conditions had a mortality rate of only 10%, despite a relatively heavy bacterial burden as determined by qPCR of posterior esophagus tissue and histological assessment at the termination of the experiment. These data support the current status of Ca. Xc as less virulent in red abalone, and may provide correlative evidence of a protective phage interaction. However, white abalone appear to remain highly susceptible to this disease. These findings have important implications for implementation of a white abalone recovery program, particularly with respect to the thermal regimes of locations where captively-reared individuals will be outplanted. creator: Ashley Vater creator: Barbara A. Byrne creator: Blythe C. Marshman creator: Lauren W. Ashlock creator: James D. Moore uri: https://doi.org/10.7717/peerj.5104 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Vater et al. title: Dry season diet composition of four-horned antelope Tetracerus quadricornis in tropical dry deciduous forests, Nepal link: https://peerj.com/articles/5102 last-modified: 2018-06-25 description: It is essential to assess the feeding strategies of threatened species during resource-scarce seasons to understand their dietary niche breadth and inform appropriate habitat management measures. In this study, we examined the diet composition of four-horned antelope (FHA) Tetracerus and quadricornis, one of the least studied ungulate species, in Banke National Park, Nepal. A total of 53 fresh pellet groups were collected between December 2015 and January 2016 and analyzed using micro-histological fecal analysis technique. First, we prepared 133 micro-histological photographs of different parts of 64 reference plant species. Then we compared 1,590 fragments of 53 fecal samples with photographs of reference plants to assess the percentage of occurrence of different plant species in FHA diet. A total of 30 plant species belonging to 18 different families were identified in fecal samples. Chi-square goodness of fit tests showed that FHA appeared not to feed all plant uniformly. Out of 1,520 identified fragments in fecal samples, 1,300 were browse species and 220 were grass species. Browse represented 85.5% of the identified plant fragments, suggesting that FHA might be adopting a browser strategy at least during winter when grasses are low in abundance and their nutritive quality is poor. Tree species had the highest contribution in the diet (46.55%) followed by shrubs (24.52%). The family Gramineae was consumed in the highest proportion (27.68%) followed by Euphorbiaceae (11.95%). Overall, our results suggest that FHA has the feeding plasticity to adapt to resource fluctuation. Based on the findings of this study, we recommend that dicot plant species—particularly fruit trees and shrubs, which are the major source of nutrients for FHA during resource-lean, dry season—be conserved and natural regeneration of these taxa be promoted. creator: Chet Bahadur Oli creator: Saroj Panthi creator: Naresh Subedi creator: Gagan Ale creator: Ganesh Pant creator: Gopal Khanal creator: Suman Bhattarai uri: https://doi.org/10.7717/peerj.5102 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Oli et al. title: Mulch and groundcover effects on soil temperature and moisture, surface reflectance, grapevine water potential, and vineyard weed management link: https://peerj.com/articles/5082 last-modified: 2018-06-25 description: The objectives of this research were to identify alternatives to glyphosate for intra-row (under-trellis) vineyard floor management and to evaluate the potential for intra-row and inter-row (alleyway) groundcovers to reduce vegetative vigor of ‘Marquette’ grapevines (Vitis spp.) in a southeast Nebraska vineyard. The experiment was a randomized factorial design with five intra-row treatments (crushed glass mulch [CG], distillers’ grain mulch [DG], creeping red fescue [CRF], non-sprayed control [NSC], and glyphosate [GLY]) and three inter-row treatments (creeping red fescue [CRF], Kentucky bluegrass [KB], and resident vegetation [RV]). Treatments were established in 2010–2011 and measurements were conducted during 2012 and 2013 on 5- and 6-year-old vines. Soil temperatures were mostly higher under mulches and lower under intra-row groundcovers, compared to GLY. Weed cover in CG, DG, and CRF treatments was the same or less than GLY. At most sampling dates, inter-row soil moisture was lowest under KB. Intra-row soil moisture was highest under DG mulch and lowest under CRF and NSC; CG had the same or lower soil moisture than GLY. Surprisingly, we did not detect differences in mid-day photosynthetically active radiation (PAR) reflectance, despite visual differences among the intra-row treatments. Mid-day vine water potential did not differ among treatments. We concluded it is not necessary to maintain a bare soil strip under established vines in this region, where soil fertility and moisture are non-limiting. creator: Christina M. Bavougian creator: Paul E. Read uri: https://doi.org/10.7717/peerj.5082 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Bavougian and Read title: It’s a matter of design—how pitfall trap design affects trap samples and possible predictions link: https://peerj.com/articles/5078 last-modified: 2018-06-25 description: BackgroundPitfall traps are commonly used to assess ground dwelling arthropod communities. The effects of different pitfall trap designs on the trapping outcome are poorly investigated however they might affect conclusions drawn from pitfall trap data greatly.MethodsWe tested four pitfall trap types which have been used in previous studies for their effectiveness: a simple type, a faster exchangeable type with an extended plastic rim plate and two types with guidance barriers (V- and X-shaped). About 20 traps were active for 10 weeks and emptied biweekly resulting in 100 trap samples.ResultsPitfall traps with guidance barriers were up to five times more effective than simple pitfall traps and trap samples resulted in more similar assemblage approximations. Pitfall traps with extended plastic rim plates did not only perform poorly but also resulted in distinct carabid assemblages with less individuals of small species and a larger variation.DiscussionDue to the obvious trait filtering and resulting altered assemblages, we suggest not to use pitfall traps with extended plastic rim plates. In comprehensive biodiversity inventories, a smaller number of pitfall traps with guidance barriers and a larger number of spatial replicates is of advantage, while due to comparability reasons, the use of simple pitfall traps will be recommended in most other cases. creator: Fabian A. Boetzl creator: Elena Ries creator: Gudrun Schneider creator: Jochen Krauss uri: https://doi.org/10.7717/peerj.5078 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Boetzl et al. title: Potamopyrgus antipodarum as a potential defender against swimmer’s itch in European recreational water bodies—experimental study link: https://peerj.com/articles/5045 last-modified: 2018-06-25 description: Swimmer’s itch is a re-emerging human disease caused by bird schistosome cercariae, which can infect bathing or working people in water bodies. Even if cercariae fail after penetrating the human skin, they can cause dangerous symptoms in atypical mammal hosts. One of the natural methods to reduce the presence of cercariae in the environment could lie in the introduction of non–host snail species to the ecosystem, which is known as the “dilution” or “decoy” effect. The caenogastropod Potamopyrgus antipodarum—an alien in Europe—could be a good candidate against swimmer’s itch because of its apparent resistance to invasion by European bird schistosome species and its high population density. As a pilot study on this topic, we have carried out a laboratory experiment on how P. antipodarum influences the infestation of the intermediate host Radix balthica (a native lymnaeid) by the bird schistosome Trichobilharzia regenti. We found that the co–exposure of 200 P. antipodarum individuals per one R. balthica to the T. regenti miracidia under experimental conditions makes the infestation ineffective. Our results show that a non–host snail population has the potential to interfere with the transmission of a trematode via suitable snail hosts. creator: Anna Marszewska creator: Anna Cichy creator: Jana Bulantová creator: Petr Horák creator: Elżbieta Żbikowska uri: https://doi.org/10.7717/peerj.5045 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Marszewska et al. title: Nitrogen addition increases the contents of glomalin-related soil protein and soil organic carbon but retains aggregate stability in a Pinus tabulaeformis forest link: https://peerj.com/articles/5039 last-modified: 2018-06-25 description: BackgroundGlomalin-related soil protein (GRSP) and soil organic carbon (SOC) contribute to the formation and stability of soil aggregates, but the mechanism by which global atmospheric nitrogen (N) deposition changes soil aggregate stability by altering the distribution of GRSP and SOC in different aggregate fractions remains unknown.MethodsWe used a gradient N addition (0–9 g N m−2 y−1) in Pinus tabulaeformis forest for two years in northeast China and then examined the changes in SOC contents, total GRSP (T-GRSP), and easily extractable GRSP (EE-GRSP) contents in three soil aggregate fractions (macro-aggregate: >250 μm, micro-aggregate: 250–53 μm, and fine material: <53 μm) and their relationship with aggregate stability.Results(1) The soil was dominated by macro-aggregates. Short term N addition had no significant effect on mean weight diameter (MWD) and geometric mean diameter (GMD). (2) GRSP varied among aggregate fractions, and N addition had different effects on the distribution of GRSP in aggregate fractions. The EE-GRSP content in the macro-aggregates increased initially and then decreased with increasing N addition levels, having a peak value of 0.480 mg g−1 at 6 g N m−2 y−1. The micro-aggregates had the lowest EE-GRSP content (0.148 mg g−1) at 6 g N m−2 y−1. Furthermore, the T-GRSP content significantly increased in the aggregate fractions with the N addition levels. (3) The macro-aggregate had the highest SOC content, followed by the micro-aggregate and the fine material had the lowest SOC content. N addition significantly increased the SOC content in all the aggregate fractions. (4) GRSP and SOC contents were not significantly correlated with MWD.ConclusionGlomalin-related soil protein and SOC contents increased by N addition, but this increase did not enhance aggregate stability in short term, and the improvement of stability might depend on binding agents and incubation time. creator: Lipeng Sun creator: Hang Jing creator: Guoliang Wang creator: Guobin Liu uri: https://doi.org/10.7717/peerj.5039 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Sun et al. title: Specalyzer—an interactive online tool to analyze spectral reflectance measurements link: https://peerj.com/articles/5031 last-modified: 2018-06-25 description: Low-cost phenotyping using proximal sensors is increasingly becoming popular in plant breeding. As these techniques generate a large amount of data, analysis pipelines that do not require expertise in computer programming can benefit a broader user base. In this work, a new online tool Specalyzer is presented that allows interactive analysis of the spectral reflectance data generated by proximal spectroradiometers. Specalyzer can be operated from any web browser allowing data uploading, analysis, interactive plots and exporting by point and click using a simple graphical user interface. Specalyzer is evaluated with case study data from a winter wheat fertilizer trial with two fertilizer treatments. Specalyzer can be accessed online at http://www.specalyzer.org. creator: Alexander Koc creator: Tina Henriksson creator: Aakash Chawade uri: https://doi.org/10.7717/peerj.5031 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Koc et al. title: Alpha-mangostin inhibits the migration and invasion of A549 lung cancer cells link: https://peerj.com/articles/5027 last-modified: 2018-06-25 description: Several studies have indicated that α-mangostin exerts anti-metastasis and anti-subsistence effects on several types of cancer cells. Especially, the anti-metastatic effect of α-mangostin on cancer cells is a prospective function in cancer treatment. However, the metastasis process is complicated, and includes migration, invasion, intravasation, and extravasation; thus, the main target of anti-metastatic effect of α-mangostin is not known. In this study, we investigated the effects of α-mangostin on the invasion, subsistence, and migration of lung cancer cells under co-culture conditions with normal cells and regular mono-culture conditions. We found that α-mangostin killed the lung cancer and normal cells in a dose-dependent manner. Furthermore, the alteration in the surface mechanical properties of cells was examined by using atomic force microscopy. Although the α-mangostin concentrations of 5 and 10 µM did not affect the short-term cell viability, they considerably decreased the Young’s modulus of lung cancer cells implying a decline in cell surface actin cytoskeletal properties. Additionally, these concentrations of α-mangostin inhibited the migration of lung cancer cells. In co-culture conditions (cancer cells with normal cells), the invasive activities of cancer cells on normal cells were discernibly observed, and was inhibited after treatment with 5 and 10 µM of α-mangostin. Taken together, α-mangostin suppressed the subsistence of lung cancer cells and displayed anti-metastatic activities by inhibiting the migration and invasion, and reducing the actin cytoskeleton of cancer cells. Our findings suggest that α-mangostin could be a potential therapeutic agent for cancer treatment. creator: Thi Kieu Trang Phan creator: Fahimeh Shahbazzadeh creator: Thi Thu Huong Pham creator: Takanori Kihara uri: https://doi.org/10.7717/peerj.5027 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Phan et al. title: DNA barcoding of marine fish species from Rongcheng Bay, China link: https://peerj.com/articles/5013 last-modified: 2018-06-25 description: Rongcheng Bay is a coastal bay of the Northern Yellow Sea, China. To investigate and monitor the fish resources in Rongcheng Bay, 187 specimens from 41 different species belonging to 28 families in nine orders were DNA-barcoded using the mitochondrial cytochrome c oxidase subunit I gene (COI). Most of the fish species could be discriminated using this COI sequence with the exception of Cynoglossus joyneri and Cynoglossus lighti. The average GC% content of the 41 fish species was 47.3%. The average Kimura 2-parameter genetic distances within the species, genera, families, and orders were 0.21%, 5.28%, 21.30%, and 23.63%, respectively. Our results confirmed that the use of combined morphological and DNA barcoding identification methods facilitated fish species identification in Rongcheng Bay, and also established a reliable DNA barcode reference library for these fish. DNA barcodes will contribute to future efforts to achieve better monitoring, conservation, and management of fisheries in this area. creator: Lijuan Wang creator: Zhihao Wu creator: Mengxia Liu creator: Wei Liu creator: Wenxi Zhao creator: Hongjun Liu creator: Feng You uri: https://doi.org/10.7717/peerj.5013 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Wang et al. title: Effects of temperature and salinity stress on DNA methylation in a highly invasive marine invertebrate, the colonial ascidian Didemnum vexillum link: https://peerj.com/articles/5003 last-modified: 2018-06-25 description: Environmentally induced epigenetic changes may contribute to phenotypic plasticity, increase adaptive potential in changing environments, and play a key role in the establishment and spread of invasive species in new habitats. In this study, we used methylation-sensitive amplified polymorphism (MSAP) to assess environmentally induced DNA methylation changes in a globally invasive clonal ascidian, Didemnum vexillum. We tested the effect of increasing temperature (19, 25 and 27 °C) and decreasing salinity (34, 32, 30, 28 and 26 practical salinity units (PSU)) on global DNA methylation, growth and survival rates. Exposure to 27 °C resulted in significant changes in DNA methylation over time. Growth also decreased in colonies exposed to high temperatures, suggesting they were under thermal stress. In contrast, no differences in growth nor DNA methylation patterns were observed in colonies exposed to a decreasing salinity gradient, potentially due to prior adaptation. The results of this study show that environmental stress can induce significant global DNA methylation changes in an invasive marine invertebrate on very rapid timescales, and that this response varies depending on the type, magnitude, and duration of the stressor. Changes in genomic DNA methylation and the rate of growth may act to ‘buy survival time’ under stressful conditions, expanding the distribution limits of this globally invasive species. creator: Nicola A. Hawes creator: Louis A. Tremblay creator: Xavier Pochon creator: Brendon Dunphy creator: Andrew E. Fidler creator: Kirsty F. Smith uri: https://doi.org/10.7717/peerj.5003 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Hawes et al. title: Disentangling the link between supplemental feeding, population density, and the prevalence of pathogens in urban stray cats link: https://peerj.com/articles/4988 last-modified: 2018-06-25 description: BackgroundSupplemental feeding of free-roaming animals, including wildlife and feral or stray animals, is well known to have a substantial impact on various aspects of animal ecology including habitat use, activity patterns, and host-pathogen interactions. Among them, an increased population density (PD) of animals receiving supplemental food raises concerns regarding the transmission of pathogens in these host populations. The primary aim of this study was to investigate how supplemental feeding is associated with host PD and prevalence of pathogens with different transmission modes in urban stray cats. We hypothesized that supplemental feeding would be positively associated with host PD and the prevalence of pathogens with density-dependent transmission modes compared with pathogens with transmission modes that are considered relatively density-independent.MethodsThis study was conducted in six districts in Seoul, Republic of Korea which were selected based on different degrees of supplemental feeding and cat caretaker activity (CCA). The PD of stray cats was estimated by mark-recapture surveys. Stray cat blood samples (N = 302) were collected from stray cats by local animal hospitals from each district performing the trap-neuter-release which tested for eight pathogens with different transmission modes (feline immunodeficiency virus, feline leukemia virus (FeLV), feline panleukopenia virus, feline calicivirus, feline herpesvirus-1, Bartonella henselae, hemoplasma, and Toxoplasma gondii) with molecular or serological assays. Associations between the prevalence of each pathogen and PD, CCA, and sex of cats were statistically analyzed.ResultsIn contrast to initial predictions, the cat PD was generally higher in low CCA districts. The prevalence of (FeLV), which is transmitted through direct contact, was significantly higher in areas with a high CCA, conforming to our hypothesis. On the other hand, the prevalence of feline parvovirus, which can be spread by environmental transmission, was higher in low CCA districts. The remaining six pathogens did not show any association with the CCA; however, they had a unique association with the PD or the sex of the stray cats.DiscussionOur findings suggest that in addition to influencing the PD, supplemental feeding may affect the prevalence of pathogens in urban animals by mechanisms such as increased aggregation and/or altered foraging strategies, with different consequences depending on the transmission mode of each pathogen. creator: Jusun Hwang creator: Nicole L. Gottdenker creator: Dae-Hyun Oh creator: Ho-Woo Nam creator: Hang Lee creator: Myung-Sun Chun uri: https://doi.org/10.7717/peerj.4988 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Hwang et al. title: Systematics and phylogeny of the Zygodactylidae (Aves, Neognathae) with description of a new species from the early Eocene of Wyoming, USA link: https://peerj.com/articles/4950 last-modified: 2018-06-25 description: Zygodactylidae are an extinct lineage of perching birds characterized by distinct morphologies of the foot and wing elements. Although the clade has a complex taxonomic history, current hypotheses place Zygodactylidae as the sister taxon to Passeriformes (i.e., songbirds). Given the rather sparse fossil record of early passeriforms, the description of zygodactylid taxa is important for inferring potentially ancestral states in the largest radiation of living birds (i.e., the ∼6,000 species of extant passeriforms). Despite the exceptional preservation of many specimens and considerable species diversity in Zygodactylidae, the relationships among species have not been previously evaluated in a phylogenetic context. Herein, we review the fossil record of Zygodactylidae from North America and describe five new well-preserved fossils from the early Eocene Green River Formation of Wyoming. Two specimens are identified as representing a new species and the first records of the taxon Zygodactylus outside Europe. Anatomical comparisons with previously named taxa and the results of phylogenetic analysis including newly described specimens and previously named zygodactylid taxa provide the first hypothesis of the species-level relationships among zygodactylids. The monophyly of Zygodactylidae is supported in these new analyses. However, the monophyly of Primozygodactylus and the taxonomic distinction between Zygodactylus and Eozygodactylus remain unresolved and would likely benefit from the description of additional specimens. creator: N. Adam Smith creator: Aj M. DeBee creator: Julia A. Clarke uri: https://doi.org/10.7717/peerj.4950 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Smith et al. title: Prevalence of extended spectrum beta lactamase and plasmid mediated quinolone resistant genes in strains of Klebsiella pneumonia, Morganella morganii, Leclercia adecarboxylata and Citrobacter freundii isolated from poultry in South Western Nigeria link: https://peerj.com/articles/5053 last-modified: 2018-06-22 description: A serious concern is arising on the coexistence of extended-spectrum beta-lactamase (ESBL) and plasmid mediated quinolone resistance (PMQR) producing bacteria in animal husbandry, which could be transferred to humans, especially in strains that may not be routinely screened for resistance. This study therefore tested the prevalence of ESBL and PMQR genes in selected bacteria isolated from poultry faeces. Faecal droppings of birds were collected from 11 farms in five states in South Western Nigeria. Bacteria were isolated from the samples on cefotaxime supplemented plates and identified with MALDI-TOF. The MIC was determined using VITEK system and resistance genes were detected with PCR. A total of 350 strains were isolated from different samples and selected strains were identified as 23 Klebsiella pneumonia, 12 Morganella morganii, seven Leclercia adecarboxylata and one Citrobacter freundii. All the species were resistant to gentamycin, trimethoprim/sulphamethaxole, tobramycin, piperacillin, cefotaxime and aztreonam (except Morganella morganii strains which were mostly susceptible to aztreonam). All the tested strains were susceptible to imipenem, meropenem and amikacin. All Leclercia adecarboxylata strains were resistant to ceftazidime, cefepime and fosfomycin while all Morganella morganii strains were resistant to fosfomycin, moxifloxacin and ciprofloxacin. All tested species were generally sensitive to ciprofloxacin except Morganella morganii strains which were resistant to ciprofloxacin. The resistance to ciprofloxacin, ceftazidime, cefepime, tigercylin, colistin and fosfomycin were 65%, 40%, 23%,, 7%, 33%, 48% respectively while the prevalence of SHV, TEM and CTX genes were 42%, 63%, 35% respectively. 9.3% of the isolates had the three ESBL genes, 2.33% had qnrA gene, 4.65% had qnr B gene while none had qnrS gene. The most prevalent PMQR gene is Oqxb (25.58%) while 6.98% had the qep gene. Klebsiella pneumoniae generally had both ESBL and PMQR genes. The high prevalence of extended spectrum beta-lactamase genes in the studied strains calls for caution in the use of beta lactam antibiotics in poultry feeds. This is the first report of the occurrence of extended spectrum beta-lactamase and plasmid mediated quinolone resistance genes in Morganella morganii and Leclercia adecarboxylata strains isolated from poultry faeces. creator: Olajumoke R. Akinbami creator: Samson Olofinsae creator: Funmilola A. Ayeni uri: https://doi.org/10.7717/peerj.5053 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Akinbami et al. title: Spatio-temporal evolution of water-related ecosystem services: Taihu Basin, China link: https://peerj.com/articles/5041 last-modified: 2018-06-22 description: Water-related ecosystem services (WESs) arise from the interaction between water ecosystems and their surrounding terrestrial ecosystems. They are critical for human well-being as well as for the whole ecological circle. An urgent service-oriented reform for the utilization and supervision of WESs can assist in avoiding ecological risks and achieving a more sustainable development in the Taihu Basin, China (THB). Spatially distributed models allow the multiple impacts of land use/land cover conversion and climate variation on WESs to be estimated and visualized efficiently, and such models can form a useful component in the toolbox for integrated water ecosystem management. The Integrated Valuation of Ecosystem Services and Tradeoffs model is used here to evaluate and visualize the spatio-temporal evolution of WESs in the THB from 2000 to 2010. Results indicate that water retention service experienced a decline from 2000 to 2005 with a recovery after 2005, while there was ongoing water scarcity in urban areas. Both the water purification service and the soil retention service underwent a slight decrease over the study period. Nutrients export mainly came from developed land and cultivated land, with the hilly areas in the south of the THB forming the primary area for soil loss. The quantity and distribution of WESs were impacted significantly by the shrinkage of cultivated land and the expansion of developed land. These findings will lay a foundation for a service-oriented management of WESs in the THB and support evidence-based decision making. creator: Junyu Chen creator: Tao Cui creator: Huimin Wang creator: Gang Liu creator: Mat Gilfedder creator: Yang Bai uri: https://doi.org/10.7717/peerj.5041 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Chen et al. title: Low resolution scans can provide a sufficiently accurate, cost- and time-effective alternative to high resolution scans for 3D shape analyses link: https://peerj.com/articles/5032 last-modified: 2018-06-22 description: BackgroundAdvances in 3D shape capture technology have made powerful shape analyses, such as geometric morphometrics, more feasible. While the highly accurate micro-computed tomography (µCT) scanners have been the “gold standard,” recent improvements in 3D surface scanners may make this technology a faster, portable, and cost-effective alternative. Several studies have already compared the two devices but all use relatively large specimens such as human crania. Here we perform shape analyses on Australia’s smallest rodent to test whether a 3D scanner produces similar results to a µCT scanner.MethodsWe captured 19 delicate mouse (Pseudomys delicatulus) crania with a µCT scanner and a 3D scanner for geometric morphometrics. We ran multiple Procrustes ANOVAs to test how variation due to scan device compared to other sources such as biologically relevant variation and operator error. We quantified operator error as levels of variation and repeatability. Further, we tested if the two devices performed differently at classifying individuals based on sexual dimorphism. Finally, we inspected scatterplots of principal component analysis (PCA) scores for non-random patterns.ResultsIn all Procrustes ANOVAs, regardless of factors included, differences between individuals contributed the most to total variation. The PCA plots reflect this in how the individuals are dispersed. Including only the symmetric component of shape increased the biological signal relative to variation due to device and due to error. 3D scans showed a higher level of operator error as evidenced by a greater spread of their replicates on the PCA, a higher level of multivariate variation, and a lower repeatability score. However, the 3D scan and µCT scan datasets performed identically in classifying individuals based on intra-specific patterns of sexual dimorphism.DiscussionCompared to µCT scans, we find that even low resolution 3D scans of very small specimens are sufficiently accurate to classify intra-specific differences. We also make three recommendations for best use of low resolution data. First, we recommend that extreme caution should be taken when analyzing the asymmetric component of shape variation. Second, using 3D scans generates more random error due to increased landmarking difficulty, therefore users should be conservative in landmark choice and avoid multiple operators. Third, using 3D scans introduces a source of systematic error relative to µCT scans, therefore we recommend not combining them when possible, especially in studies expecting little biological variation. Our findings support increased use of low resolution 3D scans for most morphological studies; they are likely also applicable to low resolution scans of large specimens made in a medical CT scanner. As most vertebrates are relatively small, we anticipate our results will bolster more researchers in designing affordable large scale studies on small specimens with 3D surface scanners. creator: Ariel E. Marcy creator: Carmelo Fruciano creator: Matthew J. Phillips creator: Karine Mardon creator: Vera Weisbecker uri: https://doi.org/10.7717/peerj.5032 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Marcy et al. title: A Miocene pygmy right whale fossil from Australia link: https://peerj.com/articles/5025 last-modified: 2018-06-22 description: Neobalaenines are an enigmatic group of baleen whales represented today by a single living species: the pygmy right whale, Caperea marginata, found only in the Southern Hemisphere. Molecular divergence estimates date the origin of pygmy right whales to 22–26 Ma, yet so far there are only three confirmed fossil occurrences. Here, we describe an isolated periotic from the latest Miocene of Victoria (Australia). The new fossil shows all the hallmarks of Caperea, making it the second-oldest described neobalaenine, and the oldest record of the genus. Overall, the new specimen resembles C. marginata in its external morphology and details of the cochlea, but is more archaic in it having a hypertrophied suprameatal area and a greater number of cochlear turns. The presence of Caperea in Australian waters during the Late Miocene matches the distribution of the living species, and supports a southern origin for pygmy right whales. creator: Felix G. Marx creator: Travis Park creator: Erich M.G. Fitzgerald creator: Alistair R. Evans uri: https://doi.org/10.7717/peerj.5025 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Marx et al. title: Effects of equal-volume resistance training with different training frequencies in muscle size and strength in trained men link: https://peerj.com/articles/5020 last-modified: 2018-06-22 description: BackgroundThe objective of the present study was to compare the effects of equal-volume resistance training (RT) performed with different training frequencies on muscle size and strength in trained young men.MethodsSixteen men with at least one year of RT experience were divided into two groups, G1 and G2, that trained each muscle group once and twice a week, respectively, for 10 weeks. Elbow flexor muscle thickness (MT) was measured using a B-Mode ultrasound and concentric peak torque of elbow extensors and flexors were assessed by an isokinetic dynamometer.ResultsANOVA did not reveal group by time interactions for any variable, indicating no difference between groups for the changes in MT or PT of elbow flexors and extensors. Notwithstanding, MT of elbow flexors increased significantly (3.1%, P < 0.05) only in G1. PT of elbow flexors and extensors did not increase significantly for any group.DiscussionThe present study suggest that there were no differences in the results promoted by equal-volume resistance training performed once or twice a week on upper body muscle strength in trained men. Only the group performing one session per week significantly increased the MT of their elbow flexors. However, with either once or twice a week training, adaptations appear largely minimal in previously trained males. creator: Paulo Gentil creator: James Fisher creator: James Steele creator: Mario H. Campos creator: Marcelo H. Silva creator: Antonio Paoli creator: Jurgen Giessing creator: Martim Bottaro uri: https://doi.org/10.7717/peerj.5020 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Gentil et al. title: Melatonin significantly influences seed germination and seedling growth of Stevia rebaudiana Bertoni link: https://peerj.com/articles/5009 last-modified: 2018-06-22 description: BackgroundMelatonin (MEL) is a signaling molecule in plants that affects developmental processes during vegetative and reproductive growth. Investigations have proved that exogenously applied MEL also has the potential to improve seed germination and plant development.MethodsIn the present study, seeds of stevia, a species with a very low germination rate, were germinated on an agar gel (AG) containing MEL at various concentrations (5, 20, 100, and 500 µM) in light. Seeds germinated on AG without MEL were used as controls. For the first 24 or 48 h of germination, the seeds were maintained in darkness as a pre-incubation step. Some seeds were not exposed to this pre-incubation step.ResultsAt concentrations of 20 and 5 µM, MEL significantly improved germination, but only in seeds pre-incubated in darkness for 24 h (p < 0.001). At concentrations of 100 and 500 µM, MEL had an inhibitory effect on germination, regardless of the pre-incubation time. Melatonin also affected plantlet properties. At a concentration of 20 µM, MEL increased plantlet fresh weight and leaf numbers. At a concentration of 5 µM, it promoted plantlet height. Regarding root development, the most favorable MEL concentration was 500 µM. Biochemical analysis revealed that MEL promoted higher pigment concentrations but hampered superoxide dismutase activity. On the other hand, the concentrations of sugars and phenolics, as well as the activities of catalase and peroxidase, increased at a MEL concentration of 500 µM.DiscussionThe results suggest that MEL can improve germination of positively photoblastic stevia seeds and that it can play a role in plantlet development. However, the effects observed in the present study depended on the quantity of MEL that was applied. creator: Magdalena Simlat creator: Agata Ptak creator: Edyta Skrzypek creator: Marzena Warchoł creator: Emilia Morańska creator: Ewa Piórkowska uri: https://doi.org/10.7717/peerj.5009 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Simlat et al. title: Vertical stratification of plant–pollinator interactions in a temperate grassland link: https://peerj.com/articles/4998 last-modified: 2018-06-22 description: Visitation of plants by different pollinators depends on individual plant traits, spatial context, and other factors. A neglected aspect of small-scale variation of plant–pollinator interactions is the role of vertical position of flowers. We conducted a series of experiments to study vertical stratification of plant–pollinator interactions in a dry grassland. We observed flower visitors on cut inflorescences of Centaurea scabiosa and Inula salicina placed at different heights above ground in two types of surrounding vegetation: short and tall. Even at such a small-scale, we detected significant shift in total visitation rate of inflorescences in response to their vertical position. In short vegetation, inflorescences close to the ground were visited more frequently, while in tall vegetation, inflorescences placed higher received more visits. Moreover, we found major differences in the composition of the pollinator community on flowers at different heights. In a second experiment, we measured flower visitation rate in inflorescences of Salvia verticillata of variable height. Total flower visitation rate increased markedly with inflorescence height in this case. Data on seed set of individual plants provide evidence for a corresponding positive pollinator-mediated selection on increased inflorescence height. Overall, our results demonstrate strong vertical stratification of plant–pollinator interactions at the scale of mere decimetres. This may have important ecological as well as evolutionary implications. creator: Jan Klecka creator: Jiří Hadrava creator: Pavla Koloušková uri: https://doi.org/10.7717/peerj.4998 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Klecka et al. title: Is publication bias present in gastroenterological research? An analysis of abstracts presented at an annual congress link: https://peerj.com/articles/4995 last-modified: 2018-06-22 description: BackgroundPublication bias is the tendency of investigators, reviewers, and editors to submit or accept manuscripts for publication based on their direction or strength of findings. In this study, we investigated if publication bias was present in gastroenterological research by evaluating abstracts at Americas Hepato-Pancreato-Biliary Congresses from 2011 to 2013.MethodsWe searched Google, Google Scholar, and PubMed to locate the published reports of research described in these abstracts. If a publication was not found, a second investigator searched to verify nonpublication. If abstract publication status remained undetermined, authors were contacted regarding reasons for nonpublication. For articles reaching publication, the P value, study design, time to publication, citation count, and journals in which the published report appeared were recorded.ResultsOur study found that of 569 abstracts presented, 297 (52.2%) reported a P value. Of these, 254 (85.5%) contained P values supporting statistical significance. The abstracts reporting a statistically significant outcome were twice as likely to reach publication than abstracts with no significant findings (OR 2.10, 95% CI [1.06–4.14]). Overall, 243 (42.7%) abstracts reached publication. The mean time to publication was 14 months and a median time of nine months.ConclusionIn conclusion, we found evidence for publication bias in gastroenterological research. Abstracts with significant P values had a higher probability of reaching publication. More than half of abstracts presented from 2011 to 2013 failed to reach publication. Readers should take these findings into consideration when reviewing medical literature. creator: Chase Meyer creator: Kaleb Fuller creator: Jared Scott creator: Matt Vassar uri: https://doi.org/10.7717/peerj.4995 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Meyer et al. title: Predicted effects of landscape change, sea level rise, and habitat management on the extirpation risk of the Hawaiian common gallinule (Gallinula galeata sandvicensis) on the island of O‘ahu link: https://peerj.com/articles/4990 last-modified: 2018-06-22 description: We conducted a spatially explicit, stochastic, individually based population viability analysis for the Hawaiian common gallinule (Gallinula galeata sandvicensis), an endangered subspecies of waterbird endemic to fragmented coastal wetlands in Hawai‘i. This subspecies persists on two islands, with no apparent movement between them. We assessed extirpation risk for birds on O‘ahu, where the resident gallinule population is made up of several fragmented subpopulations. Data on genetic differentiation were used to delineate subpopulations and estimate dispersal rates between them. We used sensitivity analyses to gauge the impact of current uncertainty of vital rate parameters on population projections, to ascertain the relative importance of gallinule vital rates to population persistence, and to compare the efficacy of potential management strategies. We used available sea level rise projections to examine the relative vulnerability of O‘ahu’s gallinule population to habitat loss arising from this threat. Our model predicted persistence of the island’s gallinule population at 160 years (∼40 generations), but with high probabilities of extirpation for small subpopulations. Sensitivity analyses highlighted the importance of juvenile and adult mortality to population persistence in Hawaiian gallinules, justifying current predator control efforts and suggesting the need for additional research on chick and fledgling survival. Subpopulation connectivity from dispersal had little effect on the persistence of the island-wide population, but strong effects on the persistence of smaller subpopulations. Our model also predicted island-wide population persistence under predicted sea level rise scenarios, but with O‘ahu’s largest gallinule populations losing >40% of current carrying capacity. creator: Charles B. van Rees creator: J. Michael Reed uri: https://doi.org/10.7717/peerj.4990 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 van Rees and Reed title: High prevalence of Lynx rufus gammaherpesvirus 1 in wild Vermont bobcats link: https://peerj.com/articles/4982 last-modified: 2018-06-22 description: Gammaherpesviruses (GHVs) are host specific DNA viruses that infect a large range of mammalian species. These viruses preferentially target host lymphocyte cell populations and infection may lead to morbidity or mortality in immunocompromised, co-infected, or non-adapted hosts. In this study, we tested for the presence of Lynx rufus gammaherpesvirus 1 (LruGHV1) in a northeastern United States population of wild bobcats (L. rufus). We estimated prevalence of infection and viral load in infected individuals using quantitative real-time PCR analysis of spleen DNA from 64 Vermont bobcats. We observed an overall prevalence of 64% using this methodology. Bobcat age was significantly positively associated with GHV infection status, and we noted a trend for higher viral loads in young animals, but prevalence and viral load were similar in male and female bobcats. A single LruGHV1 variant was identified from the sequencing of the viral glycoprotein B gene of Vermont bobcats. This gene sequence was 100% similar to that reported in Florida bobcats and slightly variant from other isolates identified in the Western USA. Our work suggests broad geographic distribution and high prevalence of LruGHV1 in bobcat populations across the United States with infection attributes that suggest horizontal transmission of the agent. Geographic differences in viral genotype may reflect historical migration and expansion events among bobcat populations. creator: Dagan A. Loisel creator: Ryan M. Troyer creator: Sue VandeWoude uri: https://doi.org/10.7717/peerj.4982 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Loisel et al. title: Cities may save some threatened species but not their ecological functions link: https://peerj.com/articles/4908 last-modified: 2018-06-22 description: BackgroundUrbanization is one of the main causes of biodiversity loss worldwide. Wildlife responses to urbanization, however, are greatly variable and, paradoxically, some threatened species may achieve much larger populations in urban than in natural habitats. Urban conservation hotspots may therefore help some species avoid regional or even global extinctions, but not conserve their often overlooked ecological functions in the wild. We aim to draw attention to this issue using two species of globally threatened parrots occurring in the Dominican Republic: the Hispaniolan amazon (Amazona ventralis) and the Hispaniolan parakeet (Psittacara chloropterus).MethodsWe conducted a large-scale roadside survey in June 2017 across the country to estimate the relative abundance of parrots in natural habitats, rural habitats, and cities. We combined this with informal interviews with local people to collect information on past and current human impacts on parrot populations. We also looked for foraging parrots to assess their potential role as seed dispersers, an ecological function that has been overlooked until very recently.ResultsRelative abundances of both parrot species were negligible in rural areas and very low in natural habitats. They were generally between one and two orders of magnitude lower than that of congeneric species inhabiting other Neotropical ecosystems. Relative abundances were six times higher in cities than in natural habitats in the case of the Hispaniolan parakeet and three times higher in the case of the Hispaniolan amazon. People indicated hunting for a source food and to mitigate crop damage as causes of parrot population declines, and a vigorous illegal trade for parrots (131 individuals recorded, 75% of them poached very recently), mostly obtained from protected areas where the last small wild populations remain. We observed parrots foraging on 19 plant species from 11 families, dispersing the fruits of 14 species by carrying them in their beaks and consuming them in distant perching trees. They discarded undamaged mature seeds, with the potential to germinate, in 99.5% of cases (n = 306), and minimum dispersal distances ranged from 8 to 155 m (median = 37 m).DiscussionThe loss of ecological functions provided by some species when they disappear from natural habitats and only persist in cities may have long-term, unexpected effects on ecosystems. Our example demonstrates how two cities may soon be the last refuges for two endemic parrots if overharvesting continues, in which case their overlooked role as seed dispersers would be completely lost in nature. The functional extinction of these species could strongly affect vegetation communities in an island environment where seed-dispersal species are naturally scarce. While conservation plans must include urban populations of threatened species, greater efforts are needed to restore their populations in natural habitats to conserve ecological functions. creator: Álvaro Luna creator: Pedro Romero-Vidal creator: Fernando Hiraldo creator: Jose L. Tella uri: https://doi.org/10.7717/peerj.4908 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Luna et al. title: Ampelisca eschrichtii Krøyer, 1842 (Ampeliscidae) of the Sakhalin Shelf in the Okhotsk Sea starve in summer and feast in winter link: https://peerj.com/articles/4841 last-modified: 2018-06-22 description: BackgroundAmpelisca eschrichtii Krøyer, 1842 of the Sakhalin