title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2016-08 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Continent-wide survey reveals massive decline in African savannah elephants link: https://peerj.com/articles/2354 last-modified: 2016-08-31 description: African elephants (Loxodonta africana) are imperiled by poaching and habitat loss. Despite global attention to the plight of elephants, their population sizes and trends are uncertain or unknown over much of Africa. To conserve this iconic species, conservationists need timely, accurate data on elephant populations. Here, we report the results of the Great Elephant Census (GEC), the first continent-wide, standardized survey of African savannah elephants. We also provide the first quantitative model of elephant population trends across Africa. We estimated a population of 352,271 savannah elephants on study sites in 18 countries, representing approximately 93% of all savannah elephants in those countries. Elephant populations in survey areas with historical data decreased by an estimated 144,000 from 2007 to 2014, and populations are currently shrinking by 8% per year continent-wide, primarily due to poaching. Though 84% of elephants occurred in protected areas, many protected areas had carcass ratios that indicated high levels of elephant mortality. Results of the GEC show the necessity of action to end the African elephants’ downward trajectory by preventing poaching and protecting habitat. creator: Michael J. Chase creator: Scott Schlossberg creator: Curtice R. Griffin creator: Philippe J.C. Bouché creator: Sintayehu W. Djene creator: Paul W. Elkan creator: Sam Ferreira creator: Falk Grossman creator: Edward Mtarima Kohi creator: Kelly Landen creator: Patrick Omondi creator: Alexis Peltier creator: S.A. Jeanetta Selier creator: Robert Sutcliffe uri: https://doi.org/10.7717/peerj.2354 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Chase et al. title: Characterization, development and multiplexing of microsatellite markers in three commercially exploited reef fish and their application for stock identification link: https://peerj.com/articles/2418 last-modified: 2016-08-31 description: Thirty-four microsatellite loci were isolated from three reef fish species; golden snapper Lutjanus johnii, blackspotted croaker Protonibea diacanthus and grass emperor Lethrinus laticaudis using a next generation sequencing approach. Both IonTorrent single reads and Illumina MiSeq paired-end reads were used, with the latter demonstrating a higher quality of reads than the IonTorrent. From the 1–1.5 million raw reads per species, we successfully obtained 10–13 polymorphic loci for each species, which satisfied stringent design criteria. We developed multiplex panels for the amplification of the golden snapper and the blackspotted croaker loci, as well as post-amplification pooling panels for the grass emperor loci. The microsatellites characterized in this work were tested across three locations of northern Australia. The microsatellites we developed can detect population differentiation across northern Australia and may be used for genetic structure studies and stock identification. creator: Laura Taillebois creator: Christine Dudgeon creator: Safia Maher creator: David A. Crook creator: Thor M. Saunders creator: Diane P. Barton creator: Jonathan A. Taylor creator: David J. Welch creator: Stephen J. Newman creator: Michael J. Travers creator: Richard J. Saunders creator: Jennifer Ovenden uri: https://doi.org/10.7717/peerj.2418 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Taillebois et al. title: Whole gut microbiome composition of damselfish and cardinalfish before and after reef settlement link: https://peerj.com/articles/2412 last-modified: 2016-08-31 description: The Pomacentridae (damselfish) and Apogonidae (cardinalfish) are among the most common fish families on coral reefs and in the aquarium trade. Members of both families undergo a pelagic larvae phase prior to settlement on the reef, where adults play key roles in benthic habitat structuring and trophic interactions. Fish-associated microbial communities (microbiomes) significantly influence fish health and ecology, yet little is known of how microbiomes change with life stage. We quantified the taxonomic (16S rRNA gene) composition of whole gut microbiomes from ten species of damselfish and two species of cardinalfish from Lizard Island, Australia, focusing specifically on comparisons between pelagic larvae prior to settlement on the reef versus post-settlement juvenile and adult individuals. On average, microbiome phylogenetic diversity increased from pre- to post-settlement, and was unrelated to the microbial composition in the surrounding water column. However, this trend varied among species, suggesting stochasticity in fish microbiome assembly. Pre-settlement fish were enriched with bacteria of the Endozoicomonaceae, Shewanellaceae, and Fusobacteriaceae, whereas settled fish harbored higher abundances of Vibrionaceae and Pasteurellaceae. Several individual operational taxonomic units, including ones related to Vibrio harveyi, Shewanella sp., and uncultured Endozoicomonas bacteria, were shared between both pre and post-settlement stages and may be of central importance in the intestinal niche across development. Richness of the core microbiome shared among pre-settlement fish was comparable to that of settled individuals, suggesting that changes in diversity with adulthood are due to the acquisition or loss of host-specific microbes. These results identify a key transition in microbiome structure across host life stage, suggesting changes in the functional contribution of microbiomes over development in two ecologically dominant reef fish families. creator: Darren J. Parris creator: Rohan M. Brooker creator: Michael A. Morgan creator: Danielle L. Dixson creator: Frank J. Stewart uri: https://doi.org/10.7717/peerj.2412 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Parris et al. title: Male foraging efficiency, but not male problem-solving performance, influences female mating preferences in zebra finches link: https://peerj.com/articles/2409 last-modified: 2016-08-31 description: Experimental evidence suggests that females would prefer males with better cognitive abilities as mates. However, little is known about the traits reflecting enhanced cognitive skills on which females might base their mate-choice decisions. In particular, it has been suggested that male foraging performance could be used as an indicator of cognitive capacity, but convincing evidence for this hypothesis is still lacking. In the present study, we investigated whether female zebra finches (Taeniopygia guttata) modify their mating preferences after having observed the performance of males on a problem-solving task. Specifically, we measured the females’ preferences between two males once before and once after an observation period, during which their initially preferred male was incapable of solving the task contrary to their initially less-preferred male. We also conducted a control treatment to test whether the shift in female preferences was attributable to differences between the two stimulus males in their foraging efficiency. Finally, we assessed each bird’s performance in a color associative task to check whether females can discriminate among males based on their learning speed. We found that females significantly increased their preference toward the most efficient male in both treatments. Yet, there was no difference between the two treatments and we found no evidence that females assess male cognitive ability indirectly via morphological traits. Thus, our results suggest that females would not use the males’ problem-solving performance as an indicator of general cognitive ability to gain indirect fitness benefits (i.e., good genes) but rather to assess their foraging efficiency and gain direct benefits. creator: Véronique Chantal creator: Julie Gibelli creator: Frédérique Dubois uri: https://doi.org/10.7717/peerj.2409 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Chantal et al. title: Influence of droplet coverage on the electrochemical response of planar microelectrodes and potential solving strategies based on nesting concept link: https://peerj.com/articles/2400 last-modified: 2016-08-31 description: Recently, biosensors have been widely used for the detection of bacteria, viruses and other toxins. Electrodes, as commonly used transducers, are a vital part of electrochemical biosensors. The coverage of the droplets can change significantly based on the hydrophobicity of the microelectrode surface materials. In the present research, screen-printed interdigitated microelectrodes (SPIMs), as one type of planar microelectrode, were applied to investigate the influence of droplet coverage on electrochemical response. Furthermore, three dimensional (3D) printing technology was employed to print smart devices with different diameters based on the nesting concept. Theoretical explanations were proposed to elucidate the influence of the droplet coverage on the electrochemical response. 3D-printed ring devices were used to incubate the SPIMs and the analytical performances of the SPIMs were tested. According to the results obtained, our device successfully improved the stability of the signal responses and eliminated irregular signal changes to a large extent. Our proposed method based on the nesting concept provides a promising method for the fabrication of stable electrochemical biosensors. We also introduced two types of electrode bases to improve the signal stability. creator: Yue Yu creator: Zhanming Li uri: https://doi.org/10.7717/peerj.2400 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Yu and Li title: Effect of pillow height on the biomechanics of the head-neck complex: investigation of the cranio-cervical pressure and cervical spine alignment link: https://peerj.com/articles/2397 last-modified: 2016-08-31 description: BackgroundWhile appropriate pillow height is crucial to maintaining the quality of sleep and overall health, there are no universal, evidence-based guidelines for pillow design or selection. We aimed to evaluate the effect of pillow height on cranio-cervical pressure and cervical spine alignment.MethodsTen healthy subjects (five males) aged 26 ± 3.6 years were recruited. The average height, weight, and neck length were 167 ± 9.3 cm, 59.6 ± 11.9 kg, and 12.9 ± 1.2 cm respectively. The subjects lay on pillows of four different heights (H0, 110 mm; H1, 130 mm; H2, 150 mm; and H3, 170 mm). The cranio-cervical pressure distribution over the pillow was recorded; the peak and average pressures for each pillow height were compared by one-way ANOVA with repeated measures. Cervical spine alignment was studied using a finite element model constructed based on data from the Visible Human Project. The coordinate of the center of each cervical vertebra were predicted for each pillow height. Three spine alignment parameters (cervical angle, lordosis distance and kyphosis distance) were identified.ResultsThe average cranial pressure at pillow height H3 was approximately 30% higher than that at H0, and significantly different from those at H1 and H2 (p < 0.05). The average cervical pressure at pillow height H0 was 65% lower than that at H3, and significantly different from those at H1 and H2 (p < 0.05). The peak cervical pressures at pillow heights H2 and H3 were significantly different from that at H0 (p < 0.05). With respect to cervical spine alignment, raising pillow height from H0 to H3 caused an increase of 66.4% and 25.1% in cervical angle and lordosis distance, respectively, and a reduction of 43.4% in kyphosis distance.DiscussionPillow height elevation significantly increased the average and peak pressures of the cranial and cervical regions, and increased the extension and lordosis of the cervical spine. The cranio-cervical pressures and cervical spine alignment were height-specific, and they were believed to reflect quality of sleep. Our results provide a quantitative and objective evaluation of the effect of pillow height on the biomechanics of the head-neck complex, and have application in pillow design and selection. creator: Sicong Ren creator: Duo Wai-Chi Wong creator: Hui Yang creator: Yan Zhou creator: Jin Lin creator: Ming Zhang uri: https://doi.org/10.7717/peerj.2397 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Ren et al. title: Effect of 8-hydroxyquinoline and derivatives on human neuroblastoma SH-SY5Y cells under high glucose link: https://peerj.com/articles/2389 last-modified: 2016-08-31 description: 8-Hydroxyquinoline and derivatives exhibit multifunctional properties, including antioxidant, antineurodegenerative, anticancer, anti-inflammatory and antidiabetic activities. In biological systems, elevation of intracellular calcium can cause calpain activation, leading to cell death. Here, the effect of 8-hydroxyquinoline and derivatives (5-chloro-7-iodo-8-hydroxyquinoline or clioquinol and 8-hydroxy-5-nitroquinoline or nitroxoline) on calpain-dependent (calpain-calpastatin) pathways in human neuroblastoma (SH-SY5Y) cells was investigated. 8-Hydroxyquinoline and derivatives ameliorated high glucose toxicity in SH-SY5Y cells. The investigated compounds, particularly clioquinol, attenuated the increased expression of calpain, even under high-glucose conditions. 8-Hydroxyquinoline and derivatives thus adversely affected the promotion of neuronal cell death by high glucose via the calpain-calpastatin signaling pathways. These findings support the beneficial effects of 8-hydroxyquinolines for further therapeutic development. creator: Wilasinee Suwanjang creator: Supaluk Prachayasittikul creator: Virapong Prachayasittikul uri: https://doi.org/10.7717/peerj.2389 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Suwanjang et al. title: Genome-wide identification and characterization of GRAS transcription factors in sacred lotus (Nelumbo nucifera) link: https://peerj.com/articles/2388 last-modified: 2016-08-31 description: The GRAS gene family is one of the most important plant-specific gene families, which encodes transcriptional regulators and plays an essential role in plant development and physiological processes. The GRAS gene family has been well characterized in many higher plants such as Arabidopsis, rice, Chinese cabbage, tomato and tobacco. In this study, we identified 38 GRAS genes in sacred lotus (Nelumbo nucifera), analyzed their physical and chemical characteristics and performed phylogenetic analysis using the GRAS genes from eight representative plant species to show the evolution of GRAS genes in Planta. In addition, the gene structures and motifs of the sacred lotus GRAS proteins were characterized in detail. Comparative analysis identified 42 orthologous and 9 co-orthologous gene pairs between sacred lotus and Arabidopsis, and 35 orthologous and 22 co-orthologous gene pairs between sacred lotus and rice. Based on publically available RNA-seq data generated from leaf, petiole, rhizome and root, we found that most of the sacred lotus GRAS genes exhibited a tissue-specific expression pattern. Eight of the ten PAT1-clade GRAS genes, particularly NnuGRAS-05, NnuGRAS-10 and NnuGRAS-25, were preferentially expressed in rhizome and root. In summary, this is the first in silico analysis of the GRAS gene family in sacred lotus, which will provide valuable information for further molecular and biological analyses of this important gene family. creator: Yu Wang creator: Shenglu Shi creator: Ying Zhou creator: Yu Zhou creator: Jie Yang creator: Xiaoqing Tang uri: https://doi.org/10.7717/peerj.2388 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Wang et al. title: Evolution of the climatic tolerance and postglacial range changes of the most primitive orchids (Apostasioideae) within Sundaland, Wallacea and Sahul link: https://peerj.com/articles/2384 last-modified: 2016-08-31 description: The location of possible glacial refugia of six Apostasioideae representatives is estimated based on ecological niche