Shelf of the Okhotsk Sea, Far Eastern Russia, comprise the highest known biomass concentration of any amphipod population in the world and are a critically important prey source for western gray whales. Growth and reproduction in this population has not been apparent in summer. However, they are not accessible for sampling in winter to test a previous default conclusion that they grow and reproduce in winter.MethodsWe tested the default winter growth and reproduction hypothesis by detailed comparisons of the brood and gonad development among 40 females and 14 males and brood sizes among females observed since 2002. Our test included six predictions of reproductive synchrony that would be apparent from gonad and brood morphology if active reproduction occurs in summer.ResultsWe found high prevalences of undersized and damaged oocytes, undersized broods, a lack of females brooding fully formed juveniles, atrophied ovaries, and males with mature sperm but lacking fully developed secondary sex morphologies required for pelagic mating. All of these conditions are consistent with trophic stress and starvation.DiscussionThese A. eschrichtii populations therefore appear to starve in summer and to grow and reproduce in winter. The Offshore A. eschrichtii populations occur in summer below water strata bearing high phytoplankton biomasses. These populations are more likely to feed successfully in winter when storms mix phytoplankton to their depths. creator: Valentina B. Durkina creator: John W. Chapman creator: Natalia L. Demchenko uri: https://doi.org/10.7717/peerj.4841 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Durkina et al. title: Psychological, pharmacological, and combined treatments for binge eating disorder: a systematic review and meta-analysis link: https://peerj.com/articles/5113 last-modified: 2018-06-21 description: ObjectiveTo systematically review the efficacy of psychological, pharmacological, and combined treatments for binge eating disorder (BED).MethodSystematic search and meta-analysis.ResultsWe found 45 unique studies with low/medium risk of bias, and moderate support for the efficacy of cognitive behavior therapy (CBT) and CBT guided self-help (with moderate quality of evidence), and modest support for interpersonal psychotherapy (IPT), selective serotonin reuptake inhibitors (SSRI), and lisdexamfetamine (with low quality of evidence) in the treatment of adults with BED in terms of cessation of or reduction in the frequency of binge eating. The results on weight loss were disappointing. Only lisdexamfetamine showed a very modest effect on weight loss (low quality of evidence). While there is limited support for the long-term effect of psychological treatments, we have currently no data to ascertain the long-term effect of drug treatments. Some undesired side effects are more common in drug treatment compared to placebo, while the side effects of psychological treatments are unknown. Direct comparisons between pharmaceutical and psychological treatments are lacking as well as data to generalize these results to adolescents.ConclusionWe found moderate support for the efficacy of CBT and guided self-help for the treatment of BED. However, IPT, SSRI, and lisdexamfetamine received only modest support in terms of cessation of or reduction in the frequency of binge eating. The lack of long-term follow-ups is alarming, especially with regard to medication. Long-term follow-ups, standardized assessments including measures of quality of life, and the study of underrepresented populations should be a priority for future research. creator: Ata Ghaderi creator: Jenny Odeberg creator: Sanna Gustafsson creator: Maria Råstam creator: Agneta Brolund creator: Agneta Pettersson creator: Thomas Parling uri: https://doi.org/10.7717/peerj.5113 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Ghaderi et al. title: Analyzing mixing systems using a new generation of Bayesian tracer mixing models link: https://peerj.com/articles/5096 last-modified: 2018-06-21 description: The ongoing evolution of tracer mixing models has resulted in a confusing array of software tools that differ in terms of data inputs, model assumptions, and associated analytic products. Here we introduce MixSIAR, an inclusive, rich, and flexible Bayesian tracer (e.g., stable isotope) mixing model framework implemented as an open-source R package. Using MixSIAR as a foundation, we provide guidance for the implementation of mixing model analyses. We begin by outlining the practical differences between mixture data error structure formulations and relate these error structures to common mixing model study designs in ecology. Because Bayesian mixing models afford the option to specify informative priors on source proportion contributions, we outline methods for establishing prior distributions and discuss the influence of prior specification on model outputs. We also discuss the options available for source data inputs (raw data versus summary statistics) and provide guidance for combining sources. We then describe a key advantage of MixSIAR over previous mixing model software—the ability to include fixed and random effects as covariates explaining variability in mixture proportions and calculate relative support for multiple models via information criteria. We present a case study of Alligator mississippiensis diet partitioning to demonstrate the power of this approach. Finally, we conclude with a discussion of limitations to mixing model applications. Through MixSIAR, we have consolidated the disparate array of mixing model tools into a single platform, diversified the set of available parameterizations, and provided developers a platform upon which to continue improving mixing model analyses in the future. creator: Brian C. Stock creator: Andrew L. Jackson creator: Eric J. Ward creator: Andrew C. Parnell creator: Donald L. Phillips creator: Brice X. Semmens uri: https://doi.org/10.7717/peerj.5096 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Stock et al. title: Effect of human recreation on bird anti-predatory response link: https://peerj.com/articles/5093 last-modified: 2018-06-21 description: Wildlife perceive humans as predators, and therefore normally flushes. Flight initiation distance (FID) is the distance a human can approach an animal at a steady pace until it flushes. Recently, several studies showed differences in within-species FID according to human presence by comparing urban and rural habitats, with urban birds showing reduced FIDs. However, urban and rural habitats also differ in structure, which might affect FID. Therefore, in order to understand the real effect of human presence, we investigated whether differences in FID are also present in natural habitats (forests), differing only in the intensity of human use for recreation. We found that human frequentation had a distinct effect on bird escape responses, with shorter FIDs in forests more-heavily frequented by humans than in forests rarely visited by humans. Whether this finding is driven by non-random spatial distribution of personalities (shy vs. bold) or phenotypic plasticity (habituation to humans) cannot be assessed with our data. Studies relying on FIDs should also incorporate human recreation intensity, as this affects the measurements strongly. creator: Yves Bötsch creator: Selina Gugelmann creator: Zulima Tablado creator: Lukas Jenni uri: https://doi.org/10.7717/peerj.5093 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Bötsch et al. title: Starch biotransformation into isomaltooligosaccharides using thermostable alpha-glucosidase from Geobacillus stearothermophilus link: https://peerj.com/articles/5086 last-modified: 2018-06-21 description: The present study first identified the biotransformation of starch as a novel preparation method was investigated using the alpha-transglucosidase-producing Geobacillus stearothermophilus U2. Subsequently, 5 L- and 20 L-scale fermentations were performed. After isolation and purification, liquid alpha-glucosidase preparations were obtained. Through covalent cross-linking and adsorption cross-linking using chitosan as the carrier and glutaraldehyde as the crosslinking agent, the conditions for immobilization of alpha-glucosidase on chitosan were determined. Moreover, Isomaltooligosaccharides (IMOs) were then prepared using chitosan membrane-immobilized alpha-glucosidase, beta-amylase, pullulanase, fungal alpha-amylase and starch as substrate. The mixed syrup that contained IMOs was evaluated and analyzed by thin-layer chromatography (TLC) and high-performance liquid chromatography (HPLC). In addition, small-scale preparation of IMOs was performed. These results are a strong indication that the alpha-transglucosidase-producing G. stearothermophilus as a potential application technique can be successfully used to prepare industrial IMOs. creator: Peng Chen creator: Ruixiang Xu creator: Jianhui Wang creator: Zhengrong Wu creator: Lei Yan creator: Wenbin Zhao creator: Yuheng Liu creator: Wantong Ma creator: Xiaofeng Shi creator: Hongyu Li uri: https://doi.org/10.7717/peerj.5086 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Chen et al. title: An integrative taxonomic analysis reveals a new species of lotic Hynobius salamander from Japan link: https://peerj.com/articles/5084 last-modified: 2018-06-21 description: We examine the phylogenetic structure and morphological differentiation within the Hynobius kimurae–H. boulengeri species complex—a widely-distributed group of stream-breeding hynobiid salamanders, inhabiting montane areas of western, central and eastern parts of Honshu Island, Japan. Phylogenetic relationships were assessed based on analyses of mitochondrial (mtDNA) and nuclear (nuDNA) gene fragments for a total of 51 samples representing 23 localities covering the entire range of the species complex. Morphological study included one-way analysis of variance (ANOVA) and principal components analysis (PCA) analyses of 26 morphometric and six meristic characters for 38 adult specimens of H. kimurae and three adult specimens of H. boulengeri. MtDNA genealogy supported monophyly of the H. kimurae–H. boulengeri complex, which is sister to all other Hynobius except H. retardatus. The complex is subdivided into three major clades, corresponding to the Eastern (Clade I) and Western (Clade II) populations of H. kimurae sensu lato, and to H. boulengeri (Clade III). Monophyly of H. kimurae sensu lato is only moderately supported by mtDNA, while nuDNA suggested that the Western form of H. kimurae is closer to H. boulengeri than to the eastern form. The time of the split of the H. kimurae–H. boulengeri complex is estimated as late Miocene and coincides with intensive crust movement in western Japan. Divergence between Clades I and II took place in early Pliocene and was likely influenced by the uplift of Central Japanese Highlands. All three clades were found to be different in a number of morphological characters, allowing us to describe the eastern form of H. kimurae as a new species, Hynobius fossigenussp. nov. creator: Hisanori Okamiya creator: Hirotaka Sugawara creator: Masahiro Nagano creator: Nikolay A. Poyarkov uri: https://doi.org/10.7717/peerj.5084 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Okamiya et al. title: Fish species richness is associated with the availability of landscape components across seasons in the Amazonian floodplain link: https://peerj.com/articles/5080 last-modified: 2018-06-21 description: Understanding environmental biodiversity drivers in freshwater systems continues to be a fundamental challenge in studies of their fish assemblages. The present study seeks to determine the degree to which landscape variables of Amazonian floodplain lakes influences fish assemblages in these environments. Fish species richness was estimated in 15 Amazonian floodplain lakes during the high and low-water phases and correlated with the areas of four inundated wetland classes: (i) open water, (ii) flooded herbaceous, (iii) flooded shrubs and (iv) flooded forest estimated in different radius circular areas around each sampling site. Data were analyzed using generalized linear models with fish species richness, total and guilds as the dependent variable and estimates of buffered landscape areas as explanatory variables. Our analysis identified the significance of landscape variables in determining the diversity of fish assemblages in Amazonian floodplain lakes. Spatial scale was also identified as a significant determinant of fish diversity as landscape effects were more evident at larger spatial scales. In particular, (1) total species richness was more sensitive to variations in the landscape areas than number of species within guilds and (2) the spatial extent of the wetland class of shrubs was consistently the more influential on fish species diversity. creator: Carlos Edwar Carvalho Freitas creator: Laurie Laurenson creator: Kedma Cristine Yamamoto creator: Bruce Rider Forsberg creator: Miguel Petrere creator: Caroline Arantes creator: Flavia Kelly Siqueira-Souza uri: https://doi.org/10.7717/peerj.5080 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Carvalho Freitas et al. title: Initial response of phenology and yield components of wheat (Triticum durum L., CIRNO C2008) under experimental warming field conditions in the Yaqui Valley link: https://peerj.com/articles/5064 last-modified: 2018-06-21 description: This work evaluates the experimental warming effects on phenology and grain yield components of wheat in the Yaqui Valley, Sonora, México, using CIRNO C2008 variety from Triticum durum L., as a model during the cropping cycle of 2016–2017 (December to April). Infrared radiators were deployed to induce experimental warming by 2 °C above ambient crop canopy temperature, in a temperature free-air controlled enhancement system. Temperature was controlled by infrared temperature sensors placed in eight plots which covered a circle of r = 1.5 m starting five days after germination until harvest. The warming treatment caused a reduction of phenophases occurrence starting at the stem extension phenophase. Such phenological responses generated a significant biological cycle reduction of 14 days. Despite this delay, CIRNO C2008 completed its biological cycle adequately. However, plant height under the warming treatment was reduced significantly and differences were particularly observed at the final phenophases of the vegetative cycle. Plant height correlated negatively with spikes length, spikes mass, and number of filled grains. Warming also reduced grain yield in 33%. The warming treatment caused a stress intensity (SI = 1-yield warming/yield control) of 39.4% and 33.2% in biomass and grain yield, respectively. The differences in stress intensities between biomass and grain yield were based on plant height reduction. Grain mass was not affected, demonstrating the crop capability for remobilization and adequate distribution of elaborated substances for the spikes under warming conditions. creator: Jaime Garatuza-Payan creator: Leandris Argentel-Martinez creator: Enrico A. Yepez creator: Tulio Arredondo uri: https://doi.org/10.7717/peerj.5064 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Garatuza-Payan et al. title: aaquetzalli is required for epithelial cell polarity and neural tissue formation in Drosophila link: https://peerj.com/articles/5042 last-modified: 2018-06-21 description: Morphogenetic movements during embryogenesis require dynamic changes in epithelial cell polarity and cytoskeletal reorganization. Such changes involve, among others, rearrangements of cell-cell contacts and protein traffic. In Drosophila melanogaster, neuroblast delamination during early neurogenesis is a well-characterized process requiring a polarized neuroepithelium, regulated by the Notch signaling pathway. Maintenance of epithelial cell polarity ensues proper Notch pathway activation during neurogenesis. We characterize here aaquetzalli (aqz), a gene whose mutations affect cell polarity and nervous system specification. The aqz locus encodes a protein that harbors a domain with significant homology to a proline-rich conserved domain of nuclear receptor co-activators. aqz expression occurs at all stages of the fly life cycle, and is dynamic. aqz mutants are lethal, showing a disruption of cell polarity during embryonic ventral neuroepithelium differentiation resulting in loss of epithelial integrity and mislocalization of membrane proteins (shown by mislocalization of Crumbs, DE-Cadherin, and Delta). As a consequence, aqz mutant embryos with compromised apical-basal cell polarity develop spotty changes of neuronal and epithelial numbers of cells. creator: Miguel A. Mendoza-Ortíz creator: Juan M. Murillo-Maldonado creator: Juan R. Riesgo-Escovar uri: https://doi.org/10.7717/peerj.5042 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Mendoza-Ortíz et al. title: Biodegradation of Crystal Violet dye by bacteria isolated from textile industry effluents link: https://peerj.com/articles/5015 last-modified: 2018-06-21 description: Industrial effluent containing textile dyes is regarded as a major environmental concern in the present world. Crystal Violet is one of the vital textile dyes of the triphenylmethane group; it is widely used in textile industry and known for its mutagenic and mitotic poisoning nature. Bioremediation, especially through bacteria, is becoming an emerging and important sector in effluent treatment. This study aimed to isolate and identify Crystal Violet degrading bacteria from industrial effluents with potential use in bioremediation. The decolorizing activity of the bacteria was measured using a photo electric colorimeter after aerobic incubation in different time intervals of the isolates. Environmental parameters such as pH, temperature, initial dye concentration and inoculum size were optimized using mineral salt medium containing different concentration of Crystal Violet dye. Complete decolorizing efficiency was observed in a mineral salt medium containing up to 150 mg/l of Crystal Violet dye by 10% (v/v) inoculums of Enterobacter sp. CV–S1 tested under 72 h of shaking incubation at temperature 35 °C and pH 6.5. Newly identified bacteria Enterobacter sp. CV–S1, confirmed by 16S ribosomal RNA sequencing, was found as a potential bioremediation biocatalyst in the aerobic degradation/de-colorization of Crystal Violet dye. The efficiency of degrading triphenylmethane dye by this isolate, minus the supply of extra carbon or nitrogen sources in the media, highlights the significance of larger-scale treatment of textile effluent. creator: Dipankar Chandra Roy creator: Sudhangshu Kumar Biswas creator: Ananda Kumar Saha creator: Biswanath Sikdar creator: Mizanur Rahman creator: Apurba Kumar Roy creator: Zakaria Hossain Prodhan creator: Swee-Seong Tang uri: https://doi.org/10.7717/peerj.5015 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Roy et al. title: Effects of anthropogenic wildfire in low-elevation Pacific island vegetation communities in French Polynesia link: https://peerj.com/articles/5114 last-modified: 2018-06-20 description: Anthropogenic (or human-caused) wildfire is an increasingly important driver of ecological change on Pacific islands including southeastern Polynesia, but fire ecology studies are almost completely absent for this region. Where observations do exist, they mostly represent descriptions of fire effects on plant communities before the introduction of invasive species in the modern era. Understanding the effects of wildfire in southeastern Polynesian island vegetation communities can elucidate which species may become problematic invasives with continued wildfire activity. We investigate the effects of wildfire on vegetation in three low-elevation sites (45–379 m) on the island of Mo’orea in the Society Islands, French Polynesia, which are already heavily impacted by past human land use and invasive exotic plants, but retain some native flora. In six study areas (three burned and three unburned comparisons), we placed 30 transects across sites and collected species and abundance information at 390 points. We analyzed each local community of plants in three categories: natives, those introduced by Polynesians before European contact (1767 C.E.), and those introduced since European contact. Burned areas had the same or lower mean species richness than paired comparison sites. Although wildfire did not affect the proportions of native and introduced species, it may increase the abundance of introduced species on some sites. Non-metric multidimensional scaling indicates that (not recently modified) comparison plant communities are more distinct from one another than are those on burned sites. We discuss conservation concerns for particular native plants absent from burned sites, as well as invasive species (including Lantana camara and Paraserianthes falcataria) that may be promoted by fire in the Pacific. creator: Erica A. Newman creator: Carlea A. Winkler creator: David H. Hembry uri: https://doi.org/10.7717/peerj.5114 license: http://creativecommons.org/publicdomain/zero/1.0/ rights: title: Comparison of the toxic effects of different mycotoxins on porcine and mouse oocyte meiosis link: https://peerj.com/articles/5111 last-modified: 2018-06-20 description: BackgroundAflatoxin B1 (AFB1), deoxynivalenol (DON), HT-2, ochratoxin A (OTA), zearalenone (ZEA) are the most common mycotoxins that are found in corn-based animal feed which have multiple toxic effects on animals and humans. Previous studies reported that these mycotoxins impaired mammalian oocyte quality. However, the effective concentrations of mycotoxins to animal oocytes were different.MethodsIn this study we aimed to compare the sensitivity of mouse and porcine oocytes to AFB1, DON, HT-2, OTA, and ZEA for mycotoxin research. We adopted the polar body extrusion rate of mouse and porcine oocyte as the standard for the effects of mycotoxins on oocyte maturation.Results and DiscussionOur results showed that 10 μM AFB1 and 1 μM DON significantly affected porcine oocyte maturation compared with 50 μM AFB1 and 2 μM DON on mouse oocytes. However, 10 nM HT-2 significantly affected mouse oocyte maturation compared with 50 nM HT-2 on porcine oocytes. Moreover, 5 μM OTA and 10 μM ZEA significantly affected porcine oocyte maturation compared with 300 μM OTA and 50 μM ZEA on mouse oocytes. In summary, our results showed that porcine oocytes were more sensitive to AFB1, DON, OTA, and ZEA than mouse oocytes except HT-2 toxin. creator: Yujie Lu creator: Yue Zhang creator: Jia-Qian Liu creator: Peng Zou creator: Lu Jia creator: Yong-Teng Su creator: Yu-Rong Sun creator: Shao-Chen Sun uri: https://doi.org/10.7717/peerj.5111 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Lu et al. title: Patients with chronic periodontitis present increased risk for primary Sjögren syndrome: a nationwide population-based cohort study link: https://peerj.com/articles/5109 last-modified: 2018-06-20 description: Many reports have mentioned the association between chronic periodontitis (CP) and primary Sjögren syndrome (pSS). However, no cohort study has been performed for the risk of pSS in patients with CP. In this study, we evaluated the risk of pSS from CP exposure in a nationwide population-based cohort study in Taiwan. We studied the claims data of Taiwanese population from 2001 to 2012. We identified 76,765 patients with CP from the National Health Insurance Database in Taiwan. We also selected 76,765 controls that were randomly frequency matched by age, sex, and index year from the general population. We analyzed the risk of pSS by using Cox proportional hazards regression models including sex, age, and comorbidities. In this study, 76,765 patients with CP (mean age: 40.8 years) and 76,765 controls (mean age: 41.0 years) were followed-up for 8.54 and 8.49 years, respectively. A total of 869 cases of pSS were identified in CP cohort and 483 cases in non-CP cohort. Multivariate Cox regression analysis indicated that the incidence rate of pSS was significantly higher in CP cohort than those who in non-CP cohort (adjusted HR: 1.79, 95% CI [1.60–2.00]). Taken together, this nationwide retrospective cohort study demonstrated that the risk of pSS was significantly higher in patients with CP than in the general population. The association between CP and pSS was significant in the female group. creator: Tai-Chen Lin creator: Chien-Fang Tseng creator: Yu-Hsun Wang creator: Hui-Chieh Yu creator: Yu-Chao Chang uri: https://doi.org/10.7717/peerj.5109 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Lin et al. title: Molecular detection and phylogenetic assessment of six honeybee viruses in Apis mellifera L. colonies in Bulgaria link: https://peerj.com/articles/5077 last-modified: 2018-06-20 description: Honey bee colonies suffer from various pathogens, including honey bee viruses. About 24 viruses have been reported so far. However, six of them are considered to cause severe infection which inflicts heavy losses on beekeeping. The aim of this study was to investigate incidence of six honey bee viruses: deformed wing virus (DWV), acute bee paralysis virus (ABPV), chronic bee paralysis virus (CBPV), sacbrood virus (SBV), kashmir bee virus (KBV), and black queen cell virus (BQCV) by a reverse transcription polymerase chain reaction (RT-PCR). A total of 250 adult honey bee samples were obtained from 50 colonies from eight apiaries situated in three different parts of the country (South, North and West Bulgaria). The results showed the highest prevalence of DWV followed by SBV and ABPV, and one case of BQCV. A comparison with homology sequences available in GenBank was performed by phylogenetic analysis, and phylogenetic relationships were discussed in the context of newly described genotypes in the uninvestigated South Eastern region of Europe. In conclusion, the present study has been the first to provide sequencing data and phylogenetics analyses of some honey bee viruses in Bulgaria. creator: Rositsa Shumkova creator: Boyko Neov creator: Daniela Sirakova creator: Ani Georgieva creator: Dimitar Gadjev creator: Denitsa Teofanova creator: Georgi Radoslavov creator: Maria Bouga creator: Peter Hristov uri: https://doi.org/10.7717/peerj.5077 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Shumkova et al. title: Plant-insect interactions patterns in three European paleoforests of the late-Neogene—early-Quaternary link: https://peerj.com/articles/5075 last-modified: 2018-06-20 description: Plants and insects are constantly interacting in complex ways through forest communities since hundreds of millions of years. Those interactions are often related to variations in the climate. Climate change, due to human activities, may have disturbed these relationships in modern ecosystems. Fossil leaf assemblages are thus good opportunities to survey responses of plant–insect interactions to climate variations over the time. The goal of this study is to discuss the possible causes of the differences of plant–insect interactions’ patterns in European paleoforests from the Neogene–Quaternary transition. This was accomplished through three fossil leaf assemblages: Willershausen, Berga (both from the late Neogene of Germany) and Bernasso (from the early Quaternary of France). In Willershausen it has been measured that half of the leaves presented insect interactions, 35% of the fossil leaves were impacted by insects in Bernasso and only 25% in Berga. The largest proportion of these interactions in Bernasso were categorized as specialist (mainly due to galling) while in Willershausen and Berga those ones were significantly more generalist. Contrary to previous studies, this study did not support the hypothesis that the mean annual precipitation and temperature were the main factors that impacted the different plant–insect interactions’ patterns. However, for the first time, our results tend to support that the hydric seasonality and the mean temperature of the coolest months could be potential factors influencing fossil plant–insect interactions. creator: Benjamin Adroit creator: Vincent Girard creator: Lutz Kunzmann creator: Jean-Frédéric Terral creator: Torsten Wappler uri: https://doi.org/10.7717/peerj.5075 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Adroit et al. title: How many fish? Comparison of two underwater visual sampling methods for monitoring fish communities link: https://peerj.com/articles/5066 last-modified: 2018-06-20 description: BackgroundUnderwater visual surveys (UVSs) for monitoring fish communities are preferred over fishing surveys in certain habitats, such as rocky or coral reefs and seagrass beds and are the standard monitoring tool in many cases, especially in protected areas. However, despite their wide application there are potential biases, mainly due to imperfect detectability and the behavioral responses of fish to the observers.MethodsThe performance of two methods of UVSs were compared to test whether they give similar results in terms of fish population density, occupancy, species richness, and community composition. Distance sampling (line transects) and plot sampling (strip transects) were conducted at 31 rocky reef sites in the Aegean Sea (Greece) using SCUBA diving.ResultsLine transects generated significantly higher values of occupancy, species richness, and total fish density compared to strip transects. For most species, density estimates differed significantly between the two sampling methods. For secretive species and species avoiding the observers, the line transect method yielded higher estimates, as it accounted for imperfect detectability and utilized a larger survey area compared to the strip transect method. On the other hand, large-scale spatial patterns of species composition were similar for both methods.DiscussionOverall, both methods presented a number of advantages and limitations, which should be considered in survey design. Line transects appear to be more suitable for surveying secretive species, while strip transects should be preferred at high fish densities and for species of high mobility. creator: Zoi Thanopoulou creator: Maria Sini creator: Konstantinos Vatikiotis creator: Christos Katsoupis creator: Panayiotis G. Dimitrakopoulos creator: Stelios Katsanevakis uri: https://doi.org/10.7717/peerj.5066 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Thanopoulou et al. title: Evaluation of the effect of chickenpox vaccination on shingles epidemiology using agent-based modeling link: https://peerj.com/articles/5012 last-modified: 2018-06-20 description: BackgroundBiological interactions between varicella (chickenpox) and herpes zoster (shingles), two diseases caused by the varicella zoster virus (VZV), continue to be debated including the potential effect on shingles cases following the introduction of universal childhood chickenpox vaccination programs. We investigated how chickenpox vaccination in Alberta impacts the incidence and age-distribution of shingles over 75 years post-vaccination, taking into consideration a variety of plausible theories of waning and boosting of immunity.MethodsWe developed an agent-based model representing VZV disease, transmission, vaccination states and coverage, waning and boosting of immunity in a stylized geographic area, utilizing a distance-based network. We derived parameters from literature, including modeling, epidemiological, and immunology studies. We calibrated our model to the age-specific incidence of shingles and chickenpox prior to vaccination to derive optimal combinations of duration of boosting (DoB) and waning of immunity. We conducted paired simulations with and without implementing chickenpox vaccination. We computed the count and cumulative incidence rate of shingles cases at 10, 25, 50, and 75 years intervals, following introduction of vaccination, and compared the difference between runs with vaccination and without vaccination using the Mann–Whitney U-test to determine statistical significance. We carried out sensitivity analyses by increasing and lowering vaccination coverage and removing biological effect of boosting.ResultsChickenpox vaccination led to a decrease in chickenpox cases. The cumulative incidence of chickenpox had dropped from 1,254 cases per 100,000 person-years pre chickenpox vaccination to 193 cases per 100,000 person-years 10 years after the vaccine implementation. We observed an increase in the all-ages shingles cumulative incidence at 10 and 25 years post chickenpox vaccination and mixed cumulative incidence change at 50 and 75 years post-vaccination. The magnitude of change was sensitive to DoB and ranged from an increase of 22–100 per 100,000 person-years at 10 years post-vaccination for two and seven years of boosting respectively (p < 0.001). At 75 years post-vaccination, cumulative incidence ranged from a decline of 70 to an increase of 71 per 100,000 person-years for two and seven years of boosting respectively (p < 0.001). Sensitivity analyses had a minimal impact on our inferences except for removing the effect of boosting.DiscussionOur model demonstrates that over the longer time period, there will be a reduction in shingles incidence driven by the depletion of the source of shingles reactivation; however in the short to medium term some age cohorts may experience an increase in shingles incidence. Our model offers a platform to further explore the relationship between chickenpox and shingles, including analyzing the impact of different chickenpox vaccination schedules and cost-effectiveness studies. creator: Ellen Rafferty creator: Wade McDonald creator: Weicheng Qian creator: Nathaniel D. Osgood creator: Alexander Doroshenko uri: https://doi.org/10.7717/peerj.5012 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Rafferty et al. title: Monitoring monthly surface water dynamics of Dongting Lake using Sentinel-1 data at 10 m link: https://peerj.com/articles/4992 last-modified: 2018-06-20 description: High temporal resolution water distribution maps are essential for surface water monitoring because surface water exhibits significant inner-annual variation. Therefore, high-frequency remote sensing data are needed for surface water mapping. Dongting Lake, the second-largest freshwater lake in China, is famous for the seasonal fluctuations of its inundation extents in the middle reaches of the Yangtze River. It is also greatly affected by the Three Gorges Project. In this study, we used Sentinel-1 data to generate surface water maps of Dongting Lake at 10 m resolution. First, we generated the Sentinel-1 time series backscattering coefficient for VH and VV polarizations at 10 m resolution by using a monthly composition method. Second, we generated the thresholds for mapping surface water at 10 m resolution with monthly frequencies using Sentinel-1 data. Then, we derived the monthly surface water distribution product of Dongting Lake in 2016, and finally, we analyzed the inner-annual surface water dynamics. The results showed that: (1) The thresholds were −21.56 and −15.82 dB for the backscattering coefficients for VH and VV, respectively, and the overall accuracy and Kappa coefficients were above 95.50% and 0.90, respectively, for the VH backscattering coefficient, and above 94.50% and 0.88, respectively, for the VV backscattering coefficient. The VV backscattering coefficient achieved lower accuracy due to the effect of the wind causing roughness on the surface of the water. (2) The maximum and minimum areas of surface water were 2040.33 km2 in July, and 738.89 km2 in December. The surface water area of Dongting Lake varied most significantly in April and August. The permanent water acreage in 2016 was 556.35 km2, accounting for 19.65% of the total area of Dongting Lake, and the acreage of seasonal water was 1525.21 km2. This study proposed a method to automatically generate monthly surface water at 10 m resolution, which may contribute to monitoring surface water in a timely manner. creator: Liwei Xing creator: Xinming Tang creator: Huabin Wang creator: Wenfeng Fan creator: Guanghui Wang uri: https://doi.org/10.7717/peerj.4992 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Xing et al. title: Dissemination of antibiotic resistance genes associated with the sporobiota in sediments impacted by wastewater link: https://peerj.com/articles/4989 last-modified: 2018-06-20 description: Aquatic ecosystems serve as a dissemination pathway and a reservoir of both antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARG). In this study, we investigate the role of the bacterial sporobiota to act as a vector for ARG dispersal in aquatic ecosystems. The sporobiota was operationally defined as the resilient fraction of the bacterial community withstanding a harsh extraction treatment eliminating the easily lysed fraction of the total bacterial community. The sporobiota has been identified as a critical component of the human microbiome, and therefore potentially a key element in the dissemination of ARG in human-impacted environments. A region of Lake Geneva in which the accumulation of ARG in the sediments has been previously linked to the deposition of treated wastewater was selected to investigate the dissemination of tet(W) and sul1, two genes conferring resistance to tetracycline and sulfonamide, respectively. Analysis of the abundance of these ARG within the sporobiome (collection of genes of the sporobiota) and correlation with community composition and environmental parameters demonstrated that ARG can spread across the environment with the sporobiota being the dispersal vector. A highly abundant OTU affiliated with the genus Clostridium was identified as a potential specific vector for the dissemination of tet(W), due to a strong correlation with tet(W) frequency (ARG copy numbers/ng DNA). The high dispersal rate, long-term survival, and potential reactivation of the sporobiota constitute a serious concern in terms of dissemination and persistence of ARG in the environment. creator: Christophe Paul creator: Zhanna Bayrychenko creator: Thomas Junier creator: Sevasti Filippidou creator: Karin Beck creator: Matthieu Bueche creator: Gilbert Greub creator: Helmut Bürgmann creator: Pilar Junier uri: https://doi.org/10.7717/peerj.4989 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Paul et al. title: Cranial morphology of Sinovenator changii (Theropoda: Troodontidae) on the new material from the Yixian Formation of western Liaoning, China link: https://peerj.com/articles/4977 last-modified: 2018-06-20 description: A new three-dimensionally preserved troodontid specimen consisting of most of the skull, partial mandibles and six articulated cervical vertebrae (PMOL-AD00102) from the Early Cretaceous Yixian Formation of Beipiao, western Liaoning, China is identified as Sinovenator changii on the basis of a surangular with a “T”-shaped cross-section. High-resolution computed tomographic data for the skull of this new specimen facilitated a detailed description of the cranial anatomy of S. changii. New diagnostic features of S. changii include a well-developed medial shelf on the jugal, a slender bar in the parasphenoid recess, a lateral groove on the pterygoid flange of the ectopterygoid, and the lateral surface of the anterior cervical vertebrae bearing two pneumatic foramina. Our new observation confirms that the braincase of Sinovenator is not as primitive as previously suggested, although it still shows an intermediate state between derived troodontids and non-troodontid paravians in having an initial stage of the subotic recess and the otosphenoidal crest. Additionally, this new specimen reveals some novel and valuable anatomical information of troodontids regarding the quadrate-quadratojugal articulation, the stapes, the epipterygoid and the atlantal ribs. creator: Ya-Lei Yin creator: Rui Pei creator: Chang-Fu Zhou uri: https://doi.org/10.7717/peerj.4977 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Yin et al. title: Comparative health assessment of urban and non-urban free-ranging mule deer (Odocoileus hemionus) in southeastern British Columbia, Canada link: https://peerj.com/articles/4968 last-modified: 2018-06-20 description: BackgroundThe provincial wildlife management agency, British Columbia Ministry of Forests, Lands, Natural Resource Operations and Rural Development, performed a translocation to control the urban mule deer (Odocoileus hemionus; uMD) overpopulation and supplement the declining non-urban mule deer (nuMD) population in the Kootenay region, British Columbia, Canada. The objectives of this cross-sectional study were to evaluate the health of the urban and nuMD populations by comparing pathogen exposure, body condition scores (BCS) and pregnancy rates, to characterize the health risks associated with the translocation and to investigate the role of infectious diseases in the decline of the nuMD deer population.MethodsTwo hundred free-ranging mule deer were captured in urban and non-urban environments in the Kootenay region from 2014 to 2017. BCS and morphometric examinations were performed for each deer. Blood samples collected from each deer were tested for exposure to selected pathogens and pregnancy status.ResultsBody condition scores averaged 3.4 on a five-point scale, was greater in nuMD, and significantly differed between years. Antibodies were detected for adenovirus hemorrhagic disease virus (38.4% (uMD 43.7%, nuMD 33.3%)), bluetongue virus (0.6% (uMD 1.2%, nuMD 0%)), bovine respiratory syncytial virus (8.4% (uMD 4.6%, nuMD 12.1%)), bovine viral diarrhea virus (1.1% (uMD 0%, nuMD 2.2%)), bovine parainfluenza-3 virus (27.0% (uMD 27.6%, nuMD 26.4%)), Neospora caninum (22.1% (uMD 24.4%, nuMD 19.7%)) and Toxoplasma gondii (8.2% (uMD 12.3%, nuMD 3.9%)). No antibodies against epizootic hemorrhagic disease virus were detected. Pregnancy rates did not differ between the two deer populations (90.7% (uMD 90.6%, nuMD 90.9%)). Exposure to N. caninum was associated with a reduced probability of being pregnant. uMD were more likely to be exposed to T. gondii than nuMD.DiscussionComparison of BCS, pregnancy rates and pathogen exposure of uMD and nuMD showed that the health of the two populations did not significantly differ, suggesting uMD translocations do not pose a severe risk of pathogen transmission between mule deer populations and that these selected pathogens do not factor in the decline of the nuMD population. However, inclusion of additional health indicators and creation of a robust predictive disease model are warranted to further characterize the health of mule deer and the health risks associated with uMD translocations. These results should be considered as part of a formal risk assessment for future uMD translocations in southeastern British Columbia. creator: Amélie Mathieu creator: Mark Flint creator: Patrick M. Stent creator: Helen M. Schwantje creator: Thomas E. Wittum uri: https://doi.org/10.7717/peerj.4968 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Mathieu et al. title: GEsture: an online hand-drawing tool for gene expression pattern search link: https://peerj.com/articles/4927 last-modified: 2018-06-20 description: Gene expression profiling data provide useful information for the investigation of biological function and process. However, identifying a specific expression pattern from extensive time series gene expression data is not an easy task. Clustering, a popular method, is often used to classify similar expression genes, however, genes with a ‘desirable’ or ‘user-defined’ pattern cannot be efficiently detected by clustering methods. To address these limitations, we developed an online tool called GEsture. Users can draw, or graph a curve using a mouse instead of inputting abstract parameters of clustering methods. GEsture explores genes showing similar, opposite and time-delay expression patterns with a gene expression curve as input from time series datasets. We presented three examples that illustrate the capacity of GEsture in gene hunting while following users’ requirements. GEsture also provides visualization tools (such as expression pattern figure, heat map and correlation network) to display the searching results. The result outputs may provide useful information for researchers to understand the targets, function and biological processes of the involved genes. creator: Chunyan Wang creator: Yiqing Xu creator: Xuelin Wang creator: Li Zhang creator: Suyun Wei creator: Qiaolin Ye creator: Youxiang Zhu creator: Hengfu Yin creator: Manoj Nainwal creator: Luis Tanon-Reyes creator: Feng Cheng creator: Tongming Yin creator: Ning Ye uri: https://doi.org/10.7717/peerj.4927 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Wang et al. title: Feeding ecology and sexual dimorphism in a speciose flower beetle clade (Hopliini: Scarabaeidae) link: https://peerj.com/articles/4632 last-modified: 2018-06-20 description: The relationship between feeding ecology and sexual dimorphism is examined in a speciose South African monkey beetle clade. We test whether feeding and mating at a fixed site (embedding guild) is associated with greater levels of sexual dimorphism and possibly sexual selection than species using unpredictable feeding resources (non-embedding guild). Sexual dimorphism was measured using a point scoring system for hind leg and colour across the two feeding guilds for >50% of the regional fauna. Quantification of hind leg dimorphism using a scoring system and allometric scaling were used to identify traits subject to sexual selection. Feeding guild had a significant effect on hind leg dimorphism, with embedders having high and non-embedders low scores. The sessile and defendable distribution of females on stable platform flowers may favour contests and associated hind leg weaponry. In contrast, degree of colour dimorphism between the sexes was not associated with any particular feeding guild, and may serve to reduce male conflict and combat. Embedder males had high proportions (∼76%) of species with positive allometric slopes for almost all hind leg traits. For male non-embedders, only ∼37% of species showed positive scaling relationships. Phylogenetic data, in conjunction with behavioural data on the function of leg weaponry and visual signalling among males is needed to better understand the link between sexual dimorphism and sexual selection in the radiation of the monkey beetles. creator: Jonathan F. Colville creator: Mike D. Picker creator: Richard M. Cowling uri: https://doi.org/10.7717/peerj.4632 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Colville et al. title: The impact of PI3K inhibitors on breast cancer cell and its tumor microenvironment link: https://peerj.com/articles/5092 last-modified: 2018-06-19 description: The phosphoinositide 3-kinase (PI3K) pathway shows frequent aberrant alterations and pathological activation in breast cancer cells. While PI3K inhibitors have not achieved expectant therapeutic efficacy in clinical trials, and several studies provide promising combination strategies to substantially maximize therapeutic outcomes. Besides its direct impact on regulating cancer cells survival, PI3K inhibitors are also demonstrated to have an immunomodulatory impact based on the tumor microenvironment. Inhibition of the leukocyte-enriched PI3K isoforms may break immune tolerance and restore cytotoxic T cell activity by reprogramming the tumor microenvironment. In addition, PI3K inhibitors have pleiotropic effects on tumor angiogenesis and even induce tumor vascular normalization. In this review, we discuss the mechanism of PI3K inhibitor suppression of breast cancer cells and modulation of the tumor microenvironment in order to provide further thoughts for breast cancer treatment. creator: Hanjiao Qin creator: Linlin Liu creator: Shu Sun creator: Dan Zhang creator: Jiyao Sheng creator: Bingjin Li creator: Wei Yang uri: https://doi.org/10.7717/peerj.5092 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Qin et al. title: Incidence of ill-health related job loss and related social and occupational factors. The “unfit for the job” study: a one-year follow-up study of 51,132 workers link: https://peerj.com/articles/5073 last-modified: 2018-06-19 description: ObjectiveThe analysis of ill-health related job loss may be a relevant indicator for the prioritization of actions in the workplace or in the field of public health, as well as a target for health promotion. The aim of this study was to analyze the medical causes, the incidence, and the characteristics of employees medically unfit to do their job.MethodsThis one-year prospective study included all workers followed by occupational physicians in an occupational health service in the south of France. The incidence of unfitness for work have been grouped according to the main medical causes and analyzed. We performed a multivariate analysis in order to adjust the observed risk of job loss based on the age groups, sex, occupation and the activity sectors.ResultsA total of 17 occupational physicians followed up 51,132 workers. The all-cause incidence of being unfit to return to one’s job was 7.8‰ (n = 398). The two main causes of being unfit for one’s job were musculoskeletal disorders (47.2%, n = 188) and mental ill-health (38.4%, n = 153). Being over 50 years old (Odds ratio (OR) 2.63, confidence interval 95% CI [2.13–3.25]) and being a woman (OR 1.52, 95% CI [1.21–1.91]) were associated with the all-cause unfitness, independent of occupation and activity sector.ConclusionsIdentification of occupational and demographic determinants independently associated with ill-health related job loss may provide significant and cost-effective arguments for health promotion and job loss prevention. creator: Francois-Xavier Lesage creator: Frederic Dutheil creator: Lode Godderis creator: Aymeric Divies creator: Guillaume Choron uri: https://doi.org/10.7717/peerj.5073 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Lesage et al. title: Floating nurseries? Scyphozoan jellyfish, their food and their rich symbiotic fauna in a tropical estuary link: https://peerj.com/articles/5057 last-modified: 2018-06-19 description: BackgroundThe anthropogenic modification of trophic pathways is seemingly prompting the increase of jellyfish populations at the expense of planktivorous fishes. However, gross generalizations are often made because the most basic aspects of trophic ecology and the diverse interactions of jellyfish with fishes remain poorly described. Here we inquire on the dynamics of food consumption of the medusoid stage of the scyphozoan jellyfish Stomolophus meleagris and characterize the traits and diversity of its symbiotic community.MethodsS. meleagris and their associated fauna were sampled in surface waters between November 2015 and April 2017 in Málaga Bay, an estuarine system at the Colombian Pacific. Stomach contents of medusae were examined and changes in prey composition and abundance over time analysed using a multivariate approach. The associated fauna was identified and the relationship between the size of medusae and the size those organisms tested using least-square fitting procedures.ResultsThe presence of S. meleagris medusa in surface waters was seasonal. The gut contents analysis revealed that algae, copepods and fish early life stages were the more abundant items, and PERMANOVA analysis showed that the diet differed within the seasons (P(perm) = 0.001) but not between seasons (P(perm) = 0.134). The majority of the collected medusae (50.4%) were associated with individuals of 11 symbiotic species, 95.3% of them fishes, 3.1% crustaceans and 1.6% molluscs. Therefore, this study reports 10 previously unknown associations. The bell diameter of S. meleagris was positively related to the body sizes of their symbionts. However, a stronger fit was observed when the size relationship between S. meleagris and the fish Hemicaranx zelotes was modelled.DiscussionThe occurrence of S. meleagris was highly seasonal, and the observed patterns of mean body size through the seasons suggested the arrival of adult medusae to the estuary from adjacent waters. The diet of S. meleagris in the study area showed differences with previous reports, chiefly because of the abundance of algae that are seemingly ingested but not digested. The low number of zooplanktonic items in gut contents suggest the contribution of alternative food sources not easily identifiable. The observed changes in the composition of food in the guts probably reflect seasonal changes in the availability of prey items. The regular pattern in the distribution of symbionts among medusae (a single symbiont per host) and the positive host-symbiont size relationship reflects antagonistic intraspecific and interspecific behaviour of the symbiont. This strongly suggest that medusa represent an “economically defendable resource” that potentially increases the survival and recruitment of the symbionts to the adult population. We argue that, if this outcome of the symbiotic association can be proven, scyphozoan jellyfish can be regarded as floating nurseries. creator: José M. Riascos creator: Willington Aguirre creator: Charlotte Hopfe creator: Diego Morales creator: Ángela Navarrete creator: José Tavera uri: https://doi.org/10.7717/peerj.5057 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Riascos et al. title: Allometric shell growth in infaunal burrowing bivalves: examples of the archiheterodonts Claibornicardia paleopatagonica (Ihering, 1903) and Crassatella kokeni Ihering, 1899 link: https://peerj.com/articles/5051 last-modified: 2018-06-19 description: We present two cases of study of ontogenetic allometry in outlines of bivalves using longitudinal data, a rarity among fossils, based on the preserved post-larval record of shells. The examples are two infaunal burrowing bivalves of the southern South America, Claibornicardia paleopatagonica (Archiheterodonta: Carditidae) (early Paleocene) and Crassatella kokeni (Archiheterodonta: Crassatellidae) (late Oligocene–late Miocene). Outline analyses were conducted using a geometric morphometric approach (Elliptic Fourier Analysis), obtaining successive outlines from shells’ growth lines, which were used to reconstruct ontogenetic trajectories. In both taxa, ontogenetic changes are characterized by the presence of positive allometry in the extension of posterior end, resulting in elongated adult shells. This particular allometric growth is known in others infaunal burrowing bivalves (Claibornicardia alticostata and some Spissatella species) and the resulting adult morphology is present in representatives of several groups (e.g., Carditidae, Crassatellidae, Veneridae, Trigoniidae). Taxonomic, ecological and evolutionary implications of this allometric growth pattern are discussed. creator: Damián Eduardo Perez creator: María Belén Santelli uri: https://doi.org/10.7717/peerj.5051 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Perez and Santelli title: Comprehensive analysis of mitogen-activated protein kinase cascades in chrysanthemum link: https://peerj.com/articles/5037 last-modified: 2018-06-19 description: BackgroundMitogen-activated protein kinase (MAPK) cascades, an important type of pathway in eukaryotic signaling networks, play a key role in plant defense responses, growth and development.MethodsPhylogenetic analysis and conserved motif analysis of the MKK and MPK families in Arabidopsis thaliana, Helianthus annuus and Chrysanthemum morifolium classified MKK genes and MPK genes. qRT-PCR was used for the expression patterns of CmMPK and CmMKK genes, and yeast two-hybrid assay was applied to clear the interaction between CmMPKs and CmMKKs.ResultsWe characterized six MKK genes and 11 MPK genes in chrysanthemum based on transcriptomic sequences and classified these genes into four groups. qRT-PCR analysis demonstrated that CmMKKs and CmMPKs exhibited various expression patterns in different organs of chrysanthemum and in response to abiotic stresses and phytohormone treatments. Furthermore, a yeast two-hybrid assay was applied to analyze the interaction between CmMKKs and CmMPKs and reveal the MAPK cascades in chrysanthemum.DiscussionOur data led us to propose that CmMKK4-CmMPK13 and CmMKK2-CmMPK4 may be involved in regulating salt resistance and in the relationship between CmMKK9 and CmMPK6 and temperature stress. creator: Aiping Song creator: Yueheng Hu creator: Lian Ding creator: Xue Zhang creator: Peiling Li creator: Ye Liu creator: Fadi Chen uri: https://doi.org/10.7717/peerj.5037 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Song et al. title: A comparative study of the gastric ossicles of Trichodactylidae crabs (Brachyura: Decapoda) with comments on the role of diet and phylogeny in shaping morphological traits link: https://peerj.com/articles/5028 last-modified: 2018-06-19 description: The gastric armature of decapod foregut is a feeding structure that sparks controversial debates about the role dietary and historical components have in shaping its morphological traits. Having previous information about the natural diet is an interesting way to gather evidence on this issue. For the present study, we analyzed the morphological traits of gastric ossicles involved directly in the maceration of food in nine species of freshwater crabs of the family Trichodactylidae (Brachyura: Decapoda) representing five genera, three tribes and two subfamilies. The analyzed gastric ossicles were quite consistent among closely related species, suggesting that the observed traits had a clear phylogenetic component. However, it was also noted that the morphological traits of the gastric teeth of trichodactylid crabs match well with the natural diet and presented likeness with general features of other species with a similar trophic habit. We discuss the influence of phylogeny and function on the design of morphological traits and propose to quantify the role of phylogeny and function in shaping morphological traits through the analysis of phylogenetic signals. creator: Débora A. Carvalho creator: Pablo A. Collins creator: Renata Lima-Gomes creator: Célio Magalhães creator: Maria Victoria Torres creator: Verónica Williner uri: https://doi.org/10.7717/peerj.5028 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Carvalho et al. title: The effect of running versus cycling high-intensity intermittent exercise on local tissue oxygenation and perceived enjoyment in 18–30-year-old sedentary men link: https://peerj.com/articles/5026 last-modified: 2018-06-19 description: BackgroundHigh-intensity interval training (HIIT) has been proposed as a time-efficient exercise format to improve exercise adherence, thereby targeting the chronic disease burden associated with sedentary behaviour. Exercise mode (cycling, running), if self-selected, will likely affect the physiological and enjoyment responses to HIIT in sedentary individuals. Differences in physiological and enjoyment responses, associated with the mode of exercise, could potentially influence the uptake and continued adherence to HIIT. It was hypothesised that in young sedentary men, local and systemic oxygen utilisation and enjoyment would be higher during a session of running HIIT, compared to a session of cycling HIIT.MethodsA total of 12 sedentary men (mean ± SD; age 24 ± 3 years) completed three exercise sessions: a maximal incremental exercise test on a treadmill (MAX) followed by two experiment conditions, (1) free-paced cycling HIIT on a bicycle ergometer (HIITCYC) and (2) constant-paced running HIIT on a treadmill ergometer (HIITRUN). Deoxygenated haemoglobin (HHb) in the gastrocnemius (GN), the left vastus lateralis (LVL) and the right vastus lateralis (RVL) muscles, oxygen consumption (VO2), heart rate (HR), ratings of perceived exertion (RPE) and physical activity enjoyment (PACES) were measured during HIITCYC and HIITRUN.ResultsThere was a higher HHb in the LVL (p = 0.001) and RVL (p = 0.002) sites and a higher VO2 (p = 0.017) and HR (p < 0.001) during HIITCYC, compared to HIITRUN. RPE was higher (p < 0.001) and PACES lower (p = 0.032) during HIITCYC compared to HIITRUN.DiscussionIn sedentary individuals, free-paced cycling HIIT produces higher levels of physiological stress when compared to constant-paced running HIIT. Participants perceived running HIIT to be more enjoyable than cycling HIIT. These findings have implications for selection of mode of HIIT for physical stress, exercise enjoyment and compliance. creator: Yuri Kriel creator: Christopher D. Askew creator: Colin Solomon uri: https://doi.org/10.7717/peerj.5026 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Kriel et al. title: Weak population structure in the ant Formica fusca link: https://peerj.com/articles/5024 last-modified: 2018-06-19 description: Dispersal is a fundamental trait of a species’ biology. High dispersal results in weakly structured or even panmictic populations over large areas, whereas weak dispersal enables population differentiation and strong spatial structuring. We report on the genetic population structure in the polygyne ant Formica fusca and the relative contribution of the dispersing males and females to this. We sampled 12 localities across a ∼35 km2 study area in Finland and generated mitochondrial DNA (mtDNA) haplotype data and microsatellite data. First, we assessed queen dispersal by estimating population differentiation from mtDNA haplotype data. Second, we analysed nuclear DNA microsatellite data to determine overall population genetic substructure in the study area with principal components analysis, Bayesian clustering, hierarchical F statistics and testing for evidence of isolation-by-distance. Third, we directly compared genetic differentiation estimates from maternally inherited mtDNA and bi-parentally inherited DNA microsatellites to test for sex-bias in dispersal. Our results showed no significant spatial structure or isolation by distance in neither mtDNA nor DNA microsatellite data, suggesting high dispersal of both sexes across the study area. However, mitochondrial differentiation was weaker (Fst-mt = 0.0047) than nuclear differentiation (Fst-nuc = 0.027), which translates into a sixfold larger female migration rate compared to that of males. We conclude that the weak population substructure reflects high dispersal in both sexes, and it is consistent with F. fusca as a pioneer species exploiting unstable habitats in successional boreal forests. creator: Helena Johansson creator: Perttu Seppä creator: Heikki Helanterä creator: Kalevi Trontti creator: Liselotte Sundström uri: https://doi.org/10.7717/peerj.5024 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Johansson et al. title: Scraping marking behaviour of the largest Neotropical felids link: https://peerj.com/articles/4983 last-modified: 2018-06-19 description: BackgroundDetails of how, why and in what conditions large felids make scrapes is unknown. Here, we examined the general hypothesis about the use of scrapes for marking proposals, as well as to communicate with other individuals to signalize particular points or areas of interest, by studying scrape-marking behaviour of jaguars and pumas.MethodsWe surveyed by scrapes between five days and two months mainly during dry season in five study areas from Mexico (El Edén and San Ignacio), Belize (Cockscomb) and Brazil (Angatuba and Serra das Almas), which differed in presence and/or abundance of jaguars and pumas. Paths were slowly walked while searching for scrapes by teams normally composed of two people and tracks were stored in GPS, distinguishing the type of path surveyed (unpaved track roads, trails and cross-country).ResultsWe found a total of 269 felid scrapes along 467 km of paths surveyed, obtaining a finding rate of 0.576 scrapes per km. Most scrapes were found in car tracks (0.629 scrapes per km), followed by trails (0.581 scrapes per km), and rarely did we find scrapes in cross country (0.094 scrapes per km). In trails, scrapes were found in a similar frequency in the centre and edge, whereas in car tracks they were mainly found in the edge. There were also clear differences in the position of the scrapes between study areas that differed in presence and/or abundance of pumas and jaguars, with scrapes located mainly in the centre in areas only with pumas, in the centre and in the edge in areas with a similar number of jaguars and pumas, and in the edge in area mainly dominated by jaguars. The remarking rate tended to be higher in one of the areas with only pumas where natural vegetation was scarcer. Felids chose sites mainly covered by leaves and located in paths less wide, clean and rarely used.DiscussionScraping was a frequent behaviour in the largest felids of America, although in some areas, scraping behaviour was rare. Scrapes seem to be signalizing some specific areas within territories and data suggest that they are made with the proposal of communication between individuals. It seems that a high scraping behaviour in pumas is not related to the presence of jaguars. creator: Francisco Palomares creator: Noa González-Borrajo creator: Cuauhtémoc Chávez creator: Yamel Rubio creator: Luciano M. Verdade creator: Rocio Monsa creator: Bart Harmsen creator: Begoña Adrados creator: Marina Zanin uri: https://doi.org/10.7717/peerj.4983 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Palomares et al. title: Biological nitrification inhibition by root exudates of native species, Hibiscus splendens and Solanum echinatum link: https://peerj.com/articles/4960 last-modified: 2018-06-19 description: Australian native species grow competitively in nutrient limited environments, particularly in nitrogen (N) limited soils; however, the mechanism that enables this is poorly understood. Biological nitrification inhibition (BNI), which is the release of root exudates into the plant rhizosphere to inhibit the nitrification process, is a hypothesized adaptive mechanism for maximizing N uptake. To date, few studies have investigated the temporal pattern and components of root exudates by Australian native plant species for BNI. This study examined root exudates from two Australian native species, Hibiscus splendens and Solanum echinatum, and contrasted with exudates of Sorghum bicolor, a plant widely demonstrated to exhibit BNI capacity. Root exudates were collected from plants at two, four, and six weeks after transplanting to solution culture. Root exudates contained three types of organic acids (OAs), oxalic, citric and succinic acids, regardless of the species. However, the two Australian natives species released larger amount of OAs in earlier development stages than S. bicolor. The total quantity of these OAs released per unit root dry mass was also seven-ten times greater for Australian native plant species compared to S. bicolor. The root exudates significantly inhibited nitrification activity over six weeks’ growth in a potential nitrification assay, with S. echinatum (ca. 81% inhibition) > S. bicolor (ca. 80% inhibition) > H. splendens (ca. 78% inhibition). The narrow range of BNI capacity in the study plants limited the determination of a relationship between OAs and BNI; however, a lack of correlation between individual OAs and inhibition of nitrification suggests OAs may not directly contribute to BNI. These results indicate that Australian native species generate a strongly N conserving environment within the rhizosphere up to six weeks after germination, establishing a competitive advantage in severely N limited environments. creator: Chelsea K. Janke creator: Laura A. Wendling creator: Ryosuke Fujinuma uri: https://doi.org/10.7717/peerj.4960 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Janke et al. title: Transcriptomic evidence for involvement of reactive oxygen species in Rhizoctonia solani AG1 IA sclerotia maturation link: https://peerj.com/articles/5103 last-modified: 2018-06-18 description: Rhizoctonia solani AG1 IA is a soil-borne fungal phytopathogen that can significantly harm crops resulting in economic loss. This species overwinters in grass roots and diseased plants, and produces sclerotia that infect future crops. R. solani AG1 IA does not produce spores; therefore, understanding the molecular mechanism of sclerotia formation is important for crop disease control. To identify the genes involved in this process for the development of disease control targets, the transcriptomes of this species were determined at three important developmental stages (mycelium, sclerotial initiation, and sclerotial maturation) using an RNA-sequencing approach. A total of 5,016, 6,433, and 5,004 differentially expressed genes (DEGs) were identified in the sclerotial initiation vs. mycelial, sclerotial maturation vs. mycelial, and sclerotial maturation vs. sclerotial initiation stages, respectively. Moreover, gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) analyses showed that these DEGs were enriched in diverse categories, including oxidoreductase activity, carbohydrate metabolic process, and oxidation-reduction processes. A total of 12 DEGs were further verified using reverse transcription quantitative PCR. Among the genes examined, NADPH oxidase 1 (NOX1) and superoxide dismutase (SOD) were highly induced in the stages of sclerotial initiation and maturation. In addition, the highest reactive oxygen species (ROS) production levels were detected during sclerotial initiation, and enzyme activities of NOX1, SOD, and catalase (CAT) matched with the gene expression profiles. To further evaluate the role of ROS in sclerotial formation, R. solani AG1 IA was treated with the CAT inhibitor aminotriazole and H2O2, resulting in the early differentiation of sclerotia. Taken together, this study provides useful information toward understanding the molecular basis of R. solani AG1 IA sclerotial formation and maturation, and identified the important role of ROS in these processes. creator: Bo Liu creator: Haode Wang creator: Zhoujie Ma creator: Xiaotong Gai creator: Yanqiu Sun creator: Shidao He creator: Xian Liu creator: Yanfeng Wang creator: Yuanhu Xuan creator: Zenggui Gao uri: https://doi.org/10.7717/peerj.5103 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Liu et al. title: Comparative demography of commercially-harvested snappers and an emperor from American Samoa link: https://peerj.com/articles/5069 last-modified: 2018-06-18 description: The age-based life history of two commercially-important species of snapper (Lutjanidae) and one emperor (Lethrinidae) were characterized from the nearshore fishery of Tutuila, American Samoa. Examination of sagittal otoliths across multiple months and years confirmed the annual deposition of increments and highlighted marked variation in life-history patterns among the three meso-predator species. The humpback red snapper Lutjanus gibbus is a medium-bodied gonochoristic species which exhibits striking sexual dimorphism in length-at-age and consequent growth trajectories and has a life span estimated to be at least 27 years. The yellow-lined snapper Lutjanus rufolineatus is a small-bodied gonochore with weak sexual dimorphism, early maturation, and a short life span of at least 12 years. The yellow-lip emperor Lethrinus xanthochilus is a large-bodied species with a moderate life span (estimated to be at least 19 years in this study), rapid initial growth, and a more complex sexual ontogeny likely involving pre- or post-maturational sex change, although this remains unresolved at present. Ratios of natural to fishing mortality indicate a low level of prevailing exploitation for all three species, which is supported by low proportions of immature female length classes captured by the fishery. However, considerable demographic variability among the three species highlights the value of detailed age-based information as a necessary component for informing monitoring efforts and future management decisions. creator: Brett M. Taylor creator: Zack S. Oyafuso creator: Cassandra B. Pardee creator: Domingo Ochavillo creator: Stephen J. Newman uri: https://doi.org/10.7717/peerj.5069 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Taylor et al. title: Intein-mediated backbone cyclization of entolimod confers enhanced radioprotective activity in mouse models link: https://peerj.com/articles/5043 last-modified: 2018-06-18 description: BackgroundEntolimod is a Salmonella enterica flagellin derivate. Previous work has demonstrated that entolimod effectively protects mice and non-human primates from ionizing radiation. However, it caused a “flu-like” syndrome after radioprotective and anticancer clinical application, indicating some type of immunogenicity and toxicity. Cyclization is commonly used to improve the in vivo stability and activity of peptides and proteins.MethodsWe designed and constructed cyclic entolimod using split Nostoc punctiforme DnaE intein with almost 100% cyclization efficiency. We adopted different strategies to purify the linear and circular entolimod due to their different topologies. Both of linear and circular entolimod were first purified by Ni-chelating affinity chromatography, and then the linear and circular entolimod were purified by size-exclusion and ion-exchange chromatography, respectively.ResultsThe circular entolimod showed significantly increased both the in vitro NF-κB signaling and in vivo radioprotective activity in mice.ConclusionOur data indicates that circular entolimod might be a good candidate for further clinical investigation. creator: Bingyu Ye creator: Wenlong Shen creator: Minglei Shi creator: Yan Zhang creator: Cunshuan Xu creator: Zhihu Zhao uri: https://doi.org/10.7717/peerj.5043 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Ye et al. title: Individual-based simulation of the spatial and temporal dynamics of macroinvertebrate functional groups provides insights into benthic community assembly mechanisms link: https://peerj.com/articles/5038 last-modified: 2018-06-18 description: The complexity and scales of the processes that shape communities of marine benthic macroinvertebrates has limited our understanding of their assembly mechanisms and the potential to make projections of their spatial and temporal dynamics. Individual-based models can shed light on community assembly mechanisms, by allowing observed spatiotemporal patterns to emerge from first principles about the modeled organisms. Previous work in the Rance estuary (Brittany, France) revealed the principal functional components of its benthic macroinvertebrate communities and derived a set of functional relationships between them. These elements were combined here for the development of a dynamic and spatially explicit model that operates at two spatial scales. At the fine scale, modeling each individual’s life cycle allowed the representation of recruitment, inter- and intra-group competition, biogenic habitat modification and predation mortality. Larval dispersal and environmental filtering due to the tidal characteristics of the Rance estuary were represented at the coarse scale. The two scales were dynamically linked and the model was parameterized on the basis of theoretical expectations and expert knowledge. The model was able to reproduce some patterns of α- and β-diversity that were observed in the Rance estuary in 1995. Model analysis demonstrated the role of local and regional processes, particularly early post-settlement mortality and spatially restricted dispersal, in shaping marine benthos. It also indicated biogenic habitat modification as a promising area for future research. The combination of this mechanism with different substrate types, along with the representation of physical disturbances and more trophic categories, could increase the model’s realism. The precise parameterization and validation of the model is expected to extend its scope from the exploration of community assembly mechanisms to the formulation of predictions about the responses of community structure and functioning to environmental change. creator: Nikolaos Alexandridis creator: Cédric Bacher creator: Nicolas Desroy creator: Fred Jean uri: https://doi.org/10.7717/peerj.5038 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Alexandridis et al. title: Safe exposure distances for transcranial magnetic stimulation based on computer simulations link: https://peerj.com/articles/5034 last-modified: 2018-06-18 description: The results of a computer simulation examining the compliance of a given transcranial magnetic stimulation device to the 2010 International Commission on Non-Ionizing Radiation Protection (ICNIRP) guidelines are presented. The objective was to update the safe distance estimates with the most current safety guidelines, as well as comparing these to values reported in previous publications. The 3D data generated was compared against results available in the literature, regarding the MCB-70 coil by Medtronic. Regarding occupational exposure, safe distances of 1.46 m and 0.96 m are derived from the simulation according to the 2003 and 2010 ICNIRP guidelines, respectively. These values are then compared to safe distances previously reported in other studies. creator: Iam Palatnik de Sousa creator: Carlos R. H. Barbosa creator: Elisabeth Costa Monteiro uri: https://doi.org/10.7717/peerj.5034 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Palatnik de Sousa et al. title: Unusually low genetic divergence at COI barcode locus between two species of intertidal Thalassaphorura (Collembola: Onychiuridae) link: https://peerj.com/articles/5021 last-modified: 2018-06-18 description: Species classification is challenging when taxa display limited morphological differences. In this paper, we combined morphology and DNA barcode data to investigate the complicated taxonomy of two Onychiurid Collembolan species. Thalassaphorura thalassophila and Thalassaphorura debilis are among the most common arthropod species in intertidal ecosystems and are often considered to be synonymous. Based on morphological and barcode analyses of fresh material collected in their type localities, we redescribed and compared the two species. However, their morphological distinctiveness was supported by a molecular divergence much smaller than previously reported at the interspecific level among Collembola. This divergence was even smaller than inter-population divergences recognized in the related edaphic species T. zschokkei, as well as those known between MOTUs within many Collembolan species. Our results may indicate a link between low genetic interspecific divergence and intertidal habitat, as the only biological peculiarity of the two species of interest compared to other Collembolan species analyzed to date is their strict intertidal life. creator: Xin Sun creator: Anne Bedos creator: Louis Deharveng uri: https://doi.org/10.7717/peerj.5021 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Sun et al. title: Availability of Nanopore sequences in the genome taxonomy for Vibrionaceae systematics: Rumoiensis clade species as a test case link: https://peerj.com/articles/5018 last-modified: 2018-06-18 description: Whole genome sequence comparisons have become essential for establishing a robust scheme in bacterial taxonomy. To generalize this genome-based taxonomy, fast, reliable, and cost-effective genome sequencing methodologies are required. MinION, the palm-sized sequencer from Oxford Nanopore Technologies, enables rapid sequencing of bacterial genomes using minimal laboratory resources. Here we tested the ability of Nanopore sequences for the genome-based taxonomy of Vibrionaceae and compared Nanopore-only assemblies to complete genomes of five Rumoiensis clade species: Vibrio aphrogenes, V. algivorus, V. casei, V. litoralis, and V. rumoiensis. Comparison of overall genome relatedness indices (OGRI) and multilocus sequence analysis (MLSA) based on Nanopore-only assembly and Illumina or hybrid assemblies revealed that errors in Nanopore-only assembly do not influence average nucleotide identity (ANI), in silico DNA-DNA hybridization (DDH), G+C content, or MLSA tree topology in Vibrionaceae. Our results show that the genome sequences from Nanopore-based approach can be used for rapid species identification based on the OGRI and MLSA. creator: Mami Tanaka creator: Sayaka Mino creator: Yoshitoshi Ogura creator: Tetsuya Hayashi creator: Tomoo Sawabe uri: https://doi.org/10.7717/peerj.5018 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Tanaka et al. title: Comparison of cryptobenthic reef fish communities among microhabitats in the Red Sea link: https://peerj.com/articles/5014 last-modified: 2018-06-18 description: Knowledge of community structure within an ecosystem is essential when trying to understand the function and importance of the system and when making related management decisions. Within the larger ecosystem, microhabitats play an important role by providing inhabitants with a subset of available resources. On coral reefs, cryptobenthic fishes encompass many groups and make up an important proportion of the biodiversity. However, these fishes are relatively small, exhibit extreme visual or behavioral camouflage, and, therefore, are often overlooked. We examined the differences in fish community structure between three common reef microhabitats (live hard coral, dead coral rubble, and sand) using ichthyocide stations in the central Red Sea. Using a combination of morphological and genetic (cytochrome oxidase I (COI) barcoding) techniques, we identified 326 individuals representing 73 species spread across 17 families, from fifteen 1 m2 quadrats. Fish assemblages in the three microhabitats were significantly different from each other. Rubble microhabitats yielded the highest levels of fish abundance, richness, and diversity, followed by hard coral, and then sand. The results show that benthic composition, even at a small scale, influences cryptobenthic communities. This study also provides new COI sequence data to public databases, in order to further the research of cryptobenthic fishes in the Red Sea region. creator: Emily M. Troyer creator: Darren J. Coker creator: Michael L. Berumen uri: https://doi.org/10.7717/peerj.5014 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Troyer et al. title: Is perfectionism associated with academic burnout through repetitive negative thinking? link: https://peerj.com/articles/5004 last-modified: 2018-06-18 description: Academic burnout is prevalent among university students, although understanding of what predicts burnout is limited. This study aimed to test the direct and indirect relationship between two dimensions of perfectionism (Perfectionistic Concerns and Perfectionistic Strivings) and the three elements of Academic Burnout (Exhaustion, Inadequacy, and Cynicism) through Repetitive Negative Thinking. In a cross-sectional survey, undergraduate students (n = 126, Mage = 23.64, 79% female) completed well-validated measures of Perfectionism, Repetitive Negative Thinking, and Academic Burnout. Perfectionistic Concerns was directly associated with all elements of burnout, as well as indirectly associated with Exhaustion and Cynicism via Repetitive Negative Thinking. Perfectionistic Strivings was directly associated with less Inadequacy and Cynicism; however, there were no indirect associations between Perfectionistic Strivings and Academic Burnout operating through Repetitive Negative Thinking. Repetitive Negative Thinking was also directly related to more burnout Exhaustion and Inadequacy, but not Cynicism. It is concluded that future research should investigate whether interventions targeting Perfectionistic Concerns and Repetitive Negative Thinking can reduce Academic Burnout in university students. creator: David Garratt-Reed creator: Joel Howell creator: Lana Hayes creator: Mark Boyes uri: https://doi.org/10.7717/peerj.5004 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Garratt-Reed et al. title: Ecotoxicity of disinfectant benzalkonium chloride and its mixture with antineoplastic drug 5-fluorouracil towards alga Pseudokirchneriella subcapitata link: https://peerj.com/articles/4986 last-modified: 2018-06-18 description: BackgroundBenzalkonium chloride (BAC) is one of the most common ingredients of the disinfectants. It is commonly detected in surface and wastewaters where it can interact with the residues of pharmaceuticals that are also common wastewater pollutants. Among the latter, the residues of antineoplastic drugs are of particular concern as recent studies showed that they can induce adverse effect in aquatic organisms at environmentally relevant concentrations.MethodsEcotoxicity of BAC as an individual compound and in a binary mixture with an antineoplastic drug 5-fluorouracil (5-FU) was determined towards alga Pseudokirchneriella subcapitata, a representative of primary producers. The toxicity of the BAC+5-FU binary mixture was predicted by the two basic models: concentration addition (CA) and independent action (IA), and compared to the experimentally determined toxicity. Additionally combination index (CI) was calculated to determine the type of interaction.ResultsAfter 72 h exposure to BAC a concentration dependent growth inhibition of P. subcapitata was observed with an EC50 0.255 mg/L. Comparing the predicted no effect concentration to the measured concentrations in the surface waters indicate that BAC at current applications and occurrence in aquatic environment may affect algal populations. The measured toxicity of the mixture was higher from the predicted and calculated CI confirmed synergistic effect on the inhibition of algal growth, at least at EC50 concentration. The observed synergism may have impact on the overall toxicity of wastewaters, whereas it is less likely for general environments because the concentrations of 5-FU are several orders of magnitude lower from its predicted no effect concentration.DiscussionThese results indicate that combined effects of mixtures of disinfectants and antineoplastic drugs should be considered in particular when dealing with environmental risk assessment as well as the management of municipal and hospital wastewaters. creator: Tina Elersek creator: Maja Ženko creator: Metka Filipič uri: https://doi.org/10.7717/peerj.4986 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Elersek et al. title: Characterization of the ATPase FlaI of the motor complex of the Pyrococcus furiosus archaellum and its interactions between the ATP-binding protein FlaH link: https://peerj.com/articles/4984 last-modified: 2018-06-18 description: The archaellum, the rotating motility structure of archaea, is best studied in the crenarchaeon Sulfolobus acidocaldarius. To better understand how assembly and rotation of this structure is driven, two ATP-binding proteins, FlaI and FlaH of the motor complex of the archaellum of the euryarchaeon Pyrococcus furiosus, were overexpressed, purified and studied. Contrary to the FlaI ATPase of S. acidocaldarius, which only forms a hexamer after binding of nucleotides, FlaI of P. furiosus formed a hexamer in a nucleotide independent manner. In this hexamer only 2 of the ATP binding sites were available for binding of the fluorescent ATP-analog MANT-ATP, suggesting a twofold symmetry in the hexamer. P. furiosus FlaI showed a 250-fold higher ATPase activity than S. acidocaldarius FlaI. Interaction studies between the isolated N- and C-terminal domains of FlaI showed interactions between the N- and C-terminal domains and strong interactions between the N-terminal domains not previously observed for ATPases involved in archaellum assembly. These interactions played a role in oligomerization and activity, suggesting a conformational state of the hexamer not observed before. Further interaction studies show that the C-terminal domain of PfFlaI interacts with the nucleotide binding protein FlaH. This interaction stimulates the ATPase activity of FlaI optimally at a 1:1 stoichiometry, suggesting that hexameric PfFlaI interacts with hexameric PfFlaH. These data help to further understand the complex interactions that are required to energize the archaellar motor. creator: Paushali Chaudhury creator: Chris van der Does creator: Sonja-Verena Albers uri: https://doi.org/10.7717/peerj.4984 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Chaudhury et al. title: Primates in peril: the significance of Brazil, Madagascar, Indonesia and the Democratic Republic of the Congo for global primate conservation link: https://peerj.com/articles/4869 last-modified: 2018-06-15 description: Primates occur in 90 countries, but four—Brazil, Madagascar, Indonesia, and the Democratic Republic of the Congo (DRC)—harbor 65% of the world’s primate species (439) and 60% of these primates are Threatened, Endangered, or Critically Endangered (IUCN Red List of Threatened Species 2017-3). Considering their importance for global primate conservation, we examine the anthropogenic pressures each country is facing that place their primate populations at risk. Habitat loss and fragmentation are main threats to primates in Brazil, Madagascar, and Indonesia. However, in DRC hunting for the commercial bushmeat trade is the primary threat. Encroachment on primate habitats driven by local and global market demands for food and non-food commodities hunting, illegal trade, the proliferation of invasive species, and human and domestic-animal borne infectious diseases cause habitat loss, population declines, and extirpation. Modeling agricultural expansion in the 21st century for the four countries under a worst-case-scenario, showed a primate range contraction of 78% for Brazil, 72% for Indonesia, 62% for Madagascar, and 32% for DRC. These pressures unfold in the context of expanding human populations with low levels of development. Weak governance across these four countries may limit effective primate conservation planning. We examine landscape and local approaches to effective primate conservation policies and assess the distribution of protected areas and primates in each country. Primates in Brazil and Madagascar have 38% of their range inside protected areas, 17% in Indonesia and 14% in DRC, suggesting that the great majority of primate populations remain vulnerable. We list the key challenges faced by the four countries to avert primate extinctions now and in the future. In the short term, effective law enforcement to stop illegal hunting and illegal forest destruction is absolutely key. Long-term success can only be achieved by focusing local and global public awareness, and actively engaging with international organizations, multinational businesses and consumer nations to reduce unsustainable demands on the environment. Finally, the four primate range countries need to ensure that integrated, sustainable land-use planning for economic development includes the maintenance of biodiversity and intact, functional natural ecosystems. creator: Alejandro Estrada creator: Paul A. Garber creator: Russell A. Mittermeier creator: Serge Wich creator: Sidney Gouveia creator: Ricardo Dobrovolski creator: K.A.I. Nekaris creator: Vincent Nijman creator: Anthony B. Rylands creator: Fiona Maisels creator: Elizabeth A. Williamson creator: Julio Bicca-Marques creator: Agustin Fuentes creator: Leandro Jerusalinsky creator: Steig Johnson creator: Fabiano Rodrigues de Melo creator: Leonardo Oliveira creator: Christoph Schwitzer creator: Christian Roos creator: Susan M. Cheyne creator: Maria Cecilia Martins Kierulff creator: Brigitte Raharivololona creator: Mauricio Talebi creator: Jonah Ratsimbazafy creator: Jatna Supriatna creator: Ramesh Boonratana creator: Made Wedana creator: Arif Setiawan uri: https://doi.org/10.7717/peerj.4869 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Estrada et al. title: MLSTar: automatic multilocus sequence typing of bacterial genomes in R link: https://peerj.com/articles/5098 last-modified: 2018-06-15 description: Multilocus sequence typing (MLST) is a standard tool in population genetics and bacterial epidemiology that assesses the genetic variation present in a reduced number of housekeeping genes (typically seven) along the genome. This methodology assigns arbitrary integer identifiers to genetic variations at these loci which allows us to efficiently compare bacterial isolates using allele-based methods. Now, the increasing availability of whole-genome sequences for hundreds to thousands of strains from the same bacterial species has allowed us to apply and extend MLST schemes by automatic extraction of allele information from the genomes. The PubMLST database is the most comprehensive resource of described schemes available for a wide variety of species. Here we present MLSTar as the first R package that allows us to (i) connect with the PubMLST database to select a target scheme, (ii) screen a desired set of genomes to assign alleles and sequence types, and (iii) interact with other widely used R packages to analyze and produce graphical representations of the data. We applied MLSTar to analyze more than 2,500 bacterial genomes from different species, showing great accuracy, and comparable performance with previously published command-line tools. MLSTar can be freely downloaded from http://github.com/iferres/MLSTar. creator: Ignacio Ferrés creator: Gregorio Iraola uri: https://doi.org/10.7717/peerj.5098 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Ferrés and Iraola title: Horizontally transferred genes in the ctenophore Mnemiopsis leidyi link: https://peerj.com/articles/5067 last-modified: 2018-06-15 description: Horizontal gene transfer (HGT) has had major impacts on the biology of a wide range of organisms from antibiotic resistance in bacteria to adaptations to herbivory in arthropods. A growing body of literature shows that HGT between non-animals and animals is more commonplace than previously thought. In this study, we present a thorough investigation of HGT in the ctenophore Mnemiopsis leidyi. We applied tests of phylogenetic incongruence to identify nine genes that were likely transferred horizontally early in ctenophore evolution from bacteria and non-metazoan eukaryotes. All but one of these HGTs (an uncharacterized protein) are homologous to characterized enzymes, supporting previous observations that genes encoding enzymes are more likely to be retained after HGT events. We found that the majority of these nine horizontally transferred genes were expressed during development, suggesting that they are active and play a role in the biology of M. leidyi. This is the first report of HGT in ctenophores, and contributes to an ever-growing literature on the