modeling analysis. The distribution of their suitable niches during the last glacial maximum (LGM) is compared with their current potential and documented geographical ranges. The climatic factors limiting the studied species occurrences are evaluated and the niche overlap between the studied orchids is assessed and discussed. The predicted niche occupancy profiles and reconstruction of ancestral climatic tolerances suggest high level of phylogenetic niche conservatism within Apostasioideae. creator: Marta Kolanowska creator: Katarzyna Mystkowska creator: Marta Kras creator: Magdalena Dudek creator: Kamil Konowalik uri: https://doi.org/10.7717/peerj.2384 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Kolanowska et al. title: Aquatic insects dealing with dehydration: do desiccation resistance traits differ in species with contrasting habitat preferences? link: https://peerj.com/articles/2382 last-modified: 2016-08-31 description: BackgroundDesiccation resistance shapes the distribution of terrestrial insects at multiple spatial scales. However, responses to drying stress have been poorly studied in aquatic groups, despite their potential role in constraining their distribution and diversification, particularly in arid and semi-arid regions.MethodsWe examined desiccation resistance in adults of four congeneric water beetle species (Enochrus, family Hydrophilidae) with contrasting habitat specificity (lentic vs. lotic systems and different salinity optima from fresh- to hypersaline waters). We measured survival, recovery capacity and key traits related to desiccation resistance (fresh mass, % water content, % cuticle content and water loss rate) under controlled exposure to desiccation, and explored their variability within and between species.ResultsMeso- and hypersaline species were more resistant to desiccation than freshwater and hyposaline ones, showing significantly lower water loss rates and higher water content. No clear patterns in desiccation resistance traits were observed between lotic and lentic species. Intraspecifically, water loss rate was positively related to specimens’ initial % water content, but not to fresh mass or % cuticle content, suggesting that the dynamic mechanism controlling water loss is mainly regulated by the amount of body water available.DiscussionOur results support previous hypotheses suggesting that the evolution of desiccation resistance is associated with the colonization of saline habitats by aquatic beetles. The interespecific patterns observed in Enochrus also suggest that freshwater species may be more vulnerable than saline ones to drought intensification expected under climate change in semi-arid regions such as the Mediterranean Basin. creator: Susana Pallarés creator: Josefa Velasco creator: Andrés Millán creator: David T. Bilton creator: Paula Arribas uri: https://doi.org/10.7717/peerj.2382 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Pallarés et al. title: Knowledge of blood loss at delivery among postpartum patients link: https://peerj.com/articles/2361 last-modified: 2016-08-31 description: BackgroundPostpartum hemorrhage (PPH) is a leading cause of obstetric morbidity. There is limited understanding of patients’ knowledge about blood loss at delivery, PPH, and PPH-related morbidities, including transfusion and anemia.MethodsWe surveyed 100 healthy postpartum patients who underwent vaginal or cesarean delivery about blood loss, and whether they received information about transfusion and peripartum hemoglobin (Hb) testing. Responses were compared between women undergoing vaginal delivery vs. cesarean delivery; P < 0.05 considered as statistically significant.ResultsIn our cohort, 49 women underwent vaginal delivery and 51 women underwent cesarean delivery. Only 29 (29%) of women provided blood loss estimates for their delivery. Women who underwent cesarean delivery were more likely to receive clear information about transfusion therapy than those undergoing vaginal delivery (43.1% vs. 20.4% respectively; P = 0.04). Women who underwent vaginal delivery were more likely to receive results of postpartum Hb tests compared to those undergoing cesarean delivery (49% vs. 29.4%; P = 0.02).ConclusionOur findings suggest that women are poorly informed about the magnitude of blood loss at delivery. Hematologic information given to patients varies according to mode of delivery. Further research is needed to better understand the clinical implications of patients’ knowledge gaps about PPH, transfusion and postpartum anemia. creator: Michaela K. Farber creator: Claire M. Miller creator: Bharathi Ramachandran creator: Priya Hegde creator: Kulsum Akbar creator: Lawrence Tim Goodnough creator: Alexander J. Butwick uri: https://doi.org/10.7717/peerj.2361 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Farber et al. title: Psychological distress of residents in Kawauchi village, Fukushima Prefecture after the accident at Fukushima Daiichi Nuclear Power Station: the Fukushima Health Management Survey link: https://peerj.com/articles/2353 last-modified: 2016-08-31 description: BackgroundTo shed light on the mental health of evacuees after the accident at Fukushima Daiichi Nuclear Power Station (FDNPS), we evaluate the results of the Fukushima Health Management Survey (FHMS) of the residents at Kawauchi village in Fukushima, which is located less than 30 km from the FDNPS.MethodsWe conducted the cross-sectional study within the framework of the FHMS. Exposure values were “anorexia,” “subjective feelings about health,” “feelings about sleep satisfaction,” and “bereavement caused by the disaster,” confounding variables were “age” and “sex,” and outcome variables were “K6 points.” We collected data from the FHMS, and employed the Kessler Psychological Distress Scale (K6) and the posttraumatic stress disorder (PTSD) Checklist Stressor-Specific Version (PCL-S) to carry out the research. A total of 13 or greater was the cut-off for identifying serious mental illness using the K6 scale. The study subjects included residents (n = 542) of over 30 years of age from Kawauchi village, and data were used from the period of January 1, 2012 to October 31, 2012.ResultsA total of 474 residents (87.5%) scored less than 13 points in the K6 and 68 (12.6%) scored 13 points or more. The proportion of elderly residents (over 65 years old) among people with K6 score above the cut-off was higher than that among people with K6 score below the cut-off (44.1 vs 31.0%, p < 0.05). In addition, the proportion of residents with anorexia and mental illness among people with K6 score above the cut-off was higher than among people with K6 score below the cut-off (p < 0.001 and p < 0.05, respectively). The amount of residents who scored 44 points or more in the PCL-S among people with K6 score above the cut-off was also considerably higher than among people with K6 score below the cut-off (79.4 vs 12.9%, p < 0.001). Interestingly, the proportion of residents who scored more than among people with K6 score above the cut-off and the among people with PCL-S score above the cut-off in Kawauchi was higher than in previous studies in other locations.ConclusionsThese results suggest that there are severe mental health problems, such as depression and PTSD, among adults as a consequence of the accident at the FDNPS. Our study showed that residents who lived in the evacuation zone before the disaster are at high risk psychological distress. To facilitate local residents’ recovery from Fukushima, there is a need to continue providing them with physical and mental support, as well as communication regarding the health risks of radiation. creator: Koji Yoshida creator: Tetsuko Shinkawa creator: Hideko Urata creator: Kanami Nakashima creator: Makiko Orita creator: Kiyotaka Yasui creator: Atsushi Kumagai creator: Akira Ohtsuru creator: Hirooki Yabe creator: Masaharu Maeda creator: Naomi Hayashida creator: Takashi Kudo creator: Shunichi Yamashita creator: Noboru Takamura uri: https://doi.org/10.7717/peerj.2353 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Yoshida et al. title: Joint estimation of crown of thorns (Acanthaster planci) densities on the Great Barrier Reef link: https://peerj.com/articles/2310 last-modified: 2016-08-31 description: Crown-of-thorns starfish (CoTS; Acanthaster spp.) are an outbreaking pest among many Indo-Pacific coral reefs that cause substantial ecological and economic damage. Despite ongoing CoTS research, there remain critical gaps in observing CoTS populations and accurately estimating their numbers, greatly limiting understanding of the causes and sources of CoTS outbreaks. Here we address two of these gaps by (1) estimating the detectability of adult CoTS on typical underwater visual count (UVC) surveys using covariates and (2) inter-calibrating multiple data sources to estimate CoTS densities within the Cairns sector of the Great Barrier Reef (GBR). We find that, on average, CoTS detectability is high at 0.82 [0.77, 0.87] (median highest posterior density (HPD) and [95% uncertainty intervals]), with CoTS disc width having the greatest influence on detection. Integrating this information with coincident surveys from alternative sampling programs, we estimate CoTS densities in the Cairns sector of the GBR averaged 44 [41, 48] adults per hectare in 2014. creator: M. Aaron MacNeil creator: Camille Mellin creator: Morgan S. Pratchett creator: Jessica Hoey creator: Kenneth R.N. Anthony creator: Alistair J. Cheal creator: Ian Miller creator: Hugh Sweatman creator: Zara L. Cowan creator: Sascha Taylor creator: Steven Moon creator: Chris J. Fonnesbeck uri: https://doi.org/10.7717/peerj.2310 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 MacNeil et al. title: A Jurassic pterosaur from Patagonia and the origin of the pterodactyloid neurocranium link: https://peerj.com/articles/2311 last-modified: 2016-08-30 description: Pterosaurs are an extinct group of highly modified flying reptiles that thrived during the Mesozoic. This group has unique and remarkable skeletal adaptations to powered flight, including pneumatic bones and an elongate digit IV supporting a wing-membrane. Two major body plans have traditionally been recognized: the primitive, primarily long-tailed paraphyletic “rhamphorhynchoids” (preferably currently recognized as non-pterodactyloids) and the derived short-tailed pterodactyloids. These two groups differ considerably in their general anatomy and also exhibit a remarkably different neuroanatomy and inferred head posture, which has been linked to different lifestyles and behaviours and improved flying capabilities in these reptiles. Pterosaur neuroanatomy, is known from just a few three-dimensionally preserved braincases of non-pterodactyloids (as Rhamphorhynchidae) and pterodactyloids, between which there is a large morphological gap. Here we report on a new Jurassic pterosaur from Argentina, Allkaruen koi gen. et sp. nov., remains of which include a superbly preserved, uncrushed braincase that sheds light on the origins of the highly derived neuroanatomy of pterodactyloids and their close relatives. A µCT ray-generated virtual endocast shows that the new pterosaur exhibits a mosaic of plesiomorphic and derived traits of the inner ear and neuroanatomy that fills an important gap between those of non-monofenestratan breviquartossans (Rhamphorhynchidae) and derived pterodactyloids. These results suggest that, while modularity may play an important role at one anatomical level, at a finer level the evolution of structures within a module may follow a mosaic pattern. creator: Laura Codorniú creator: Ariana Paulina Carabajal creator: Diego Pol creator: David Unwin creator: Oliver W.M. Rauhut uri: https://doi.org/10.7717/peerj.2311 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Codorniú et al. title: Osteology of the Late Triassic aetosaur Scutarx deltatylus (Archosauria: Pseudosuchia) link: https://peerj.com/articles/2411 last-modified: 2016-08-30 description: Aetosaurians are some of the most common fossils collected from the Upper Triassic Chinle Formation of Arizona, especially at the Petrified Forest National Park (PEFO). Aetosaurians collected from lower levels of the park include Desmatosuchus spurensis, Paratypothorax, Adamanasuchus eisenhardtae, Calyptosuchus wellesi, and Scutarx deltatylus. Four partial skeletons collected from the park between 2002 and 2009 represent the holotype and referred specimens of Scutarx deltatylus. These specimens include much of the carapace, as well as the vertebral column, and shoulder and pelvic girdles, and a new naming convention proposed for osteoderms descriptions better differentiates portions of the carapace and ventral armor. A partial skull from the holotype specimen represents the first aetosaur skull recovered and described from Arizona since the 1930s. The key morphological feature distinguishing Scutarx deltatylus is the presence of a prominent, triangular boss located in the posteromedial corner of the dorsal surface of the dorsal paramedian osteoderms. Scutarx deltatylus can be distinguished from closely related forms Calyptosuchus wellesi and Adamanasuchus eisenhardtae not only morphologically, but also stratigraphically. Thus, Scutarx deltatylus is potentially an index taxon for the upper part of the Adamanian biozone. creator: William G. Parker uri: https://doi.org/10.7717/peerj.2411 license: http://creativecommons.org/publicdomain/zero/1.0/ rights: title: Short and long term representation of an unfamiliar tone distribution link: https://peerj.com/articles/2399 last-modified: 2016-08-30 description: We report on a study conducted to extend our knowledge about the process of gaining a mental representation of music. Several studies, inspired by research on the statistical learning of language, have investigated statistical learning of sequential rules underlying tone sequences. Given that the mental representation of music correlates with distributional properties of music, we tested whether participants are able to abstract distributional information contained in tone sequences to form a mental representation. For this purpose, we created an unfamiliar music genre defined by an underlying tone distribution, to which 40 participants were exposed. Our stimuli allowed us to differentiate between sensitivity to the distributional properties contained in test stimuli and long term representation of the distributional properties of the music genre overall. Using a probe tone paradigm and a two-alternative forced choice discrimination task, we show that listeners are able to abstract distributional properties of music through mere exposure into a long term representation of music. This lends support to the idea that statistical learning is involved in the process of gaining musical knowledge. creator: Anja X. Cui creator: Charlette Diercks creator: Nikolaus F. Troje creator: Lola L. Cuddy uri: https://doi.org/10.7717/peerj.2399 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Cui et al. title: Epidemiology of Salmonella sp. in California cull dairy cattle: prevalence of fecal shedding and diagnostic accuracy of pooled enriched broth culture of fecal samples link: https://peerj.com/articles/2386 last-modified: 2016-08-30 description: BackgroundThe primary objective of this cross-sectional study was to estimate the crude, seasonal and cull-reason stratified prevalence of Salmonella fecal shedding in cull dairy cattle on seven California dairies. A secondary objective was to estimate and compare the relative sensitivity (Se) and specificity (Sp) for pools of 5 and 10 enriched broth cultures of fecal samples for Salmonella sp. detection.MethodsSeven dairy farms located in the San Joaquin Valley of California were identified and enrolled in the study as a convenience sample. Cull cows were identified for fecal sampling once during each season between 2014 and 2015, specifically during spring, summer, fall, and winter, and 10 cows were randomly selected for fecal sampling at the day of their sale. In addition, study personnel completed a survey based on responses of the