prevalence of genetic information flowing between non-animals and animals. creator: Alexandra M. Hernandez creator: Joseph F. Ryan uri: https://doi.org/10.7717/peerj.5067 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Hernandez and Ryan title: Transcriptional regulation of metabolism in disease: From transcription factors to epigenetics link: https://peerj.com/articles/5062 last-modified: 2018-06-15 description: Every cell in an individual has largely the same genomic sequence and yet cells in different tissues can present widely different phenotypes. This variation arises because each cell expresses a specific subset of genomic instructions. Control over which instructions, or genes, are expressed is largely controlled by transcriptional regulatory pathways. Each cell must assimilate a huge amount of environmental input, and thus it is of no surprise that transcription is regulated by many intertwining mechanisms. This large regulatory landscape means there are ample possibilities for problems to arise, which in a medical context means the development of disease states. Metabolism within the cell, and more broadly, affects and is affected by transcriptional regulation. Metabolism can therefore contribute to improper transcriptional programming, or pathogenic metabolism can be the result of transcriptional dysregulation. Here, we discuss the established and emerging mechanisms for controling transcription and how they affect metabolism in the context of pathogenesis. Cis- and trans-regulatory elements, microRNA and epigenetic mechanisms such as DNA and histone methylation, all have input into what genes are transcribed. Each has also been implicated in diseases such as metabolic syndrome, various forms of diabetes, and cancer. In this review, we discuss the current understanding of these areas and highlight some natural models that may inspire future therapeutics. creator: Liam J. Hawkins creator: Rasha Al-attar creator: Kenneth B. Storey uri: https://doi.org/10.7717/peerj.5062 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Hawkins et al. title: A novel thymidylate synthase from the Vibrionales, Alteromonadales, Aeromonadales, and Pasteurellales (VAAP) clade with altered nucleotide and folate binding sites link: https://peerj.com/articles/5023 last-modified: 2018-06-15 description: Thymidylate synthase (TS, E.C. 2.1.1.45) is a crucial enzyme for de novo deoxythymidine monophosphate (dTMP) biosynthesis. The gene for this enzyme is thyA, which encodes the folate-dependent TS that converts deoxyuridine monophosphate group (dUMP) into (dTMP) using the cofactor 5,10-methylenetetrahydrofolate (mTHF) as a carbon donor. We identified the thyA gene in the genome of the Vibrio parahaemolyticus strain FIM-S1708+ that is innocuous to humans but pathogenic to crustaceans. Surprisingly, we found changes in the residues that bind the substrate dUMP and mTHF, previously postulated as invariant among all TSs known (Finer-Moore, Santi & Stroud, 2003). Interestingly, those amino acid changes were also found in a clade of microorganisms that contains Vibrionales, Alteromonadales, Aeromonadales, and Pasteurellales (VAAP) from the Gammaproteobacteria class. In this work, we studied the biochemical properties of recombinant TS from V. parahemolyticus FIM-S1708+ (VpTS) to address the natural changes in the TS amino acid sequence of the VAAP clade. Interestingly, the Km for dUMP was 27.3 ± 4.3 µM, about one-fold larger compared to other TSs. The Km for mTHF was 96.3 ± 18 µM, about three- to five-fold larger compared to other species, suggesting also loss of affinity. Thus, the catalytic efficiency was between one or two orders of magnitude smaller for both substrates. We used trimethoprim, a common antibiotic that targets both TS and DHFR for inhibition studies. The IC50 values obtained were high compared to other results in the literature. Nonetheless, this molecule could be a lead for the design antibiotics towards pathogens from the VAAP clade. Overall, the experimental results also suggest that in the VAAP clade the nucleotide salvage pathway is important and should be investigated, since the de novo dTMP synthesis appears to be compromised by a less efficient thymidylate synthase. creator: Alonso A. Lopez-Zavala creator: Eduardo Guevara-Hernandez creator: Luz H. Vazquez-Lujan creator: Arturo Sanchez-Paz creator: Karina D. Garcia-Orozco creator: Carmen A. Contreras-Vergara creator: Gamaliel Lopez-Leal creator: Aldo A. Arvizu-Flores creator: Adrian Ochoa-Leyva creator: Rogerio R. Sotelo-Mundo uri: https://doi.org/10.7717/peerj.5023 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Lopez-Zavala et al. title: Relationship between Acropora millepora juvenile fluorescence and composition of newly established Symbiodinium assemblage link: https://peerj.com/articles/5022 last-modified: 2018-06-15 description: Coral-dinoflagellate symbiosis is the key biological interaction enabling existence of modern-type coral reefs, but the mechanisms regulating initial host–symbiont attraction, recognition and symbiont proliferation thus far remain largely unclear. A common reef-building coral, Acropora millepora, displays conspicuous fluorescent polymorphism during all phases of its life cycle, due to the differential expression of fluorescent proteins (FPs) of the green fluorescent protein family. In this study, we examine whether fluorescent variation in young coral juveniles exposed to natural sediments is associated with the uptake of disparate Symbiodinium assemblages determined using ITS-2 deep sequencing. We found that Symbiodinium assemblages varied significantly when redness values varied, specifically in regards to abundances of clades A and C. Whether fluorescence was quantified as a categorical or continuous trait, clade A was found at higher abundances in redder juveniles. These preliminary results suggest juvenile fluorescence may be associated with Symbiodinium uptake, potentially acting as either an attractant to ecologically specific types or as a mechanism to modulate the internal light environment to control Symbiodinium physiology within the host. creator: Kate M. Quigley creator: Marie E. Strader creator: Mikhail V. Matz uri: https://doi.org/10.7717/peerj.5022 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Quigley et al. title: Comprehensive circular RNA expression profile in radiation-treated HeLa cells and analysis of radioresistance-related circRNAs link: https://peerj.com/articles/5011 last-modified: 2018-06-15 description: BackgroundCervical cancer is one of the most common cancers in women worldwide. Malignant tumors develop resistance mechanisms and are less sensitive to or do not respond to irradiation. With the development of high-throughput sequencing technologies, circular RNA (circRNA) has been identified in an increasing number of diseases, especially cancers. It has been reported that circRNA can compete with microRNAs (miRNAs) to change the stability or translation of target RNAs, thus regulating gene expression at the transcriptional level. However, the role of circRNAs in cervical cancer and the radioresistance mechanisms of HeLa cells are unknown. The objective of this study is to investigate the role of circRNAs in radioresistance in HeLa cells.MethodsHigh-throughput sequencing and bioinformatics analysis of irradiated and sham-irradiated HeLa cells. The reliability of high-throughput RNA sequencing was validated using quantitative real-time polymerase chain reaction. The most significant circRNA functions and pathways were selected by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. A circRNA–miRNA–target gene interaction network was used to find circRNAs associated with radioresistance. Moreover, a protein–protein interaction network was constructed to identify radioresistance-related hub proteins.ResultsHigh-throughput sequencing allowed the identification of 16,893 circRNAs involved in the response of HeLa cells to radiation. Compared with the control group, there were 153 differentially expressed circRNAs, of which 76 were up-regulated and 77 were down-regulated. GO covered three domains: biological process (BP), cellular component (CC) and molecular function (MF). The terms assigned to the BP domain were peptidyl-tyrosine dephosphorylation and regulation of cell migration. The identified CC terms were cell–cell adherens junction, nucleoplasm and cytosol, and the identified MF terms were protein binding and protein tyrosine phosphatase activity. The top five KEGG pathways were MAPK signaling pathway, endocytosis, axon guidance, neurotrophin signaling pathway, and SNARE interactions in vesicular transport. The protein–protein interaction analysis indicated that 19 proteins might be hub proteins.ConclusionsCircRNAs may play a major role in the response to radiation. These findings may improve our understanding of the role of circRNAs in radioresistance in HeLa cells and allow the development of novel therapeutic approaches. creator: Duo Yu creator: Yunfeng Li creator: Zhihui Ming creator: Hongyong Wang creator: Zhuo Dong creator: Ling Qiu creator: Tiejun Wang uri: https://doi.org/10.7717/peerj.5011 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Yu et al. title: Highly efficient removal of ammonia nitrogen from wastewater by dielectrophoresis-enhanced adsorption link: https://peerj.com/articles/5001 last-modified: 2018-06-15 description: A new approach, based on dielectrophoresis (DEP), was developed in this work to enhance traditional adsorption for the removal of ammonia nitrogen (NH3-N) from wastewater. The factors that affected the removal efficiency were systematically investigated, which allowed us to determine optimal operation parameters. With this new method we found that the removal efficiency was significantly improved from 66.7% by adsorption only to 95% by adsorption-DEP using titanium metal mesh as electrodes of the DEP and zeolite as the absorbent material. In addition, the dosage of the absorbent/zeolite and the processing time needed for the removal were greatly reduced after the introduction of DEP into the process. In addition, a very low discharge concentration (C, 1.5 mg/L) of NH3-N was achieved by the new method, which well met the discharge criterion of C < 8 mg/L (the emission standard of pollutants for rare earth industry in China). creator: Dongyang Liu creator: Chenyang Cui creator: Yanhong Wu creator: Huiying Chen creator: Junfeng Geng creator: Jianxin Xia uri: https://doi.org/10.7717/peerj.5001 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Liu et al. title: Drinking water and rural schools in the Western Amazon: an environmental intervention study link: https://peerj.com/articles/4993 last-modified: 2018-06-15 description: BackgroundAlthough water and sanitation are considered human rights, worldwide approximately three of 10 people (2.1 billion) do not have access to safe drinking water. In 2016, 5.6 million students were enrolled in the 34% of Brazilian schools located in rural areas, but only 72% had a public water supply network. The objective was to evaluate effectiveness of environmental intervention for water treatment in rural schools of the Western Amazonia, and determine the efficacy of water treatment using a simplified chlorinator on potability standards for turbidity, fecal coliforms and Escherichia coli.MethodsA simplified chlorinator was installed for treatment of potable water in 20 public schools in the rural area of Rio Branco municipality, Acre state, Brazil.ResultsBefore the intervention, 20% (n = 4), 100% (n = 20) and 70% (n = 14) of schools had water that failed to meet potability standards for turbidity, fecal coliforms and E. coli, respectively. However, after intervention, 70% (p = 0.68), 75% (p < 0.001) and 100% (p < 0.001) of schools complied with potability standards.DiscussionThis intervention considerably improved schools’ water quality, thus decreasing children’s health vulnerability due to inadequate water. Ancillary activities including training, educational lectures, installation of equipment, supply of materials and supplies (65% calcium hypochlorite and reagents) were considered fundamental to achieving success full outcomes. Installation of a simplified chlorinator in rural schools of the Western Amazon is therefore proposed as a social technology aiming at social inclusion, as well as economic and environmental sustainability. creator: Maura Regina Ribeiro creator: Luiz Carlos de Abreu creator: Gabriel Zorello Laporta uri: https://doi.org/10.7717/peerj.4993 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Ribeiro et al. title: The use of chloroplast genome sequences to solve phylogenetic incongruences in Polystachya Hook (Orchidaceae Juss) link: https://peerj.com/articles/4916 last-modified: 2018-06-15 description: BackgroundCurrent evidence suggests that for more robust estimates of species tree and divergence times, several unlinked genes are required. However, most phylogenetic trees for non-model organisms are based on single sequences or just a few regions, using traditional sequencing methods. Techniques for massive parallel sequencing or next generation sequencing (NGS) are an alternative to traditional methods that allow access to hundreds of DNA regions. Here we use this approach to resolve the phylogenetic incongruence found in Polystachya Hook. (Orchidaceae), a genus that stands out due to several interesting aspects, including cytological (polyploid and diploid species), evolutionary (reticulate evolution) and biogeographical (species widely distributed in the tropics and high endemism in Brazil). The genus has a notoriously complicated taxonomy, with several sections that are widely used but probably not monophyletic.MethodsWe generated the complete plastid genome of 40 individuals from one clade within the genus. The method consisted in construction of genomic libraries, hybridization to RNA probes designed from available sequences of a related species, and subsequent sequencing of the product. We also tested how well a smaller sample of the plastid genome would perform in phylogenetic inference in two ways: by duplicating a fast region and analyzing multiple copies of this dataset, and by sampling without replacement from all non-coding regions in our alignment. We further examined the phylogenetic implications of non-coding sequences that appear to have undergone hairpin inversions (reverse complemented sequences associated with small loops).ResultsWe retrieved 131,214 bp, including coding and non-coding regions of the plastid genome. The phylogeny was able to fully resolve the relationships among all species in the targeted clade with high support values. The first divergent species are represented by African accessions and the most recent ones are among Neotropical species.DiscussionOur results indicate that using the entire plastid genome is a better option than screening highly variable markers, especially when the expected tree is likely to contain many short branches. The phylogeny inferred is consistent with the proposed origin of the genus, showing a probable origin in Africa, with later dispersal into the Neotropics, as evidenced by a clade containing all Neotropical individuals. The multiple positions of Polystachya concreta (Jacq.) Garay & Sweet in the phylogeny are explained by allotetraploidy. Polystachya estrellensis Rchb.f. can be considered a genetically distinct species from P. concreta and P. foliosa (Lindl.) Rchb.f., but the delimitation of P. concreta remains uncertain. Our study shows that NGS provides a powerful tool for inferring relationships at low taxonomic levels, even in taxonomically challenging groups with short branches and intricate morphology. creator: Narjara Lopes de Abreu creator: Ruy José Válka Alves creator: Sérgio Ricardo Sodré Cardoso creator: Yann J.K. Bertrand creator: Filipe Sousa creator: Climbiê Ferreira Hall creator: Bernard E. Pfeil creator: Alexandre Antonelli uri: https://doi.org/10.7717/peerj.4916 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Abreu et al. title: Is right coronary artery chronic total vessel occlusion impacting the surgical revascularization results of patients with multivessel disease? A retrospective study link: https://peerj.com/articles/4909 last-modified: 2018-06-15 description: IntroductionChronic total occlusion (CTO) is common in the presence of other significantly narrowed coronary arteries. The impact of total occlusion and its association with completeness of revascularization on patients with multivessel disease undergoing coronary artery bypass graft (CABG) remains largely unknown.AimThe aim of our study was to compare CABG operation characteristics, as well as 30-day mortality, incidence of post-operative major adverse cardiac and cerebrovascular events (MACCE) between patients with and without CTO in right coronary artery (RCA).Materials and MethodsA total of 156 consecutive patients were included in the analysis. CTO of RCA or right posterior descending artery (RPD) was diagnosed in 57 patients (CTO-RCA group). Coronary stenosis without CTO in RCA was diagnosed in 99 patients (nonCTO-RCA group). Baseline characteristics were comparable in both groups.ResultsThe majority of patients had class II (49.1% vs. 46%, p = 0.86) or class III (42.1% vs. 43%, p = 1.0) Canadian Cardiovascular Society grading system symptoms. Patients in the CTO-RCA group had in average 2.2 grafts implanted, as opposed to 2.4 grafts in patients in the nonCTO-RCA group (p = 0.003). Graft to the RCA was performed in 40.3% patients in the CTO-RCA group and in 81% patients in the nonCTO-RCA group (p = 0.001). The 30-day mortality from any cause or cardiac cause did not differ between groups (7% vs. 2%, p = 0.14 and 3.5% vs. 2%, p = 0.57 respectively). In a multivariate analysis CTO in RCA or RPD and peripheral artery disease were independent predictors of post-operative MACCE (7.9 (1.434–43.045) p = 0.02; 18.8 (3.451–101.833) p < 0.01, respectively).ConclusionsChronic total occlusion of RCA was found to be associated with smaller number of grafts performed during the CABG procedure. Although mortality between patients in the CTO-RCA and nonCTO-RCA groups did not differ, patients in the CTO-RCA group had higher incidence of post-operative MACCE. creator: Janusz Konstanty-Kalandyk creator: Krzysztof Bartuś creator: Jacek Piątek creator: Anna Kędziora creator: Tomasz Darocha creator: Krzysztof L. Bryniarski creator: Marcin Wróżek creator: Piotr Ceranowicz creator: Stanisław Bartuś creator: Leszek Bryniarski creator: Bogusław Kapelak uri: https://doi.org/10.7717/peerj.4909 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Konstanty-Kalandyk et al. title: The effect of recent competition between the native Anolis oculatus and the invasive A. cristatellus on display behavior link: https://peerj.com/articles/4888 last-modified: 2018-06-15 description: Invasive species are a global threat to biodiversity. Cases where the invasion has been tracked since its beginning are rare, however, such that the first interactions between invasive and native species remain poorly understood. Communication behavior is an integral part of species identity and is subject to selection. Consequently, resource use and direct interference competition between native and invasive species may drive its evolution. Here, we tested the role of interactions between the recently introduced invasive lizard Anolis cristatellus and the native Anolis oculatus on variation in behavior and communication in Calibishie (Dominica). From May to June 2016, we filmed 122 adult males of both species displaying in banana farms under two contexts (allopatry and sympatry). We then recorded (i) the proportion of time spent displaying and (ii) the relative frequency of dewlap vs. push-up displays. To control for habitat variation, we measured and compared the habitat characteristics (canopy openness and habitat openness) of 228 males in allopatry and sympatry. While the habitat characteristics and total display-time did not differ between the contexts for the two species, the proportion of display-time spent dewlapping by A. cristatellus decreased in sympatry. The display of A. oculatus did not differ between the contexts, however. Shifts in microhabitat use, predation pressure, or interspecific interference are potential factors which might explain the behavioral changes in display observed in A. cristatellus. This study highlights the role of behavioral traits as a first response of an invasive species to recent competition with a closely related native species. creator: Claire M. S. Dufour creator: Anthony Herrel creator: Jonathan B. Losos uri: https://doi.org/10.7717/peerj.4888 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Dufour et al. title: A new minute ectosymbiotic harpacticoid copepod living on the sea cucumber Eupentacta fraudatrix in the East/Japan Sea link: https://peerj.com/articles/4979 last-modified: 2018-06-14 description: The ectosymbiotic copepods, Vostoklaophonte eupenta gen. & sp. nov. associated with the sea cucumber Eupentacta fraudatrix, was found in the subtidal zone of Peter the Great Bay, East/Japan Sea. The new genus, Vostoklaophonte, is similar to Microchelonia in the flattened body form, reduced mandible, maxillule and maxilla, but with well-developed prehensile maxilliped, and in the reduced segmentation and setation of legs 1–5. Most appendages of the new genus are more primitive than those of Microchelonia. The inclusion of the symbiotic genera Microchelonia and Vostoklaophonte gen. nov. in Laophontidae, as well as their close phylogenetic relationships, are supported by morphological observations and molecular data. This is the third record of laophontid harpacticoid copepods living in symbiosis with sea cucumbers recorded from the Korean and Californian coasts. creator: Jisu Yeom creator: Mikhail A. Nikitin creator: Viatcheslav N. Ivanenko creator: Wonchoel Lee uri: https://doi.org/10.7717/peerj.4979 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Yeom et al. title: Reproductive ecology of the endangered Beal’s-eyed turtle, Sacalia bealei link: https://peerj.com/articles/4997 last-modified: 2018-06-14 description: The Beal’s-eyed turtle (Sacalia bealei) is endemic to southeastern China and endangered due to poaching and habitat loss. Knowledge of S. bealei ecology is lacking and this study provides baseline information of its reproduction in a natural environment. We studied the reproductive ecology of S. bealei using X-ray, spool-and-line tracking, and direct observation. Six nesting females were successfully tracked and their nesting behaviors are documented in detail. Females produced a mean clutch size of 2.2 eggs (range 1–3). The hard-shelled eggs were ellipsoidal with a mean length of 45.50 mm, a mean width of 23.20 mm, and mean weight of 14.8 g. The relative clutch mass was 9.47%, while the relative egg mass was 4.60%. The mean incubation period was 94.7 days with a mean nest temperature of 25.08 °C. Hatchlings had a mean weight of 9.7 g, carapace length of 40.1 mm, carapace width of 33.3 mm, carapace height of 17.4 mm, plastron length of 31.6 mm, and plastron width of 25.4 mm. The results of this study provide important information to inform conservation plans and ex-situ breeding for this endangered species. creator: Liu Lin creator: Qingru Hu creator: Jonathan J. Fong creator: Jiangbo Yang creator: Zhongdong Chen creator: Feiyu Zhou creator: Jichao Wang creator: Fanrong Xiao creator: Haitao Shi uri: https://doi.org/10.7717/peerj.4997 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Lin et al. title: Structural insights and characterization of human Npas4 protein link: https://peerj.com/articles/4978 last-modified: 2018-06-14 description: Npas4 is an activity dependent transcription factor which is responsible for gearing the expression of target genes involved in neuro-transmission. Despite the importance of Npas4 in many neuronal diseases, the tertiary structure of Npas4 protein along with its physico-chemical properties is limited. In the current study, first we perfomed the phylogenetic analysis of Npas4 and determined the content of hydrophobic, flexible and order-disorder promoting amino acids. The protein binding regions, post-translational modifications and crystallization propensity of Npas4 were predicted through different in-silico methods. The three dimensional model of Npas4 was predicted through LOMET, SPARSKS-X, I-Tasser, RaptorX, MUSTER and Pyhre and the best model was selected on the basis of Ramachandran plot, PROSA, and Qmean scores. The best model was then subjected to further refinement though MODREFINER. Finally the interacting partners of Npas4 were identified through STRING database. The phylogenetic analysis showed the human Npas4 gene to be closely related to other primates such as chimpanzees, monkey, gibbon. The physiochemical properties of Npas4 showed that it is an intrinsically disordered protein with N-terminal ordered region. The post-translational modification analyses indicated absence of acetylation and mannosylation sites. Three potential phosphorylation sites (S108, T130 and T136) were found in PAS A domain whilst a single phosphorylation site (S273) was present in PAS B domain. The predicted tertiary structure of Npas4 showed that bHLH domain and PAS domain possess tertiary structures while the rest of the protein exhibited disorder property. Protein-protein interaction analysis revealed NPas4 interaction with various proteins which are mainly involved in nuclear trafficking of proteins to cytoplasm, activity regulated gene transcription and neurodevelopmental disorders. Moreover the analysis also highlighted the direct relation to proteins involved in promoting neuronal survival, plasticity and cAMP responsive element binding protein proteins. The current study helps in understanding the physicochemical properties and reveals the neuro-modulatory role of Npas4 in crucial pathways involved in neuronal survival and neural signalling hemostasis. creator: Ammad Fahim creator: Zaira Rehman creator: Muhammad Faraz Bhatti creator: Amjad Ali creator: Nasar Virk creator: Amir Rashid creator: Rehan Zafar Paracha uri: https://doi.org/10.7717/peerj.4978 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Fahim et al. title: Histology of 24 organs from Asian elephant calves (Elephas maximus) link: https://peerj.com/articles/4947 last-modified: 2018-06-14 description: BackgroundElephants are the largest and heaviest living terrestrial animals, but information on their histology is still lacking. This study provides a unique insight into the elephant’s organs and also provides a comparison between juvenile Asian elephants and adult Asian elephants or other species. Here we report on the histological structure of 24 organs, including the skin, brain (cerebrum, cerebellar hemisphere, vermis, thalamus, midbrain), spinal cord, sciatic nerve, striated skeletal muscle, cardiac muscle, bone (flat bone and long bone), cartilage (hyaline cartilage and fibrocartilage), heart (right atrium, right ventricle), blood vessels (aorta, pulmonary artery and caudal vena cava), trunk, trachea, lung, tongue, esophagus, stomach, small intestine (duodenum, jejunum, ileum), large intestine (cecum, colon, rectum), liver and pancreas, kidney, ovary, uterus (body and horn) and spleen of two juvenile Asian elephants.MethodsTissue sections were stained with Harris’s hematoxylin and eosin Y.ResultsWhile almost all structures were similar to those of other species or adult elephants, some structures were different from other mammalian species, such as: plexiform bone was found in flat bone only; a thin trachealismuscle was observed in the trachea; and no serous or mucinous glands were found in the submucosa of the trachea.DiscussionHistological information from various organs can serve as an important foundation of basal data for future microanatomical studies, and help in the diagnosis and pathogenesis in sick elephants or those with an unknown cause of death. creator: Chatchote Thitaram creator: Pitchaya Matchimakul creator: Wanpitak Pongkan creator: Wasan Tangphokhanon creator: Raktham Maktrirat creator: Jaruwan Khonmee creator: Anucha Sathanawongs creator: Piyamat Kongtueng creator: Korakot Nganvongpanit uri: https://doi.org/10.7717/peerj.4947 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Thitaram et al. title: Changes in DNA methylation assessed by genomic bisulfite sequencing suggest a role for DNA methylation in cotton fruiting branch development link: https://peerj.com/articles/4945 last-modified: 2018-06-14 description: Cotton plant architecture, including fruit branch formation and flowering pattern, influences plant light exploitation, cotton yield and planting cost. DNA methylation has been widely observed at different developmental stages in both plants and animals and is associated with regulation of gene expression, chromatin remodelling, genome protection and other functions. Here, we investigated the global epigenetic reprogramming during the development of fruiting branches and floral buds at three developmental stages: the seedling stage, the pre-squaring stage and the squaring stage. We first identified 22 cotton genes which potentially encode DNA methyltransferases and demethylases. Among them, the homologous genes of CMT, DRM2 and MET1 were upregulated at pre-squaring and squaring stages, suggesting that DNA methylation is involved in the development of floral buds and fruit branches. Although the global methylation at all of three developmental stages was not changed, the CHG-type methylation of non-expressed genes was higher than those of expressed genes. In addition, we found that the expression of the homologous genes of the key circadian rhythm regulators, including CRY, LHY and CO, was associated with changes of DNA methylation at three developmental stages. creator: Quan Sun creator: Jing Qiao creator: Sai Zhang creator: Shibin He creator: Yuzhen Shi creator: Youlu Yuan creator: Xiao Zhang creator: Yingfan Cai uri: https://doi.org/10.7717/peerj.4945 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Sun et al. title: Establishment of a 12-gene expression signature to predict colon cancer prognosis link: https://peerj.com/articles/4942 last-modified: 2018-06-14 description: A robust and accurate gene expression signature is essential to assist oncologists to determine which subset of patients at similar Tumor-Lymph Node-Metastasis (TNM) stage has high recurrence risk and could benefit from adjuvant therapies. Here we applied a two-step supervised machine-learning method and established a 12-gene expression signature to precisely predict colon adenocarcinoma (COAD) prognosis by using COAD RNA-seq transcriptome data from The Cancer Genome Atlas (TCGA). The predictive performance of the 12-gene signature was validated with two independent gene expression microarray datasets: GSE39582 includes 566 COAD cases for the development of six molecular subtypes with distinct clinical, molecular and survival characteristics; GSE17538 is a dataset containing 232 colon cancer patients for the generation of a metastasis gene expression profile to predict recurrence and death in COAD patients. The signature could effectively separate the poor prognosis patients from good prognosis group (disease specific survival (DSS): Kaplan Meier (KM) Log Rank p = 0.0034; overall survival (OS): KM Log Rank p = 0.0336) in GSE17538. For patients with proficient mismatch repair system (pMMR) in GSE39582, the signature could also effectively distinguish high risk group from low risk group (OS: KM Log Rank p = 0.005; Relapse free survival (RFS): KM Log Rank p = 0.022). Interestingly, advanced stage patients were significantly enriched in high 12-gene score group (Fisher’s exact test p = 0.0003). After stage stratification, the signature could still distinguish poor prognosis patients in GSE17538 from good prognosis within stage II (Log Rank p = 0.01) and stage II & III (Log Rank p = 0.017) in the outcome of DFS. Within stage III or II/III pMMR patients treated with Adjuvant Chemotherapies (ACT) and patients with higher 12-gene score showed poorer prognosis (III, OS: KM Log Rank p = 0.046; III & II, OS: KM Log Rank p = 0.041). Among stage II/III pMMR patients with lower 12-gene scores in GSE39582, the subgroup receiving ACT showed significantly longer OS time compared with those who received no ACT (Log Rank p = 0.021), while there is no obvious difference between counterparts among patients with higher 12-gene scores (Log Rank p = 0.12). Besides COAD, our 12-gene signature is multifunctional in several other cancer types including kidney cancer, lung cancer, uveal and skin melanoma, brain cancer, and pancreatic cancer. Functional classification showed that seven of the twelve genes are involved in immune system function and regulation, so our 12-gene signature could potentially be used to guide decisions about adjuvant therapy for patients with stage II/III and pMMR COAD. creator: Dalong Sun creator: Jing Chen creator: Longzi Liu creator: Guangxi Zhao creator: Pingping Dong creator: Bingrui Wu creator: Jun Wang creator: Ling Dong uri: https://doi.org/10.7717/peerj.4942 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Sun et al. title: Crucial biological functions of CCL7 in cancer link: https://peerj.com/articles/4928 last-modified: 2018-06-14 description: Chemokine (C-C motif) ligand 7 (CCL7), a CC chemokine, is a chemotactic factor and attractant for various kinds of leukocytes, including monocytes and neutrophils. CCL7 is widely expressed in multiple cell types and can participate in anti-inflammatory responses through binding to its receptors to mediate the recruitment of immune cells. Abnormal CCL7 expression is associated with certain immune diseases. Furthermore, CCL7 plays a pivotal role in tumorigenesis. CCL7 promotes tumor progression by supporting the formation of the tumor microenvironment and facilitating tumor invasion and metastasis, although some studies have suggested that CCL7 has tumor suppressor effects. In this review, we summarize the currently available information regarding the influence of CCL7 on tumors. creator: Yangyang Liu creator: Yadi Cai creator: Li Liu creator: Yudong Wu creator: Xiangyang Xiong uri: https://doi.org/10.7717/peerj.4928 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Liu et al. title: What killed Frame Lake? A precautionary tale for urban planners link: https://peerj.com/articles/4850 last-modified: 2018-06-14 description: Frame Lake, located within the city of Yellowknife, Northwest Territories, Canada, has been identified as requiring significant remediation due to its steadily declining water quality and inability to support fish by the 1970s. Former gold mining operations and urbanization around the lake have been suspected as probable causes for the decline in water quality. While these land-use activities are well documented, little information is available regarding their impact on the lake itself. For this reason, Arcellinida, a group of shelled protozoans known to be reliable bioindicators of land-use change, were used to develop a hydroecological history of the lake. The purpose of this study was to use Arcellinida to: (1) document the contamination history of the lake, particularly related to arsenic (As) associated with aerial deposition from mine roaster stacks; (2) track the progress of water quality deterioration in Frame Lake related to mining, urbanization and other activities; and (3) identify any evidence of natural remediation within the lake. Arcellinida assemblages were assessed at 1-cm intervals through the upper 30 cm of a freeze core obtained from Frame Lake. The assemblages were statistically compared to geochemical and loss-on-ignition results from the core to document the contamination and degradation of conditions in the lake. The chronology of limnological changes recorded in the lake sediments were derived from 210Pb, 14C dating and known stratigraphic events. The progress of urbanization near the lake was tracked using aerial photography. Using Spearman correlations, the five most significant environmental variables impacting Arcellinida distribution were identified as minerogenics, organics, As, iron and mercury (p < 0.05; n = 30). Based on CONISS and ANOSIM analysis, three Arcellinida assemblages are identified. These include the Baseline Limnological Conditions Assemblage (BLCA), ranging from 17–30 cm and deposited in the early Holocene >7,000 years before present; the As Contamination Assemblage (ACA), ranging from 7–16 cm, deposited after ∼1962 when sedimentation began in the lake again following a long hiatus that spanned to the early Holocene; and the Eutrophication Assemblage (EA), ranging from 1–6 cm, comprised of sediments deposited after 1990 following the cessation of As and other metal contaminations. The EA developed in response to nutrient-rich waters entering the lake derived from the urbanization of the lake catchment and a reduction in lake circulation associated with the development at the lake outlet of a major road, later replaced by a causeway with rarely open sluiceways. The eutrophic condition currently charactering the lake—as evidenced by a population explosion of eutrophication indicator taxa Cucurbitella tricuspis—likely led to a massive increase in macrophyte growth and winter fish-kills. This ecological shift ultimately led to a system dominated by Hirudinea (leeches) and cessation of the lake as a recreational area. creator: Melody J. Gavel creator: R. Timothy Patterson creator: Nawaf A. Nasser creator: Jennifer M. Galloway creator: Bruce W. Hanna creator: Peter A. Cott creator: Helen M. Roe creator: Hendrik Falck uri: https://doi.org/10.7717/peerj.4850 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Gavel et al. title: Population diversity and relatedness in Sugarbirds (Promeropidae: Promerops spp.) link: https://peerj.com/articles/5000 last-modified: 2018-06-13 description: Sugarbirds are a family of two socially-monogamous passerine species endemic to southern Africa. Cape and Gurney’s Sugarbird (Promerops cafer and P. gurneyi) differ in abundance, dispersion across their range and in the degree of sexual dimorphism in tail length, factors that affect breeding systems and potentially genetic diversity. According to recent data, P. gurneyi are in decline and revision of the species’ IUCN conservation status to a threatened category may be warranted. It is therefore necessary to understand genetic diversity and risk of inbreeding in this species. We used six polymorphic microsatellite markers and one mitochondrial gene (ND2) to compare genetic diversity in P. cafer from Helderberg Nature Reserve and P. gurneyi from Golden Gate Highlands National Park, sites at the core of each species distribution. We describe novel universal avian primers which amplify the entire ND2 coding sequence across a broad range of bird orders. We observed high mitochondrial and microsatellite diversity in both sugarbird populations, with no detectable inbreeding and large effective population sizes. creator: Evan S. Haworth creator: Michael J. Cunningham creator: Kathleen M. Calf Tjorve uri: https://doi.org/10.7717/peerj.5000 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Haworth et al. title: Epidemiology of Haemophilus parasuis isolates from pigs in China using serotyping, antimicrobial susceptibility, biofilm formation and ERIC-PCR genotyping link: https://peerj.com/articles/5040 last-modified: 2018-06-13 description: BackgroundHaemophilus parasuis is a commensal organism of the upper respiratory tract of healthy pigs and causes high morbidity and mortality in piglets. The aim of this study was to investigate the epidemiology of H. parasuis in China from 2014 to 2017.MethodsWe characterized 143 H. parasuis isolates by serotyping, antimicrobial susceptibility, biofilm formation and with enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) assays.ResultsSerotyping revealed serovar 5 as the most prevalent (26.6%) followed by serovars 4 (22.4%), 7 (9.1 %), 13 (6.3%), 12 (5.6 %), and non-typeable (8.4%). In a panel of 23 antimicrobials, the minimum inhibitory concentration 50% (MIC50) were in the range of 0.25–16 μg/mL and MIC90 were 2–>512 μg/mL. A total of 99 isolates of H. parasuis (69.2%) were able to form biofilms and 59.6% (59/99) performed weak biofilm-forming ability. ERIC-PCR revealed a very heterogeneous pattern with 87 clusters.DiscussionThese H. parasuis isolates showed a high serovar and genotypic lineage diversity, different abilities to form biofilms and a high degree of genetic diversity. Biofilm formation was related to antimicrobial susceptibility but there were no statistically significant associations between the antimicrobial susceptibility and either the serovars or the ERIC-PCR clusters. This study showed a high prevalence of high-MIC H. parasuis strains and suggests the need for a continuous surveillance of clinical isolates of H. parasuis. creator: Yongda Zhao creator: Qin Wang creator: Jie Li creator: Xiaohuan Lin creator: Xianhui Huang creator: Binghu Fang uri: https://doi.org/10.7717/peerj.5040 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Zhao et al. title: Increased chronic kidney disease development and progression in diabetic patients after appendectomy: a population-based cohort study link: https://peerj.com/articles/5019 last-modified: 2018-06-13 description: BackgroundThe vermiform appendix serves as a “safe house” for maintaining normal gut bacteria and appendectomy may impair the intestinal microbiota. Appendectomy is expected to profoundly alter the immune system and modulate the pathogenic inflammatory immune responses of the gut. Recent studies have shown that a dysbiotic gut increases the risk of cardiovascular disease and chronic kidney disease (CKD). Therefore, we hypothesized that appendectomy would increase the risk of CKD.MethodsThis nationwide, population-based, propensity-score-matched cohort study included 10,383 patients who underwent appendectomy and 41,532 propensity-score-matched controls. Data were collected by the National Health Insurance Research Database of Taiwan from 2000 to 2013. We examined the associations between appendectomy and CKD and end-stage renal disease (ESRD). The major outcome was a new diagnosis of CKD based on an outpatient diagnosis made at least three times or hospital discharge diagnosis made once during the follow-up period. ESRD was defined as undergoing dialysis therapy for at least 90 days, as in previous studies.ResultsThe incidence rates of CKD and ESRD were higher in the appendectomy group than in the control cohort (CKD: 6.52 vs. 5.93 per 1,000 person-years, respectively; ESRD: 0.49 vs. 0.31 per 1,000 person-years, respectively). Appendectomy patients also had a higher risk of developing CKD (adjusted hazard ratio [aHR] 1.13; 95% CI [1.01–1.26]; P = 0.037) and ESRD (aHR 1.59; 95% CI [1.06–2.37]; P = 0.024) than control group patients. Subgroup analysis showed that appendectomy patients with concomitant diabetes mellitus (aHR 2.08; P = 0.004) were at higher risk of incident ESRD than those without diabetes mellitus. The interaction effects of appendectomy and diabetes mellitus were significant for ESRD risk (P = 0.022); no interaction effect was found for CKD risk (P = 0.555).ConclusionsAppendectomy increases the risk of developing CKD and ESRD, especially in diabetic patients. Physicians should pay close attention to renal function prognosis in appendectomy patients. creator: Chin-Hua Chang creator: Chew-Teng Kor creator: Chia-Lin Wu creator: Ping-Fang Chiu creator: Jhao-Rong Li creator: Chun-Chieh Tsai creator: Teng-Hsiang Chang creator: Chia-Chu Chang uri: https://doi.org/10.7717/peerj.5019 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Chang et al. title: Evaluating the utility of the female-specific mitochondrial f-orf gene for population genetic, phylogeographic and systematic studies in freshwater mussels (Bivalvia: Unionida) link: https://peerj.com/articles/5007 last-modified: 2018-06-13 description: Freshwater mussels (order: Unionida) represent one of the most critically imperilled groups of animals; consequently, there exists a need to establish a variety of molecular markers for population genetics and systematic studies in this group. Recently, two novel mitochondrial protein-coding genes were described in unionoids with doubly uniparental inheritance of mtDNA. These genes are the f-orf in female-transmitted mtDNA and the m-orf in male-transmitted mtDNA. In this study, whole F-type mitochondrial genome sequences of two morphologically similar Lampsilis spp. were compared to identify the most divergent protein-coding regions, including the f-orf gene, and evaluate its utility for population genetic and phylogeographic studies in the subfamily Ambleminae. We also tested whether the f-orf gene is phylogenetically informative at the species level. Our preliminary results indicated that the f-orf gene could represent a viable molecular marker for population- and species-level studies in freshwater mussels. creator: Brent M. Robicheau creator: Emily E. Chase creator: Walter R. Hoeh creator: John L. Harris creator: Donald T. Stewart creator: Sophie Breton uri: https://doi.org/10.7717/peerj.5007 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Robicheau et al. title: Efficient dispersal and substrate acquisition traits in a marine invasive species via transient chimerism and colony mobility link: https://peerj.com/articles/5006 last-modified: 2018-06-13 description: Over the past three decades the colonial ascidian Didemnum vexillum has been expanding its global range, significantly impacting marine habitats and aquaculture facilities. What biological features make D. vexillum so highly invasive? Here, we show that juxtaposed allogeneic D. vexillum colony fragments (‘ramets’) may, initially, form chimeric entities. Subsequently, zooids of the differing genotypes within such chimeras coordinately retreat away from fusion zones. A few days following such post-fusion retreat movements there is further ramet fission and the formation of zooid-depauperate tunic zones. Using polymorphic microsatellite loci to distinguish between genotypes, we found that they were sectorial at the fusion zones and the subsequent ramet movements resulted in further spatial separation of the paired-genotypes indicating that the fusion events observed did not lead to formation of long-term, stable chimeras. Thus, movements of D. vexillum colony ramets from initial fusion zones lead to progressive segregation of genotypes probably minimizing potential somatic/germ-cell competition/parasitism. We speculate that relatively fast (≤10 mm/day) movement of D. vexillum colonies on substrates along with frequent, and perhaps unrestrained, transient allogeneic fusions play significant roles in this species’ striking invasiveness and capacity to colonize new substrates. creator: Andrew E. Fidler creator: Aurelie Bacq-Labreuil creator: Elad Rachmilovitz creator: Baruch Rinkevich uri: https://doi.org/10.7717/peerj.5006 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Fidler et al. title: Synergistic and antagonistic effects of immunomodulatory drugs on the action