herd manager to questions related to the previous four month’s herd management. Fecal samples were frozen until testing for Salmonella. After overnight enrichment in liquid broth, pools of enrichment broth (EBP) were created for 5 and 10 samples. All individual and pooled broths were cultured on selective media with putative Salmonella colonies confirmed by biochemical testing before being serogrouped and serotyped.ResultsA total of 249 cull cows were enrolled into the study and their fecal samples tested for Salmonella. The survey-weighted period prevalence of fecal shedding of all Salmonella sp. in the cull cow samples across all study herds and the entire study period was 3.42% (N = 249; SE 1.07). The within herd prevalence of Salmonella shed in feces did not differ over the four study seasons (P = 0.074). The Se of culture of EBP of five samples was 62.5% (SE = 17.12), which was not statistically different from the Se of culture of EBP of 10 (37.5%, SE = 17.12, P = 0.48). The Sp of culture of EBP of five samples was 95.24% (SE = 3.29) and for pools of 10 samples was 100.00% (SE = 0). There was no statistical difference between the culture relative specificities of EBP of 5 and 10 (P > 0.99).DiscussionOur study showed a numerically higher prevalence of Salmonella shedding in the summer, although the results were not significant, most likely due to a lack of power from the small sample size. A higher prevalence in summer months may be related to heat stress. To detect Salmonella, investigators may expect a 62.5% sensitivity for culture of EBP of five, relative to individual fecal sample enrichment and culture. In contrast, culture of EBP of 10 samples resulted in a numerically lower Se. Culture of EBP of size 5 or 10 samples, given similar prevalence and limit of detection, can be expected to yield specificities of 95 and 100%, respectively. creator: Omran A. Abu Aboud creator: John M. Adaska creator: Deniece R. Williams creator: Paul V. Rossitto creator: John D. Champagne creator: Terry W. Lehenbauer creator: Robert Atwill creator: Xunde Li creator: Sharif S. Aly uri: https://doi.org/10.7717/peerj.2386 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Abu Aboud et al. title: An examination of species limits in the Aulacorhynchus “prasinus” toucanet complex (Aves: Ramphastidae) link: https://peerj.com/articles/2381 last-modified: 2016-08-30 description: The number of species recognized in Aulacorhynchus toucanets has varied tremendously over the past century. Revisors seem to disagree on whether head and bill coloration are useful indicators of species limits, especially in the A. “prasinus” complex. Using morphometrics, I tested the hypothesis that the major color-based subspecific groups of A. “prasinus” sensu lato are simply “cookie-cutter” (i.e., morphologically nearly identical) toucanets with different head and bill colorations. Univariate and multivariate analyses show that they are not simply morphological replicates of different colors: a complex array of morphometric similarities and dissimilarities occur between the major subspecific groups, and these variations differ between the sexes. Latitude and longitude had a small but significant association with female (but not male) PC1 and PC2. Hybridization and intergradation were also considered using plumage and bill characters as a surrogate to infer gene flow. Hybridization as indicated by phenotype appears to be substantial between A. “p.” cyanolaemus and A. “p.” atrogularis and nonexistent between other major groups, although from genetic evidence it is likely rare between A. “p.” albivitta and A. “p.” cyanolaemus. The congruence and complexities of the morphological and color changes occurring among these groups suggest that ecological adaptation (through natural selection) and social selection have co-occurred among these groups and that species limits are involved. Further, hybridization is not evident at key places, despite in many cases (hypothetical) opportunity for gene flow. Consequently, I recommend that this complex be recognized as comprising five biological species: A. wagleri, prasinus, caeruleogularis, albivitta, and atrogularis. Four of these also have valid subspecies within them, and additional work may eventually support elevation of some of these subspecies to full species. Species limits in South America especially need more study. creator: Kevin Winker uri: https://doi.org/10.7717/peerj.2381 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Winker title: A heritability-based comparison of methods used to cluster 16S rRNA gene sequences into operational taxonomic units link: https://peerj.com/articles/2341 last-modified: 2016-08-30 description: A variety of methods are available to collapse 16S rRNA gene sequencing reads to the operational taxonomic units (OTUs) used in microbiome analyses. A number of studies have aimed to compare the quality of the resulting OTUs. However, in the absence of a standard method to define and enumerate the different taxa within a microbial community, existing comparisons have been unable to compare the ability of clustering methods to generate units that accurately represent functional taxonomic segregation. We have previously demonstrated heritability of the microbiome and we propose this as a measure of each methods’ ability to generate OTUs representing biologically relevant units. Our approach assumes that OTUs that best represent the functional units interacting with the hosts’ properties will produce the highest heritability estimates. Using 1,750 unselected individuals from the TwinsUK cohort, we compared 11 approaches to OTU clustering in heritability analyses. We find that de novo clustering methods produce more heritable OTUs than reference based approaches, with VSEARCH and SUMACLUST performing well. We also show that differences resulting from each clustering method are minimal once reads are collapsed by taxonomic assignment, although sample diversity estimates are clearly influenced by OTU clustering approach. These results should help the selection of sequence clustering methods in future microbiome studies, particularly for studies of human host-microbiome interactions. creator: Matthew A. Jackson creator: Jordana T. Bell creator: Tim D. Spector creator: Claire J. Steves uri: https://doi.org/10.7717/peerj.2341 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Jackson et al. title: Genome sequencing-assisted identification and the first functional validation of N-acyl-homoserine-lactone synthases from the Sphingomonadaceae family link: https://peerj.com/articles/2332 last-modified: 2016-08-30 description: BackgroundMembers of the genus Novosphingobium have been isolated from a variety of environmental niches. Although genomics analyses have suggested the presence of genes associated with quorum sensing signal production e.g., the N-acyl-homoserine lactone (AHL) synthase (luxI) homologs in various Novosphingobium species, to date, no luxI homologs have been experimentally validated.MethodsIn this study, we report the draft genome of the N-(AHL)-producing bacterium Novosphingobium subterraneum DSM 12447 and validate the functions of predicted luxI homologs from the bacterium through inducible heterologous expression in Agrobacterium tumefaciens strain NTL4. We developed a two-dimensional thin layer chromatography bioassay and used LC-ESI MS/MS analyses to separate, detect and identify the AHL signals produced by the N. subterraneum DSM 12447 strain.ResultsThree predicted luxI homologs were annotated to the locus tags NJ75_2841 (NovINsub1), NJ75_2498 (NovINsub2), and NJ75_4146 (NovINsub3). Inducible heterologous expression of each luxI homologs followed by LC-ESI MS/MS and two-dimensional reverse phase thin layer chromatography bioassays followed by bioluminescent ccd camera imaging indicate that the three LuxI homologs are able to produce a variety of medium-length AHL compounds. New insights into the LuxI phylogeny was also gleemed as inferred by Bayesian inference.DiscussionThis study significantly adds to our current understanding of quorum sensing in the genus Novosphingobium and provide the framework for future characterization of the phylogenetically interesting LuxI homologs from members of the genus Novosphingobium and more generally the family Sphingomonadaceae. creator: Han Ming Gan creator: Lucas K. Dailey creator: Nigel Halliday creator: Paul Williams creator: André O. Hudson creator: Michael A. Savka uri: https://doi.org/10.7717/peerj.2332 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Gan et al. title: Minimum information about tolerogenic antigen-presenting cells (MITAP): a first step towards reproducibility and standardisation of cellular therapies link: https://peerj.com/articles/2300 last-modified: 2016-08-30 description: Cellular therapies with tolerogenic antigen-presenting cells (tolAPC) show great promise for the treatment of autoimmune diseases and for the prevention of destructive immune responses after transplantation. The methodologies for generating tolAPC vary greatly between different laboratories, making it difficult to compare data from different studies; thus constituting a major hurdle for the development of standardised tolAPC therapeutic products. Here we describe an initiative by members of the tolAPC field to generate a minimum information model for tolAPC (MITAP), providing a reporting framework that will make differences and similarities between tolAPC products transparent. In this way, MITAP constitutes a first but important step towards the production of standardised and reproducible tolAPC for clinical application. creator: Phillip Lord creator: Rachel Spiering creator: Juan C. Aguillon creator: Amy E. Anderson creator: Silke Appel creator: Daniel Benitez-Ribas creator: Anja ten Brinke creator: Femke Broere creator: Nathalie Cools creator: Maria Cristina Cuturi creator: Julie Diboll creator: Edward K. Geissler creator: Nick Giannoukakis creator: Silvia Gregori creator: S. Marieke van Ham creator: Staci Lattimer creator: Lindsay Marshall creator: Rachel A. Harry creator: James A. Hutchinson creator: John D. Isaacs creator: Irma Joosten creator: Cees van Kooten creator: Ascension Lopez Diaz de Cerio creator: Tatjana Nikolic creator: Haluk Barbaros Oral creator: Ljiljana Sofronic-Milosavljevic creator: Thomas Ritter creator: Paloma Riquelme creator: Angus W. Thomson creator: Massimo Trucco creator: Marta Vives-Pi creator: Eva M. Martinez-Caceres creator: Catharien M.U. Hilkens uri: https://doi.org/10.7717/peerj.2300 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Lord et al. title: Microsatellite loci in the tiger shark and cross-species amplification using pyrosequencing technology link: https://peerj.com/articles/2205 last-modified: 2016-08-30 description: The tiger shark (Galeocerdo cuvier) has a global distribution in tropical and warm temperate seas, and it is caught in numerous fisheries worldwide, mainly as bycatch. It is currently assessed as near threatened by the International Union for Conservation of Nature (IUCN) Red List. In this study, we identified nine microsatellite loci through next generation sequencing (454 pyrosequencing) using 29 samples from the western Atlantic. The genetic diversity of these loci were assessed and revealed a total of 48 alleles ranging from 3 to 7 alleles per locus (average of 5.3 alleles). Cross-species amplification was successful at most loci for other species such as Carcharhinus longimanus, C. acronotus and Alopias superciliosus. Given the potential applicability of genetic markers for biological conservation, these data may contribute to the population assessment of this and other species of sharks worldwide. creator: Natália J. Mendes creator: Vanessa P. Cruz creator: Fernando Y. Ashikaga creator: Sâmia M. Camargo creator: Claudio Oliveira creator: Andrew N. Piercy creator: George H. Burgess creator: Rui Coelho creator: Miguel N. Santos creator: Fernando F. Mendonça creator: Fausto Foresti uri: https://doi.org/10.7717/peerj.2205 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Mendes et al. title: Depression, anxiety, and stress in partners of Australian combat veterans and military personnel: a comparison with Australian population norms link: https://peerj.com/articles/2373 last-modified: 2016-08-25 description: Partners of Australian combat veterans are at an increased risk of experiencing mental health problems. The present study provides a comparative analysis of the mental health of partners of veterans with that of the Australian normative data. To compare different types of groups of partners, the study samples comprised: (a) partners of Australian combat veterans (Sample 1: n = 282, age M = 60.79, SD = 5.05), (b) a sub-sample of partners of Australian combat veterans from the previous sample (Sample 2: n = 50; M = 60.06, SD = 4.80), (c) partners of Special Air Services Regiment (SASR) personnel (Sample 3: n = 40, age M = 34.39SD = 7.01), and (d) partners of current serving military (non-SASR) personnel (Sample 4: n = 38, age M = 32.37, SD = 6.20). Respondents completed measures assessing their reported levels of depression, anxiety, and stress. Samples 1 and 2 comprised partners of Australian military veterans who reported significantly greater symptoms of depression, anxiety, and stress than the comparative population norms. The sample of SASR personnel partners (Sample 3) reported significantly lower levels of depression and anxiety, whereas the sample with non-SASR personnel partners (Sample 4) reported a significantly greater stress symptomatology than the comparative norms. Number of deployments was found to be associated with depression, anxiety, and stress in partners of non-SASR veterans (Sample 4). Lessons and protective factors can be learnt from groups within the current military as to what may assist partners and families to maintain a better level of psychosocial health. creator: Gail V. MacDonell creator: Navjot Bhullar creator: Einar B. Thorsteinsson uri: https://doi.org/10.7717/peerj.2373 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 MacDonell et al. title: Thermal treatment and leaching of biochar alleviates plant growth inhibition from mobile organic compounds link: https://peerj.com/articles/2385 last-modified: 2016-08-25 description: Recent meta-analyses of plant responses to biochar boast positive average effects of between 10 and 40%. Plant responses, however, vary greatly across systems, and null or negative biochar effects are increasingly reported. The mechanisms responsible for such responses remain unclear. In a glasshouse experiment we tested the effects of three forestry residue wood biochars, applied at five dosages (0, 5, 10, 20, and 50 t/ha) to a temperate forest drystic cambisol as direct surface applications and as complete soil mixes on the herbaceous pioneers Lolium multiflorum and Trifolium repens. Null and negative effects of biochar on growth were found in most cases. One potential cause for null and negative plant responses to biochar is plant exposure to mobile compounds produced during pyrolysis that leach or evolve following additions of biochars to soil. In a second glasshouse experiment we examined the effects of simple leaching and heating techniques to ameliorate potentially phytotoxic effects of volatile and leachable compounds released from biochar. We used Solid Phase Microextraction (SPME)–gas chromatography–mass spectrometry (GC-MS) to qualitatively describe organic compounds in both biochar (through headspace extraction), and in the water leachates (through direct injection). Convection heating and water leaching of biochar prior to application alleviated growth inhibition. Additionally, growth was inhibited when filtrate from water-leached biochar was applied following germination. SPME-GC-MS detected primarily short-chained carboxylic acids and phenolics in both the leachates and solid chars, with relatively high concentrations of several known phytotoxic compounds including acetic acid, butyric acid, 2,4-di-tert-butylphenol and benzoic acid. We speculate