of antifungals against Candida glabrata and Saccharomyces cerevisiae link: https://peerj.com/articles/4999 last-modified: 2018-06-13 description: Candidemia and other forms of invasive fungal infections caused by Candida glabrata and to a lesser extent Saccharomyces cerevisiae are a serious health problem, especially if their steadily rising resistance to the limited range of antifungal drugs is taken into consideration. Various drug combinations are an attractive solution to the resistance problem, and some drug combinations are already common in the clinical environment due to the nature of diseases or therapies. We tested a few of the common antifungal-immunomodulatory drug combinations and evaluated their effect on selected strains of C. glabrata and S. cerevisiae. The combinations were performed using the checkerboard microdilution assay and interpreted using the Loewe additivity model and a model based on the Bliss independence criterion. A synergistic interaction was confirmed between calcineurin inhibitors (Fk506 and cyclosporine A) and antifungals (fluconazole, itraconazole, and amphotericin B). A new antagonistic interaction between mycophenolic acid (MPA) and azole antifungals was discovered in non-resistant strains. A possible mechanism that explains this is induction of the Cdr1 efflux pump by MPA in C. glabrata ATCC 2001. The Pdr1 regulatory cascade plays a role in overall resistance to fluconazole, but it is not essential for the antagonistic interaction. This was confirmed by the Cgpdr1Δ mutant still displaying the antagonistic interaction between the drugs, although at lower concentrations of fluconazole. This antagonism calls into question the use of simultaneous therapy with MPA and azoles in the clinical environment. creator: Miha Tome creator: Jure Zupan creator: Zorica Tomičić creator: Tadeja Matos creator: Peter Raspor uri: https://doi.org/10.7717/peerj.4999 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Tome et al. title: Identifying the predisposing factors, signs and symptoms of overreaching and overtraining in physical education professionals link: https://peerj.com/articles/4994 last-modified: 2018-06-13 description: BackgroundIt is possible that physical education professionals, especially those who participate in aerobic activities, have predisposing factors, signs and symptoms of overreaching (OVR) and overtraining (OVT) due to a high load and volume of exercise followed by suboptimal recovery time. The present study aimed to identify the predisposing factors, signs and symptoms of OVR and OVT in physical education professionals.MethodsA questionnaire consisting of 42 questions (10 questions group) about predisposing factors and signs/symptoms was answered by 132 physical education professionals from both sexes (83 men and 49 women) who were allocated into a resistance training group (RG, n = 74), aerobic training group (AG, n = 20) and resistance and aerobic training group (RAG, n = 38). A mean score was calculated ranging from 1 (completely absent) to 5 (severe) for each question group. A low occurrence of predisposing factors and signs and symptoms of OVR and OVT was considered to be a question group score 4 or lower. Profile of Mood State Questionnaire (POMS) was also applied.ResultsA mean score of 2.5 ± 0.7, 2.7 ± 0.7 and 2.7 ± 0.8 was found for all question groups for RG, AG and RAG, respectively. Of the total sample, 40.6% trained at least five times/week. The POMS revealed that 67.5% of the RG (n = 50), 80% of the AG (n = 16) and 60.5% of the RAG (n = 23) were classified as having no mood disorders and a standard graphic iceberg was presented. There were no statistical differences (p > 0.05) in the total mood disorders among RG (13.9 ± 24.5), AG (10.3 ± 25.1) and RAG (14.6 ± 27.9) groups.ConclusionDespite the volume of training/body working performed by the physical education professionals surveyed being greater than the recommended to achieve improvements on physical fitness, they did not show predisposing factors, signs or symptoms of OVR and OVT. creator: Ricardo B. Viana creator: Paulo Gentil creator: Vinício S. Lorenço creator: Carlos A. Vieira creator: Mário H. Campos creator: Douglas A.T. Santos creator: Wellington F. Silva creator: Marilia S. Andrade creator: Rodrigo L. Vancini creator: Claudio A.B. de Lira uri: https://doi.org/10.7717/peerj.4994 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Viana et al. title: Seasonal dynamics alter taxonomical and functional microbial profiles in Pampa biome soils under natural grasslands link: https://peerj.com/articles/4991 last-modified: 2018-06-13 description: Soil microbial communities’ assembly is strongly tied to changes in temperature and moisture. Although microbial functional redundancy seems to overcome taxonomical composition changes, the sensitivity and resilience of soil microbial communities from subtropical regions in response to seasonal variations are still poorly understood. Thus, the development of new strategies for biodiversity conservation and sustainable management require a complete understanding of the soil abiotic process involved in the selection of microbial taxa and functions. In this work, we used state of the art molecular methodologies (Next Generation Sequencing) to compare the taxonomic (metataxonomics) and functional (metatranscriptomics) profiles among soil samples from two subtropical natural grasslands located in the Pampa biome, Brazil, in response to short-term seasonal variations. Our data suggest that grasslands maintained a stable microbial community membership along the year with oscillation in abundance. Apparently soil microbial taxa are more susceptible to natural climatic disturbances while functions are more stable and change with less intensity along the year. Finally, our data allow us to conclude that the most abundant microbial groups and functions were shared between seasons and locations reflecting the existence of a stable taxonomical and functional core microbiota. creator: Anthony Diego Muller Barboza creator: Victor Satler Pylro creator: Rodrigo Josemar Seminot Jacques creator: Paulo Ivonir Gubiani creator: Fernando Luiz Ferreira de Quadros creator: Júlio Kuhn da Trindade creator: Eric W. Triplett creator: Luiz Roesch uri: https://doi.org/10.7717/peerj.4991 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Barboza et al. title: Can non-destructive DNA extraction of bulk invertebrate samples be used for metabarcoding? link: https://peerj.com/articles/4980 last-modified: 2018-06-13 description: BackgroundHigh throughput DNA sequencing of bulk invertebrate samples or metabarcoding is becoming increasingly used to provide profiles of biological communities for environmental monitoring. As metabarcoding becomes more widely applied, new reference DNA barcodes linked to individual specimens identified by taxonomists are needed. This can be achieved through using DNA extraction methods that are not only suitable for metabarcoding but also for building reference DNA barcode libraries.MethodsIn this study, we test the suitability of a rapid non-destructive DNA extraction method for metabarcoding of freshwater invertebrate samples.ResultsThis method resulted in detection of taxa from many taxonomic groups, comparable to results obtained with two other tissue-based extraction methods. Most taxa could also be successfully used for subsequent individual-based DNA barcoding and taxonomic identification. The method was successfully applied to field-collected invertebrate samples stored for taxonomic studies in 70% ethanol at room temperature, a commonly used storage method for freshwater samples.DiscussionWith further refinement and testing, non-destructive extraction has the potential to rapidly characterise species biodiversity in invertebrate samples, while preserving specimens for taxonomic investigation. creator: Melissa E. Carew creator: Rhys A. Coleman creator: Ary A. Hoffmann uri: https://doi.org/10.7717/peerj.4980 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Carew et al. title: Dynamic succession of substrate-associated bacterial composition and function during Ganoderma lucidum growth link: https://peerj.com/articles/4975 last-modified: 2018-06-13 description: BackgroundGanoderma lucidum, a valuable medicinal fungus, is widely distributed in China. It grows alongside with a complex microbial ecosystem in the substrate. As sequencing technology advances, it is possible to reveal the composition and functions of substrate-associated bacterial communities.MethodsWe analyzed the bacterial community dynamics in the substrate during the four typical growth stages of G. lucidum using next-generation sequencing.ResultsThe physicochemical properties of the substrate (e.g. acidity, moisture, total nitrogen, total phosphorus and total potassium) changed between different growth stages. A total of 598,771 sequences from 12 samples were obtained and assigned to 22 bacterial phyla. Proteobacteria and Firmicutes were the dominant phyla. Bacterial community composition and diversity significantly differed between the elongation stage and the other three growth stages. LEfSe analysis revealed a large number of bacterial taxa (e.g. Bacteroidetes, Acidobacteria and Nitrospirae) with significantly higher abundance at the elongation stage. Functional pathway prediction uncovered significant abundance changes of a number of bacterial functional pathways between the elongation stage and other growth stages. At the elongation stage, the abundance of the environmental information processing pathway (mainly membrane transport) decreased, whereas that of the metabolism-related pathways increased.DiscussionThe changes in bacterial community composition, diversity and predicted functions were most likely related to the changes in the moisture and nutrient conditions in the substrate with the growth of G. lucidum, particularly at the elongation stage. Our findings shed light on the G. lucidum-bacteria-substrate relationships, which should facilitate the industrial cultivation of G. lucidum. creator: Bo Zhang creator: Lijuan Yan creator: Qiang Li creator: Jie Zou creator: Hao Tan creator: Wei Tan creator: Weihong Peng creator: Xiaolin Li creator: Xiaoping Zhang uri: https://doi.org/10.7717/peerj.4975 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Zhang et al. title: Multi-omic profiling to assess the effect of iron starvation in Streptococcus pneumoniae TIGR4 link: https://peerj.com/articles/4966 last-modified: 2018-06-13 description: We applied multi-omics approaches (transcriptomics, proteomics and metabolomics) to study the effect of iron starvation on the Gram-positive human pathogen Streptococcus pneumoniae to elucidate global changes in the bacterium in a condition similar to what can be found in the host during an infectious episode. We treated the reference strain TIGR4 with the iron chelator deferoxamine mesylate. DNA microarrays revealed changes in the expression of operons involved in multiple biological processes, with a prevalence of genes coding for ion binding proteins. We also studied the changes in protein abundance by 2-DE followed by MALDI-TOF/TOF analysis of total cell extracts and secretome fractions. The main proteomic changes were found in proteins related to the primary and amino sugar metabolism, especially in enzymes with divalent cations as cofactors. Finally, the metabolomic analysis of intracellular metabolites showed altered levels of amino sugars involved in the cell wall peptidoglycan metabolism. This work shows the utility of multi-perspective studies that can provide complementary results for the comprehension of how a given condition can influence global physiological changes in microorganisms. creator: Irene Jiménez-Munguía creator: Mónica Calderón-Santiago creator: Antonio Rodríguez-Franco creator: Feliciano Priego-Capote creator: Manuel J. Rodríguez-Ortega uri: https://doi.org/10.7717/peerj.4966 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Jiménez-Munguía et al. title: Long-term experimental in situ farming of Crambe crambe (Demospongiae: Poecilosclerida) link: https://peerj.com/articles/4964 last-modified: 2018-06-13 description: BackgroundThe marine sponge Crambe crambe was chosen as an experimental model of sustainable shallow-water mariculture in the Sardinian Sea (Western Mediterranean) to provide biomass with high potential in applied research.MethodsExplants were cultured in four long-term experiments (19 and 31 months at ca. 2.5 m depth), to determine the suitability of new culture techniques by testing substrata and seeding time (season), and monitoring survival and growth. Explants were excised and grown in an experimental plant close to the wild donor sponge population. Percentage growth rate (GR%) was measured in terms of surface cover area, and explant survival was monitored in situ by means of a digital photo camera.ResultsExplant survival was high throughout the trial, ranging from 78.57% to 92.85% on travertine tiles and from 50% to 71.42% on oyster shells. A few instances of sponge regression were observed. Explant cover area correlated positively with season on two substrata, i.e., tiles and shells. The surface cover area and GR% of explants were measured in the starting phase and monitored up to the end of the trial. High GR% values were observed both on tiles (>21%) and on oyster shells (>15%).DiscussionThe data on the behaviour and life-style of cultured fragments, together with an increase >2,400% in cover area, demonstrate that in situ aquaculture is a viable and sustainable method for the shallow-water biomass supply of Crambe crambe. creator: Andrea Padiglia creator: Fabio D. Ledda creator: Bachisio M. Padedda creator: Roberto Pronzato creator: Renata Manconi uri: https://doi.org/10.7717/peerj.4964 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Padiglia et al. title: Suitable oasis scales under a government plan in the Kaidu-Konqi River Basin of northwest arid region, China link: https://peerj.com/articles/4943 last-modified: 2018-06-13 description: The Yanqi Basin and the Konqi River Basin of the Kaidu-Konqi River Basin were chosen as the study sites in this paper in order to investigate suitable scales of natural and artificial oases with a specified water resource and water quantity planned by the local government. Combined with remote-sensing images from 2013, water resources in 2013, 2025 and 2035, and weather and socioeconomic data, suitable scales of oases were analyzed. The results showed that: (1) The total available water quantities in the Yanqi Basin and the Konqi River Basin without river base flow, and the input of water into Bosten Lake and Tarim River, over high-, normal and low-flow periods, in 2025 and 2035, were 19.04 × 108 m3, 10.52 × 108 m3, 4.95 × 108 m3, 9.95 × 108 m3 and 9.95 × 108 m3, as well as 21.77 × 108 m3, 13.95 × 108 m3, 10.11 × 108 m3, 12.50 × 108 m3, and 9.74 × 108 m3. (2) The water demand of the natural oasis in the Yanqi Basin and the Konqi River Basin was 2.59 × 108 m3, and 4.59 × 108 m3, respectively. (3) The total water consumption of the artificial oasis in 2013, 2025, and 2035 were 10.51 × 108 m3, 10.99 × 108 m3 and 10.74 × 108 m3 in the Yanqi Basin, respectively, and 18.59 × 108 m3, 14.07 × 108 m3 and 13.30 × 108m3 in the Kongqi River Basin, respectively. (4) Under government planning, the optimal area in 2025 and 2035 should be 5,100.06 km2 and 5,096.15 km2 in the Yanqi Basin oases, and 6,008.53 km2 and 4,691.36 km2 in the Konqi River Basin oases, respectively, under the different inflow variations, and 4,972.71 km2 and 4,969.22 km2 in the Yanqi Basin oases, and 5,975.17 km2 and 4,665.67 km2 in the Kongqi River Basin oases, respectively, under the appropriate proportion. (5) The artificial oases in these basins should be greatly decreased in the future due to limited water resources. creator: Aihong Fu creator: Weihong Li creator: Yaning Chen creator: Yuting Liu uri: https://doi.org/10.7717/peerj.4943 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Fu et al. title: First use of molecular evidence to match sexes in the Monstrilloida (Crustacea: Copepoda), and taxonomic implications of the newly recognized and described, partly Maemonstrilla-like females of Monstrillopsis longilobata Lee, Kim & Chang, 2016 link: https://peerj.com/articles/4938 last-modified: 2018-06-13 description: Two forms of the monstrilloid copepod, one represented by males, the other by females, were dominant among the monstrilloids collected while sampling zooplankton with a light trap in southern coastal waters of Korea. Morphological examination revealed that the males are conspecific with the previously reported and rather specialized Korean species Monstrillopsis longilobata Lee, Kim & Chang, 2016, hitherto known only from males that have extremely long genital lappets. The females also show several diagnostic features of Monstrillopsis, such as prominent eyes, bilobed fifth legs with the inner lobe unarmed and reduced, and four urosomal somites. In addition, though, these females are extraordinary among all Monstrilloida in that their ovigerous spines are directed ventrally, not posteriorly as in most species or anteriorly as in those assigned to Maemonstrilla. Genetic divergence analyses based on partial mitochondrial cytochrome c oxidase subunit I, complete Internal Transcribed Spacer 1 (ITS1)–5.8S–ITS2, and partial 28S rRNA revealed little or no genetic divergence between the present males and females, thus demonstrating that they are mutually conspecific. The present report (1) provides the first morphological description of female M. longilobata with the proposal of a revised nomenclature for antennular setal armament; (2) presents the molecular evidence for conspecificity of the males and females; and (3) lists several morphological characteristics that are sexually dimorphic in this species, and thus likely also in other monstrilloids. Matters bearing on the validity of the genera Haemocera, Monstrillopsis, and Maemonstrilla are discussed. creator: Donggu Jeon creator: Donghyun Lim creator: Wonchoel Lee creator: Ho Young Soh uri: https://doi.org/10.7717/peerj.4938 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Jeon et al. title: Genetic differentiation, local adaptation and phenotypic plasticity in fragmented populations of a rare forest herb link: https://peerj.com/articles/4929 last-modified: 2018-06-13 description: BackgroundDue to habitat loss and fragmentation, numerous forest species are subject to severe population decline. Investigating variation in genetic diversity, phenotypic plasticity and local adaptation should be a prerequisite for implementing conservation actions. This study aimed to explore these aspects in ten fragmented populations of Physospermum cornubiense in view of translocation measures across its Italian range.MethodsFor each population we collected environmental data on landscape (habitat size, quality and fragmentation) and local conditions (slope, presence of alien species, incidence of the herbivorous insect Metcalfa pruinosa and soil parameters). We measured vegetative and reproductive traits in the field and analysed the genetic population structure using ISSR markers (STRUCTURE and AMOVA). We then estimated the neutral (FST) and quantitative (PST) genetic differentiation of populations.ResultsThe populations exhibited moderate phenotypic variation. Population size (range: 16–655 individuals), number of flowering adults (range: 3–420 individuals) and inflorescence size (range: 5.0–8.4 cm) were positively related to Mg soil content. Populations’ gene diversity was moderate (Nei-H = 0.071–0.1316); STRUCTURE analysis identified five different clusters and three main geographic groups: upper, lower, and Apennine/Western Po plain. Fragmentation did not have an influence on the local adaptation of populations, which for all measured traits showed PST < FST, indicating convergent selection.DiscussionThe variation of phenotypic traits across sites was attributed to plastic response rather than local adaptation. Plant translocation from suitable source populations to endangered ones should particularly take into account provenance according to identified genetic clusters and specific soil factors. creator: Rodolfo Gentili creator: Aldo Solari creator: Martin Diekmann creator: Cecilia Duprè creator: Gianna Serafina Monti creator: Stefano Armiraglio creator: Silvia Assini creator: Sandra Citterio uri: https://doi.org/10.7717/peerj.4929 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Gentili et al. title: Tackling critical parameters in metazoan meta-barcoding experiments: a preliminary study based on coxI DNA barcode link: https://peerj.com/articles/4845 last-modified: 2018-06-13 description: Nowadays DNA meta-barcoding is a powerful instrument capable of quickly discovering the biodiversity of an environmental sample by integrating the DNA barcoding approach with High Throughput Sequencing technologies. It mainly consists of the parallel reading of informative genomic fragment/s able to discriminate living entities. Although this approach has been widely studied, it still needs optimization in some necessary steps requested in its advanced accomplishment. A fundamental element concerns the standardization of bioinformatic analyses pipelines. The aim of the present study was to underline a number of critical parameters of laboratory material preparation and taxonomic assignment pipelines in DNA meta-barcoding experiments using the cytochrome oxidase subunit-I (coxI) barcode region, known as a suitable molecular marker for animal species identification. We compared nine taxonomic assignment pipelines, including a custom in-house method, based on Hidden Markov Models. Moreover, we evaluated the potential influence of universal primers amplification bias in qPCR, as well as the correlation between GC content with taxonomic assignment results. The pipelines were tested on a community of known terrestrial invertebrates collected by pitfall traps from a chestnut forest in Italy. Although the present analysis was not exhaustive and needs additional investigation, our results suggest some potential improvements in laboratory material preparation and the introduction of additional parameters in taxonomic assignment pipelines. These include the correct setup of OTU clustering threshold, the calibration of GC content affecting sequencing quality and taxonomic classification, as well as the evaluation of PCR primers amplification bias on the final biodiversity pattern. Thus, careful attention and further validation/optimization of the above-mentioned variables would be required in a DNA meta-barcoding experimental routine. creator: Bachir Balech creator: Anna Sandionigi creator: Caterina Manzari creator: Emiliano Trucchi creator: Apollonia Tullo creator: Flavio Licciulli creator: Giorgio Grillo creator: Elisabetta Sbisà creator: Stefano De Felici creator: Cecilia Saccone creator: Anna Maria D’Erchia creator: Donatella Cesaroni creator: Maurizio Casiraghi creator: Saverio Vicario uri: https://doi.org/10.7717/peerj.4845 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Balech et al. title: Surface electromyographic analysis of differential effects in kettlebell carries for the serratus anterior muscles link: https://peerj.com/articles/5044 last-modified: 2018-06-12 description: The purpose of this study was to examine differences in the Electromyography (EMG) amplitude of the serratus anterior between 45° kettlebell carries and 90° kettlebell carries. Thirty-three men aged roughly between 19 and 23 and who were either college or professional baseball pitchers were chosen and randomly assigned to either perform the 45° kettlebell carry followed by the 90° kettlebell carry (n = 17) or the 90° kettlebell carry followed by the 45° kettlebell carry (n = 16). Each pitcher was instructed in the proper usage of the exercise and assigned a short break between the two carries. Changes in EMG amplitude were examined after proper band-pass filtering, normalization, and moving average-smoothing of the raw EMG signal. Differences of the EMG amplitude mean frequencies were examined between each subject’s individual carries and the clumped groups of all 45° and 90° carries. Among each individual comparison, eight pitchers had “large” Effect Size differences between the EMG amplitudes of their two carries, with seven of them signaling the 45° carry as the larger value. In addition, when examining the grouped mean differences of the EMG amplitudes, we found the 45° carries to be significantly higher (p-value of 0.018). creator: Alex Caravan creator: John O. Scheffey creator: Sam J. Briend creator: Kyle J. Boddy uri: https://doi.org/10.7717/peerj.5044 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Caravan et al. title: Taxonomy annotation and guide tree errors in 16S rRNA databases link: https://peerj.com/articles/5030 last-modified: 2018-06-12 description: Sequencing of the 16S ribosomal RNA (rRNA) gene is widely used to survey microbial communities. Specialized 16S rRNA databases have been developed to support this approach including Greengenes, RDP and SILVA. Most taxonomy annotations in these databases are predictions from sequence rather than authoritative assignments based on studies of type strains or isolates. In this work, I investigated the taxonomy annotations and guide trees provided by these databases. Using a blinded test, I estimated that the annotation error rate of the RDP database is ∼10%. The branching orders of the Greengenes and SILVA guide trees were found to disagree at comparable rates with each other and with taxonomy annotations according to the training set (authoritative reference) provided by RDP, indicating that the trees have comparable quality. Pervasive conflicts between tree branching order and type strain taxonomies strongly suggest that the guide trees are unreliable guides to phylogeny. I found 249,490 identical sequences with conflicting annotations in SILVA v128 and Greengenes v13.5 at ranks up to phylum (7,804 conflicts), indicating that the annotation error rate in these databases is ∼17%. creator: Robert Edgar uri: https://doi.org/10.7717/peerj.5030 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Edgar title: Neural correlates of executive functions in patients with obesity link: https://peerj.com/articles/5002 last-modified: 2018-06-12 description: Obesity is one of the most challenging problems in human health and is recognized as an important risk factor for many chronic diseases. It remains unclear how the neural systems (e.g., the mesolimbic “reward” and the prefrontal “control” neural systems) are correlated with patients’ executive function (EF), conceptualized as the integration of “cool” EF and “hot” EF. “Cool” EF refers to relatively abstract, non-affective operations such as inhibitory control and mental flexibility. “Hot” EF refers to motivationally significant affective operations such as affective decision-making. We tried to find the correlation between structural and functional neuroimaging indices and EF in obese patients. The study population comprised seventeen patients with obesity (seven males and 10 females, BMI = 37.99 ± 5.40, age = 31.82 ± 8.75 year-old) preparing to undergo bariatric surgery. We used noninvasive diffusion tensor imaging, generalized q-sampling imaging, and resting-state functional magnetic resonance imaging to examine the neural correlations between structural and functional neuroimaging indices and EF performances in patients with obesity. We reported that many brain areas are correlated to the patients’ EF performances. More interestingly, some correlations may implicate the possible associations of EF and the incentive motivational effects of food. The neural correlation between the left precuneus and middle occipital gyrus and inhibitory control may suggest that patients with a better ability to detect appetitive food may have worse inhibitory control. Also, the neural correlation between the superior frontal blade and affective decision-making may suggest that patients’ affective decision-making may be associated with the incentive motivational effects of food. Our results provide evidence suggesting neural correlates of EF in patients with obesity. creator: Ming-Chou Ho creator: Vincent Chin-Hung Chen creator: Seh-Huang Chao creator: Ching-Tzu Fang creator: Yi-Chun Liu creator: Jun-Cheng Weng uri: https://doi.org/10.7717/peerj.5002 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Ho et al. title: The restoration of the endangered Sambucus palmensis after 30 years of conservation actions in the Garajonay National Park: genetic assessment and niche modeling link: https://peerj.com/articles/4985 last-modified: 2018-06-12 description: The translocation of individuals or the reinforcement of populations are measures in the genetic rescue of endangered species. Although it can be controversial to decide which and how many individuals must be reintroduced, populations can benefit from reinforcements. Sambucus palmensis is a critically endangered endemic to the Canary Islands. During the past 30 years, the Garajonay National Park (La Gomera) has carried out an intensive program of translocations using cuttings, due to the low germination rates of seeds. To assess the effect of the restorations on the population genetics of S. palmensis in La Gomera, we collected 402 samples from all the restored sites and all known natural individuals, which were genotyped with seven microsatellite markers. In addition, we conducted a species distribution modeling approach to assess how restorations fit the ecological niche of the species. Results show that there is a high proportion of clone specimens due to the propagation method, and the natural clonal reproduction of the species. Nonetheless, the observed heterozygosity has increased with the restorations and there still are private alleles and unique genotypes in the natural populations that have not been considered in the restorations. The population of Liria constitutes a very important genetic reservoir for the species. To optimize future reintroductions, we have proposed a list of specimens that are suitable for the extraction of seeds or cuttings in a greenhouse, as well as new suitable areas obtained by the species distribution models. creator: Priscila Rodríguez-Rodríguez creator: Alejandro G. Fernández de Castro creator: Pedro A. Sosa uri: https://doi.org/10.7717/peerj.4985 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Rodríguez-Rodríguez et al. title: Biofilms and antibiotic susceptibility of multidrug-resistant bacteria from wild animals link: https://peerj.com/articles/4974 last-modified: 2018-06-12 description: BackgroundThe “One Health” concept recognizes that human health and animal health are interdependent and bound to the health of the ecosystem in which they (co)exist. This interconnection favors the transmission of bacteria and other infectious agents as well as the flow of genetic elements containing antibiotic resistance genes. This problem is worsened when pathogenic bacteria have the ability to establish as biofilms. Therefore, it is important to understand the characteristics and behaviour of microorganisms in both planktonic and biofilms states from the most diverse environmental niches to mitigate the emergence and dissemination of resistance.MethodsThe purpose of this work was to assess the antibiotic susceptibility of four bacteria (Acinetobacter spp., Klebsiella pneumoniae, Pseudomonas fluorescens and Shewanella putrefaciens) isolated from wild animals and their ability to form biofilms. The effect of two antibiotics, imipenem (IPM) and ciprofloxacin (CIP), on biofilm removal was also assessed. Screening of resistance genetic determinants was performed by PCR. Biofilm tests were performed by a modified microtiter plate method. Bacterial surface hydrophobicity was determined by sessile drop contact angles.ResultsThe susceptibility profile classified the bacteria as multidrug-resistant. Three genes coding for β-lactamases were detected in K. pneumoniae (TEM, SHV, OXA-aer) and one in P. fluorescens (OXA-aer). K. pneumoniae was the microorganism that carried more β-lactamase genes and it was the most proficient biofilm producer, while P. fluorescens demonstrated the highest adhesion ability. Antibiotics at their MIC, 5 × MIC and 10 × MIC were ineffective in total biofilm removal. The highest biomass reductions were found with IPM (54% at 10 × MIC) against K. pneumoniae biofilms and with CIP (40% at 10 × MIC) against P. fluorescens biofilms.DiscussionThe results highlight wildlife as important host reservoirs and vectors for the spread of multidrug-resistant bacteria and genetic determinants of resistance. The ability of these bacteria to form biofilms should increase their persistence. creator: Carla Dias creator: Anabela Borges creator: Diana Oliveira creator: Antonio Martinez-Murcia creator: Maria José Saavedra creator: Manuel Simões uri: https://doi.org/10.7717/peerj.4974 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Dias et al. title: Biomechanical evidence suggests extensive eggshell thinning during incubation in the Sanagasta titanosaur dinosaurs link: https://peerj.com/articles/4971 last-modified: 2018-06-12 description: The reproduction of titanosaur dinosaurs is still a complex and debated topic. Their Late Cretaceous nesting sites are distributed worldwide and their eggs display substantial morphological variations according to the parent species. In contrast to the typical 1.3–2.0 mm thick shells common to eggs of most titanosaur species (e.g., those that nested in Auca Mahuevo, Tama, Toteşti or Boseong), the Cretaceous Sanagasta eggs of Argentina display an unusual shell thickness of up to 7.9 mm. Their oviposition was synchronous with a palaeogeothermal process, leading to the hypothesis that their extra thick eggshell was an adaptation to this particular nesting environment. Although this hypothesis has already been supported indirectly through several investigations, the mechanical implications of developing such thick shells and how this might have affected the success of hatching remains untested. Finite element analyses estimate that the breaking point of the thick-shelled Sanagasta eggs is 14–45 times higher than for other smaller and equally sized titanosaur eggs. The considerable energetic disadvantage for piping through these thick eggshells suggests that their dissolution during incubation would have been paramount for a successful hatching. creator: E. Martín Hechenleitner creator: Jeremías R. A. Taborda creator: Lucas E. Fiorelli creator: Gerald Grellet-Tinner creator: Segundo R. Nuñez-Campero uri: https://doi.org/10.7717/peerj.4971 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Hechenleitner et al. title: Odor-dependent temporal dynamics in Caenorhabitis elegans adaptation and aversive learning behavior link: https://peerj.com/articles/4956 last-modified: 2018-06-12 description: Animals sense an enormous number of cues in their environments, and, over time, can form learned associations and memories with some of these. The nervous system remarkably maintains the specificity of learning and memory to each of the cues. Here we asked whether the nematode Caenorhabditis elegans adjusts the temporal dynamics of adaptation and aversive learning depending on the specific odor sensed. C. elegans senses a multitude of odors, and adaptation and learned associations to many of these odors requires activity of the cGMP-dependent protein kinase EGL-4 in the AWC sensory neuron. We identified a panel of 17 attractive odors, some of which have not been tested before, and determined that the majority of these odors require the AWC primary sensory neuron for sensation. We then devised a novel assay to assess odor behavior over time for a single population of animals. We used this assay to evaluate the temporal dynamics of adaptation and aversive learning to 13 odors and find that behavior change occurs early in some odors and later in others. We then examined EGL-4 localization in early-trending and late-trending odors over time. We found that the timing of these behavior changes correlated with the timing of nuclear accumulation of EGL-4 in the AWC neuron suggesting that temporal changes in behavior may be mediated by aversive learning mechanisms. We demonstrate that temporal dynamics of adaptation and aversive learning in C. elegans can be used as a model to study the timing of memory formation to different sensory cues. creator: Jae Im Choi creator: Hee Kyung Lee creator: Hae Su Kim creator: So Young Park creator: Tong Young Lee creator: Kyoung-hye Yoon creator: Jin I. Lee uri: https://doi.org/10.7717/peerj.4956 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Choi et al. title: A relationship between species richness and evenness that depends on specific relative abundance distribution link: https://peerj.com/articles/4951 last-modified: 2018-06-12 description: Although many ecologists focus on the relationship between species richness (S) and evenness (E), conflicts between observation and theory are difficult to reconcile. Empirical S–E relationships were not consistent, while relationships show strong correlation between S and E. Since E essentially depended on the relative abundance distribution (RAD), the hypothesis of this paper was that the S–E relationship should be determined by RAD. Theoretical S–E relationships for various RADs have already been reported, but they were rarely assessed by the raw data. This study constructed S–E relationships for a specific RAD, which indicated that if the community had a fractal distribution of rank abundance, E would decrease with S, and the S–E relationship would be unique for a given RAD. Such theoretical expectations were supported by three datasets with 82 samples, which suggested that the S–E relationship were controlled by RAD and inconsistent S–E relationships in statistical analyses could be accounted for by the variation of underlying RAD model between communities. From the perspective of RAD, it could be too early to split the diversity into S and E only based on the S–E relationship in statistical analyses. creator: Qiang Su uri: https://doi.org/10.7717/peerj.4951 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Su title: RNA interference-mediated silencing of genes involved in the immune responses of the soybean pod borer Leguminivora glycinivorella (Lepidoptera: Olethreutidae) link: https://peerj.com/articles/4931 last-modified: 2018-06-12 description: RNA interference (RNAi) technology may be useful for developing new crop protection strategies against the soybean pod borer (SPB; Leguminivora glycinivorella), which is a critical soybean pest in northeastern Asia. Immune-related genes have been recently identified as potential RNAi targets for controlling insects. However, little is known about these genes or mechanisms underlying their expression in the SPB. In this study, we completed a transcriptome-wide analysis of SPB immune-related genes. We identified 41 genes associated with SPB microbial recognition proteins, immune-related effectors or signalling molecules in immune response pathways (e.g., Toll and immune deficiency pathways). Eleven of these genes were selected for a double-stranded RNA artificial feeding assay. The down-regulated expression levels of LgToll-5-1a and LgPGRP-LB2a resulted in relatively high larval mortality rates and abnormal development. Our data represent a comprehensive genetic resource for immune-related SPB genes, and may contribute to the elucidation of the mechanism regulating innate immunity in Lepidoptera species. Furthermore, two immune-related SPB genes were identified as potential RNAi targets, which may be used in the development of RNAi-mediated SPB control methods. creator: Ruixue Ran creator: Tianyu Li creator: Xinxin Liu creator: Hejia Ni creator: Wenbin Li creator: Fanli Meng uri: https://doi.org/10.7717/peerj.4931 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Ran et al. title: Does bariatric surgery influence plasma levels of fetuin-A and leukocyte cell-derived chemotaxin-2 in patients with type 2 diabetes mellitus? link: https://peerj.com/articles/4884 last-modified: 2018-06-12 description: BackgroundFetuin-A and leukocyte cell-derived chemotaxin-2 (LECT-2) are liver-derived proteins. Fetuin-A is an independent risk factor for type 2 diabetes (T2D) and obese patients with T2D have higher plasma fetuin-A levels than those without T2D. LECT-2 has positive correlation with the severity of both obesity and insulin resistance. The changes in plasma fetuin-A are not consistent after bariatric surgery and no studies have investigated the changes in LECT-2 on the obese patients with T2D after bariatric surgery.MethodsOverall, 18 patients undergoing gastric bypass (GB) and 16 patients undergoing sleeve gastrectomy (SG) were enrolled. The fasting plasma fetuin-A and LECT-2 levels were measured at baseline, one week, three months, and one year after surgery.ResultsBoth the GB and SG groups significantly decreased the body mass index (BMI), waist-to-hip ratio, a body shape index; the triglyceride, fasting blood sugar (FBS), hemoglobin A1c, C-peptide levels; and homeostatic model assessment (HOMA-IR) one year after surgery. The SG group showed a decreasing trend in plasma fetuin-A levels one year after SG surgery. There are no significant changes in LECT-2 one year after either GB or SG. Fetuin-A had a near significant negative relationship with insulin (P = 0.056) and HOMA-IR (P = 0.050) in the SG group. Changes in fetuin-A had a significant positive relationship with changes in BMI (P = 0.031) and waist-to-hip ratio (P = 0.031) in the GB group and had a near significant positive correlation with FBS (P = 0.051) in the SG group.DiscussionNeither GB nor SG modifies plasma levels of plasma fetuin-A or LECT-2 in T2D patients after surgery. The changes in plasma fetuin-A have a positive correlation with those of the BMI and waist-to-hip ratio 12 months after GB. creator: Hsien-Hao Huang creator: Chun Yeh creator: Jung-Chien Chen creator: Tzong-Hsi Lee creator: Shu-Chun Chen creator: Wei-Jei Lee creator: Chih-Yen Chen uri: https://doi.org/10.7717/peerj.4884 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Huang et al. title: Unfamiliar face matching with photographs of infants and children link: https://peerj.com/articles/5010 last-modified: 2018-06-11 description: BackgroundInfants and children travel using passports that are typically valid for five years (e.g. Canada, United Kingdom, United States and Australia). These individuals may also need to be identified using images taken from videos and other sources in forensic situations including child exploitation cases. However, few researchers have examined how useful these images are as a means of identification.MethodsWe investigated the effectiveness of photo identification for infants and children using a face matching task, where participants were presented with two images simultaneously and asked whether the images depicted the same child or two different children. In Experiment 1, both images showed an infant (<1 year old), whereas in Experiment 2, one image again showed an infant but the second image of the child was taken at 4–5 years of age. In Experiments 3a and 3b, we asked participants to complete shortened versions of both these tasks (selecting the most difficult trials) as well as the short version Glasgow face matching test. Finally, in Experiment 4, we investigated whether information regarding the sex of the infants and children could be accurately perceived from the images.ResultsIn Experiment 1, we found low levels of performance (72% accuracy) for matching two infant photos. For Experiment 2, performance was lower still (64% accuracy) when infant and child images were presented, given the significant changes in appearance that occur over the first five years of life. In Experiments 3a and 3b, when participants completed both these tasks, as well as a measure of adult face matching ability, we found lowest performance for the two infant tasks, along with mixed evidence of within-person correlations in sensitivities across all three tasks. The use of only same-sex pairings on mismatch trials, in comparison with random pairings, had little effect on performance measures. In Experiment 4, accuracy when judging the sex of infants was at chance levels for one image set and above chance (although still low) for the other set. As expected, participants were able to judge the sex of children (aged 4–5) from their faces.DiscussionIdentity matching with infant and child images resulted in low levels of performance, which were significantly worse than for an adult face matching task. Taken together, the results of the experiments presented here provide evidence that child facial photographs are ineffective for use in real-world identification. creator: Robin S.S. Kramer creator: Jerrica Mulgrew creator: Michael G. Reynolds uri: https://doi.org/10.7717/peerj.5010 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Kramer et al. title: Expressional and functional interactions of two Apis cerana cerana olfactory receptors link: https://peerj.com/articles/5005 last-modified: 2018-06-11 description: Apis cerana cerana relies on its sensitive olfactory system to perform foraging activities in the surrounding environment. Olfactory receptors (ORs) are a primary requirement for odorant recognition and coding. However, the molecular recognition of volatile compounds with ORs in A. cerana cerana is still not clear. Hence, in the present study, we achieved transient transfection and cell surface expression of A. cerana cerana ORs (AcerOr1 and AcerOr2; AcerOr2 is orthologous to the co-receptor) in Spodoptera frugiperda (Sf9) cells. AcerOr2 narrowly responded to N-(4-ethylphenyl)-2-((4-ethyl-5-(3-pyridinyl)-4H-1,2,4-triazol-3-yl) thio) acetamide (VUAA1), whereas AcerOr1 was sensitive to eugenol, lauric acid, ocimene, 1-nonanol, linolenic acid, hexyl acetate, undecanoic acid, 1-octyl alcohol, and nerol. Of the compounds tested, AcerOr1 showed the highest sensitivity to these odorants with EC50 values of 10−7 and 10−8 M, and AcerOr2 recognized VUAA1 with higher sensitivity [EC50 = (6.621 ± 0.26) × 10−8]. These results indicate that AcerOr2 is an essential gene for olfactory signaling, and AcerOr1 is a broadly tuned receptor. We discovered ligands that were useful for probing receptor activity during odor stimulation and validated three of them by electroantennography. The response increased with concentration of the odorant. The present study provides insight into the mechanism of olfactory discrimination in A. cerana cerana. creator: Lina Guo creator: Huiting Zhao creator: Yusuo Jiang uri: https://doi.org/10.7717/peerj.5005 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Guo et al. title: Sorption to soil, biochar and compost: is prediction to multicomponent mixtures possible based on single sorbent measurements? link: https://peerj.com/articles/4996 last-modified: 2018-06-11 description: Amendment with biochar and/or compost has been proposed as a strategy to remediate soil contaminated with low levels of polycyclic aromatic hydrocarbons. The