that variable plant responses to phytotoxic organic compounds leached from biochars may largely explain negative plant growth responses and also account for strongly species-specific patterns of plant responses to biochar amendments in short-term experiments. creator: Nigel V. Gale creator: Tara E. Sackett creator: Sean C. Thomas uri: https://doi.org/10.7717/peerj.2385 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Gale et al. title: Electrophysiological assessment of auditory processing disorder in children with non-syndromic cleft lip and/or palate link: https://peerj.com/articles/2383 last-modified: 2016-08-25 description: ObjectivesCleft lip and/or palate is a common congenital craniofacial malformation found worldwide. A frequently associated disorder is conductive hearing loss, and this disorder has been thoroughly investigated in children with non-syndromic cleft lip and/or palate (NSCL/P). However, analysis of auditory processing function is rarely reported for this population, although this issue should not be ignored since abnormal auditory cortical structures have been found in populations with cleft disorders. The present study utilized electrophysiological tests to assess the auditory status of a large group of children with NSCL/P, and investigated whether this group had less robust central auditory processing abilities compared to craniofacially normal children.Methods146 children with NSCL/P who had normal peripheral hearing thresholds, and 60 craniofacially normal children aged from 6 to 15 years, were recruited. Electrophysiological tests, including auditory brainstem response (ABR), P1-N1-P2 complex, and P300 component recording, were conducted.ResultsABR and N1 wave latencies were significantly prolonged in children with NSCL/P. An atypical developmental trend was found for long latency potentials in children with cleft compared to control group children. Children with unilateral cleft lip and palate showed a greater level of abnormal results compared with other cleft subgroups, whereas the cleft lip subgroup had the most robust responses for all tests.ConclusionChildren with NSCL/P may have slower than normal neural transmission times between the peripheral auditory nerve and brainstem. Possible delayed development of myelination and synaptogenesis may also influence auditory processing function in this population. Present research outcomes were consistent with previous, smaller sample size, electrophysiological studies on infants and children with cleft lip/palate disorders. In view of the these findings, and reports of educational disadvantage associated with cleft disorders, further research that focuses on the auditory processing abilities of children with cleft lip/palate disorder is warranted. creator: Xiaoran Ma creator: Bradley McPherson creator: Lian Ma uri: https://doi.org/10.7717/peerj.2383 license: http://creativecommons.org/licenses/by/3.0/ rights: ©2016 Ma et al. title: Antioxidant-rich leaf extract of Barringtonia racemosa significantly alters the in vitro expression of genes encoding enzymes that are involved in methylglyoxal degradation III link: https://peerj.com/articles/2379 last-modified: 2016-08-25 description: BackgroundBarringtonia racemosa is a medicinal plant belonging to the Lecythidaceae family. The water extract of B. racemosa leaf (BLE) has been shown to be rich in polyphenols. Despite the diverse medicinal properties of B. racemosa, information on its major biological effects and the underlying molecular mechanisms are still lacking.MethodsIn this study, the effect of the antioxidant-rich BLE on gene expression in HepG2 cells was investigated using microarray analysis in order to shed more light on the molecular mechanism associated with the medicinal properties of the plant.ResultsMicroarray analysis showed that a total of 138 genes were significantly altered in response to BLE treatment (p < 0.05) with a fold change difference of at least 1.5. SERPINE1 was the most significantly up-regulated gene at 2.8-fold while HAMP was the most significantly down-regulated gene at 6.5-fold. Ingenuity Pathways Analysis (IPA) revealed that “Cancer, cell death and survival, cellular movement” was the top network affected by the BLE with a score of 44. The top five canonical pathways associated with BLE were Methylglyoxal Degradation III followed by VDR/RXR activation, TR/RXR activation, PXR/RXR activation and gluconeogenesis. The expression of genes that encode for enzymes involved in methylglyoxal degradation (ADH4, AKR1B10 and AKR1C2) and glycolytic process (ENO3, ALDOC and SLC2A1) was significantly regulated. Owing to the Warburg effect, aerobic glycolysis in cancer cells may increase the level of methylglyoxal, a cytotoxic compound.ConclusionsBLE has the potential to be developed into a novel chemopreventive agent provided that the cytotoxic effects related to methylglyoxal accumulation are minimized in normal cells that rely on aerobic glycolysis for energy supply. creator: Kin Weng Kong creator: Azlina Abdul Aziz creator: Nurhanani Razali creator: Norhaniza Aminuddin creator: Sarni Mat Junit uri: https://doi.org/10.7717/peerj.2379 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Kong et al. title: Rapid induction of GFP expression by the nitrate reductase promoter in the diatom Phaeodactylum tricornutum link: https://peerj.com/articles/2344 last-modified: 2016-08-25 description: An essential prerequisite for a controlled transgene expression is the choice of a suitable promoter. In the model diatom Phaeodactylum tricornutum, the most commonly used promoters for trans-gene expression are the light dependent lhcf1 promoters (derived from two endogenous genes encoding fucoxanthin chlorophyll a/c binding proteins) and the nitrate dependent nr promoter (derived from the endogenous nitrate reductase gene). In this study, we investigated the time dependent expression of the green fluorescent protein (GFP) reporter under control of the nitrate reductase promoter in independently genetically transformed P. tricornutum cell lines following induction of expression by change of the nitrogen source in the medium via flow cytometry, microscopy and western blotting. In all investigated cell lines, GFP fluorescence started to increase 1 h after change of the medium, the fastest increase rates were observed between 2 and 3 h. Fluorescence continued to increase slightly for up to 7 h even after transfer of the cells to ammonium medium. The subsequent decrease of GFP fluorescence was much slower than the increase, probably due to the stability of GFP. The investigation of several cell lines transformed with nr based constructs revealed that, also in the absence of nitrate, the promoter may show residual activity. Furthermore, we observed a strong variation of gene expression between independent cell lines, emphasising the importance of a thorough characterisation of genetically modified cell lines and their individual expression patterns. creator: Lili Chu creator: Daniela Ewe creator: Carolina Río Bártulos creator: Peter G. Kroth creator: Ansgar Gruber uri: https://doi.org/10.7717/peerj.2344 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Chu et al. title: Morpho-histological characterisation of the alimentary canal of an important food fish, Asian seabass (Lates calcarifer) link: https://peerj.com/articles/2377 last-modified: 2016-08-24 description: Asian seabass (Lates calcarifer) is a food fish of increasing aquaculture importance. In order to improve our understanding on the digestive system and feeding of this species, morphological and histological features of the gut were studied. Morphologically, the Asian seabass gut is defined by a short and muscular esophagus, well-developed stomach and comparatively short intestine. Mucous secreting goblet cells reactive to PAS (Periodic Acid Schiff) and AB (Alcian Blue) stain were present throughout the esophagus. The stomach was sac-like and could be distinguished into the cardiac, fundic and pyloric regions. Gastric glands and mucus cells were predominately present in the cardiac and fundic regions. Five finger-like pyloric caeca were present between the stomach and intestine. The intestine was a short, tubular structure with no morphological differences between the various regions. Histologically, the intestinal regions were similar, the main difference being in the number of goblet cells that increased from anterior to posterior intestine, with 114 ± 9, 153 ± 7 and 317 ± 21 goblet cells in the anterior, mid and posterior regions, respectively. The intestinal epithelium stained positively for PAS, but the staining was stronger for acidic glycoproteins. The rectum was similar to intestine, except for increased goblet cell numbers (anterior rectum: 529 ± 26; posterior rectum: 745 ± 29). Gut morpho-histology did not respond to salinity changes, however, there was a significant reduction of mucosal height, goblet cell numbers and muscularis thickness upon food deprivation. creator: Kathiresan Purushothaman creator: Doreen Lau creator: Jolly M. Saju creator: Syed Musthaq SK creator: Declan Patrick Lunny creator: Shubha Vij creator: László Orbán uri: https://doi.org/10.7717/peerj.2377 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Purushothaman et al. title: The incidence rates of endometrial hyperplasia and endometrial cancer: a four-year population-based study link: https://peerj.com/articles/2374 last-modified: 2016-08-24 description: IntroductionThe aim of this study was to determine the incidence rates of endometrial hyperplasia (EH) and endometrial cancer (EC) in the Republic of Korea using national insurance claim data generated from 2009 to 2012.Materials and MethodsData that were generated from 2009 to 2012 were sourced from the Korean Health Insurance Review and Assessment Service-National Inpatients Sample database. The data from women who were assigned diagnosis codes representing EH or EC within 1 month of being assigned codes that corresponded to procedures that included endometrial biopsies and several types of gynecologic surgeries to obtain endometrial pathology samples, were selected for analysis.ResultsData from 2,477,424 women were entered into the database between 2009 and 2012, and the data from 1,868 women with EH and 868 women with EC were extracted for analysis. The mean ages of the patients were 44.1 ± 0.4 years for those with EH and 52.7 ± 0.6 years for those with EC. The EH and EC incidence rates were 37 per 100,000 woman-years and 8 per 100,000 woman-years, respectively. The EH and EC incidence rates peaked when the women were in their late forties and fifties, respectively.ConclusionsThe EH and EC incidence rates determined in this study were somewhat lower than those determined from previous studies. Further studies are required that adjust the data for race, menopausal hormone therapy, and obesity. creator: Jin-Sung Yuk uri: https://doi.org/10.7717/peerj.2374 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Yuk title: Effects of yearling, juvenile and adult survival on reef manta ray (Manta alfredi) demography link: https://peerj.com/articles/2370 last-modified: 2016-08-24 description: BackgroundThe trade in manta ray gill plates has considerably increased over the last two decades. The resulting increases in ray mortality, in addition to mortality caused by by-catch, has caused many ray populations to decrease in size. The aim of this study was to ascertain how yearling and juvenile growth and survival, and adult survival and reproduction affect reef manta ray (Manta alfredi) population change, to increase our understanding of manta ray demography and thereby improve conservation research and measures for these fish.MethodsWe developed a population projection model for reef manta rays, and used published life history data on yearling and juvenile growth and adult reproduction to parameterise the model. Because little is known about reef manta ray yearling and juvenile survival, we conducted our analyses using a range of plausible survival rate values for yearlings, juveniles and adults.ResultsThe model accurately captured observed variation in population growth rate, lifetime reproductive success and cohort generation time in different reef manta ray populations. Our demographic analyses revealed a range of population consequences in response to variation in demographic rates. For example, an increase in yearling or adult survival rates always elicited greater responses in population growth rate, lifetime reproductive success and cohort generation time than the same increase in juvenile survival rate. The population growth rate increased linearly, but lifetime reproductive success and cohort generation time increased at an accelerating rate with increasing yearling or adult survival rates. Hence, even a small increase in survival rate could increase lifetime reproductive success by one pup, and cohort generation time by several years. Elasticity analyses revealed that, depending on survival rate values of all life stages, the population growth rate is either most sensitive to changes in the rate with which juveniles survive but stay juveniles (i.e., do not mature into adults) or to changes in adult survival rate. However, when assessing these results against estimates on population growth and adult survival rates for populations off the coasts of Mozambique and Japan, we found that the population growth rate is predicted to be always most sensitive to changes in the adult survival rate.DiscussionIt is important to gain an in-depth understanding of reef manta ray life histories, particularly of yearling and adult survival rates, as these can influence reef manta ray population dynamics in a variety of ways. For declining populations in particular, it is crucial to know which life stage should be targeted for their conservation. For one such declining population off the coast of Mozambique, adult annual survival rate has the greatest effect on population growth, and by increasing adult survival by protecting adult aggregation sites, this population’s decline could be halted or even reversed. creator: Isabel M. Smallegange creator: Isabelle B.C. van der Ouderaa creator: Yara Tibiriçá uri: https://doi.org/10.7717/peerj.2370 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Smallegange et al. title: Tree phyllosphere bacterial communities: exploring the magnitude of intra- and inter-individual variation among host species link: https://peerj.com/articles/2367 last-modified: 2016-08-24 description: BackgroundThe diversity and composition of the microbial community of tree leaves (the phyllosphere) varies among trees and host species and along spatial, temporal, and environmental gradients. Phyllosphere community variation within the canopy of an individual tree exists but the importance of this variation relative to among-tree and among-species variation is poorly understood. Sampling techniques employed for phyllosphere studies include picking leaves from one canopy location to mixing randomly selected leaves from throughout the canopy. In this context, our goal was to characterize the relative importance of intra-individual variation in phyllosphere communities across multiple species, and compare this variation to inter-individual and interspecific variation of phyllosphere epiphytic bacterial communities in a natural temperate forest in Quebec, Canada.MethodsWe targeted five dominant temperate forest tree species including angiosperms and gymnosperms: Acer saccharum, Acer rubrum, Betula papyrifera, Abies balsamea and Picea glauca. For one randomly selected tree of each species, we sampled microbial communities at six distinct canopy locations: bottom-canopy (1–2 m height), the four cardinal points of mid-canopy (2–4 m height), and the top-canopy (4–6 m height). We also collected bottom-canopy leaves from five additional trees from each species.ResultsBased on an analysis of bacterial community structure measured via Illumina sequencing of the bacterial 16S gene, we demonstrate that 65% of the intra-individual variation in leaf bacterial