strong sorption potential of biochar can help sequestering contaminants while the compost may promote their degradation. An improved understanding of how sorption evolves upon soil amendment is an essential step towards the implementation of the approach. The present study reports on the sorption of pyrene to two soils, four biochars and one compost. Detailed isotherm analyzes across a wide range of concentration confirmed that soil amendments can significantly increase the sorption of pyrene. Comparisons of data obtained by a classical batch and a passive sampling method suggest that dissolved organic matter did not play a significant role on the sorption of pyrene. The addition of 10% compost to soil led to a moderate increase in sorption (<2-fold), which could be well predicted based on measurements of sorption to the individual components. Hence, our result suggest that the sorption of pyrene to soil and compost can be relatively well approximated by an additive process. The addition of 5% biochar to soil (with or without compost) led to a major increase in the sorption of pyrene (2.5–4.7-fold), which was, however, much smaller than that suggested based on the sorption measured on the three individual components. Results suggest that the strong sorption to the biochar was attenuated by up to 80% in the presence of soil and compost, much likely due to surface and pore blockage. Results were very similar in the two soils considered, and collectively suggest that combined amendments with compost and biochar may be a useful approach to remediate soils with low levels of contamination. Further studies carried out in more realistic settings and over longer periods of time are the next step to evaluate the long term viability of remediation approaches based on biochar amendments. creator: Melanie Kah creator: Gabriel Sigmund creator: Pedro Luis Manga Chavez creator: Lucie Bielská creator: Thilo Hofmann uri: https://doi.org/10.7717/peerj.4996 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Kah et al. title: Trace fossils on dinosaur bones reveal ecosystem dynamics along the coast of eastern North America during the latest Cretaceous link: https://peerj.com/articles/4973 last-modified: 2018-06-11 description: Direct evidence of paleoecological processes is often rare when the fossil record is poor, as in the case of the Cretaceous of eastern North America. Here, I describe a femur and partial tibia shaft assignable to theropods from two Late Cretaceous sites in New Jersey. The former, identifiable as the femur of a large ornithomimosaur, bears several scores interpreted as shark feeding traces. The tibia shaft has punctures and flaked bone from the bites of mid-sized crocodyliforms, the first documented occurrence of crocodyliform traces on dinosaur bone from the Maastrichtian of the Atlantic Coastal Plain. The surface of the partial tibia is also littered with indentations interpreted as the traces of invertebrates, revealing a microcosm of biological interaction on the coastal seafloor of the Cretaceous Atlantic Ocean. Massive crocodyliforms, such as Deinosuchus rugosus and the slightly smaller Deltasuchus motherali, maintained the role of terrestrial vertebrate taphonomic process drivers in eastern North America during the Cretaceous. The report of crocodyliform bite marks on the ornithomimosaur tibia shaft in this manuscript reinforces the importance of the role of crocodyliforms in the modification of terrestrial vertebrate remains during the Cretaceous in North America. The preserved invertebrate traces add to the sparse record of the presence of barnacles and other marine invertebrates on dinosaur bone, and the evidence of shark feeding on the ornithomimosaur femur support the “bloat-and-float” model of terrestrial vertebrate fossil deposition in marine deposits from the Cretaceous of eastern North America. creator: Chase D. Brownstein uri: https://doi.org/10.7717/peerj.4973 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Brownstein title: How well do force fields capture the strength of salt bridges in proteins? link: https://peerj.com/articles/4967 last-modified: 2018-06-11 description: Salt bridges form between pairs of ionisable residues in close proximity and are important interactions in proteins. While salt bridges are known to be important both for protein stability, recognition and regulation, we still do not have fully accurate predictive models to assess the energetic contributions of salt bridges. Molecular dynamics simulation is one technique that may be used study the complex relationship between structure, solvation and energetics of salt bridges, but the accuracy of such simulations depends on the force field used. We have used NMR data on the B1 domain of protein G (GB1) to benchmark molecular dynamics simulations. Using enhanced sampling simulations, we calculated the free energy of forming a salt bridge for three possible lysine-carboxylate ionic interactions in GB1. The NMR experiments showed that these interactions are either not formed, or only very weakly formed, in solution. In contrast, we show that the stability of the salt bridges is overestimated, to different extents, in simulations of GB1 using seven out of eight commonly used combinations of fixed charge force fields and water models. We also find that the Amber ff15ipq force field gives rise to weaker salt bridges in good agreement with the NMR experiments. We conclude that many force fields appear to overstabilize these ionic interactions, and that further work may be needed to refine our ability to model quantitatively the stability of salt bridges through simulations. We also suggest that comparisons between NMR experiments and simulations will play a crucial role in furthering our understanding of this important interaction. creator: Mustapha Carab Ahmed creator: Elena Papaleo creator: Kresten Lindorff-Larsen uri: https://doi.org/10.7717/peerj.4967 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Ahmed et al. title: Pretreating mesenchymal stem cells with electrical stimulation causes sustained long-lasting pro-osteogenic effects link: https://peerj.com/articles/4959 last-modified: 2018-06-11 description: BackgroundElectrical stimulation (ES) has a long history of successful use in the clinical treatment of refractory, non-healing bone fractures and has recently been proposed as an adjunct to bone tissue-engineering treatments to optimize their therapeutic potential. This idea emerged from ES’s demonstrated positive effects on stem cell migration, proliferation, differentiation and adherence to scaffolds, all cell behaviors recognized to be advantageous in Bone Tissue Engineering (BTE). In previous in vitro experiments we demonstrated that direct current ES, administered daily, accelerates Mesenchymal Stem Cell (MSC) osteogenic differentiation. In the present study, we sought to define the optimal ES regimen for maximizing this pro-osteogenic effect.MethodsRat bone marrow-derived MSC were exposed to 100 mV/mm, 1 hr/day for three, seven, and 14 days, then osteogenic differentiation was assessed at Day 14 of culture by measuring collagen production, calcium deposition, alkaline phosphatase activity and osteogenic marker gene expression.ResultsWe found that exposing MSC to ES for three days had minimal effect, while seven and 14 days resulted in increased osteogenic differentiation, as indicated by significant increases in collagen and calcium deposits, and expression of osteogenic marker genes Col1a1, Osteopontin, Osterix and Calmodulin. We also found that cells treated with ES for seven days, maintained this pro-osteogenic activity long (for at least seven days) after discontinuing ES exposure.DiscussionThis study showed that while three days of ES is insufficient to solicit pro-osteogenic effects, seven and 14 days significantly increases osteogenic differentiation. Importantly, we found that cells treated with ES for only seven days, maintained this pro-osteogenic activity long after discontinuing ES exposure. This sustained positive osteogenic effect is likely due to the enhanced expression of RunX2 and Calmodulin we observed. This prolonged positive osteogenic effect, long after discontinuing ES treatment, if incorporated into BTE treatment protocols, could potentially improve outcomes and in doing so help BTE achieve its full therapeutic potential. creator: Maria Eischen-Loges creator: Karla M.C. Oliveira creator: Mit B. Bhavsar creator: John H. Barker creator: Liudmila Leppik uri: https://doi.org/10.7717/peerj.4959 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Eischen-Loges et al. title: Two new species of Primulina (Gesneriaceae) from limestone karsts of China link: https://peerj.com/articles/4946 last-modified: 2018-06-11 description: The limestone karst area of South China is a major biodiversity hotspot of global terrestrial biomes. During extensive field work on the Guangxi limestone formations, two unknown species of Gesneriaceae were collected. After conducting a comprehensive study of the literature and herbarium specimens, Primulina davidioides and P. hiemalis are recognized as two species new to science, and described and illustrated here. P. davidioides is morphologically close to P. lunglinensis based on the shape of the leaf and flower, but it can be easily distinguished by the shape of the bracts, corolla and stigma, indumentum of peduncles, pedicels and pistil and number of staminodes. P. hiemalis is closely relate to P. luzhaiensis in vegetative appearance, but differs in the shape of the calyx and stigma, number of bracts and staminodes, indumentum of the leaf blade and peduncle, and position of stamens in the corolla tube. Considering that not enough is known about their populations, it is proposed that their conservation statuses should currently be classed as data deficient (DD) according to the IUCN Red List Category and Criteria. creator: Xin Hong creator: Zhong-Lin Li creator: Jia-Zhi Liu creator: Shou-Biao Zhou creator: Wei-Hua Qin creator: Fang Wen uri: https://doi.org/10.7717/peerj.4946 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Hong et al. title: Cortical bone adaptation and mineral mobilization in the subterranean mammal Bathyergus suillus (Rodentia: Bathyergidae): effects of age and sex link: https://peerj.com/articles/4944 last-modified: 2018-06-11 description: The patterns of bone modeling and mineral mobilization (skeletal homeostasis) among mammals other than humans and laboratory rodents are still poorly known. In this study we assessed the pattern of bone formation and bone resorption in the femur of a wild population of Cape dune molerats, Bathyergus suillus (n = 41) (Bathyergidae), a solitary subterranean mammal with a marked extended longevity among rodents, and which also lives in a naturally deficient state of vitamin D. In order to determine ontogenetic and sex effects on histomorphometric parameters of transversal undecalcified bone sections, two-way ANOVA, linear mixed-effects model and regression statistical analyses were performed. During ontogeny, B. suillus increased their cross sectional area, cortical area and cortical thickness, and most importantly, they showed scarce endosteal bone resorption which resulted in a retained medullary cavity size during ontogeny. This resulted in a positively imbalanced bone modeling, where bone formation considerably surpasses bone loss by almost 100-fold in adulthood. This differs markedly from other terrestrial mammals with relatively thin cortical walls. Regarding bone loss and remodeling, three main processes involving intracortical resorption were observed: modeling-related bone loss in early postnatal growth; secondary osteon formation occurring in both sexes; and subendosteal secondary reconstruction observed only in females. The latter is accompanied by females having six-fold more relative bone loss than males, which is evidenced by the development of enlarged resorption cavities (RCs) distributed circumferentially around the medullary cavity. Males have smaller, more circular and randomly distributed RCs. In general, our data indicate no age-related decline in mineral content in B. suillus, and provides strong support for a pattern of sexual dimorphism in skeletal homeostasis, similar to that occurring in humans and other mammals, with females losing more bone throughout aging as compared to males due to reproductive factors. Interestingly as well, despite the high mechanical loads experienced during burrow construction, bone remodeling in B. suillus is kept at very low levels throughout their lifespan, and dense Haversian tissue never forms. This study represents the first comprehensive assessment of skeletal homeostasis in a subterranean mammal, and it enables a better understanding of the complex processes governing the acquisition and maintenance of bone properties in this species with extraordinary fossorial adaptations. creator: Germán Montoya-Sanhueza creator: Anusuya Chinsamy uri: https://doi.org/10.7717/peerj.4944 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Montoya-Sanhueza and Chinsamy title: Sex-based differences in anti-predator response of crickets to chemical cues of a mammalian predator link: https://peerj.com/articles/4923 last-modified: 2018-06-11 description: Anti-predator behaviors like vigilance or hiding come at the expense of other fitness increasing behaviors such as foraging. To compensate for this trade-off, prey assess predation risk and modify the frequency of anti-predator behaviors according to the likelihood of the threat. In this study, we tested the ability of house crickets (Acheta domesticus) to indirectly assess predation risk via odors from a mammalian predator, Elliot’s short-tailed shrew (Blarina hylophaga). As natural differences in encounter rates and predation risk differs between sexes, we tested if male and female crickets perceive similar rates of predation risk from the presence of shrew odor measured via anti-predator behavioral response. Crickets were placed in enclosed, cardboard-lined chambers either treated with shrew odor or control, along with a food source. Time until foraging was measured for each individual and compared across treatment and sex. We found that in the presence of shrew odor, female crickets delayed foraging while males showed no response. These results suggest adult crickets can use chemical cues to detect mammalian predators. Furthermore, we demonstrate that female crickets associate greater predation risk from shrew predators than do male crickets, which are more stationary yet acoustically conspicuous. As predation risk potentially differs drastically for each sex, changes to the operational sex ratios of wild cricket populations could be influenced by the identity of the predator community. creator: Brian P. Tanis creator: Bradley Bott creator: Brian J. Gaston uri: https://doi.org/10.7717/peerj.4923 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Tanis et al. title: Diversity and abundance of conspicuous macrocrustaceans on coral reefs differing in level of degradation link: https://peerj.com/articles/4922 last-modified: 2018-06-11 description: Coral reefs sustain abundant and diverse macrocrustaceans that perform multiple ecological roles, but coral reefs are undergoing massive degradation that may be driving changes in the species composition and abundance of reef-associated macrocrustaceans. To provide insight into this issue, we used non-destructive visual census techniques to compare the diversity and abundance of conspicuous macrocrustaceans (i.e., those >1 cm and visible without disturbance) between two shallow Caribbean coral reefs similar in size (∼1.5 km in length) and close to each other, but one (“Limones”) characterized by extensive stands of the branching coral Acropora palmata, and the other (“Bonanza”) dominated by macroalgae and relic coral skeletons and rubble (i.e., degraded). We also assessed the structural complexity of each reef and the percent cover of various benthic community components. Given the type of growth of A. palmata, we expected to find a greater structural complexity, a higher cover of live coral, and a lower cover of macroalgae on Limones, and hence a more diverse and abundant macrocrustacean community on this reef compared with Bonanza. Overall, we identified 63 macrocrustacean species (61 Decapoda and two Stomatopoda). Contrary to our expectations, structural complexity did not differ significantly between the back-reef zones of these reefs but varied more broadly on Limones, and the diversity and abundance of macrocrustaceans were higher on Bonanza than on Limones despite live coral cover being higher on Limones and macroalgal cover higher on Bonanza. However, the use of various types of microhabitats by macrocrustaceans differed substantially between reefs. On both reefs, the dominant species were the clinging crab Mithraculus coryphe and the hermit crab Calcinus tibicen, but the former was more abundant on Bonanza and the latter on Limones. M. coryphe occupied a diverse array of microhabitats but mostly coral rubble and relic skeletons, whereas C. tibicen was often, but not always, found associated with colonies of Millepora spp. A small commensal crab of A. palmata, Domecia acanthophora, was far more abundant on Limones, emerging as the main discriminant species between reefs. Our results suggest that local diversity and abundance of reef-associated macrocrustaceans are partially modulated by habitat degradation, the diversity of microhabitat types, and the establishment of different commensal associations rather than by structural complexity alone. creator: Roberto González-Gómez creator: Patricia Briones-Fourzán creator: Lorenzo Álvarez-Filip creator: Enrique Lozano-Álvarez uri: https://doi.org/10.7717/peerj.4922 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 González-Gómez et al. title: BCD Beam Search: considering suboptimal partial solutions in Bad Clade Deletion supertrees link: https://peerj.com/articles/4987 last-modified: 2018-06-08 description: Supertree methods enable the reconstruction of large phylogenies. The supertree problem can be formalized in different ways in order to cope with contradictory information in the input. Some supertree methods are based on encoding the input trees in a matrix; other methods try to find minimum cuts in some graph. Recently, we introduced Bad Clade Deletion (BCD) supertrees which combines the graph-based computation of minimum cuts with optimizing a global objective function on the matrix representation of the input trees. The BCD supertree method has guaranteed polynomial running time and is very swift in practice. The quality of reconstructed supertrees was superior to matrix representation with parsimony (MRP) and usually on par with SuperFine for simulated data; but particularly for biological data, quality of BCD supertrees could not keep up with SuperFine supertrees. Here, we present a beam search extension for the BCD algorithm that keeps alive a constant number of partial solutions in each top-down iteration phase. The guaranteed worst-case running time of the new algorithm is still polynomial in the size of the input. We present an exact and a randomized subroutine to generate suboptimal partial solutions. Both beam search approaches consistently improve supertree quality on all evaluated datasets when keeping 25 suboptimal solutions alive. Supertree quality of the BCD Beam Search algorithm is on par with MRP and SuperFine even for biological data. This is the best performance of a polynomial-time supertree algorithm reported so far. creator: Markus Fleischauer creator: Sebastian Böcker uri: https://doi.org/10.7717/peerj.4987 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Fleischauer and Böcker title: Archaeal and bacterial diversity and community composition from 18 phylogenetically divergent sponge species in Vietnam link: https://peerj.com/articles/4970 last-modified: 2018-06-08 description: Sponge-associated prokaryotic diversity has been studied from a wide range of marine environments across the globe. However, for certain regions, e.g., Vietnam, Thailand, Cambodia, and Singapore, an overview of the sponge-associated prokaryotic communities is still pending. In this study we characterized the prokaryotic communities from 27 specimens, comprising 18 marine sponge species, sampled from the central coastal region of Vietnam. Illumina MiSeq sequencing of 16S ribosomal RNA (rRNA) gene fragments was used to investigate sponge-associated bacterial and archaeal diversity. Overall, 14 bacterial phyla and one archaeal phylum were identified among all 27 samples. The phylum Proteobacteria was present in all sponges and the most prevalent phylum in 15 out of 18 sponge species, albeit with pronounced differences at the class level. In contrast, Chloroflexi was the most abundant phylum in Halichondria sp., whereas Spirastrella sp. and Dactylospongia sp. were dominated by Actinobacteria. Several bacterial phyla such as Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Deferribacteres, Gemmatimonadetes, and Nitrospirae were found in two-thirds of the sponge species. Moreover, the phylum Thaumarchaeota (Archaea), which is known to comprise nitrifying archaea, was highly abundant among the majority of the 18 investigated sponge species. Altogether, this study demonstrates that the diversity of prokaryotic communities associated with Vietnamese sponges is comparable to sponge-prokaryotic assemblages from well-documented regions. Furthermore, the phylogenetically divergent sponges hosted species-specific prokaryotic communities, thus demonstrating the influence of host identity on the composition and diversity of the associated communities. Therefore, this high-throughput 16S rRNA gene amplicon analysis of Vietnamese sponge-prokaryotic communities provides a foundation for future studies on sponge symbiont function and sponge-derived bioactive compounds from this region. creator: Ton That Huu Dat creator: Georg Steinert creator: Nguyen Thi Kim Cuc creator: Hauke Smidt creator: Detmer Sipkema uri: https://doi.org/10.7717/peerj.4970 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Dat et al. title: Gorgonopsian therapsids (Nochnitsa gen. nov. and Viatkogorgon) from the Permian Kotelnich locality of Russia link: https://peerj.com/articles/4954 last-modified: 2018-06-08 description: The early evolution of gorgonopsians is poorly understood. New material from the Kotelnich locality in Russia expands our knowledge of middle/earliest late Permian gorgonopsians from Laurasia. Two gorgonopsian taxa are recognized from Kotelnich: Viatkogorgon ivakhnenkoi Tatarinov, 1999 and Nochnitsa geminidens gen. et sp. nov. Nochnitsa can be distinguished from all known gorgonopsians by its unique upper postcanine tooth row, composed of pairs of teeth (a small anterior and larger posterior) separated by diastemata. Both Viatkogorgon and Nochnitsa are relatively small gorgonopsians, comparable in size to the South African middle Permian taxon Eriphostoma. Inclusion of Viatkogorgon and Nochnitsa in a phylogenetic analysis of gorgonopsians recovers them in basal positions, with Nochnitsa representing the earliest-diverging gorgonopsian genus. All other sampled gorgonopsians fall into two major subclades: one made up entirely of Russian taxa (Inostrancevia, Pravoslavlevia, Sauroctonus, and Suchogorgon) and the other containing only African gorgonopsians. The high degree of endemism indicated in this analysis for gorgonopsians is remarkable, especially given the extensive intercontinental dispersal inferred for coeval therapsid groups. creator: Christian F. Kammerer creator: Vladimir Masyutin uri: https://doi.org/10.7717/peerj.4954 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Kammerer et al. title: Process-based allometry describes the influence of management on orchard tree aboveground architecture link: https://peerj.com/articles/4949 last-modified: 2018-06-08 description: We evaluated allometric relationships in length, diameter, and mass of branches for two variably managed orchard tree species (tart cherry, Prunus cerasus; apple, Malus spp.). The empirically estimated allometric exponents (a) of the orchard trees were described in the context of two processed-based allometry models that make predictions for a: the West, Brown and Enquist fractal branching model (WBE) and the recently introduced Flow Similarity model (FS). These allometric models make predictions about relationships in plant morphology (e.g., branch mass, diameter, length, volume, surface area) based on constraints imposed on plant growth by physical and physiological processes. We compared our empirical estimates of a to the model predictions to interpret the physiological implications of pruning and management in orchard systems. Our study found strong allometric relationships among the species and individuals studied with limited agreement with the expectations of either model. The 8/3-power law prediction of the mass ∼ diameter relationship by the WBE, indicative of biomechanical limitations, was marginally supported by this study. Length-including allometric relationships deviated from predictions of both models, but shift toward the expectation of flow similarity. In this way, managed orchard trees deviated from strict adherence to the idealized expectations of the models, but still fall within the range of model expectations in many cases despite intensive management. creator: Zachary T. Brym creator: S.K. Morgan Ernest uri: https://doi.org/10.7717/peerj.4949 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Brym and Ernest title: A new therocephalian (Gorynychus masyutinae gen. et sp. nov.) from the Permian Kotelnich locality, Kirov Region, Russia link: https://peerj.com/articles/4933 last-modified: 2018-06-08 description: A new therocephalian taxon (Gorynychus masyutinae gen. et sp. nov.) is described based on a nearly complete skull and partial postcranium from the Permian Kotelnich locality of Russia. Gorynychus displays an unusual mixture of primitive (“pristerosaurian”) and derived (eutherocephalian) characters. Primitive features of Gorynychus include extensive dentition on the palatal boss and transverse process of the pterygoid, paired vomers, and a prominent dentary angle; derived features include the absence of the postfrontal. Gorynychus can be distinguished from all other therocephalians by its autapomorphic dental morphology, with roughly denticulated incisors and postcanines. Phylogenetic analysis recovers Gorynychus as a non-lycosuchid, non-scylacosaurid therocephalian situated as sister-taxon to Eutherocephalia. The identification of Gorynychus as the largest predator from Kotelnich indicates that therocephalians acted as apex predators in middle–late Permian transition ecosystems in Russia, corroborating a pattern observed in South African faunas. However, other aspects of the Kotelnich fauna, and Permian Russian tetrapod faunas in general, differ markedly from those of South Africa and suggest that Karoo faunas are not necessarily representative of global patterns. creator: Christian F. Kammerer creator: Vladimir Masyutin uri: https://doi.org/10.7717/peerj.4933 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Kammerer and Masyutin title: Literature-based latitudinal distribution and possible range shifts of two US east coast dune grass species (Uniola paniculata and Ammophila breviligulata) link: https://peerj.com/articles/4932 last-modified: 2018-06-08 description: Previous work on the US Atlantic coast has generally shown that coastal foredunes are dominated by two dune grass species, Ammophila breviligulata (American beachgrass) and Uniola paniculata (sea oats). From Virginia northward, A. breviligulata dominates, while U. paniculata is the dominant grass south of Virginia. Previous work suggests that these grasses influence the shape of coastal foredunes in species-specific ways, and that they respond differently to environmental stressors; thus, it is important to know which species dominates a given dune system. The range boundaries of these two species remains unclear given the lack of comprehensive surveys. In an attempt to determine these boundaries, we conducted a literature survey of 98 studies that either stated the range limits and/or included field-based studies/observations of the two grass species. We then produced an interactive map that summarizes the locations of the surveyed papers and books. The literature review suggests that the current southern range limit for A. breviligulata is Cape Fear, NC, and the northern range limit for U. paniculata is Assateague Island, on the Maryland and Virginia border. Our data suggest a northward expansion of U. paniculata, possibly associated with warming trends observed near the northern range limit in Painter, VA. In contrast, the data regarding a range shift for A. breviligulata remain inconclusive. We also compare our literature-based map with geolocated records from the Global Biodiversity Information Facility and iNaturalist research grade crowd-sourced observations. We intend for our literature-based map to aid coastal researchers who are interested in the dynamics of these two species and the potential for their ranges to shift as a result of climate change. creator: Evan B. Goldstein creator: Elsemarie V. Mullins creator: Laura J. Moore creator: Reuben G. Biel creator: Joseph K. Brown creator: Sally D. Hacker creator: Katya R. Jay creator: Rebecca S. Mostow creator: Peter Ruggiero creator: Julie C. Zinnert uri: https://doi.org/10.7717/peerj.4932 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Goldstein et al. title: MipLAAO, a new L-amino acid oxidase from the redtail coral snake Micrurus mipartitus link: https://peerj.com/articles/4924 last-modified: 2018-06-08 description: L-amino acid oxidases (LAAOs) are ubiquitous enzymes in nature. Bioactivities described for these enzymes include apoptosis induction, edema formation, induction or inhibition of platelet aggregation, as well as antiviral, antiparasite, and antibacterial actions. With over 80 species, Micrurus snakes are the representatives of the Elapidae family in the New World. Although LAAOs in Micrurus venoms have been predicted by venom gland transcriptomic studies and detected in proteomic studies, no enzymes of this kind have been previously purified from their venoms. Earlier proteomic studies revealed that the venom of M. mipartitus from Colombia contains ∼4% of LAAO. This enzyme, here named MipLAAO, was isolated and biochemically and functionally characterized. The enzyme is found in monomeric form, with an isotope-averaged molecular mass of 59,100.6 Da, as determined by MALDI-TOF. Its oxidase activity shows substrate preference for hydrophobic amino acids, being optimal at pH 8.0. By nucleotide sequencing of venom gland cDNA of mRNA transcripts obtained from a single snake, six isoforms of MipLAAO with minor variations among them were retrieved. The deduced sequences present a mature chain of 483 amino acids, with a predicted pI of 8.9, and theoretical masses between 55,010.9 and 55,121.0 Da. The difference with experimentally observed mass is likely due to glycosylation, in agreement with the finding of three putative N-glycosylation sites in its amino acid sequence. A phylogenetic analysis of MmipLAAO placed this new enzyme within the clade of homologous proteins from elapid snakes, characterized by the conserved Serine at position 223, in contrast to LAAOs from viperids. MmipLAAO showed a potent bactericidal effect on S. aureus (MIC: 2 µg/mL), but not on E. coli. The former activity could be of interest to future studies assessing its potential as antimicrobial agent. creator: Paola Rey-Suárez creator: Cristian Acosta creator: Uday Torres creator: Mónica Saldarriaga-Córdoba creator: Bruno Lomonte creator: Vitelbina Núñez uri: https://doi.org/10.7717/peerj.4924 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Rey-Suárez et al. title: ­Characterization of pyruvate kinase from the anoxia tolerant turtle, Trachemys scripta elegans: a potential role for enzyme methylation during metabolic rate depression link: https://peerj.com/articles/4918 last-modified: 2018-06-08 description: BackgroundPyruvate kinase (PK) is responsible for the final reaction in glycolysis. As PK is a glycolytic control point, the analysis of PK posttranslational modifications (PTM) and kinetic changes reveals a key piece of the reorganization of energy metabolism in an anoxia tolerant vertebrate.MethodsTo explore PK regulation, the enzyme was isolated from red skeletal muscle and liver of aerobic and 20-hr anoxia-exposed red eared-slider turtles (Trachemys scripta elegans). Kinetic analysis and immunoblotting were used to assess enzyme function and the corresponding covalent modifications to the enzymes structure during anoxia.ResultsBoth muscle and liver isoforms showed decreased affinity for phosphoenolpyruvate substrate during anoxia, and muscle PK also had a lower affinity for ADP. I50 values for the inhibitors ATP and lactate were lower for PK from both tissues after anoxic exposure while I50 L-alanine was only reduced in the liver. Both isozymes showed significant increases in threonine phosphorylation (by 42% in muscle and 60% in liver) and lysine methylation (by 43% in muscle and 70% in liver) during anoxia which have been linked to suppression of PK activity in other organisms. Liver PK also showed a 26% decrease in tyrosine phosphorylation under anoxia.DiscussionAnoxia responsive changes in turtle muscle and liver PK coordinate with an overall reduced activity state. This reduced affinity for the forward glycolytic reaction is likely a key component of the overall metabolic rate depression that supports long term survival in anoxia tolerant turtles. The coinciding methyl- and phospho- PTM alterations present the mechanism for tissue specific enzyme modification during anoxia. creator: Amanda M.S. Mattice creator: Isabelle A. MacLean creator: Christine L. Childers creator: Kenneth B. Storey uri: https://doi.org/10.7717/peerj.4918 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Mattice et al. title: Does bathymetry drive coastal whale shark (Rhincodon typus) aggregations? link: https://peerj.com/articles/4904 last-modified: 2018-06-08 description: BackgroundThe whale shark (Rhincodon typus) is known to aggregate in a number of coastal locations globally, however what causes these aggregations to form where they do is largely unknown. This study examines whether bathymetry is an important driver of coastal aggregation locations for R. typus through bathymetry’s effect on primary productivity and prey availability. This is a global study taking into account all coastal areas within R. typus’ range.MethodsR. typus aggregation locations were identified through an extensive literature review. Global bathymetric data were compared at R. typus aggregation locations and a large random selection of non-aggregation areas. Generalised linear models were used to assess which bathymetric characteristic had the biggest influence on aggregation presence.ResultsAggregation sites were significantly shallower than non-aggregation sites and in closer proximity to deep water (the mesopelagic zone) by two orders of magnitude. Slope at aggregation sites was significantly steeper than non-aggregation sites. These three bathymetric variables were shown to have the biggest association with aggregation sites, with up to 88% of deviation explained by the GLMs.DiscussionThe three key bathymetric characteristics similar at the aggregation sites are known to induce upwelling events, increase primary productivity and consequently attract numerous other filter feeding species. The location of aggregation sites in these key areas can be attributed to this increased prey availability, thought to be the main reason R. typus aggregations occur, extensively outlined in the literature. The proximity of aggregations to shallow areas such as reefs could also be an important factor why whale sharks thermoregulate after deep dives to feed. These findings increase our understanding of whale shark behaviour and may help guide the identification and conservation of further aggregation sites. creator: Joshua P. Copping creator: Bryce D. Stewart creator: Colin J. McClean creator: James Hancock creator: Richard Rees uri: https://doi.org/10.7717/peerj.4904 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Copping et al. title: Actively transcribed and expressed atp8 gene in Mytilus edulis mussels link: https://peerj.com/articles/4897 last-modified: 2018-06-08 description: BackgroundAnimal mitochondrial genomes typically encode 37 genes: 13 proteins, 22 tRNAs and two rRNAs. However, many species represent exceptions to that rule. Bivalvia along with Nematoda and Platyhelminthes are often suspected to fully or partially lack the ATP synthase subunit 8 (atp8) gene. This raises the question as to whether they are really lacking this gene or is this maybe an annotation problem? Among bivalves, Mytilus edulis has been inferred to lack an ATP8 gene since the characterization of its mitochondrial genome in 1992. Even though recent bioinformatic analyses suggested that atp8 is present in Mytilus spp., due to high divergence in predicted amino acid sequences, the existence of a functional atp8 gene in this group remains controversial.ResultsHere we demonstrate that M. edulis mitochondrial open reading frames suggested to be atp8 (in male and female mtDNAs) are actively translated proteins. We also provide evidence that both proteins are an integral part of the ATP synthase complex based on in-gel detection of ATP synthase activity and two-dimensional Blue-Native and SDS polyacrylamide electrophoresis.ConclusionMany organisms (e.g., Bivalvia along with Nematoda and Platyhelminthes) are considered to be lacking certain mitochondrial genes often only based on poor similarity between protein coding gene sequences in genetically closed species. In some situations, this may lead to the inference that the ATP8 gene is absent, when it is in fact present, but highly divergent. This shows how important complementary role protein-based approaches, such as those in the present study, can provide to bioinformatic, genomic studies (i.e., ability to confirm the presence of a gene). creator: Marek Lubośny creator: Aleksandra Przyłucka creator: Beata Śmietanka creator: Sophie Breton creator: Artur Burzyński uri: https://doi.org/10.7717/peerj.4897 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Lubośny et al. title: The first tetrapod from the mid-Miocene Clarkia lagerstätte (Idaho, USA) link: https://peerj.com/articles/4880 last-modified: 2018-06-08 description: The Clarkia lagerstätte (Latah Formation) of Idaho is well known for its beautifully preserved plant fossils as well as a fauna of insects and fish. Here we present the first known tetrapod fossil from these deposits. This specimen, recovered from the lower anoxic zone of the beds, is preserved as a carbonaceous film of a partial skeleton associated with a partial lower incisor and some tooth fragments. The morphology of the teeth indicates that the first tetrapod reported from Clarkia is a rodent. Its skeletal morphology as well as its bunodont and brachydont dentition suggests that it is a member of the squirrel family (Sciuridae). It is a large specimen that cannot be assigned to a known genus. Instead, it appears to represent the first occurrence of a new taxon with particularly gracile postcranial morphology likely indicative of an arboreal ecology. This new specimen is a rare glimpse into the poorly known arboreal mammal fossil record of the Neogene. It supports a greater taxonomic and ecological diversity of Miocene Sciuridae than previously recognized and offers new lines of inquiry in the paleoecological research enabled by the unique preservation conditions of the Clarkia biota. creator: Jonathan J. M. Calede creator: John D. Orcutt creator: Winifred A. Kehl creator: Bill D. Richards uri: https://doi.org/10.7717/peerj.4880 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Calede et al. title: Scan, extract, wrap, compute—a 3D method to analyse morphological shape differences link: https://peerj.com/articles/4861 last-modified: 2018-06-08 description: Quantitative analysis of shape and form is critical in many biological disciplines, as context-dependent morphotypes reflect changes in gene expression and physiology, e.g., in comparisons of environment-dependent phenotypes, forward/reverse genetic assays or shape development during ontogenesis. 