community structure could be attributed to the effect of inter-individual and inter-specific differences while the effect of canopy location was not significant. In comparison, host species identity explains 47% of inter-individual and inter-specific variation in leaf bacterial community structure followed by individual identity (32%) and canopy location (6%).DiscussionOur results suggest that individual samples from consistent positions within the tree canopy from multiple individuals per species can be used to accurately quantify variation in phyllosphere bacterial community structure. However, the considerable amount of intra-individual variation within a tree canopy ask for a better understanding of how changes in leaf characteristics and local abiotic conditions drive spatial variation in the phyllosphere microbiome. creator: Isabelle Laforest-Lapointe creator: Christian Messier creator: Steven W. Kembel uri: https://doi.org/10.7717/peerj.2367 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Laforest-Lapointe et al. title: Fine structure of the spermatozoon in three species of Cambaridae (Arthropoda: Crustacea: Decapoda) Cambarus robustus, Orconectes propinquus and Orconectes rusticus: a comparative biometrical study link: https://peerj.com/articles/2363 last-modified: 2016-08-24 description: The ultrastructure of spermatozoa in three species of cambarid crayfish, Cambarus robustus, Orconectes propinquus, and Orconectes rusticus, were studied and compared with eight previously studied species from different crayfish families using morphological features and biometrical data. The ultrastructure of spermatozoa show a generally conserved pattern including an acrosome and nucleus in the anterior and posterior parts of the cell, respectively, radial arms that wrap around the nucleus, and the whole cell is enclosed by an extracellular capsule. The most outstanding morphological feature in spermatozoa of three studied cambarid crayfish is the crest-like protrusions in the anterior part of the acrosome that can be used as one of the features for distinguishing the members of this family. Results of biometrical data reveal that acrosome size in the representatives of Parastacidae are the smallest, while representatives of Astacidae show the biggest acrosome. The acrosome size in species belonging to Cambaridae occupy an intermediate position between the two other families of freshwater crayfish. In conclusion, a combination of morphological features and biometrical data of spermatozoa can help distinguishing different species of the freshwater crayfish. creator: Buket Yazicioglu creator: Přemek Hamr creator: Pavel Kozák creator: Antonín Kouba creator: Hamid Niksirat uri: https://doi.org/10.7717/peerj.2363 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Yazicioglu et al. title: Transmission of a heterologous clade C Symbiodinium in a model anemone infection system via asexual reproduction link: https://peerj.com/articles/2358 last-modified: 2016-08-24 description: Anemones of genus Exaiptasia are used as model organisms for the study of cnidarian-dinoflagellate (genus Symbiodinium) endosymbiosis. However, while most reef-building corals harbor Symbiodinium of clade C, Exaiptasia spp. anemones mainly harbor clade B Symbiodinium (ITS2 type B1) populations. In this study, we reveal for the first time that bleached Exaiptasia pallida anemones can establish a symbiotic relationship with a clade C Symbiodinium (ITS2 type C1). We further found that anemones can transmit the exogenously supplied clade C Symbiodinium cells to their offspring by asexual reproduction (pedal laceration). In order to corroborate the establishment of stable symbiosis, we used microscopic techniques and genetic analyses to examine several generations of anemones, and the results of these endeavors confirmed the sustainability of the system. These findings provide a framework for understanding the differences in infection dynamics between homologous and heterologous dinoflagellate types using a model anemone infection system. creator: Wan-Nan U. Chen creator: Ya-Ju Hsiao creator: Anderson B. Mayfield creator: Ryan Young creator: Ling-Lan Hsu creator: Shao-En Peng uri: https://doi.org/10.7717/peerj.2358 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Chen et al. title: Taxonomic revision of Eoalligator (Crocodylia, Brevirostres) and the paleogeographic origins of the Chinese alligatoroids link: https://peerj.com/articles/2356 last-modified: 2016-08-24 description: Background. The primarily Neotropical distribution of living alligatoroids raises questions as to when and how the ancestors of Alligator sinensis migrated to China. As phylogeny provides a necessary framework for historical biogeographic issues, determining the phylogenetic positions of the Chinese alligatoroids is a crucial step towards understanding global alligatoroid paleobiogeography. Besides the unnamed alligatoroids from the Eocene of Guangdong Province, three Chinese fossil taxa have been referred to Alligatoroidea: Alligator luicus, Eoalligator chunyii and Eoalligator huiningensis. However, none of these fossil taxa has been included in a phylogenetic analysis. The genus Eoalligator was established to accommodate E. chunyii from Guangdong Province. E. huiningensis from Anhui Province was later erected as a second species, despite no distinctive similarities with E. chunyii. By contrast, the putative crocodyline Asiatosuchus nanlingensis was established based on material from Guangdong Province, close to the E. chunyii specimens geographically and stratigraphically. Furthermore, specimens of A. nanlingensis and E. chunyii share four distinctive characters, but display no evident differences. As a result, the taxonomic relationships of these three species require restudy.Methods. In this paper, all specimens of E. chunyii and E. huiningensis are reassessed in detail, and compared to specimens of A. nanlingensis. Detailed re-descriptions and revised diagnoses are provided, and a cladistic analysis is carried out to assess the phylogenetic positions of E. chunyii, E. huiningensis and A. nanlingensis.Results. The analysis recovers E. chunyii and A. nanlingensis as sister taxa among basal Crocodylidae, while P. huiningensis is posited as an alligatoroid. Two key characters support the monophyly E. chunyii + A. nanlingensis: sulcus within surangular, and anteroposteriorly oriented surangular-articular suture. The former character is unique to E. chunyii and A. nanlingensis among crocodyloids, although a smaller and more posteriorly positioned surangular fossa is known in Diplocynodon. Detailed comparisons show the two species to be synonymous, with E. chunyii as the junior synonym of A. nanlingensis based on page priority. Because E. chunyii was erected as the type species of Eoalligator, the genus is now invalid. We establish the new genus Protoalligator to accommodate “Eoalligator” huiningensis, an alligatoroid whose exact phylogenetic position is uncertain. In particular, P. huiningensis retains primitive characters such as a lacrimal that extends further anteriorly than the prefrontal, and a notch at the premaxilla-maxilla suture. However, P. huiningensis also appears to share one important derived character, a complete nasal bar, with alligators. Our taxonomic revisions imply that four alligatoroids are currently known from China, and these species must have dispersed from North America to Asia in more than one event. creator: Yan-yin Wang creator: Corwin Sullivan creator: Jun Liu uri: https://doi.org/10.7717/peerj.2356 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Wang et al. title: Anxiolytic effects of fluoxetine and nicotine exposure on exploratory behavior in zebrafish link: https://peerj.com/articles/2352 last-modified: 2016-08-24 description: Zebrafish (Danio rerio) have emerged as a popular model for studying the pharmacology and behavior of anxiety. While there have been numerous studies documenting the anxiolytic and anxiogenic effects of common drugs in zebrafish, many do not report or test for behavioral differences between the sexes. Previous studies have indicated that males and females differ in their baseline level of anxiety. In this study, we test for a sex interaction with fluoxetine and nicotine. We exposed fish to system water (control), 10 mg/L fluoxetine, or 1 mg/L nicotine for three minutes prior to being subjected to four minutes in an open-field drop test. Video recordings were tracked using ProAnalyst. Fish from both drug treatments reduced swimming speed, increased vertical position, and increased use of the top half of the open field when compared with the control, though fluoxetine had a larger effect on depth related behaviors while nicotine mostly affected swimming speed. A significant sex effect was observed where females swam at a slower and more constant speed than males, however neither drug produced a sex-dependent response. creator: Matthew L. Singer creator: Kris Oreschak creator: Zachariah Rhinehart creator: Barrie D. Robison uri: https://doi.org/10.7717/peerj.2352 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Singer et al. title: Identification of biomarkers for periodontal disease using the immunoproteomics approach link: https://peerj.com/articles/2327 last-modified: 2016-08-24 description: BackgroundPeriodontitis is one of the most common oral diseases associated with the host’s immune response against periodontopathogenic infection. Failure to accurately diagnose the stage of periodontitis has limited the ability to predict disease status. Therefore, we aimed to look for reliable diagnostic markers for detection or differentiation of early stage periodontitis using the immunoprotemic approach.MethodIn the present study, patient serum samples from four distinct stages of periodontitis (i.e., mild chronic, moderate chronic, severe chronic, and aggressive) and healthy controls were subjected to two-dimensional gel electrophoresis (2-DE), followed by silver staining. Notably, we consistently identified 14 protein clusters in the sera of patients and normal controls.ResultsOverall, we found that protein levels were comparable between patients and controls, with the exception of the clusters corresponding to A1AT, HP, IGKC and KNG1 (p < 0.05). In addition, the immunogenicity of these proteins was analysed via immunoblotting, which revealed differential profiles for periodontal disease and controls. For this reason, IgM obtained from severe chronic periodontitis (CP) sera could be employed as a suitable autoantibody for the detection of periodontitis.DiscussionTaken together, the present study suggests that differentially expressed host immune response proteins could be used as potential biomarkers for screening periodontitis. Future studies exploring the diagnostic potential of such factors are warranted. creator: Jesinda P. Kerishnan creator: Sani Mohammad creator: Muhamad Shaifunizam Alias creator: Alan Kang-Wai Mu creator: Rathna Devi Vaithilingam creator: Nor Adinar Baharuddin creator: Syarida H. Safii creator: Zainal Ariff Abdul Rahman creator: Yu Nieng Chen creator: Yeng Chen uri: https://doi.org/10.7717/peerj.2327 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Kerishnan et al. title: Analysis of genotype diversity and evolution of Dengue virus serotype 2 using complete genomes link: https://peerj.com/articles/2326 last-modified: 2016-08-24 description: BackgroundDengue is one of the most common arboviral diseases prevalent worldwide and is caused by Dengue viruses (genus Flavivirus, family Flaviviridae). There are four serotypes of Dengue Virus (DENV-1 to DENV-4), each of which is further subdivided into distinct genotypes. DENV-2 is frequently associated with severe dengue infections and epidemics. DENV-2 consists of six genotypes such as Asian/American, Asian I, Asian II, Cosmopolitan, American and sylvatic. Comparative genomic study was carried out to infer population structure of DENV-2 and to analyze the role of evolutionary and spatiotemporal factors in emergence of diversifying lineages.MethodsComplete genome sequences of 990 strains of DENV-2 were analyzed using Bayesian-based population genetics and phylogenetic approaches to infer genetically distinct lineages. The role of spatiotemporal factors, genetic recombination and selection pressure in the evolution of DENV-2 is examined using the sequence-based bioinformatics approaches.ResultsDENV-2 genetic structure is complex and consists of fifteen subpopulations/lineages. The Asian/American genotype is observed to be diversified into seven lineages. The Asian I, Cosmopolitan and sylvatic genotypes were found to be subdivided into two lineages, each. The populations of American and Asian II genotypes were observed to be homogeneous. Significant evidence of episodic positive selection was observed in all the genes, except NS4A. Positive selection operational on a few codons in envelope gene confers antigenic and lineage diversity in the American strains of Asian/American genotype. Selection on codons of non-structural genes was observed to impact diversification of lineages in Asian I, cosmopolitan and sylvatic genotypes. Evidence of intra/inter-genotype recombination was obtained and the uncertainty in classification of recombinant strains was resolved using the population genetics approach.DiscussionComplete genome-based analysis revealed that the worldwide population of DENV-2 strains is subdivided into fifteen lineages. The population structure of DENV-2 is spatiotemporal and is shaped by episodic positive selection and recombination. Intra-genotype diversity was observed in four genotypes (Asian/American, Asian I, cosmopolitan and sylvatic). Episodic positive selection on envelope and non-structural genes translates into antigenic diversity and appears to be responsible for emergence of strains/lineages in DENV-2 genotypes. Understanding of the genotype diversity and emerging lineages will be useful to design strategies for epidemiological surveillance and vaccine design. creator: Vaishali P. Waman creator: Pandurang Kolekar creator: Mukund R. Ramtirthkar creator: Mohan M. Kale creator: Urmila Kulkarni-Kale uri: https://doi.org/10.7717/peerj.2326 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Waman et al. title: Investigation of the mechanisms of action behind Electromotive Drug Administration (EMDA) link: https://peerj.com/articles/2309 last-modified: 2016-08-24 description: ObjectiveBladder cancer is a cause of considerable morbidity worldwide. Electromotive Drug Administration is a method that combines intravesical chemotherapy with local electric field application. Electroporation has been suggested among other mechanisms as having a possible role in the therapy, so the goal of the present study was to investigate the electric fields present in the bladder wall during the treatment to determine which mechanisms might be involved.Material and MethodsElectromotive Drug Administration involves applying intravesical mitomycin C with direct current of 20 mA delivered through a catheter electrode for 30 min. For numerical electric field computation we built a 3-D nonhomogeneous patient specific model based on CT images and used finite element method simulations to determine the electric fields in the whole body.ResultsResults indicate that highest electric field in the bladder wall was 37.7 V/m. The mean electric field magnitude in the bladder wall was 3.03 V/m. The mean magnitude of the current density in the bladder wall was 0.61 A/m2.ConclusionsThe present study shows that electroporation is not the mechanism of action in EMDA. A more likely explanation of the mechanism of action is iontophoretic forces increasing the mitomycin C concentration in the bladder wall. creator: Bor Kos creator: Juan Luis Vásquez creator: Damijan Miklavčič creator: Gregers G.G. Hermann creator: Julie Gehl uri: https://doi.org/10.7717/peerj.2309 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Kos et al. title: I-HEDGE: determining the optimum complementary sets of taxa for conservation using evolutionary