3D-shape rendering methods produce models with arbitrarily numbered, and therefore non-comparable, mesh points. However, this prevents direct comparisons. We introduce a workflow that allows the generation of comparable 3D models based on several specimens. Translocations between points of modelled morphotypes are plotted as heat maps and statistically tested. With this workflow, we are able to detect, model and investigate the significance of shape and form alterations in all spatial dimensions, demonstrated with different morphotypes of the pond-dwelling microcrustacean Daphnia. Furthermore, it allows the detection even of inconspicuous morphological features that can be exported to programs for subsequent analysis, e.g., streamline- or finite-element analysis. creator: Martin Horstmann creator: Alexander T. Topham creator: Petra Stamm creator: Sebastian Kruppert creator: John K. Colbourne creator: Ralph Tollrian creator: Linda C. Weiss uri: https://doi.org/10.7717/peerj.4861 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Horstmann et al. title: Soft-bottom fishes and spatial protection: findings from a temperate marine protected area link: https://peerj.com/articles/4653 last-modified: 2018-06-08 description: Numerous studies over the last decades have focused on marine protected areas (MPAs) and their effects on fish communities. However, there is a knowledge gap regarding how species that live associated with soft-substrates (e.g., sand, mud) respond to spatial protection. We analyzed abundance, biomass and total lengths of the soft-bottom fishes in a multiple-use MPA in the north-eastern Atlantic, the Luiz Saldanha Marine Park (Portugal), during and after the implementation of its management plan. Data were collected by experimental fishing in areas with three different levels of protection, during the implementation period and for three years after full implementation of the MPA. Univariate analysis detected significant biomass increases between the two periods. Fish assemblages were mainly structured by depth and substrate, followed by protection level. Community composition analyses revealed significant differences between protection levels and between the two periods. Species exhibited a broad variation in their response to protection, and we hypothesize that factors such as species habitat preferences, body size and late maturity might be underlying determinants. Overall, this study provides some evidence of protection effectiveness in soft-bottom fish communities, supported by the significant increase in biomass in the protected areas and the positive trends of some species. creator: Inês Sousa creator: Jorge M.S. Gonçalves creator: Joachim Claudet creator: Rui Coelho creator: Emanuel J. Gonçalves creator: Karim Erzini uri: https://doi.org/10.7717/peerj.4653 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Sousa et al. title: Effect of acute augmented feedback on between limb asymmetries and eccentric knee flexor strength during the Nordic hamstring exercise link: https://peerj.com/articles/4972 last-modified: 2018-06-07 description: BackgroundHamstring strain injuries (HSI) are one of the most prevalent and serious injuries affecting athletes, particularly those in team ball sports or track and field. Recent evidence demonstrates that eccentric knee flexor weakness and between limb asymmetries are possible risk factors for HSIs. While eccentric hamstring resistance training, e.g. the Nordic hamstring exercise (NHE) significantly increases eccentric hamstring strength and reduces HSI risk, little research has examined whether between limb asymmetries can be reduced with training. As augmented feedback (AF) can produce significant acute and chronic increases in muscular strength and reduce injury risk, one way to address the limitation in the eccentric hamstring training literature may be to provide athletes real-time visual AF of their NHE force outputs with the goal to minimise the between limb asymmetry.MethodsUsing a cross over study design, 44 injury free, male cricket players from two skill levels performed two NHE sessions on a testing device. The two NHE sessions were identical with the exception of AF, with the two groups randomised to perform the sessions with and without visual feedback of each limb’s force production in real-time. When performing the NHE with visual AF, the participants were provided with the following instructions to ‘reduce limb asymmetries as much as possible using the real-time visual force outputs displayed in front them’. Between limb asymmetries and mean peak force outputs were compared between the two feedback conditions (FB1 and FB2) using independent t-tests to ensure there was no carryover effect, and to determine any period and treatment effects. The magnitude of the differences in the force outputs were also examined using Cohen d effect size.ResultsThere was a significant increase in mean peak force production when feedback was provided (mean difference, 21.7 N; 95% CI [0.2–42.3 N]; P = 0.048; d = 0.61) and no significant difference in between limb asymmetry for feedback or no feedback (mean difference, 5.7%; 95% CI [−2.8% to 14.3%]; P = 0.184; d = 0.41). Increases in force production under feedback were a result of increased weak limb (mean difference, 15.0 N; 95% CI [1.6–28.5 N]; P = 0.029; d = 0.22) force contribution compared to the strong limb.DiscussionThe results of this study further support the potential utility of AF in improving force production and reducing risk in athletic populations. While there are currently some financial limitations to the application of this training approach, even in high-performance sport, such an approach may improve outcomes for HSI prevention programs. Further research with more homogenous populations over greater periods of time that assess the chronic effect of such training practices on injury risk factors and injury rates are also recommended. creator: Wade J. Chalker creator: Anthony J. Shield creator: David A. Opar creator: Evelyne N. Rathbone creator: Justin W.L. Keogh uri: https://doi.org/10.7717/peerj.4972 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Chalker et al. title: High similarity in the microbiota of cold-water sponges of the Genus Mycale from two different geographical areas link: https://peerj.com/articles/4935 last-modified: 2018-06-07 description: Sponges belonging to genus Mycale are common and widely distributed across the oceans and represent a significant component of benthic communities in term of their biomass, which in many species is largely composed by bacteria. However, the microbial communities associated with Mycale species inhabiting different geographical areas have not been previously compared. Here, we provide the first detailed description of the microbiota of two Mycale species inhabiting the sub-Antarctic Magellan region (53°S) and the Western Antarctic Peninsula (62–64°S), two geographically distant areas (>1,300 km) with contrasting environmental conditions. The sponges Mycale (Aegogropila) magellanica and Mycale (Oxymycale) acerata are both abundant members of benthic communities in the Magellan region and in Antarctica, respectively. High throughput sequencing revealed a remarkable similarity in the microbiota of both sponge species, dominated by Proteobacteria and Bacteroidetes, with both species sharing more than 74% of the OTUs. In contrast, 16% and 10% of the OTUs were found only in either M. magellanica or M. acerata, respectively. Interestingly, despite slight differences in the relative abundance, the most dominant OTUs were present in both species, whereas the unique OTUs had very low abundances (less than 1% of the total abundance). These results show a significant overlap among the microbiota of both Mycale species and also suggest the existence of a low level of specificity of the most dominant symbiont groups. creator: César A. Cárdenas creator: Marcelo González-Aravena creator: Alejandro Font creator: Jon T. Hestetun creator: Eduardo Hajdu creator: Nicole Trefault creator: Maja Malmberg creator: Erik Bongcam-Rudloff uri: https://doi.org/10.7717/peerj.4935 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Cárdenas et al. title: Metal-binding polymorphism in late embryogenesis abundant protein AtLEA4-5, an intrinsically disordered protein link: https://peerj.com/articles/4930 last-modified: 2018-06-07 description: Late embryogenesis abundant (LEA) proteins accumulate in plants during adverse conditions and their main attributed function is to confer tolerance to stress. One of the deleterious effects of the adverse environment is the accumulation of metal ions to levels that generate reactive oxygen species, compromising the survival of cells. AtLEA4-5, a member of group 4 of LEAs in Arabidopsis, is an intrinsically disordered protein. It has been shown that their N-terminal region is able to undergo transitions to partially folded states and prevent the inactivation of enzymes. We have characterized metal ion binding to AtLEA4-5 by circular dichroism, electronic absorbance spectroscopy (UV–vis), electron paramagnetic resonance, dynamic light scattering, and isothermal titration calorimetry. The data shows that AtLEA4-5 contains a single binding site for Ni(II), while Zn(II) and Cu(II) have multiple binding sites and promote oligomerization. The Cu(II) interacts preferentially with histidine residues mostly located in the C-terminal region with moderate affinity and different coordination modes. These results and the lack of a stable secondary structure formation indicate that an ensemble of conformations remains accessible to the metal for binding, suggesting the formation of a fuzzy complex. Our results support the multifunctionality of LEA proteins and suggest that the C-terminal region of AtLEA4-5 could be responsible for antioxidant activity, scavenging metal ions under stress conditions while the N-terminal could function as a chaperone. creator: Leidys French-Pacheco creator: Cesar L. Cuevas-Velazquez creator: Lina Rivillas-Acevedo creator: Alejandra A. Covarrubias creator: Carlos Amero uri: https://doi.org/10.7717/peerj.4930 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 French-Pacheco et al. title: Spatial-temporal variation and impacts of drought in Xinjiang (Northwest China) during 1961–2015 link: https://peerj.com/articles/4926 last-modified: 2018-06-07 description: Observations indicate that temperature and precipitation patterns changed dramatically in Xinjiang, northwestern China, between 1961 and 2015. Dramatic changes in climatic conditions can bring about adverse effects. Specifically, meteorological drought severity based on the standardized precipitation index (SPI) and the standardized precipitation evapotranspiration index (SPEI) showed a decreasing trend in Xinjiang prior to 1997, after which the trend reversed. SPEI-based drought severity shows a much stronger change during 1997–2015 than the SPI, which is independent of the effect of evaporative demand. Meteorological drought severity has been aggravated by a significant rise in temperature (1.1 °C) over the last two decades that has not been accompanied by a corresponding increase in precipitation. As a result, the evaporative demand in Xinjiang has risen. An examination of a large spatio-temporal extent has made the aggravated drought conditions more evident. Our results indicate that increased meteorological drought severity has had a direct effect on the normalized difference vegetation index (NDVI) and river discharge. The NDVI exhibited a significant decrease during the period 1998–2013 compared to 1982–1997, a decrease that was found to be caused by increased soil moisture loss. A positive relationship was recorded between evaporative demand and the runoff coefficients of the 68 inland river catchments in northwestern China. In the future, meteorological drought severity will likely increase in arid and semiarid regions as global warming continues. creator: Junqiang Yao creator: Yong Zhao creator: Xiaojing Yu uri: https://doi.org/10.7717/peerj.4926 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Yao et al. title: Modelling daily water temperature from air temperature for the Missouri River link: https://peerj.com/articles/4894 last-modified: 2018-06-07 description: The bio-chemical and physical characteristics of a river are directly affected by water temperature, which thereby affects the overall health of aquatic ecosystems. It is a complex problem to accurately estimate water temperature. Modelling of river water temperature is usually based on a suitable mathematical model and field measurements of various atmospheric factors. In this article, the air–water temperature relationship of the Missouri River is investigated by developing three different machine learning models (Artificial Neural Network (ANN), Gaussian Process Regression (GPR), and Bootstrap Aggregated Decision Trees (BA-DT)). Standard models (linear regression, non-linear regression, and stochastic models) are also developed and compared to machine learning models. Analyzing the three standard models, the stochastic model clearly outperforms the standard linear model and nonlinear model. All the three machine learning models have comparable results and outperform the stochastic model, with GPR having slightly better results for stations No. 2 and 3, while BA-DT has slightly better results for station No. 1. The machine learning models are very effective tools which can be used for the prediction of daily river temperature. creator: Senlin Zhu creator: Emmanuel Karlo Nyarko creator: Marijana Hadzima-Nyarko uri: https://doi.org/10.7717/peerj.4894 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Zhu et al. title: Beef tenderness and intramuscular fat proteomic biomarkers: muscle type effect link: https://peerj.com/articles/4891 last-modified: 2018-06-07 description: Tenderness and intramuscular fat content are key attributes for beef sensory qualities. Recently some proteomic analysis revealed several proteins which are considered as good biomarkers of these quality traits. This study focuses on the analysis of 20 of these proteins representative of several biological functions: muscle structure and ultrastructure, muscle energetic metabolism, cellular stress and apoptosis. The relative abundance of the proteins was measured by Reverse Phase Protein Array (RPPA) in five muscles known to have different tenderness and intramuscular lipid contents: Longissimus thoracis (LT), Semimembranosus (SM), Rectus abdominis (RA), Triceps brachii (TB) and Semitendinosus (ST). The main results showed a muscle type effect on 16 among the 20 analyzed proteins. They revealed differences in protein abundance depending on the contractile and metabolic properties of the muscles. The RA muscle was the most different by 11 proteins differentially abundant comparatively to the four other muscles. Among these 11 proteins, six were less abundant namely enolase 3 (ENO3), phosphoglucomutase 1 (PGK1), aldolase (ALDOA), myosin heavy chain IIX (MyHC-IIX), fast myosin light chain 1 (MLC1F), triosephosphate isomerase 1 (TPI1) and five more abundant: Heat shock protein (HSP27, HSP70-1A1, αB-crystallin (CRYAB), troponin T slow (TNNT1), and aldolase dehydrogenase 1 (ALDH1A1). Four proteins: HSP40, four and a half LIM domains protein 1 (FHL1), glycogen phosphorylase B (PYGB) and malate dehydrogenase (MDH1) showed the same abundance whatever the muscle. The correlations observed between the 20 proteins in all the five muscles were used to construct a correlation network. The proteins the most connected with the others were in the following order MyHC-IIX, CRYAB, TPI1, PGK1, ALDH1A1, HSP27 and TNNT1. This knowledge is important for understanding the biological functions related to beef tenderness and intramuscular fat content. creator: Brigitte Picard creator: Mohammed Gagaoua creator: Marwa Al-Jammas creator: Leanne De Koning creator: Albéric Valais creator: Muriel Bonnet uri: https://doi.org/10.7717/peerj.4891 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Picard et al. title: A new predator connecting the abyssal with the hadal in the Kuril-Kamchatka Trench, NW Pacific link: https://peerj.com/articles/4887 last-modified: 2018-06-07 description: The bathyal to hadal deep sea of north-west Pacific Ocean was recently intensively sampled during four international expeditions (KuramBio I and II, SoJaBio and SokhoBio). A large amphipod, Rhachotropis saskia n. sp., was sampled in the Kuril-Kamchatka Trench and increases the number of described hadal species of that area to eight. A detailed description of the new species is provided, including illustrations, scanning-microscope images and molecular analysis. This predatory species was sampled at both continental and ocean abyssal margins of the Kuril-Kamchatka Trench as well as at hadal depths of the trench. The wide bathymetric distribution of the new species over more than 3,000 m is confirmed by molecular analysis, indicating that the Kuril Kamchatka Trench is not a distribution barrier for this species. However, the molecular analysis indicated the presence of isolation by distance of the populations of the studied taxon. creator: Anne-Nina Lörz creator: Anna Maria Jażdżewska creator: Angelika Brandt uri: https://doi.org/10.7717/peerj.4887 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Lörz et al. title: ­Chemical profiling and biological activity of Peperomia blanda (Jacq.) Kunth link: https://peerj.com/articles/4839 last-modified: 2018-06-07 description: Background Peperomia belongs to the family of Piperaceae. It has different uses in folk medicine and contains rare compounds that have led to increased interest in this genus. Peperomia blanda (Jacq.) Kunth is used as an injury disinfectant by Yemeni people. In addition, the majority of Yemen’s population still depend on the traditional remedy for serious diseases such as cancer, inflammation and infection. Currently, there is a deficiency of scientific evidence with regards to the medicinal plants from Yemen. Therefore, this study was performed to assess the chemical profile and in vitro antioxidant and cytotoxic activities of P. blanda.MethodsChemical profiling of P. blanda was carried out using gas chromatography mass spectrometry (GCMS) followed by isolation of bioactive compounds by column chromatography. DPPH• and FRAP assays were used to evaluate antioxidant activity and the MTT assay was performed to estimate the cytotoxicity activity against three cancer cell lines, namely MCF-7, HL-60 and WEHI-3, and three normal cell lines, MCF10A, WRL-68 and HDFa.ResultsX-ray crystallographic data for peperomin A is reported for the first time here and N,N′-diphenethyloxamide was isolated for the first time from Peperomia blanda. Methanol and dichloromethane extracts showed high radical scavenging activity with an IC50 of 36.81 ± 0.09 µg/mL, followed by the dichloromethane extract at 61.78 ± 0.02 µg/mL, whereas the weak ferric reducing activity of P. blanda extracts ranging from 162.2 ± 0.80 to 381.5 ± 1.31 µg/mL were recorded. In addition, petroleum ether crude extract exhibited the highest cytotoxic activity against all the tested cancer cell lines with IC50 values of 9.54 ± 0.30, 4.30 ± 0.90 and 5.39 ± 0.34 µg/mL, respectively. Peperomin A and the isolated mixture of phytosterol (stigmasterol and β-sitosterol) exhibited cytotoxic activity against MCF-7 and WE-HI cell lines with an IC50 of (5.58 ± 0.47, 4.62 ± 0.03 µg/mL) and (8.94 ± 0.05, 9.84 ± 0.61 µg/mL), respectively, compared to a standard drug, taxol, that has IC50 values of 3.56 ± 0.34 and 1.90 ± 0.9 µg/mL, respectively.ConclusionThe activities of P. blanda extracts and isolated compounds recorded in this study underlines the potential that makes this plant a valuable source for further study on anticancer and antioxidant activities. creator: Wafa M. Al-Madhagi creator: Najihah Mohd Hashim creator: Nasser A. Awad Ali creator: Abeer A. Alhadi creator: Siti Nadiah Abdul Halim creator: Rozana Othman uri: https://doi.org/10.7717/peerj.4839 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Al-Madhagi et al. title: Physiological and behavioral responses of house sparrows to repeated stressors link: https://peerj.com/articles/4961 last-modified: 2018-06-06 description: Despite decades of research, we still lack a complete understanding of what factors influence the transition of the necessary and adaptive acute stress response to what has become known as chronic stress. This gap in knowledge has illuminated the necessity for studies that examine the thresholds between these two sides of the stress response. Here, we determine how repeated exposure to acute stressors influences physiological and behavioral responses. In this repeated measures study, house sparrows (Passer domesticus) were exposed to a chronic stress protocol. We took physiological and behavioral measurements before, during, and after the protocol. Blood samples were used to assess four aspects of hypothalamic-pituitary-adrenal (HPA) axis function: baseline corticosterone, stress-induced corticosterone, negative feedback, and the maximal capacity to secrete corticosterone. We also assessed bacterial killing capacity and changes in uric acid concentration. Neophobia trials were used to assess behavioral changes throughout the protocol. We found no significant changes in HPA axis regulation in any of the four aspects we tested. However, we found that uric acid concentrations and neophobia significantly decreased after only four days of the chronic stress protocol, while bacterial killing capacity did not decrease until after eight days of exposure. These results indicate that different components of the stress response can be impacted by chronic stress on different timescales. Our results further indicate the importance of assessing multiple aspects of both physiology and behavior in order to understand how exposure to chronic stress may influence ability to cope with future challenges. creator: Brenna M.G. Gormally creator: Jessica Wright-Lichter creator: J. Michael Reed creator: L. Michael Romero uri: https://doi.org/10.7717/peerj.4961 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Gormally et al. title: Quantitative histological models suggest endothermy in plesiosaurs link: https://peerj.com/articles/4955 last-modified: 2018-06-06 description: BackgroundPlesiosaurs are marine reptiles that arose in the Late Triassic and survived to the Late Cretaceous. They have a unique and uniform bauplan and are known for their very long neck and hydrofoil-like flippers. Plesiosaurs are among the most successful vertebrate clades in Earth’s history. Based on bone mass decrease and cosmopolitan distribution, both of which affect lifestyle, indications of parental care, and oxygen isotope analyses, evidence for endothermy in plesiosaurs has accumulated. Recent bone histological investigations also provide evidence of fast growth and elevated metabolic rates. However, quantitative estimations of metabolic rates and bone growth rates in plesiosaurs have not been attempted before.MethodsPhylogenetic eigenvector maps is a method for estimating trait values from a predictor variable while taking into account phylogenetic relationships. As predictor variable, this study employs vascular density, measured in bone histological sections of fossil eosauropterygians and extant comparative taxa. We quantified vascular density as primary osteon density, thus, the proportion of vascular area (including lamellar infillings of primary osteons) to total bone area. Our response variables are bone growth rate (expressed as local bone apposition rate) and resting metabolic rate (RMR).ResultsOur models reveal bone growth rates and RMRs for plesiosaurs that are in the range of birds, suggesting that plesiosaurs were endotherm. Even for basal eosauropterygians we estimate values in the range of mammals or higher.DiscussionOur models are influenced by the availability of comparative data, which are lacking for large marine amniotes, potentially skewing our results. However, our statistically robust inference of fast growth and fast metabolism is in accordance with other evidence for plesiosaurian endothermy. Endothermy may explain the success of plesiosaurs consisting in their survival of the end-Triassic extinction event and their global radiation and dispersal. creator: Corinna V. Fleischle creator: Tanja Wintrich creator: P. Martin Sander uri: https://doi.org/10.7717/peerj.4955 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Fleischle et al. title: Restriction digest screening facilitates efficient detection of site-directed mutations introduced by CRISPR in C. albicans UME6 link: https://peerj.com/articles/4920 last-modified: 2018-06-06 description: Introduction of point mutations to a gene of interest is a powerful tool when determining protein function. CRISPR-mediated genome editing allows for more efficient transfer of a desired mutation into a wide range of model organisms. Traditionally, PCR amplification and DNA sequencing is used to determine if isolates contain the intended mutation. However, mutation efficiency is highly variable, potentially making sequencing costly and time consuming. To more efficiently screen for correct transformants, we have identified restriction enzymes sites that encode for two identical amino acids or one or two stop codons. We used CRISPR to introduce these restriction sites directly upstream of the Candida albicans UME6 Zn2+-binding domain, a known regulator of C. albicans filamentation. While repair templates coding for different restriction sites were not equally successful at introducing mutations, restriction digest screening enabled us to rapidly identify isolates with the intended mutation in a cost-efficient manner. In addition, mutated isolates have clear defects in filamentation and virulence compared to wild type C. albicans. Our data suggest restriction digestion screening efficiently identifies point mutations introduced by CRISPR and streamlines the process of identifying residues important for a phenotype of interest. creator: Ben A. Evans creator: Olivia L. Smith creator: Ethan S. Pickerill creator: Mary K. York creator: Kristen J.P. Buenconsejo creator: Antonio E. Chambers creator: Douglas A. Bernstein uri: https://doi.org/10.7717/peerj.4920 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Evans et al. title: Gastrointestinal transit time and heart rate variability in patients with mild acquired brain injury link: https://peerj.com/articles/4912 last-modified: 2018-06-06 description: BackgroundConstipation is suspected to occur frequently after acquired brain injury (ABI). In patients with ABI, heart rate variability (HRV) is reduced suggesting autonomic dysfunction. Autonomic dysfunction may be associated with prolonged gastrointestinal transit time (GITT). The primary aim of this study was to investigate if GITT is prolonged in patients with ABI. Secondarily, HRV and its correlation with GITT was investigated.MethodsWe included 25 patients with ABI (18 men, median age: 61.3 years, range [30.7–74.5]). GITT was assessed using radio-opaque markers and HRV was calculated from 24-hour electrocardiograms. Medical records were reviewed for important covariates, including primary diagnosis, time since injury, functional independence measure, and use of medication. The GITT assessed in patients was compared to a control group of 25 healthy subjects (18 men, median age: 61.5 years, range [34.0–70.9]).ResultsIn ABI patients, the mean GITT was significantly longer than in healthy controls (2.68 days, 95% CI [2.16–3.19] versus (1.92 days, 95% CI [1.62–2.22], p = 0.011)). No correlation was found between HRV and GITT.ConclusionPatients with mild to moderate ABI have prolonged GITT unrelated to the HRV. creator: Johannes Enevoldsen creator: Simon T. Vistisen creator: Klaus Krogh creator: Jørgen F. Nielsen creator: Karoline Knudsen creator: Per Borghammer creator: Henning Andersen uri: https://doi.org/10.7717/peerj.4912 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Enevoldsen et al. title: Modeling and analysis of the impacts of jet lag on circadian rhythm and its role in tumor growth link: https://peerj.com/articles/4877 last-modified: 2018-06-06 description: Circadian rhythms maintain a 24 h oscillation pattern in metabolic, physiological and behavioral processes in all living organisms. Circadian rhythms are organized as biochemical networks located in hypothalamus and peripheral tissues. Rhythmicity in the expression of circadian clock genes plays a vital role in regulating the process of cell division and DNA damage control. The oncogenic protein, MYC and the tumor suppressor, p53 are directly influenced by the circadian clock. Jet lag and altered sleep/wake schedules prominently affect the expression of molecular clock genes. This study is focused on developing a Petri net model to analyze the impacts of long term jet lag on the circadian clock and its probable role in tumor progression. The results depict that jet lag disrupts the normal rhythmic behavior and expression of the circadian clock proteins. This disruption leads to persistent expression of MYC and suppressed expression of p53. Thus, it is inferred that jet lag altered circadian clock negatively affects the expressions of cell cycle regulatory genes and contribute in uncontrolled proliferation of tumor cells. creator: Azka Hassan creator: Jamil Ahmad creator: Hufsah Ashraf creator: Amjad Ali uri: https://doi.org/10.7717/peerj.4877 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Hassan et al. title: Comparative description and ossification patterns of Dendropsophus labialis (Peters, 1863) and Scinax ruber (Laurenti, 1758) (Anura: Hylidae) link: https://peerj.com/articles/4525 last-modified: 2018-06-06 description: Although comparative studies of anuran ontogeny have provided new data on heterochrony in the life cycles of frogs, most of them have not included ossification sequences. Using differential staining techniques, we observe and describe differences and similarities of cranial and postcranial development in two hylid species, Scinax ruber (Scinaxinae) and Dendropsophus labialis (Hylinae), providing new data of ontogenetic studies in these Colombian species. We examined tadpoles raining from Gosner Stages 25 to 45. We found differences between species in the infrarostral and suprarostral cartilages, optic foramen, planum ethmoidale, and gill apparatus. In both species, the first elements to ossify were the atlas and transverse processes of the vertebral column and the parasphenoid. Both species exhibited suprascapular processes as described in other hylids. Although the hylids comprise a large group (over 700 species), postcranial ossification sequence is only known for 15 species. Therefore, the descriptions of the skeletal development and ossification sequences provided herein will be useful for future analyses of heterochrony in the group. creator: Angélica Arenas-Rodríguez creator: Juan Francisco Rubiano Vargas creator: Julio Mario Hoyos uri: https://doi.org/10.7717/peerj.4525 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Arenas-Rodríguez et al. title: Coupling GIS spatial analysis and Ensemble Niche Modelling to investigate climate change-related threats to the Sicilian pond turtle Emys trinacris, an endangered species from the Mediterranean link: https://peerj.com/articles/4969 last-modified: 2018-06-05 description: The pond turtle Emys trinacris is an endangered endemic species of Sicily showing a fragmented distribution throughout the main island. In this study, we applied “Ensemble Niche Modelling”, combining more classical statistical techniques as Generalized Linear Models and Multivariate Adaptive Regression Splines with machine-learning approaches as Boosted Regression Trees and Maxent, to model the potential distribution of the species under current and future climatic conditions. Moreover, a “gap analysis” performed on both the species’ presence sites and the predictions from the Ensemble Models is proposed to integrate outputs from these models, in order to assess the conservation status of this threatened species in the context of biodiversity management. For this aim, four “Representative Concentration Pathways”, corresponding to different greenhouse gases emissions trajectories were considered to project the obtained models to both 2050 and 2070. Areas lost, gained or remaining stable for the target species in the projected models were calculated. E. trinacris’ potential distribution resulted to be significantly dependent upon precipitation-linked variables, mainly precipitation of wettest and coldest quarter. Future negative effects for the conservation of this species, because of more unstable precipitation patterns and extreme meteorological events, emerged from our analyses. Further, the sites currently inhabited by E. trinacris are, for more than a half, out of the Protected Areas network, highlighting an inadequate management of the species by the authorities responsible for its protection. Our results, therefore, suggest that in the next future the Sicilian pond turtle will need the utmost attention by the scientific community to avoid the imminent risk of extinction. Finally, the gap analysis performed in GIS environment resulted to be a very informative post-modeling technique, potentially applicable to the management of species at risk and to Protected Areas’ planning in many contexts. creator: Mattia Iannella creator: Francesco Cerasoli creator: Paola D’Alessandro creator: Giulia Console creator: Maurizio Biondi uri: https://doi.org/10.7717/peerj.4969 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Iannella et al. title: Molecular attributes and apoptosis-inducing activities of a putative serine protease isolated from Tiger Milk mushroom (Lignosus rhinocerus) sclerotium against breast cancer cells in vitro link: https://peerj.com/articles/4940 last-modified: 2018-06-05 description: BackgroundThe highly valued medicinal tiger milk mushroom (also known as Lignosus rhinocerus) has the ability to cure numerous ailments. Its anticancer activities are well explored, and recently a partially purified cytotoxic protein fraction termed F5 from the mushroom’s sclerotial cold water extract consisting mainly of fungal serine proteases was found to exhibit potent selective cytotoxicity against a human breast adenocarcinoma cell line (MCF7) with IC50 value of 3.00 μg/ml. However, characterization of its cell death-inducing activity has yet to be established.MethodsThe mechanism involved in the cytotoxic activities of F5 against MCF7 cells was elucidated by flow cytometry-based apoptosis detection, caspases activity measurement, and expression profiling of apoptosis markers by western blotting. Molecular attributes of F5 were further mined from L. rhinocerus’s published genome and transcriptome for future exploration.Results and DiscussionApoptosis induction in MCF7 cells by F5 may involve a cross-talk between the extrinsic and intrinsic apoptotic pathways with upregulation of caspase-8 and -9 activities and a marked decrease of Bcl-2. On the other hand, the levels of pro-apoptotic Bax, BID, and cleaved BID were increased accompanied by observable actin cleavage. At gene level, F5 composed of three predicted non-synonymous single nucleotide polymorphisms (T > C) and an alternative 5′ splice site.ConclusionsFindings from this study provide an advanced framework for further investigations on cancer therapeutics development from L. rhinocerus. creator: Hui Yeng Y. Yap creator: Nget Hong Tan creator: Szu Ting Ng creator: Chon Seng Tan creator: Shin Yee Fung uri: https://doi.org/10.7717/peerj.4940 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Yap et al. title: An inexpensive, customizable microscopy system for the automated quantification and characterization of multiple adherent cell types link: https://peerj.com/articles/4937 last-modified: 2018-06-05 description: Cell quantification assays are essential components of most biological and clinical labs. However, many currently available quantification assays, including flow cytometry and commercial cell counting systems, suffer from unique drawbacks that limit their overall efficacy. In order to address the shortcomings of traditional quantification assays, we have designed a robust, low-cost, automated microscopy-based cytometer that quantifies individual cells in a multiwell plate using tools readily available in most labs. Plating and subsequent quantification of various dilution series using the automated microscopy-based cytometer demonstrates the single-cell sensitivity, near-perfect R2 accuracy, and greater than 5-log dynamic range of our system. Further, the microscopy-based cytometer is capable of obtaining absolute counts of multiple cell types in one well as part of a co-culture setup. To demonstrate this ability, we recreated an experiment that assesses the tumoricidal properties of primed macrophages on co-cultured tumor cells as a proof-of-principle test. The results of the experiment reveal that primed macrophages display enhanced cytotoxicity toward tumor cells while simultaneously losing the ability to proliferate, an example of a dynamic interplay between two cell populations that our microscopy-based cytometer is successfully able to elucidate. creator: Vishwaratn Asthana creator: Yuqi Tang creator: Adam Ferguson creator: Pallavi Bugga creator: Anantratn Asthana creator: Emily R. Evans creator: Allen L. Chen creator: Brett S. Stern creator: Rebekah A. Drezek uri: https://doi.org/10.7717/peerj.4937 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Asthana et al. title: The mitochondrial genomes of two walnut pests, Gastrolina depressa depressa and G. depressa thoracica (Coleoptera: Chrysomelidae), and phylogenetic analyses link: https://peerj.com/articles/4919 last-modified: 2018-06-05 description: In this study, the mitochondrial genomes (mitogenomes) of two walnut leaf insect pests, Gastrolina depressa depressa and G. depressa thoracica, were sequenced by Sanger sequencing technology. The mitogenome of G. depressa thoracica was complete at 16,109 bp in length, while the mitogenome of G. depressa depressa (14,277 bp) was partial. The genomic analyses indicated that both mitogenomes have the typical gene content and arrangement. The formerly identified elements, ‘TAGTA’ between trnSer(UCN) and nad2, and ‘ATGATAA’ between atp8 and atp6, were more conserved than that between nad4L and nad4, which was ‘ATGTTAA’ in Coleoptera excluding Polyphaga. Phylogenetic analyses of the 13 protein-coding genes from 36 coleopteran species well supported a close affinity between the subfamily Chrysomelinae including G. depressa thoracica and G. depressa depressa and Galerucinae, as well as a sister relationship of ((Eumolpinae + Cryptocephalinae) + Cassidinae) within Chrysomelidae. creator: Qiqi Wang creator: Guanghui Tang uri: https://doi.org/10.7717/peerj.4919 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Wang and Tang title: Shift in VEGFA isoform balance towards more angiogenic variants is associated with tumor stage and differentiation of human hepatocellular carcinoma link: https://peerj.com/articles/4915 last-modified: 2018-06-05 description: BackgroundHepatocellular carcinoma (HCC) is the most common and aggressive type of malignant liver tumor. HCC progression depends significantly on its vascularization and formation of new blood vessels. Vascular endothelial growth factor A (VEGFA) is a crucial regulator of tumor vascularization and components of VEGF-induced cell signaling pathways are important targets of therapeutical drugs that demonstrated the highest efficiency in case of advanced HCC (sorafenib and regorafenib). VEGFA is expressed as a set of isoforms with different functional properties, thus VEGFA isoform expression pattern may affect tumor sensitivity to anti-angiogenic drugs. However, information about VEGFA isoforms expression in HCC is still incomplete and contradictory. The present study aims to quantitatively investigate VEGFA isoform expression aberrations in HCC tissue.MethodsA total of 50 pairs of HCC and non-tumor tissue samples were used to evaluate the VEGFA isoform spectrum using RT-PCR and quantitatively estimate changes in isoform expression using RT-qPCR. Correlations between these changes and tumor clinicopathological characteristics were analyzed.ResultsWe identified VEGFA-189, VEGFA-165, and VEGFA-121 as predominant isoforms in liver tissue. Anti-angiogenic VEGFA-xxxb variants constituted no more than 5% of all mature VEGFA transcripts detected and their expression was not changed significantly in HCC tissue. We demonstrated for the first time that the least active variant VEGFA-189 is frequently repressed in HCC (p < 0.001), while no uniform changes were detected for potent angiogenesis stimulators VEGFA-165 and VEGFA-121. Isoform balance in HCC shifts from VEGFA-189 towards VEGFA-165 or VEGFA-121 in the majority of cases (p < 0.001). Changes in fractions, but not expression levels, of VEGFA-189 (decrease) and VEGFA-121 (increase) correlated with advanced Tumor-Node-Metastasis (TNM) and Barcelona Clinic Liver Cancer (BCLC) tumor stages (p < 0.05), VEGFA-189 fraction reduction was also associated with poor tumor differentiation (p < 0.05).DiscussionA distinct shift in VEGFA isoform balance towards more pro-angiogenic variants occurs in HCC tissue and may modulate overall impact of VEGFA signaling. We suppose that the ratio between VEGFA isoforms is an important parameter governing HCC angiogenesis that may affect HCC progression and be used for optimizing the strategy of HCC therapy by predicting the response to anti-angiogenic drugs. creator: Mikhail S. Chesnokov creator: Polina A. Khesina creator: Darya A. Shavochkina creator: Inna F. Kustova creator: Leonid M. Dyakov creator: Olga V. Morozova creator: Nikolai S. Mugue creator: Nikolay E. Kudashkin creator: Ekaterina A. Moroz creator: Yuri I. Patyutko creator: Natalia L. Lazarevich uri: https://doi.org/10.7717/peerj.4915 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Chesnokov et al. title: Discovery of digestive enzymes in carnivorous plants with focus on proteases link: https://peerj.com/articles/4914 last-modified: 2018-06-05 description: BackgroundCarnivorous plants have been fascinating researchers with their unique characters and bioinspired applications. These include medicinal trait of some carnivorous plants with potentials for pharmaceutical industry.MethodsThis review will cover recent progress based on current studies on digestive enzymes secreted by different genera of carnivorous plants: Drosera (sundews), Dionaea (Venus flytrap), Nepenthes (tropical pitcher plants), Sarracenia (North American pitcher plants), Cephalotus (Australian pitcher plants), Genlisea (corkscrew plants), and Utricularia (bladderworts).ResultsSince the discovery of secreted protease nepenthesin in Nepenthes pitcher, digestive enzymes from carnivorous plants have been the focus of many studies. Recent genomics approaches have accelerated digestive enzyme discovery. Furthermore, the advancement in recombinant technology and protein purification helped in the identification and characterisation of enzymes in carnivorous plants.DiscussionThese different aspects will be described and discussed in this review with focus on the role of secreted plant proteases and their potential industrial applications. creator: Rishiesvari Ravee creator: Faris ‘Imadi Mohd Salleh creator: Hoe-Han Goh uri: https://doi.org/10.7717/peerj.4914 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Ravee et al. title: Hindering the illegal trade in dog and cat furs through a DNA-based protocol for species identification link: https://peerj.com/articles/4902 last-modified: 2018-06-05 description: In Western countries dogs and cats are the most popular pets, and people are increasingly opposed to their rearing for the fur industry. In 2007, a Regulation of the European Union (EU) banned the use and trade of dog and cat furs, but an official analytical protocol to identify them as source species was not provided, and violations of law are still frequent in all Member States. In this paper we report on the development and validation of a simple and affordable DNA method for species detection in furs to use as an effective tool to combat illegal trade in fur products. A set of mitochondrial primers was designed for amplification of partial cytochrome b, control region and ND1 gene in highly degraded samples, like furs and pelts. Our amplification workflow involved the use of a non-specific primer pair to perform a first test to identify the species through sequencing, then the application of species-specific primer pairs to use in singleplex end-point PCRs as confirmation tests. The advantage of this two-step procedure is twofold: on the one hand it minimises the possibility of negative test results from degraded samples, since failure of amplification with a first set of primers can be offset by successful amplification of the second, and on the other it adds confidence and reliability to final authentication of species. All designed primers were validated on a reference collection of tissue samples, obtaining solid results in terms of specificity, sensitivity, repeatability and reproducibility. Application of the protocol on real caseworks from seized furs yielded successful results also from old and dyed furs, suggesting that age and chemical staining do not necessarily affect positive amplifications. Major pros of this approach are: (1) sensitive and informative primer sets for detection of species; (2) short PCR amplicons for the analysis of poor quality DNA; (3) binding primers that avoid contamination from human DNA; (4) user-friendly protocol for any laboratory equipped for analysis of low-copy-number DNA. Our molecular procedure proved to be a good starting point for enforcing the EU Regulation against dog and cat fur trade in forensic contexts where source attribution is essential to the assignment of responsibilities. creator: Luisa Garofalo creator: Alessia Mariacher creator: Rita Fanelli creator: Rosario Fico creator: Rita Lorenzini uri: https://doi.org/10.7717/peerj.4902 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Garofalo et al. title: In quest of contact: phylogeography of helmeted terrapins (Pelomedusa galeata, P. subrufa sensu stricto) link: https://peerj.com/articles/4901 last-modified: 2018-06-05 description: Based on rangewide sampling and three mitochondrial and two nuclear markers (together up to 1,850 bp and 1,840 bp, respectively), we examine the phylogeography of two helmeted terrapin species (Pelomedusa galeata and P. subrufa sensu stricto) and infer shifts of climatically suitable spaces since the Last Glacial Maximum using a modeling approach. Whilst P. galeata displays significant phylogeographic structuring across its range and consists of two deeply divergent lineages that could represent distinct species, P. subrufa shows no obvious phylogeographic differentiation. This seems to be related to historically stable or fluctuating ranges. One of the lineages within P. galeata appears to be confined to the westernmost, winter-rainfall region of South Africa and deserves special conservational attention due to the scarcity of surface water. The other lineage is distributed further east and is differentiated in three weakly supported subclades with parapatric distribution; one occurring inland, and two along the south and east coasts, respectively. As far as is known, P. subrufa occurs in South Africa only in the northeast of the country (Limpopo, Mpumalanga) and we report the species for the first time from the Lapalala Wilderness Area in the Waterberg region (Limpopo), approximately 350 km further west than previously recorded. We confirmed the occurrence of P. galeata only 80 km south of Lapalala. Thus, a sympatric occurrence of P. galeata and P. subrufa is possible. Another putative contact zone, for the two lineages within P. galeata, must be located in the Western Cape region, and further contact zones are likely for the eastern subclades within P. galeata. The nuclear loci provided no evidence for gene flow across taxa or genetic clusters within taxa. Future investigations should use denser sampling from putative contact zones and more nuclear markers to re-examine this situation. Despite few phylogeographic studies published for southern African biota, it seems likely that differentiation follows general rules, and that climate and physiographic barriers (e.g., the Great Escarpment) have shaped phylogeographic patterns. creator: Melita Vamberger creator: Margaretha D. Hofmeyr creator: Flora Ihlow creator: Uwe Fritz uri: https://doi.org/10.7717/peerj.4901 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Vamberger et al. title: Growth, biochemical response and liver health of juvenile barramundi (Lates calcarifer) fed fermented and non-fermented tuna hydrolysate as fishmeal protein replacement ingredients link: https://peerj.com/articles/4870 last-modified: 2018-06-05 description: Conventional aquaculture feed materials available in Australia are expensive, which has prompted the search for alternatives that would be cost-effective and locally available. The present study was undertaken in order to maximize the use of a tuna hydrolysate (TH), which was produced locally from the tuna-processing discards. The growth performance, biochemical status, antioxidant capacity and liver health of juvenile barramundi (Lates calcarifer) were assessed. Two series of isonitrogenous and isocaloric diets labelled as TH50, TH75 (non-fermented tuna hydrolysate) and FTH50, FTH75 (fermented tuna hydrolysate) were formulated to replace FM at 50% and 75%, respectively. A basal diet without the TH supplementation was used as a control. The experimental diets were fed to the triplicate groups of fish three times a day for 56 days. The results of the experiment revealed that fish fed on both fermented and non-fermented TH-containing diets significantly reduced (p < 0.05) the final body weight, weight gain and specific growth rate compared to the control. The highest apparent digestibility coefficients for dry matter, protein and lipid were obtained in the control group, and decreased with the increasing level of TH in the diets. However, the whole-body proximate compositions and the blood biochemical indices of fish were not affected by the TH inclusion in the diets. The fish fed on TH diets of TH50, FTH50 and TH75 exhibited reduced (p < 0.05) glutathione peroxidase (GPx) activity compared to the control; whereas the FTH75 exhibited no difference with the control. The excessive inclusion of TH in the diets of TH75 and FTH75 resulted in cytoplasmic vacuolization, with an increased amount of lipid accumulation, and necrosis in the liver tissue. These results indicated that the replacement of the FM protein with TH at 50% and 75% inclusion levels negatively affected the growth performance, feed utilization, and digestibility in juvenile barramundi; and it also increased the potential risk of hepatic failure in the fish. Further investigation is, therefore, required in order to optimize the TH levels in the fish diets which would be suitable for the growth of fish, as well as for maintaining the enhanced biochemical response in juvenile barramundi. creator: Muhammad A.B. Siddik creator: Janet Howieson creator: Ilham Ilham creator: Ravi Fotedar uri: https://doi.org/10.7717/peerj.4870 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Siddik et al. title: Biochemical and genetic analyses of the oomycete Pythium insidiosum provide new insights into clinical identification and urease-based evolution of metabolism-related traits link: https://peerj.com/articles/4821 last-modified: 2018-06-05 description: The oomycete microorganism, Pythium insidiosum, causes the life-threatening infectious condition, pythiosis, in humans and animals worldwide. Affected individuals typically endure surgical removal of the infected organ(s). Detection of P. insidiosum by the established microbiological, immunological, or molecular methods is not feasible in non-reference laboratories, resulting in delayed diagnosis. Biochemical assays have been used to characterize P. insidiosum, some of which could aid in the clinical identification of this organism. Although hydrolysis of maltose and sucrose has been proposed as the key biochemical feature useful in discriminating P. insidiosum from other oomycetes and fungi, this technique requires a more rigorous evaluation involving a wider selection of P. insidiosum strains. Here, we evaluated 10 routinely available biochemical assays for characterization of 26 P. insidiosum strains, isolated from different hosts and geographic origins. Initial assessment revealed diverse biochemical characteristics across the P. insidiosum strains tested. Failure to hydrolyze sugars is observed, especially in slow-growing strains. Because hydrolysis of maltose and sucrose varied among different strains, use of the biochemical assays for identification of P. insidiosum should be cautioned. The ability of P. insidiosum to hydrolyze urea is our focus, because this metabolic process relies on the enzyme urease, an important virulence factor of other pathogens. The ability to hydrolyze urea varied among P. insidiosum strains and was not associated with growth rates. Genome analyses demonstrated that urease- and urease accessory protein-encoding genes are present in both urea-hydrolyzing and non-urea-hydrolyzing strains of P. insidiosum. Urease genes are phylogenetically conserved in P. insidiosum and related oomycetes, while the presence of urease accessory protein-encoding genes is markedly diverse in these organisms. In summary, we dissected biochemical characteristics and drew new insights into clinical identification and