isolation link: https://peerj.com/articles/2350 last-modified: 2016-08-23 description: In the midst of the current biodiversity crisis, conservation efforts might profitably be directed towards ensuring that extinctions do not result in inordinate losses of evolutionary history. Numerous methods have been developed to evaluate the importance of species based on their contribution to total phylogenetic diversity on trees and networks, but existing methods fail to take complementarity into account, and thus cannot identify the best order or subset of taxa to protect. Here, we develop a novel iterative calculation of the heightened evolutionary distinctiveness and globally endangered metric (I-HEDGE) that produces the optimal ranked list for conservation prioritization, taking into account complementarity and based on both phylogenetic diversity and extinction probability. We applied this metric to a phylogenetic network based on mitochondrial control region data from extant and recently extinct giant Galápagos tortoises, a highly endangered group of closely related species. We found that the restoration of two extinct species (a project currently underway) will contribute the greatest gain in phylogenetic diversity, and present an ordered list of rankings that is the optimum complementarity set for conservation prioritization. creator: Evelyn L. Jensen creator: Arne Ø. Mooers creator: Adalgisa Caccone creator: Michael A. Russello uri: https://doi.org/10.7717/peerj.2350 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Jensen et al. title: Investigation of population structure in Gulf of Mexico Seepiophila jonesi (Polychaeta, Siboglinidae) using cross-amplified microsatellite loci link: https://peerj.com/articles/2366 last-modified: 2016-08-23 description: BackgroundVestimentiferan tubeworms are some of the most recognizable fauna found at deep-sea cold seeps, isolated environments where hydrocarbon rich fluids fuel biological communities. Several studies have investigated tubeworm population structure; however, much is still unknown about larval dispersal patterns at Gulf of Mexico (GoM) seeps. As such, researchers have applied microsatellite markers as a measure for documenting the transport of vestimentiferan individuals. In the present study, we investigate the utility of microsatellites to be cross-amplified within the escarpiid clade of seep vestimentiferans, by determining if loci originally developed for Escarpia spp. could be amplified in the GoM seep tubeworm, Seepiophila jonesi. Additionally, we determine if cross-amplified loci can reliably uncover the same signatures of high gene flow seen in a previous investigation of S. jonesi.MethodsSeventy-seven S. jonesi individuals were collected from eight seep sites across the upper Louisiana slope (<1,000 m) in the GoM. Forty-eight microsatellite loci that were originally developed for Escarpia laminata (18 loci) and Escarpia southwardae (30 loci) were tested to determine if they were homologous and polymorphic in S. jonesi. Loci found to be both polymorphic and of high quality were used to test for significant population structuring in S. jonesi.ResultsMicrosatellite pre-screening identified 13 (27%) of the Escarpia loci were homologous and polymorphic in S. jonesi, revealing that microsatellites can be amplified within the escarpiid clade of vestimentiferans. Our findings uncovered low levels of heterozygosity and a lack of genetic differentiation amongst S. jonesi from various sites and regions, in line with previous investigations that employed species-specific polymorphic loci on S. jonesi individuals retrieved from both the same and different seep sites. The lack of genetic structure identified from these populations supports the presence of significant gene flow via larval dispersal in mixed oceanic currents.DiscussionThe ability to develop “universal” microsatellites reduces the costs associated with these analyses and allows researchers to track and investigate a wider array of taxa, which is particularly useful for organisms living at inaccessible locations such as the deep sea. Our study highlights that non-species specific microsatellites can be amplified across large evolutionary distances and still yield similar findings as species-specific loci. Further, these results show that S. jonesi collected from various localities in the GoM represents a single panmictic population, suggesting that dispersal of lecithotrophic larvae by deep sea currents is sufficient to homogenize populations. These data are consistent with the high levels of gene flow seen in Escarpia spp., which advocates that differences in microhabitats of seep localities lead to variation in biogeography of separate species. creator: Chunya Huang creator: Stephen W. Schaeffer creator: Charles R. Fisher creator: Dominique A. Cowart uri: https://doi.org/10.7717/peerj.2366 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Huang et al. title: SICLE: a high-throughput tool for extracting evolutionary relationships from phylogenetic trees link: https://peerj.com/articles/2359 last-modified: 2016-08-23 description: We present the phylogeny analysis software SICLE (Sister Clade Extractor), an easy-to-use, high-throughput tool to describe the nearest neighbors to a node of interest in a phylogenetic tree as well as the support value for the relationship. The application is a command line utility that can be embedded into a phylogenetic analysis pipeline or can be used as a subroutine within another C++ program. As a test case, we applied this new tool to the published phylome of Salinibacter ruber, a species of halophilic Bacteriodetes, identifying 13 unique sister relationships to S. ruber across the 4,589 gene phylogenies. S. ruber grouped with bacteria, most often other Bacteriodetes, in the majority of phylogenies, but 91 phylogenies showed a branch-supported sister association between S. ruber and Archaea, an evolutionarily intriguing relationship indicative of horizontal gene transfer. This test case demonstrates how SICLE makes it possible to summarize the phylogenetic information produced by automated phylogenetic pipelines to rapidly identify and quantify the possible evolutionary relationships that merit further investigation. SICLE is available for free for noncommercial use at http://eebweb.arizona.edu/sicle/. creator: Dan F. DeBlasio creator: Jennifer H. Wisecaver uri: https://doi.org/10.7717/peerj.2359 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 DeBlasio and Wisecaver title: Reliability and validity of an iPhone® application for the measurement of lumbar spine flexion and extension range of motion link: https://peerj.com/articles/2355 last-modified: 2016-08-23 description: BackgroundMeasurement of lumbar spine range of motion (ROM) is often considered to be an essential component of lumbar spine physiotherapy and orthopedic assessment. The measurement can be carried out through various instruments such as inclinometers, goniometers, and etc. Recent smartphones have been equipped with accelerometers and magnetometers, which, through specific software applications (apps) can be used for inclinometric functions.PurposeThe main purpose was to investigate the reliability and validity of an iPhone® app (TiltMeter© -advanced level and inclinometer) for measuring standing lumbar spine flexion–extension ROM in asymptomatic subjects.DesignA cross-sectional study was carried out.SettingThis study was conducted in a physiotherapy clinic located at School of Rehabilitation Sciences, Iran University of Medical Science and Health Services, Tehran, Iran.SubjectsA convenience sample of 30 asymptomatic adults (15 males; 15 females; age range = 18–55 years) was recruited between August 2015 and December 2015.MethodsFollowing a 2–minute warm-up, the subjects were asked to stand in a relaxed position and their skin was marked at the T12–L1 and S1–S2 spinal levels. From this position, they were asked to perform maximum lumbar flexion followed by maximum lumbar extension with their knees straight. Two blinded raters each used an inclinometer and the iPhone ® app to measure lumbar spine flexion–extension ROM. A third rater read the measured angles. To calculate total lumbar spine flexion–extension ROM, the measurement from S1–S2 was subtracted from T12–L1. The second (2 hours later) and third (48 hours later) sessions were carried out in the same manner as the first session. All of the measurements were conducted 3 times and the mean value of 3 repetitions for each measurement was used for analysis. Intraclass correlation coefficient (ICC) models (3, k) and (2, k) were used to determine the intra-rater and inter-rater reliability, respectively. The Pearson correlation coefficients were used to establish concurrent validity of the iPhone® app. Furthermore, minimum detectable change at the 95% confidence level (MDC95) was computed as 1.96 × standard error of measurement × $\sqrt{2}$2.ResultsGood to excellent intra-rater and inter-rater reliability were demonstrated for both the gravity-based inclinometer with ICC values of ≥0.84 and ≥0.77 and the iPhone® app with ICC values of ≥0.85 and ≥0.85, respectively. The MDC95 ranged from 5.82°to 8.18°for the intra-rater analysis and from 7.38°to 8.66° for the inter-rater analysis. The concurrent validity for flexion and extension between the 2 instruments was 0.85 and 0.91, respectively.ConclusionsThe iPhone®app possesses good to excellent intra-rater and inter-rater reliability and concurrent validity. It seems that the iPhone® app can be used for the measurement of lumbar spine flexion–extension ROM.Level of evidenceIIb. creator: Mohammad Reza Pourahmadi creator: Morteza Taghipour creator: Elham Jannati creator: Mohammad Ali Mohseni-Bandpei creator: Ismail Ebrahimi Takamjani creator: Fatemeh Rajabzadeh uri: https://doi.org/10.7717/peerj.2355 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Pourahmadi et al. title: Effects of cattle grazing on small mammal communities in the Hulunber meadow steppe link: https://peerj.com/articles/2349 last-modified: 2016-08-23 description: Small mammals play important roles in many ecosystems, and understanding their response to disturbances such as cattle grazing is fundamental for developing sustainable land use strategies. However, how small mammals respond to cattle grazing remains controversial. A potential cause is that most of previous studies adopt rather simple experimental designs based solely on the presence/absence of grazing, and are thus unable to detect any complex relationships between diversity and grazing intensity. In this study, we conducted manipulated experiments in the Hulunber meadow steppe to survey small mammal community structures under four levels of grazing intensities. We found dramatic changes in species composition in native small mammal communities when grazing intensity reached intermediate levels (0.46 animal unit/ha). As grazing intensity increased, Spermophilus dauricus gradually became the single dominant species. Species richness and diversity of small mammals in ungrazed and lightly grazed (0.23 animal unit/ha) area were much higher than in intermediately and heavily grazed area. We did not detect a humped relationship between small mammal diversity and disturbance levels predicted by the intermediate disturbance hypothesis (IDH). Our study highlighted the necessity of conducting manipulated experiments under multiple grazing intensities. creator: Chan Cao creator: Ling-Ying Shuai creator: Xiao-Ping Xin creator: Zhi-Tao Liu creator: Yan-Ling Song creator: Zhi-Gao Zeng uri: https://doi.org/10.7717/peerj.2349 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Cao et al. title: CardioTF, a database of deconstructing transcriptional circuits in the heart system link: https://peerj.com/articles/2339 last-modified: 2016-08-23 description: Background: Information on cardiovascular gene transcription is fragmented and far behind the present requirements of the systems biology field. To create a comprehensive source of data for cardiovascular gene regulation and to facilitate a deeper understanding of genomic data, the CardioTF database was constructed. The purpose of this database is to collate information on cardiovascular transcription factors (TFs), position weight matrices (PWMs), and enhancer sequences discovered using the ChIP-seq method.Methods: The Naïve-Bayes algorithm was used to classify literature and identify all PubMed abstracts on cardiovascular development. The natural language learning tool GNAT was then used to identify corresponding gene names embedded within these abstracts. Local Perl scripts were used to integrate and dump data from public databases into the MariaDB management system (MySQL). In-house R scripts were written to analyze and visualize the results.Results: Known cardiovascular TFs from humans and human homologs from fly, Ciona, zebrafish, frog, chicken, and mouse were identified and deposited in the database. PWMs from Jaspar, hPDI, and UniPROBE databases were deposited in the database and can be retrieved using their corresponding TF names. Gene enhancer regions from various sources of ChIP-seq data were deposited into the database and were able to be visualized by graphical output. Besides biocuration, mouse homologs of the 81 core cardiac TFs were selected using a Naïve-Bayes approach and then by intersecting four independent data sources: RNA profiling, expert annotation, PubMed abstracts and phenotype.Discussion: The CardioTF database can be used as a portal to construct transcriptional network of cardiac development.Availability and Implementation: Database URL: http://www.cardiosignal.org/database/cardiotf.html. creator: Yisong Zhen uri: https://doi.org/10.7717/peerj.2339 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Zhen title: The larvae of Epigomphus jannyae Belle, 1993 and E. tumefactus Calvert, 1903 (Insecta: Odonata: Gomphidae) link: https://peerj.com/articles/2338 last-modified: 2016-08-23 description: The taxonomic knowledge about immature stages of the insect order Odonata (dragonflies and damselflies) is rather limited in tropical America. Here, the larvae of Epigomphus jannyae Belle, 1993 and E. tumefactus Calvert, 1903 are described, figured, and compared with other described congeners. E. jannyae larva is characterized by 3rd antennomere 1.6 times longer than its widest part; ligula very poorly developed, with ten short, truncate teeth on middle; apical lobe of labial palp rounded and smooth. Lateral margins on abdominal segments (S5–9) serrated, lateral spines on S6–9 small and divergent; male epiproct with a pair of dorsal tubercles at basal 0.66; tips of cerci and paraprocts strongly divergent. The larva of E. tumefactus is characterized by 3rd antennomere 2.3 times longer than its widest part, ligula with 6–7 truncate teeth, apical lobe of labial palp acute and finely serrate. Lateral margins of S6–9 serrate, lateral spines on S7–9; male epiproct with a pair of dorsal tubercles at basal 0.50. Differences with other species were found in 3rd antennomere, lateral spines of S7–9, and the caudal appendages. Epigomphus larvae inhabit small, shallow creeks (1st order streams) where they live in fine benthic sediments. When mature, the larva leaves the water in shady places, climbing small rocks at the water’s edge and metamorphosing horizontally on flat rocks. These new descriptions bring the total number of Epigomphus species with known larval stages to eight; only 28% of the species in this genus are known as larva. creator: Rodolfo Novelo-Gutiérrez creator: Alonso Ramírez creator: Débora Delgado uri: https://doi.org/10.7717/peerj.2338 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Novelo-Gutiérrez et al. title: You can hide but you can’t run: apparent competition, predator responses and the decline of Arctic ground squirrels in boreal forests of the southwest Yukon link: https://peerj.com/articles/2303 last-modified: 2016-08-23 description: Throughout much of North America’s boreal forest, the cyclical fluctuations of snowshoe hare populations (Lepus americanus) may cause other herbivores to become entrained in similar cycles. Alternating apparent competition via prey switching followed by positive indirect effects are the mechanisms behind this interaction. Our purpose is to document a change in the role of indirect interactions between sympatric populations of hares and arctic ground squirrels (Urocitellus parryii plesius), and to emphasize the influence of predation for controlling ground squirrel numbers. We used mark-recapture to estimate the population densities of both species over a 25-year period that covered two snowshoe hare cycles. We analysed the strength of association between snowshoe hare and ground squirrel numbers, and the changes to the seasonal and annual population growth rates of ground squirrels over time. A hyperbolic curve best describes the per capita rate of increase of ground squirrels relative to their population size, with a single stable equilibrium and a lower critical threshold below which populations drift to extinction. The crossing of this unstable boundary resulted in the subsequent uncoupling of ground squirrel and hare populations following the decline phase of their cycles in 1998. The implications are that this sustained Type II predator response led to the local extinction of ground squirrels. When few individuals are left in a colony, arctic ground squirrels may also have exhibited an Allee effect caused by the disruption of social signalling of approaching predators. creator: Jeffery R. Werner creator: Elizabeth A. Gillis creator: Rudy Boonstra creator: Charles J. Krebs uri: https://doi.org/10.7717/peerj.2303 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Werner et al. title: Sedimentology and ichnology of the Mafube dinosaur track site (Lower Jurassic, eastern Free State, South Africa): a report on footprint preservation and palaeoenvironment link: https://peerj.com/articles/2285 last-modified: 2016-08-23 description: Footprint morphology (e.g., outline shape, depth of impression) is one of the key diagnostic features used in the interpretation of ancient vertebrate tracks. Over 80 tridactyl tracks, confined to the same bedding surface in the Lower Jurassic Elliot Formation at Mafube (eastern Free State, South Africa), show large shape variability over the length of the study site. These morphological differences are considered here to be mainly due to variations in the substrate rheology as opposed to differences in the trackmaker’s foot anatomy, foot kinematics or recent weathering of the bedding surface. The sedimentary structures (e.g., desiccation cracks, ripple marks) preserved in association with and within some of the Mafube tracks suggest that the imprints were produced essentially contemporaneous and are true dinosaur tracks rather than undertracks or erosional remnants. They are therefore valuable not only for the interpretation of the ancient environment (i.e., seasonally dry river channels) but also for taxonomic assessments as some of them closely resemble the original anatomy of the trackmaker’s foot. The tracks are grouped, based on size, into two morphotypes that can be identified as Eubrontes-like and Grallator-like ichnogenera. The Mafube morphotypes are tentatively attributable to large and small tridactyl theropod trackmakers, possibly to Dracovenator and Coelophysis based on the following criteria: (a) lack of manus impressions indicative of obligate bipeds; (b) long, slender-digits that are asymmetrical and taper; (c) often end in a claw impression or point; and (d) the tracks that are longer than broad. To enable high-resolution preservation, curation and subsequent remote studying of the morphological variations of and the secondary features in the tracks, low viscosity silicone rubber was used to generate casts of the Mafube tracks. creator: Lara Sciscio creator: Emese M. Bordy creator: Mhairi Reid creator: Miengah Abrahams uri: https://doi.org/10.7717/peerj.2285 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Sciscio et al. title: Developmental toxicity from exposure to various forms of mercury compounds in medaka fish (Oryzias latipes) embryos link: https://peerj.com/articles/2282 last-modified: 2016-08-23 description: This study examined developmental toxicity of different mercury compounds, including some used in traditional medicines. Medaka (Oryzias latipes) embryos were exposed to 0.001–10 µM concentrations of MeHg, HgCl2, α-HgS (Zhu Sha), and β-HgS (Zuotai) from stage 10 (6–7 hpf) to 10 days post fertilization (dpf). Of the forms of mercury in this study, the organic form (MeHg) proved the most toxic followed by inorganic mercury (HgCl2), both producing embryo developmental toxicity. Altered phenotypes included pericardial edema with elongated or tube heart, reduction of eye pigmentation, and failure of swim bladder inflation. Both α-HgS and β-HgS were less toxic than MeHg and HgCl2. Total RNA was extracted from survivors three days after exposure to MeHg (0.1 µM), HgCl2 (1 µM), α-HgS (10 µM), or β-HgS (10 µM) to examine toxicity-related gene expression. MeHg and HgCl2 markedly induced metallothionein (MT) and heme oxygenase-1 (Ho-1), while α-HgS and β-HgS failed to induce either gene. Chemical forms of mercury compounds proved to be a major determinant in their developmental toxicity. creator: Wu Dong creator: Jie Liu creator: Lixin Wei creator: Yang Jingfeng creator: Melissa Chernick creator: David E. Hinton uri: https://doi.org/10.7717/peerj.2282 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Dong et al. title: In vitro evaluation of osteoprotegerin in chitosan for potential bone defect applications link: https://peerj.com/articles/2229 last-modified: 2016-08-23 description: BackgroundThe receptor activator of nuclear factor kappa-B (RANK)/RANK ligand/osteoprotegerin (OPG) system plays a critical role in bone remodelling by regulating osteoclast formation and activity. OPG has been used systemically in the treatment of bone diseases. In searching for more effective and safer treatment for bone diseases, we investigated newly formulated OPG-chitosan complexes, which is prepared as a local application for its osteogenic potential to remediate bone defects.MethodsWe examined high, medium and low molecular weights of chitosan combined with OPG. The cytotoxicity of OPG in chitosan and its proliferation in vitro was evaluated using normal, human periodontal ligament (NHPL) fibroblasts in 2D and 3D cell culture. The cytotoxicity of these combinations was compared by measuring cell survival with a tetrazolium salt reduction (MTT) assay and AlamarBlue assay. The cellular morphological changes were observed under an inverted microscope. A propidium iodide and acridine orange double-staining assay was used to evaluate the morphology and quantify the viable and nonviable cells. The expression level of osteopontin and osteocalcin protein in treated normal human osteoblast cells was evaluated by using Western blot.ResultsThe results demonstrated that OPG in combination with chitosan was non-toxic, and OPG combined with low molecular weight chitosan has the most significant effect on NHPL fibroblasts and stimulates proliferation of cells over the period of treatment. creator: Soher Nagi Jayash creator: Najihah M. Hashim creator: Misni Misran creator: NA Baharuddin uri: https://doi.org/10.7717/peerj.2229 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Jayash et al. title: Microendemicity in the northern Hajar Mountains of Oman and the United Arab Emirates with the description of two new species of geckos of the genus Asaccus (Squamata: Phyllodactylidae) link: https://peerj.com/articles/2371 last-modified: 2016-08-18 description: BackgroundThe Hajar Mountains of Oman and the United Arab Emirates (UAE) is the highest mountain range in Eastern Arabia. As a result of their old geological origin, geographical isolation, complex topography and local climate, these mountains provide an important refuge for endemic and relict species of plants and animals with strong Indo-Iranian affinities. Among vertebrates, the rock climbing nocturnal geckos of the genus Asaccus represent the genus with the highest number of endemic species in the Hajar Mountains. Recent taxonomic studies on the Zagros populations of Asaccus have shown that this genus is much richer than it was previously thought and preliminary morphological and molecular data suggest that its diversity in Arabia may also be underestimated.MethodsA total of 83 specimens originally classified as Asaccus caudivolvulus (including specimens of the two new species described herein), six other Asaccus species from the Hajar and the Zagros Mountains and two representatives of the genus Haemodracon were sequenced for up to 2,311 base pairs including the mitochondrial 12S and cytb and the nuclear c-mos, MC1R and ACM4 genes. Phylogenetic relationships were inferred using both Bayesian and maximum-likelihood approaches and the former method was also used to calibrate the phylogenetic tree. Haplotype networks and phylogenetic trees were inferred from the phased nuclear genes only. Sixty-one alcohol-preserved adult specimens originally classified as Asaccus caudivolvulus from the northern Hajar Mountains were examined for 13 morphometric and the five meristic variables using multivariate methods and were also used to diagnose and describe the two new species.ResultsThe results of the molecular and morphological analyses indicate that the species originally classified as Asaccus caudivolvulus is, in fact, an assemblage of three different species that started diversifying during the Mid-Miocene. The molecular phylogenies consistently recovered the Hajar endemic A. montanus as sister taxon to all the other Asaccus species included in the analyses, rendering the Arabian species of Asaccus polyphyletic.DiscussionUsing this integrative approach we have uncovered a very old diversification event that has resulted in a case of microendemicity, where three morphologically and ecologically similar medium-sized lizard species coexist in a very short and narrow mountain stretch. Asaccus caudivolvulus is restricted to a small coastal area of the UAE and at risk from heavy development, while the two new species described herein are widely distributed across the northern tip of the Hajar Mountains and seem to segregate in altitude when found in close proximity in the Musandam Peninsula (Oman). Similarly to other integrative analyses of Hajar reptiles, this study highlights the high level of diversity and endemicity of this arid mountain range, underscoring its status as one of the top hotspots of reptile diversity in Arabia. creator: Salvador Carranza creator: Marc Simó-Riudalbas creator: Sithum Jayasinghe creator: Thomas Wilms creator: Johannes Els uri: https://doi.org/10.7717/peerj.2371 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Carranza et al. title: Agricultural land-use change in a Mexican oligotrophic desert depletes ecosystem stability link: https://peerj.com/articles/2365 last-modified: 2016-08-18 description: BackgroundGlobal demand for food has led to increased land-use change, particularly in dry land ecosystems, which has caused several environmental problems due to the soil degradation. In the Cuatro Cienegas Basin (CCB), alfalfa production irrigated by flooding impacts strongly on the soil.MethodsIn order to analyze the effect of such agricultural land-use change on soil nutrient dynamics and soil bacterial community composition, this work examined an agricultural gradient within the CCB which was comprised of a native desert grassland, a plot currently cultivated with alfalfa and a former agricultural field that had been abandoned for over 30 years. For each site, we analyzed C, N and P dynamic fractions, the activity of the enzyme phosphatase and the bacterial composition obtained using 16S rRNA clone libraries.ResultsThe results showed that the cultivated site presented a greater availability of water and dissolved organic carbon, these conditions promoted mineralization processes mediated by heterotrophic microorganisms, while the abandoned land was limited by water and dissolved organic nitrogen. The low amount of dissolved organic matter promoted nitrification, which is mediated by autotrophic microorganisms. The microbial N immobilization process and specific phosphatase activity were both favored in the native grassland. As expected, differences in bacterial taxonomical composition were observed among sites. The abandoned site exhibited similar compositions than native grassland, while the cultivated site differed.DiscussionThe results suggest that the transformation of native grassland into agricultural land induces drastic changes in soil nutrient dynamics as well as in the bacterial community. However, with the absence of agricultural practices, some of the soil characteristics analyzed slowly recovers their natural state. creator: Natali Hernández-Becerra creator: Yunuen Tapia-Torres creator: Ofelia Beltrán-Paz creator: Jazmín Blaz creator: Valeria Souza creator: Felipe García-Oliva uri: https://doi.org/10.7717/peerj.2365 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Hernández-Becerra et al. title: Evaluation of outbreak response immunization in the control of pertussis using agent-based modeling link: https://peerj.com/articles/2337 last-modified: 2016-08-18 description: BackgroundPertussis control remains a challenge due to recently observed effects of waning immunity to acellular vaccine and suboptimal vaccine coverage. Multiple outbreaks have been reported in different ages worldwide. For certain outbreaks, public health authorities can launch an outbreak response immunization (ORI) campaign to control pertussis spread. We investigated effects of an outbreak response immunization targeting young adolescents in averting pertussis cases.MethodsWe developed an agent-based model for pertussis transmission representing disease mechanism, waning immunity, vaccination schedule and pathogen transmission in a spatially-explicit 500,000-person contact network representing a typical Canadian Public Health district. Parameters were derived from literature and calibration. We used published cumulative incidence and dose-specific vaccine coverage to calibrate the model’s epidemiological curves. We endogenized outbreak response by defining thresholds to trigger simulated immunization campaigns in the 10–14 age group offering 80% coverage. We ran paired simulations with and without outbreak response immunization and included those resulting in a single ORI within a 10-year span. We calculated the number of cases averted attributable to outbreak immunization campaign in all ages, in the 10–14 age group and in infants. The count of cases averted were tested using Mann–Whitney U test to determine statistical significance. Numbers needed to vaccinate during immunization campaign to prevent a single case in respective age groups were derived from the model. We varied adult vaccine coverage, waning immunity parameters, immunization campaign eligibility and tested stronger vaccination boosting effect in sensitivity analyses.Results189 qualified paired-runs were analyzed. On average, ORI was triggered every 26 years. On a per-run basis, there were an average of 124, 243 and 429 pertussis cases averted across all age groups within 1, 3 and 10 years of a campaign, respectively. During the same time periods, 53, 96, and 163 cases were averted in the 10–14 age group, and 6, 11, 20 in infants under 1 (p < 0.001, all groups). Numbers needed to vaccinate ranged from 49 to 221, from 130 to 519 and from 1,031 to 4,903 for all ages, the 10–14 age group and for infants, respectively. Most sensitivity analyses resulted in minimal impact on a number of cases averted.DiscussionOur model generated 30 years of longitudinal data to evaluate effects of outbreak response immunization in a controlled study. Immunization campaign implemented as an outbreak response measure among adolescents may confer benefits across all ages accruing over a 10-year period. Our inference is dependent on having an outbreak of