urease-related evolution of P. insidiosum. creator: Theerapong Krajaejun creator: Thidarat Rujirawat creator: Teerat Kanpanleuk creator: Pitak Santanirand creator: Tassanee Lohnoo creator: Wanta Yingyong creator: Yothin Kumsang creator: Pattarana Sae-Chew creator: Weerayuth Kittichotirat creator: Preecha Patumcharoenpol uri: https://doi.org/10.7717/peerj.4821 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Krajaejun et al. title: The energetic cost of mounting an immune response for Pallas’s long-tongued bat (Glossophaga soricina) link: https://peerj.com/articles/4627 last-modified: 2018-06-05 description: The acute phase response (APR) is the first line of defense of the vertebrate immune system against pathogens. Mounting an immune response is believed to be energetically costly but direct measures of metabolic rate during immune challenges contradict this assumption. The energetic cost of APR for birds is higher than for rodents, suggesting that this response is less expensive for mammals. However, the particularly large increase in metabolic rate after APR activation for a piscivorous bat (Myotis vivesi) suggests that immune response might be unusually costly for bats. Here we quantified the energetic cost and body mass change associated with APR for the nectarivorous Pallas’s long-tongued bat (Glossophaga soricina). Activation of the APR resulted in a short-term decrease in body mass and an increase in resting metabolic rate (RMR) with a total energy cost of only 2% of the total energy expenditure estimated for G. soricina. This increase in RMR was far from the large increase measured for piscivorous bats; rather, it was similar to the highest values reported for birds. Overall, our results suggest that the costs of APR for bats may vary interspecifically. Measurement of the energy cost of vertebrate immune response is limited to a few species and further work is warranted to evaluate its significance for an animal’s energy budget. creator: Lucia V. Cabrera-Martínez creator: L. Gerardo Herrera M. creator: Ariovaldo P. Cruz-Neto uri: https://doi.org/10.7717/peerj.4627 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Cabrera-Martínez et al. title: Diversity, host-specificity and stability of sponge-associated fungal communities of co-occurring sponges link: https://peerj.com/articles/4965 last-modified: 2018-06-04 description: Fungi play a critical role in a range of ecosystems; however, their interactions and functions in marine hosts, and particular sponges, is poorly understood. Here we assess the fungal community composition of three co-occurring sponges (Cymbastela concentrica, Scopalina sp., Tedania anhelans) and the surrounding seawater over two time points to help elucidate host-specificity, stability and potential core members, which may shed light into the ecological function of fungi in sponges. The results showed that ITS-amplicon-based community profiling likely provides a more realistic assessment of fungal diversity in sponges than cultivation-dependent approaches. The sponges studied here were found to contain phylogenetically diverse fungi (eight fungal classes were observed), including members of the family Togniniaceae and the genus Acrostalagmus, that have so far not been reported to be cultured from sponges. Fungal communities within any given sponge species were found to be highly variable compared to bacterial communities, and influenced in structure by the community of the surrounding seawater, especially considering temporal variation. Nevertheless, the sponge species studied here contained a few “variable/core” fungi that appeared in multiple biological replicates and were enriched in their relative abundance compared to seawater communities. These fungi were the same or highly similar to fungal species detected in sponges around the world, which suggests a prevalence of horizontal transmission where selectivity and enrichment of some fungi occur for those that can survive and/or exploit the sponge environment. Our current sparse knowledge about sponge-associated fungi thus indicate that fungal communities may perhaps not play as an important ecological role in the sponge holobiont compared to bacterial or archaeal symbionts. creator: Mary T.H.D. Nguyen creator: Torsten Thomas uri: https://doi.org/10.7717/peerj.4965 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Nguyen and Thomas title: D-GENIES: dot plot large genomes in an interactive, efficient and simple way link: https://peerj.com/articles/4958 last-modified: 2018-06-04 description: Dot plots are widely used to quickly compare sequence sets. They provide a synthetic similarity overview, highlighting repetitions, breaks and inversions. Different tools have been developed to easily generated genomic alignment dot plots, but they are often limited in the input sequence size. D-GENIES is a standalone and web application performing large genome alignments using minimap2 software package and generating interactive dot plots. It enables users to sort query sequences along the reference, zoom in the plot and download several image, alignment or sequence files. D-GENIES is an easy-to-install, open-source software package (GPL) developed in Python and JavaScript. The source code is available at https://github.com/genotoul-bioinfo/dgenies and it can be tested at http://dgenies.toulouse.inra.fr/. creator: Floréal Cabanettes creator: Christophe Klopp uri: https://doi.org/10.7717/peerj.4958 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Cabanettes and Klopp title: Adaptive genetic variation at three loci in South African vervet monkeys (Chlorocebus pygerythrus) and the role of selection within primates link: https://peerj.com/articles/4953 last-modified: 2018-06-04 description: Vervet monkeys (Chlorocebus pygerythrus) are one of the most widely distributed non-human primate species found in South Africa. They occur across all the South African provinces, inhabiting a large variety of habitats. These habitats vary sufficiently that it can be assumed that various factors such as pathogen diversity could influence populations in different ways. In turn, these factors could lead to varied levels of selection at specific fitness linked loci. The Toll-like receptor (TLR) gene family, which play an integral role in vertebrate innate immunity, is a group of fitness linked loci which has been the focus of much research. In this study, we assessed the level of genetic variation at partial sequences of two TLR loci (TLR4 and 7) and a reproductively linked gene, acrosin (ACR), across the different habitat types within the vervet monkey distribution range. Gene variation and selection estimates were also made among 11–21 primate species. Low levels of genetic variation for all three gene regions were observed within vervet monkeys, with only two polymorphic sites identified for TLR4, three sites for TLR7 and one site for ACR. TLR7 variation was positively correlated with high mean annual rainfall, which was linked to increased pathogen abundance. The observed genetic variation at TLR4 might have been influenced by numerous factors including pathogens and climatic conditions. The ACR exonic regions showed no variation in vervet monkeys, which could point to the occurrence of a selective sweep. The TLR4 and TLR7 results for the among primate analyses was mostly in line with previous studies, indicating a higher rate of evolution for TLR4. Within primates, ACR coding regions also showed signs of positive selection, which was congruent with previous reports on mammals. Important additional information to the already existing vervet monkey knowledge base was gained from this study, which can guide future research projects on this highly researched taxon as well as help conservation agencies with future management planning involving possible translocations of this species. creator: Willem G. Coetzer creator: Trudy R. Turner creator: Christopher A. Schmitt creator: J. Paul Grobler uri: https://doi.org/10.7717/peerj.4953 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Coetzer et al. title: Bioheat transfer model of transcutaneous spinal cord stimulation-induced temperature changes link: https://peerj.com/articles/4921 last-modified: 2018-06-04 description: Transcutaneous spinal cord stimulation (tSCS) has been extensively studied due to its promising application in motor function restoration. Many previous studies have explored both the essential mechanism of action and the methods for determining optimal stimulation parameters. In contrast, the bioheat transfer analysis of tSCS therapy has not been investigated to the same extent, despite widely existing, and being of great significance in assuring a stable and thermally safe treatment. In this paper, we concentrated on the thermal effects of tSCS using a finite element-based method. By coupling the electric field and bioheat field, systematic finite element simulations were performed on a human spinal cord model to survey the influence of anatomical structures, blood perfusion, and stimulation parameters on temperature changes for the first time. The results show that tSCS-induced temperature rise mainly occurs in the skin and fat layers and varies due to individual differences. The current density distribution along with the interactions of multiple biothermal effects synthetically determines the thermal status of the whole spinal cord model. Smaller stimulation electrodes have a higher risk of thermal damage when compared with larger electrodes. Increasing the stimulation intensity will result in more joule heat accumulation, hence an increase in the temperature. Among all configurations in this study that simulated the clinical tSCS protocols, the temperature rise could reach up to 9.4 °C on the skin surface depending on the stimulation parameters and tissue blood perfusion. creator: Luyao Chen creator: Ang Ke creator: Peng Zhang creator: Zhaolong Gao creator: Xuecheng Zou creator: Jiping He uri: https://doi.org/10.7717/peerj.4921 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Chen et al. title: Pro-inflammatory AGE-RAGE signaling is activated during arousal from hibernation in ground squirrel adipose link: https://peerj.com/articles/4911 last-modified: 2018-06-04 description: BackgroundInflammation is generally suppressed during hibernation, but select tissues (e.g. lung) have been shown to activate both antioxidant and pro-inflammatory pathways, particularly during arousal from torpor when breathing rates increase and oxidative metabolism fueling the rewarming process produces more reactive oxygen species. Brown and white adipose tissues are now understood to be major hubs for the regulation of immune and inflammatory responses, yet how these potentially damaging processes are regulated by fat tissues during hibernation has hardly been studied. The advanced glycation end-product receptor (RAGE) can induce pro-inflammatory responses when bound by AGEs (which are glycated and oxidized proteins, lipids, or nucleic acids) or damage associated molecular pattern molecules (DAMPs, which are released from dying cells).MethodsSince gene expression and protein synthesis are largely suppressed during torpor, increases in AGE-RAGE pathway proteins relative to a euthermic control could suggest some role for these pro-inflammatory mediators during hibernation. This study determined how the pro-inflammatory AGE-RAGE signaling pathway is regulated at six major time points of the torpor-arousal cycle in brown and white adipose from a model hibernator, Ictidomys tridecemlineatus. Immunoblotting, RT-qPCR, and a competitive ELISA were used to assess the relative gene expression and protein levels of key regulators of the AGE-RAGE pathway during a hibernation bout.ResultsThe results of this study revealed that RAGE is upregulated as animals arouse from torpor in both types of fat, but AGE and DAMP levels either remain unchanged or decrease. Downstream of the AGE-RAGE cascade, nfat5 was more highly expressed during arousal in brown adipose.DiscussionAn increase in RAGE protein levels and elevated mRNA levels of the downstream transcription factor nfat5 during arousal suggest the pro-inflammatory response is upregulated in adipose tissue of the hibernating ground squirrel. It is unlikely that this cascade is activated by AGEs or DAMPs. This research sheds light on how a fat-but-fit organism with highly regulated metabolism may control the pro-inflammatory AGE-RAGE pathway, a signaling cascade that is often dysregulated in other obese organisms. creator: Samantha M. Logan creator: Kenneth B. Storey uri: https://doi.org/10.7717/peerj.4911 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Logan and Storey title: Teleost and elasmobranch eye lenses as a target for life-history stable isotope analyses link: https://peerj.com/articles/4883 last-modified: 2018-06-04 description: Incrementally grown, metabolically inert tissues such as fish otoliths provide biochemical records that can used to infer behavior and physiology throughout the lifetime of the individual. Organic tissues are particularly useful as the stable isotope composition of the organic component can provide information about diet, trophic level and location. Unfortunately, inert, incrementally grown organic tissues are relatively uncommon. The vertebrate eye lens, however, is formed via sequential deposition of protein-filled fiber cells, which are subsequently metabolically inert. Lenses therefore have the potential to serve as biochemical data recorders capturing life-long variations in dietary and spatial ecology. Here we review the state of knowledge regarding the structure and formation of fish eye lenses in the context of using lens tissue for retrospective isotopic analysis. We discuss the relationship between eye lens diameter and body size, describe the successful recovery of expected isotopic gradients throughout ontogeny and between species, and quantify the isotopic offset between lens protein and white muscle tissue. We show that fish eye lens protein is an attractive host for recovery of stable isotope life histories, particularly for juvenile life stages, and especially in elasmobranchs lacking otoliths, but interpretation of lens-based records is complicated by species-specific uncertainties associated with lens growth rates. creator: Katie Quaeck-Davies creator: Victoria A. Bendall creator: Kirsteen M. MacKenzie creator: Stuart Hetherington creator: Jason Newton creator: Clive N. Trueman uri: https://doi.org/10.7717/peerj.4883 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Quaeck-Davies et al. title: Cytotoxicity and antimicrobial action of selected phytochemicals against planktonic and sessile Streptococcus mutans link: https://peerj.com/articles/4872 last-modified: 2018-06-04 description: BackgroundDental caries remains the most prevalent and costly oral infectious disease worldwide, encouraging the search for new and more effective antimicrobials. Therefore, the aim of this work was to study the antimicrobial action of selected phytochemicals (eugenol, citronellol, sabinene hydrate, trans-cinnamaldehyde, terpineol and cinnamic acid) against Streptococcus mutans in planktonic and biofilm states as well as the cytotoxicity of these compounds.MethodsThe antibacterial activity of the selected compounds was evaluated by the determination of the minimal bactericidal concentration. The resazurin assay was used to assess the metabolic activity of sessile S. mutans. The cytotoxicity was determined using a fibroblast cell line.ResultsAmong the tested phytochemicals, citronellol, cinnamic acid and trans-cinnamaldehyde were the most effective against both planktonic and sessile S. mutans, an effect apparently related to their hydrophobic character. Additionally, these three compounds did not compromise fibroblasts cell viability.DiscussionCitronellol, cinnamic acid and trans-cinnamaldehyde demonstrated significant antimicrobial activity and low cytotoxicity proposing their potential as a novel group of therapeutic compounds to control oral infectious diseases. Moreover, their effects are particularly relevant when benchmarked against eugenol, a phytochemical commonly used for prosthodontic applications in dentistry. creator: Marta Ribeiro creator: Joana Malheiro creator: Liliana Grenho creator: Maria Helena Fernandes creator: Manuel Simões uri: https://doi.org/10.7717/peerj.4872 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Ribeiro et al. title: Bullying victimization and child sexual abuse among left-behind and non-left-behind children in China link: https://peerj.com/articles/4865 last-modified: 2018-06-04 description: BackgroundBullying is one of the most important factors associated with child abuse. However, robust tests supporting the assumption that being bullied can contribute to child sexual abuse (CSA) among left-behind children (LBC) remain sparse. This study aims to investigate the association of bullying victimization with CSA among LBC in China.MethodsA cross-sectional study was conducted in six middle schools of Sichuan and Anhui province in 2015. The bullying victimization was assessed by seven items from the Revised Olweus Bully/Victim Questionnaire. The experience of CSA was measured by ten items CSA scale with good consistency.ResultsA total of 1,030 children met the sampling criteria, including 284 LBC and 746 non-LBC. The prevalence of CSA was 22.89% in LBC and 20.19% in non-LBC (p > 0.05). Bullying victimization was related to CSA among both LBC (adjusted Odds Ratio [aOR] = 2.52, 95% CI [1.34–4.73]) and non-LBC (aOR = 2.35, 95% CI [1.58–3.53]). The association between bullying victimization and CSA was much higher among left-behind girls (left-behind girls: aOR = 7.36, 95% CI [2.16–24.99]; non-left-behind girls: aOR = 2.38, 95% CI [1.08–5.27]). Also, LBC of a young age (11–15), children with siblings, living in rural areas and non-traditional family structure who were bullied were more likely to suffer CSA than their non-LBC peers.ConclusionsBullying victimization is associated with a significant increase in CSA among both LBC and non-LBC. Anti-bullying programs should target vulnerable populations including female LBC and LBC with siblings to reduce the risk of CSA. creator: Li Yan creator: Qianqian Zhu creator: Xiaowen Tu creator: Xiayun Zuo creator: Chunyan Yu creator: Chaohua Lou creator: Qiguo Lian uri: https://doi.org/10.7717/peerj.4865 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Yan et al. title: Seasonal fluctuation of oribatid mite communities in forest microhabitats link: https://peerj.com/articles/4863 last-modified: 2018-06-04 description: Oribatid mites are abundant and diverse decomposers in almost all terrestrial microhabitats, especially in temperate forests. Although their functional importance in the decomposition system in these forests has been investigated, spatio-temporal patterns of oribatid mite communities inhabiting different microhabitats have largely been neglected. Therefore, we (i) investigated seasonal fluctuation (monthly over one year) in oribatid-mite community structure and specificity to three microhabitats (moss, dead wood and litter) and (ii) analyzed the influence of air temperature and overall air humidity on seasonal community changes. In total, 57,398 adult oribatid mite individuals were collected. Total abundance, species richness and diversity differed among microhabitats. Seasonal changes were most pronounced in moss and least in litter. While overall air humidity had no influence on species distribution and community changes, air temperature positively influenced species richness and diversity, again most pronounced in moss. The calculated environmental temperature occurrence niche showed that 35% of adult oribatid mite species occurred at higher air temperatures. Furthermore, interaction/bipartite networks were more generalized—i.e., species were more equally distributed among moss, dead wood and litter—when ambient air temperatures were higher. This pattern is probably due to the dispersal ability of adult oribatid mites, i.e., species enter a dispersal mode only at higher air temperatures. creator: Katja Wehner creator: Michael Heethoff creator: Adrian Brückner uri: https://doi.org/10.7717/peerj.4863 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Wehner et al. title: Combined therapy of pulsed radiofrequency and nerve block in postherpetic neuralgia patients: a randomized clinical trial link: https://peerj.com/articles/4852 last-modified: 2018-06-04 description: Caused by viral infection, postherpetic neuralgia (PHN) is the most common chronic neuropathic pain. Various treatment modalities such as early use of nerve block therapy (NBT) and pulsed radiofrequency (PRF) have been studied in reducing pain, however, no consistent success was achieved in all the patients treated with single regimen. The combined therapy of PRF and NBT with different targeting mechanism are of interest and remains to be determined. Here we investigated the combined effects of pulsed radiofrequency (PRF) with nerve block therapy (NBT) in PHN patients in a prospective randomized clinical trial. Sixty PHN patients were divided into four groups (n = 15 each): the conventional puncture group (group CP), the nerve block therapy group (group NB), the PRF group (group PRF), and the combined treatment group (PRF combined with nerve block therapy (group CT). To evaluate the extent of remission of hyperalgesia, we recorded the visual analogue scale (VAS) scores during cotton swab reaction before and after treatment and in the resting and active pain states. In addition, blood samples were collected and plasma cytokine and neuropeptides such as interleukin-6 (IL-6), substance P (SP), and β-endorphin (β-EP) were measured by enzyme-linked immunosorbent assay (ELISA) at the admission (basic state), before the operation, and at 12 h postoperatively. The number of adverse events (nausea, vomiting, constipation, puncture point hemorrhage, swelling and redness) within 12 h of the treatment were also documented. Our results showed that VAS scores during cotton swab reaction decreased after treatment in all patients (p < 0.05). Compared to group CP, plasma IL-6 and SP levels decreased (p < 0.05) and β-EP levels increased (p < 0.05) in groups NB, PRF, and CT. There were no significant differences in adverse events among groups (p > 0.05). We found that PRF in combination with NBT increased β-EP levels and decreased plasma IL-6 and SP, thereby alleviating pain and hyperalgesia in PHN patients. Taken together, our data suggest combined therapy of PRF and NBT is effective and safe for PHN patients. creator: Dan Li creator: Guohua Sun creator: Hanzhe Sun creator: Yanjuan Wang creator: Zhiping Wang creator: Jianping Yang uri: https://doi.org/10.7717/peerj.4852 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Li et al. title: Exploring constructs of well-being, happiness and quality of life link: https://peerj.com/articles/4903 last-modified: 2018-06-01 description: BackgroundExisting definitions of happiness, subjective well-being, and quality of life suggest conceptual overlap between these constructs. This study explored the relationship between these well-being constructs by applying widely used measures with satisfactory psychometric properties.Materials and MethodsUniversity students (n = 180) completed widely used well-being measures including the Oxford Happiness Questionnaire (OHQ), the World Health Organization Quality of Life Questionnaire, the Satisfaction with Life Scale, and the Positive and Negative Affect Scale. We analyzed the data using correlation, regression, and exploratory factor analysis.ResultsAll included well-being measures demonstrated high loadings on the global well-being construct that explains about 80% of the variance in the OHQ, the psychological domain of Quality of Life and subjective well-being. The results show high positive correlations between happiness, psychological and health domains of quality of life, life satisfaction, and positive affect. Social and environmental domains of quality of life were poor predictors of happiness and subjective well-being after controlling for psychological quality of life.ConclusionTogether, these data provide support for a global well-being dimension and interchangeable use of terms happiness, subjective well-being, and psychological quality of life with the current sample and measures. Further investigation with larger heterogeneous samples and other well-being measures is warranted. creator: Oleg N. Medvedev creator: C. Erik Landhuis uri: https://doi.org/10.7717/peerj.4903 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Medvedev and Landhuis title: N-acetylcysteine protects against motor, optomotor and morphological deficits induced by 6-OHDA in zebrafish larvae link: https://peerj.com/articles/4957 last-modified: 2018-06-01 description: BackgroundParkinson’s disease (PD) is the second most common neurodegenerative disorder. In addition to its highly debilitating motor symptoms, non-motor symptoms may precede their motor counterparts by many years, which may characterize a prodromal phase of PD. A potential pharmacological strategy is to introduce neuroprotective agents at an earlier stage in order to prevent further neuronal death. N-acetylcysteine (NAC) has been used against paracetamol overdose hepatotoxicity by restoring hepatic concentrations of glutathione (GSH), and as a mucolytic in chronic obstructive pulmonary disease by reducing disulfide bonds in mucoproteins. It has been shown to be safe for humans at high doses. More recently, several studies have evidenced that NAC has a multifaceted mechanism of action, presenting indirect antioxidant effect by acting as a GSH precursor, besides its anti-inflammatory and neurotrophic effects. Moreover, NAC modulates glutamate release through activation of the cystine-glutamate antiporter in extra-synaptic astrocytes. Its therapeutic benefits have been demonstrated in clinical trials for several neuropsychiatric conditions but has not been tested in PD models yet.MethodsIn this study, we evaluated the potential of NAC to prevent the damage induced by 6-hydroxydopamine (6-OHDA) on motor, optomotor and morphological parameters in a PD model in larval zebrafish.ResultsNAC was able to prevent the motor deficits (total distance, mean speed, maximum acceleration, absolute turn angle and immobility time), optomotor response impairment and morphological alterations (total length and head length) caused by exposure to 6-OHDA, which reinforce and broaden the relevance of its neuroprotective effects.DiscussionNAC acts in different targets relevant to PD pathophysiology. Further studies and clinical trials are needed to assess this agent as a candidate for prevention and adjunctive treatment of PD. creator: Radharani Benvenutti creator: Matheus Marcon creator: Carlos G. Reis creator: Laura R. Nery creator: Camila Miguel creator: Ana P. Herrmann creator: Monica R.M. Vianna creator: Angelo Piato uri: https://doi.org/10.7717/peerj.4957 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Benvenutti et al. title: Occupational health and safety characteristics of agricultural workers in Adana, Turkey: a cross-sectional study link: https://peerj.com/articles/4952 last-modified: 2018-06-01 description: BackgroundAmong agricultural workers, especially in the seasonal migratory ones, housing and hygiene related issues, occupational accidents, low levels of education, poverty and absence of social security problems emerge as significant public health problems. This study aims to compare migrant-seasonal workers (MSWs) and resident agricultural workers (RAWs) in terms of socio-demographic characteristics and occupational health and safety in Adana, one of Turkey’s most important agricultural cities.MethodsThis cross-sectional study was conducted on RAWs and MSWs, aged 15–65, operating in the province of Adana. The calculated sample sizes for both MSWs and RAWs were distributed using stratified simple random sampling to five districts of Adana.ResultsThe mean age of the 798 participating agricultural workers was 34.6 ± 14.2. Of the RAWs, 78.8% and of the MSWs 57.0% were male; 5.8% of RAWs and 32.8% of MSWs were illiterate. The mean number of people in the households of the participating workers was 5.1 for RAWs and 6.6 for MSWs. Of the RAWs, 20.5% were not covered by any social security scheme while this percentage was 35.1% in MSWs. RAWs worked 9.9 h a day while MSWs worked 10.9 h a day. Of the agricultural workers, 12.9% had injuries caused by occupational accidents.DiscussionAgricultural workers, who are a large part of Turkey’s economically active population, do not have healthy and safe working conditions. New regulations in the fields of social security, record keeping, monitoring, supervision, education and occupational health have been implemented recently to solve these problems. Despite the recent improvements there are still some problematic issues in the auditing of the necessary practices. creator: Ramazan Azim Okyay creator: Ferdi Tanır creator: Pelin Mutlu Ağaoğlu uri: https://doi.org/10.7717/peerj.4952 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Okyay et al. title: Understanding the cone scale in Cupressaceae: insights from seed-cone teratology in Glyptostrobus pensilis link: https://peerj.com/articles/4948 last-modified: 2018-06-01 description: Both wild-type and teratological seed cones are described in the monoecious conifer Glyptostrobus pensilis and compared with those of other Cupressaceae sensu lato and other conifers. Some Cupressaceae apparently possess a proliferation of axillary structures in their cone scales. In our interpretation, in Glyptostrobus each bract of both typical and atypical seed cones bears two descending accessory shoots, interpreted here as seed scales (ovuliferous scales). The primary seed scale is fertile and forms the ovules, the second is sterile and forms characteristic tooth-like structures. The bract and the two axillary seed scales are each supplied with a single distinct vascular bundle that enters the cone axis as a separate strand; this vasculature also characterises the descending accessory short shoots in the vegetative parts of the crown. In wild-type seed cones, the fertile seed scale is reduced to its ovules, and the ovules are always axillary. In contrast, the ovules of some of the teratological seed cones examined were located at the centre of the cone scale. An additional tissue found on the upper surface of the sterile lower seed scale is here interpreted as the axis of the fertile seed scale. Thus, the central position of the ovules can be explained by recaulescent fusion of the upper fertile and lower sterile seed scales. In several teratological cone scales, the ovules were enveloped by an additional sterile tissue that is uniseriate and represents an epidermal outgrowth of the fertile seed scale. Close to the ovules, the epidermis was detached from lower tissue and surrounded the ovule completely, except at the micropyle. These teratological features are potentially significant in understanding seed-cone homologies among extant conifers. creator: Veit Martin Dörken creator: Paula J. Rudall uri: https://doi.org/10.7717/peerj.4948 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Dörken and Rudall title: Some maternal lineages of domestic horses may have origins in East Asia revealed with further evidence of mitochondrial genomes and HVR-1 sequences link: https://peerj.com/articles/4896 last-modified: 2018-06-01 description: ObjectivesThere are large populations of indigenous horse (Equus caballus) in China and some other parts of East Asia. However, their matrilineal genetic diversity and origin remained poorly understood. Using a combination of mitochondrial DNA (mtDNA) and hypervariable region (HVR-1) sequences, we aim to investigate the origin of matrilineal inheritance in these domestic horses.MethodsTo investigate patterns of matrilineal inheritance in domestic horses, we conducted a phylogenetic study using 31 de novo mtDNA genomes together with 317 others from the GenBank. In terms of the updated phylogeny, a total of 5,180 horse mitochondrial HVR-1 sequences were analyzed.ResultsEightteen haplogroups (Aw-Rw) were uncovered from the analysis of the whole mitochondrial genomes. Most of which have a divergence time before the earliest domestication of wild horses (about 5,800 years ago) and during the Upper Paleolithic (35–10 KYA). The distribution of some haplogroups shows geographic patterns. The Lw haplogroup contained a significantly higher proportion of European horses than the horses from other regions, while haplogroups Jw, Rw, and some maternal lineages of Cw, have a higher frequency in the horses from East Asia. The 5,180 sequences of horse mitochondrial HVR-1 form nine major haplogroups (A-I). We revealed a corresponding relationship between the haplotypes of HVR-1 and those of whole mitochondrial DNA sequences. The data of the HVR-1 sequences also suggests that Jw, Rw, and some haplotypes of Cw may have originated in East Asia while Lw probably formed in Europe.ConclusionsOur study supports the hypothesis of the multiple origins of the maternal lineage of domestic horses and some maternal lineages of domestic horses may have originated from East Asia. creator: Hongying Ma creator: Yajiang Wu creator: Hai Xiang creator: Yunzhou Yang creator: Min Wang creator: Chunjiang Zhao creator: Changxin Wu uri: https://doi.org/10.7717/peerj.4896 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Ma et al. title: Cranial anatomy of Bellusaurus sui (Dinosauria: Eusauropoda) from the Middle-Late Jurassic Shishugou Formation of northwest China and a review of sauropod cranial ontogeny link: https://peerj.com/articles/4881 last-modified: 2018-06-01 description: Bellusaurus sui is an enigmatic sauropod dinosaur from the Middle-Late Jurassic Shishugou Formation of northwest China. Bellusaurus is known from a monospecific bonebed preserving elements from more than a dozen juvenile individuals, including numerous bones of the skull, providing rare insight into the cranial anatomy of juvenile sauropods. Here, we present a comprehensive description of the cranial anatomy of Bellusaurus, supplementing the holotypic cranial material with additional elements recovered from recent joint Sino-American field expeditions. Bellusaurus is diagnosed by several unique autapomorphies, including a neurovascular foramen piercing the ascending process of the maxilla at midheight, the frontal process of the nasal extending farther posteriorly onto the frontal than the prefrontal, and U-shaped medial and lateral notches in the posterior margin of the ventral process of the squamosal. Several features identified here, including a preantorbital opening in the maxilla, a stepped dorsal margin of the vomerine process of the pterygoid, and the partitioning of the dorsal midline endocranial fossae associated with the dural venous sinuses into anterior and posterior components by a transverse ridge of the parietal, are consistent with recent phylogenetic hypotheses that recover Bellusaurus as a basal macronarian or close relative of Neosauropoda. We review the current state of knowledge of sauropod cranial ontogeny, placing several aspects of the cranial anatomy of Bellusaurus in an ontogenetic context and providing explicit hypotheses of ontogenetic transformations that can be tested by future discoveries of ontogenetic variants of sauropod skulls. While scoring ontogenetically variable characters as unknown may help to alleviate the biasing effects of ontogeny on the phylogenetic position of juvenile specimens, we caution that this approach may remove phylogenetically informative character information, and argue that inference methods that are known to be less sensitive to homoplasy than equal weights parsimony (i.e., implied weights parsimony; Bayesian approaches) should also be employed. creator: Andrew J. Moore creator: Jinyou Mo creator: James M. Clark creator: Xing Xu uri: https://doi.org/10.7717/peerj.4881 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Moore et al. title: Community involvement works where enforcement fails: conservation success through community-based management of Amazon river turtle nests link: https://peerj.com/articles/4856 last-modified: 2018-06-01 description: Law enforcement is widely regarded as a cornerstone to effective natural resource management. Practical guidelines for the optimal use of enforcement measures are lacking particularly in areas protected under sustainable and/or mixed use management regimes and where legal institution are weak. Focusing on the yellow-spotted river turtles (Podocnemis unifilis) along 33 km of river that runs between two sustainable–use reserves in the Brazilian Amazon as an illustrative example, we show that two years of patrols to enforce lawful protection regulations had no effect on nest harvesting. In contrast, during one year when community-based management approaches were enacted harvest levels dropped nearly threefold to a rate (26%) that is likely sufficient for river turtle population recovery. Our findings support previous studies that show how community participation, if appropriately implemented, can facilitate effective natural resource management where law enforcement is limited or ineffective. creator: Darren Norris creator: Fernanda Michalski creator: James P. Gibbs uri: https://doi.org/10.7717/peerj.4856 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Norris et al. title: Phytoregionalisation of the Andean páramo link: https://peerj.com/articles/4786 last-modified: 2018-06-01 description: BackgroundThe páramo is a high-elevation biogeographical province in the northern Andes, known for its great biodiversity and ecosystem services. Because there have been very few biogeographic studies encompassing the entire province to date, this study aimed at conducting a phytogeographical regionalisation of the páramo. Specifically, (1) clustering analyses were conducted to identify the main phytogeographical units in the three altitudinal belts: sub-páramo, mid-páramo and super-páramo, and examine their diagnostic flora, (2) an ordination complemented the geo-climatic characterization of the obtained units and (3) a hierarchical classification transformation was obtained to evaluate the relationships between units.MethodsThe study area included the entire Andean páramo range in northern Peru, Ecuador, Colombia and Venezuela. The analyses were based on 1,647 phytosociological plots from the VegPáramo database. The K-means non-hierarchical clustering technique was used to obtain clusters identifiable as phytogeographical units, and the Ochiai fidelity index was calculated to identify their diagnostic species. A principal component analysis was conducted to obtain the geo-climatic characterization of each unit. Finally, the relationships between clusters were traced using a hierarchical plot-based classification.ResultsFifteen clusters were obtained, 13 natural and two artificial, of which two represented the sub-páramo, nine the mid-páramo and four the super-páramo. Even though data representativeness was a potential limitation to segregate certain sub-páramo and super-páramo units, the overall bioregionalisation was robust and represented important latitudinal, altitudinal and climatic gradients.DiscussionThis study is the first to bioregionalise the páramo province based on a substantial widely distributed biological dataset, and therefore provides important novel scientific insight on its biogeography. The obtained phytogeographical units can be used to support further research on the páramo at smaller scale and on the humid Neotropical high-elevation ecosystems at broader-scale. Finally, several units were highlighted in our results as particularly worthy of further scientific and conservation focus. creator: Gwendolyn Peyre creator: Henrik Balslev creator: Xavier Font uri: https://doi.org/10.7717/peerj.4786 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Peyre et al. title: Comparing the biomechanical characteristics between squat and standing serves in female table tennis athletes link: https://peerj.com/articles/4760 last-modified: 2018-06-01 description: BackgroundThe table tennis serve involves complex spatial movements combined with biomechanial characteristics. Although the differences in lower-limb biomechanial characteristics to a great extent influence the translational and spinning velocity of the ball when using the different styles of table tennis serve, few researchers have studied their mechanics. Therefore, the aim of this study was to investigate the differences in lower-limb activity between the squat and standing serves during a table tennis short serve.MethodsTen advanced female table tennis participants performed a squat serve and standing serve in random order. A Vicon motion analysis system and a Novel Pedar insole plantar pressure measurement system were used to record kinematics and kinetics data, respectively.ResultsKey findings from the study were that the squat serve not only showed significantly larger hip and knee flexion, as well as ankle dorsiflexion, it also showed significantly larger hip adduction and external knee rotation, with larger changing angular rate of the lower limb joints in the sagittal and the transverse planes when the two serving styles were compared. In addition, the force-time integral (FTI) was higher in the rear foot area for the standing serve.DiscussionThe results demonstrated that the squat serve needs higher lower limb drive during a table tennis short serve compared with a standing serve. These biomechanical considerations may be beneficial for table tennis athletes and coaches as a method of optimizing performance characteristics during both competition and training. creator: Changxiao Yu creator: Shirui Shao creator: Julien S. Baker creator: Yaodong Gu uri: https://doi.org/10.7717/peerj.4760 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Yu et al. title: Sexually dimorphic venom proteins in long-jawed orb-weaving spiders (Tetragnatha) comprise novel gene families link: https://peerj.com/articles/4691 last-modified: 2018-06-01 description: Venom has been associated with the ecological success of many groups of organisms, most notably reptiles, gastropods, and arachnids. In some cases, diversification has been directly linked to tailoring of venoms for dietary specialization. Spiders in particular are known for their diverse venoms and wide range of predatory behaviors, although there is much to learn about scales of variation in venom composition and function. The current study focuses on venom characteristics in different sexes within a species of spider. We chose the genus Tetragnatha (Tetragnathidae) because of its unusual courtship behavior involving interlocking of the venom delivering chelicerae (i.e., the jaws), and several species in the genus are already known to have sexually dimorphic venoms. Here, we use transcriptome and proteome analyses to identify venom components that are dimorphic in Tetragnatha versicolor. We present cDNA sequences including unique, male-specific high molecular weight proteins that have remote, if any, detectable similarity to known venom components in spiders or other venomous lineages and have no detectable homologs in existing databases. While the function of these proteins is not known, their presence in association with the cheliceral locking mechanism during mating together with the presence of prolonged male-male mating attempts in a related, cheliceral-locking species (Doryonychus raptor) lacking the dimorphism suggests potential for a role in sexual communication. creator: Pamela A. Zobel-Thropp creator: Emily A. Bulger creator: Matthew H.J. Cordes creator: Greta J. Binford creator: Rosemary G. Gillespie creator: Michael S. Brewer uri: https://doi.org/10.7717/peerj.4691 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Zobel-Thropp et al. title: Cytotoxic effects of zinc oxide nanoparticles on cyanobacterium Spirulina (Arthrospira) platensis link: https://peerj.com/articles/4682 last-modified: 2018-06-01 description: BackgroundThe extensive usage of zinc oxide nanoparticles (ZnO NPs) in industrial and consumer products raises the risk of releasing their residues into the aquatic environment. The presence of ZnO NPs in the aquatic environment could potentially cause cytotoxic effects on aquatic organisms. Thus, investigating the cytotoxic effects of ZnO NPs on microalgae, which form the base for the food web of aquatic biota, is essential to gain information regarding the ecotoxicological effects of metallic oxide nanoparticles in the aquatic ecosystem. Therefore, the present study has investigated in detail the assorted cytotoxic effects of ZnO NPs on S. platensis using various concentrations of ZnO NPs (10–200 mg/L) from 6 to 96 h to explore the dose- and time-dependent cytotoxic effects.MethodsThe cytotoxic effects were all assessed through quantification of loss in cell viability, reduction in biomass and decrease in photosynthetic pigments such as chlorophyll-a, carotenoids and phycocyanin. The surface interactions of nanoparticles and the subsequent morphological alterations on algal cells were examined by optical and scanning electron microscopy (SEM). The intracellular alterations of algal cells were studied using transmission electron microscopy. Furthermore, Fourier transformed infrared (FTIR) spectrum was obtained to investigate the involvement of algal surface biomolecules in surface binding of ZnO NPs on algal cells.ResultsThe treatment of ZnO NPs on S. platensis exhibited a typical concentration- and time-dependent cytotoxicity. Results showed a significant (p < 0.05) cytotoxicity from 24 h onwards for all tested concentrations of ZnO NPs. The maximum cytotoxicity on algal cells was achieved at 96 h of exposure to ZnO NPs. In comparison with control, the algal cells that interacted with 200 mg/L of ZnO NPs for 96 h showed 87.3 ± 1% loss in cell viability, 76.1 ± 1.7% reduction in algal biomass, 92.5 ± 2.2%, 76.2 ± 2.2% and 74.1 ± 3.4% decrease in chlorophyll-a, carotenoids and phycocyanin contents respectively. Our study confirmed the cytotoxicity of ZnO NPs through the algal growth inhibition with 72 h EC10 and EC50 values of 1.29 and 31.56 mg/L, respectively. The microscopic examinations of the algal cells that interacted with ZnO NPs showed severe cell membrane and intracellular damage. The SEM EDX spectrum of ZnO NPs treated algal biomass evidenced the surface accumulation of zinc in the biomass. Finally, the FTIR spectrum confirmed the involvement of amino, hydroxyl and carboxylic groups of algal cell wall in the surface interaction of ZnO NPs on the algal cells.DiscussionThe results showed that the treatment of ZnO NPs on S. platensis triggered substantial cytotoxicity and caused cell death. Hence, S. platensis could be potentially used as a bioindicator for testing toxicity of ZnO NPs in aquatic environment. creator: Sinouvassane Djearamane creator: Yang Mooi Lim creator: Ling Shing Wong creator: Poh Foong Lee uri: https://doi.org/10.7717/peerj.4682 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Djearamane et al.