significant magnitude affecting predominantly the selected age and achieving a comprehensive vaccine coverage during the campaign. Economic evaluations and comparisons with other control measures can add to conclusions generated by our work. creator: Alexander Doroshenko creator: Weicheng Qian creator: Nathaniel D. Osgood uri: https://doi.org/10.7717/peerj.2337 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Doroshenko et al. title: Population genetic structure between Yap and Palau for the coral Acropora hyacinthus link: https://peerj.com/articles/2330 last-modified: 2016-08-18 description: Information on connectivity is becoming increasingly in demand as marine protected areas are being designed as an integral part of a network to protect marine resources at the ecosystem level. Larval dispersal and population structure, however, remain very difficult to assess. Here, we tested the predictions of a detailed oceanographic connectivity model of larval dispersal and coral recruitment within Palau and between Palau and Yap, which was developed to support the review of the existing network of marine protected areas in Palau. We used high throughput microsatellite genotyping of the coral Acropora hyacinthus to characterize population genetic structure. Pairwise F′ST values between Palau and Yap (0.10), Palau and Ngulu (0.09) and Yap and Ngulu (0.09) were all significant and similar to pairwise F′ST values of sites within Palau (0.02–0.12) and within Yap (0.02–0.09) highlighting structure at island scale and indicating that recruitment may be even more localized than previously anticipated. A bottleneck test did not reveal any signs of a founder effect between Yap and Palau. Overall, the data supports the idea that recovery of A. hyacinthus in Palau did not come exclusively from a single source but most likely came from a combination of areas, including sites within Palau. In light of these results there seems to be very little connectivity around the barrier reef and management recommendation would be to increase the number or the size of MPAs within Palau. creator: Annick Cros creator: Robert J. Toonen creator: Sarah W. Davies creator: Stephen A. Karl uri: https://doi.org/10.7717/peerj.2330 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Cros et al. title: A resource-based game theoretical approach for the paradox of the plankton link: https://peerj.com/articles/2329 last-modified: 2016-08-18 description: The maintenance of species diversity is a central focus in ecology. It is not rare to observe more species than the number of limiting resources, especially in plankton communities. However, such high species diversity is hard to achieve in theory under the competitive exclusion principles, known as the plankton paradox. Previous studies often focus on the coexistence of predefined species and ignore the fact that species can evolve. We model multi-resource competitions using evolutionary games, where the number of species fluctuates under extinction and the appearance of new species. The interspecific and intraspecific competitions are captured by a dynamical payoff matrix, which has a size of the number of species. The competition strength (payoff entries) is obtained from comparing the capability of species in consuming resources, which can change over time. This allows for the robust coexistence of a large number of species, providing a possible solution to the plankton paradox. creator: Weini Huang creator: Paulo Roberto de Araujo Campos creator: Viviane Moraes de Oliveira creator: Fernando Fagundes Ferrreira uri: https://doi.org/10.7717/peerj.2329 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Huang et al. title: Effects of social isolation and re-socialization on cognition and ADAR1 (p110) expression in mice link: https://peerj.com/articles/2306 last-modified: 2016-08-18 description: It has been reported that social isolation stress could be a key factor that leads to cognitive deficit for both humans and rodent models. However, detailed mechanisms are not yet clear. ADAR1 (Adenosine deaminase acting on RNA) is an enzyme involved in RNA editing that has a close relation to cognitive function. We have hypothesized that social isolation stress may impact the expression of ADAR1 in the brain of mice with cognitive deficit. To test our hypothesis, we evaluated the cognition ability of mice isolated for different durations (2, 4, and 8 weeks) using object recognition and object location tests; we also measured ADAR1 expression in hippocampus and cortex using immunohistochemistry and western blot. Our study showed that social isolation stress induced spatial and non-spatial cognition deficits of the tested mice. In addition, social isolation significantly increased both the immunoreactivity and protein expression of ADAR1 (p110) in the hippocampus and frontal cortex. Furthermore, re-socialization could not only recover the cognition deficits, but also bring ADAR1 (p110) immunoreactivity of hippocampus and frontal cortex, as well as ADAR1 (p110) protein expression of hippocampus back to the normal level for the isolated mice in adolescence. In conclusion, social isolation stress significantly increases ADAR1 (p110) expression in the hippocampus and frontal cortex of the mice with cognitive deficit. This finding may open a window to better understand the reasons (e.g., epigenetic change) that are responsible for social isolation-induced cognitive deficit and help the development of novel therapies for the resulted diseases. creator: Wei Chen creator: Dong An creator: Hong Xu creator: Xiaoxin Cheng creator: Shiwei Wang creator: Weizhi Yu creator: Deqin Yu creator: Dan Zhao creator: Yiping Sun creator: Wuguo Deng creator: Yiyuan Tang creator: Shengming Yin uri: https://doi.org/10.7717/peerj.2306 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Chen et al. title: Temporal overlaps of feral cats with prey and competitors in primary and human-altered habitats on Bohol Island, Philippines link: https://peerj.com/articles/2288 last-modified: 2016-08-18 description: The vertebrate fauna of the Philippines, known for its diversity and high proportion of endemic species, comprises mainly small- to medium-sized forms with a few large exceptions. As with other tropical ecosystems, the major threats to wildlife are habitat loss, hunting and invasive species, of which the feral cat (Felis catus) is considered the most damaging. Our camera-trapping study focused on a terrestrial vertebrate species inventory on Bohol Island and tempo-spatial co-occurrences of feral cats with their prey and competitors. The survey took place in the Rajah Sikatuna Protected Landscape, and we examined the primary rainforest, its border with agricultural land, and rural areas in the vicinity of villages. Altogether, over 2,885 trap days we captured 30 species of vertebrates–10 mammals (including Sus philippensis), 19 birds and one reptile, Varanus cumingi. We trapped 81.8% of expected vertebrates. Based on the number of events, the most frequent native species was the barred rail (Gallirallus torquatus). The highest overlap in diel activity between cats and potential prey was recorded with rodents in rural areas (Δ = 0.62); the lowest was in the same habitat with ground-dwelling birds (Δ = 0.40). Cat activity was not recorded inside the rainforest; in other habitats their diel activity pattern differed. The cats’ activity declined in daylight in the proximity of humans, while it peaked at the transition zone between rainforest and fields. Both rodents and ground-dwelling birds exhibited a shift in activity levels between sites where cats were present or absent. Rodents tend to become active by day in cat-free habitats. No cats’ temporal response to co-occurrences of civets (Paradoxurus hermaphroditus and Viverra tangalunga) was found but cats in diel activity avoided domestic dogs (Canis lupus familiaris). Our first insight into the ecology of this invasive predator in the Philippines revealed an avoidance of homogeneous primary rainforest and a tendency to forage close to human settlements in heterogeneous habitats. A detailed further investigation of the composition of the cat’s diet, as well as ranging pattern, is still needed. creator: Vlastimil Bogdan creator: Tomáš Jůnek creator: Pavla Jůnková Vymyslická uri: https://doi.org/10.7717/peerj.2288 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Bogdan et al. title: Microbe-ID: an open source toolbox for microbial genotyping and species identification link: https://peerj.com/articles/2279 last-modified: 2016-08-18 description: Development of tools to identify species, genotypes, or novel strains of invasive organisms is critical for monitoring emergence and implementing rapid response measures. Molecular markers, although critical to identifying species or genotypes, require bioinformatic tools for analysis. However, user-friendly analytical tools for fast identification are not readily available. To address this need, we created a web-based set of applications called Microbe-ID that allow for customizing a toolbox for rapid species identification and strain genotyping using any genetic markers of choice. Two components of Microbe-ID, named Sequence-ID and Genotype-ID, implement species and genotype identification, respectively. Sequence-ID allows identification of species by using BLAST to query sequences for any locus of interest against a custom reference sequence database. Genotype-ID allows placement of an unknown multilocus marker in either a minimum spanning network or dendrogram with bootstrap support from a user-created reference database. Microbe-ID can be used for identification of any organism based on nucleotide sequences or any molecular marker type and several examples are provided. We created a public website for demonstration purposes called Microbe-ID (microbe-id.org) and provided a working implementation for the genus Phytophthora (phytophthora-id.org). In Phytophthora-ID, the Sequence-ID application allows identification based on ITS or cox spacer sequences. Genotype-ID groups individuals into clonal lineages based on simple sequence repeat (SSR) markers for the two invasive plant pathogen species P. infestans and P. ramorum. All code is open source and available on github and CRAN. Instructions for installation and use are provided at https://github.com/grunwaldlab/Microbe-ID. creator: Javier F. Tabima creator: Sydney E. Everhart creator: Meredith M. Larsen creator: Alexandra J. Weisberg creator: Zhian N. Kamvar creator: Matthew A. Tancos creator: Christine D. Smart creator: Jeff H. Chang creator: Niklaus J. Grünwald uri: https://doi.org/10.7717/peerj.2279 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Tabima et al. title: Isolation of an antimicrobial compound produced by bacteria associated with reef-building corals link: https://peerj.com/articles/2275 last-modified: 2016-08-18 description: Bacterial communities associated with healthy corals produce antimicrobial compounds that inhibit the colonization and growth of invasive microbes and potential pathogens. To date, however, bacteria-derived antimicrobial molecules have not been identified in reef-building corals. Here, we report the isolation of an antimicrobial compound produced by Pseudovibrio sp. P12, a common and abundant coral-associated bacterium. This strain was capable of metabolizing dimethylsulfoniopropionate (DMSP), a sulfur molecule produced in high concentrations by reef-building corals and playing a role in structuring their bacterial communities. Bioassay-guided fractionation coupled with nuclear magnetic resonance (NMR) and mass spectrometry (MS), identified the antimicrobial as tropodithietic acid (TDA), a sulfur-containing compound likely derived from DMSP catabolism. TDA was produced in large quantities by Pseudovibrio sp., and prevented the growth of two previously identified coral pathogens, Vibrio coralliilyticus and V. owensii, at very low concentrations (0.5 μg/mL) in agar diffusion assays. Genome sequencing of Pseudovibrio sp. P12 identified gene homologs likely involved in the metabolism of DMSP and production of TDA. These results provide additional evidence for the integral role of DMSP in structuring coral-associated bacterial communities and underline the potential of these DMSP-metabolizing microbes to contribute to coral disease prevention. creator: Jean-Baptiste Raina creator: Dianne Tapiolas creator: Cherie A. Motti creator: Sylvain Foret creator: Torsten Seemann creator: Jan Tebben creator: Bette L. Willis creator: David G. Bourne uri: https://doi.org/10.7717/peerj.2275 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Raina et al. title: Diet of otters (Lutra lutra) in various habitat types in the Pannonian biogeographical region compared to other regions of Europe link: https://peerj.com/articles/2266 last-modified: 2016-08-18 description: Knowledge of the effect of habitat type and region on diet and feeding behaviours of a species facilitates a better understanding of factors impacting populations, which contributes to effective conservation management. Using spraint analysis and relative frequency of occurrence data from the literature, we described the dietary patterns of Eurasian otters (Lutra lutra) in 23 study sites within the Pannonian biogeographical region in Hungary. Our results indicated that diet composition varied by habitat type and is therefore context dependant. The differences among habitat types were however lower than expected. We noticed a decline in the fish consumption with a concomitant increase in trophic niche breadth and amphibian consumption in rivers, ponds (fish farms), backwaters, marshes and small watercourses. The main differences in diet were not attributed to the consumption of primary and secondary food types (fish and amphibians), but rather to differences in other, less important food types (mammals, birds). Using hierarchical cluster analysis, rivers and ponds could clearly be separated from other habitat types. We found the main fish diet of otters in most of these areas consisted of small (<100 g), eurytopic, littoral and non-native, mostly invasive species. Dietary studies from 91 sites in six European biogeographical regions showed that fish are consumed most frequently in the Atlantic and Boreal, less in the Continental and Pannonian, and least in the Alpine and Mediterranean regions. Comparative analysis indicated that the Mediterranean region (with frequent crayfish consumption) and Alpine region (frequent amphibian consumption) cluster separate from the other regions. creator: József Lanszki creator: István Lehoczky creator: Antoinette Kotze creator: Michael J. Somers uri: https://doi.org/10.7717/peerj.2266 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Lanszki et al. title: Proteomic profiling analysis reveals that glutathione system plays important roles responding to osmotic stress in wheat (Triticum aestivum L.) roots link: https://peerj.com/articles/2334 last-modified: 2016-08-17 description: Wheat is one of the most important crops in the world, and osmotic stress has become one of the main factors affecting wheat production. Understanding the mechanism of the response of wheat to osmotic stress would be greatly significant. In the present study, isobaric tag for relative and absolute quantification (iTRAQ) was used to analyze the changes of protein expression in the wheat roots exposed to different osmotic stresses. A total of 2,228 expressed proteins, including 81 differentially expressed proteins, between osmotic stress and control, were found. The comprehensive analysis of these differentially expressed proteins revealed that osmotic stress increased the variety of expressed proteins and suppressed the quantity of expressed proteins in wheat roots. Furthermore, the proteins for detoxifying and reactive oxygen species scavenging, especially the glutathione system, played important roles in maintaining organism balance in response to osmotic stress in wheat roots. Thus, the present study comprehensively describes the protein expression changes in wheat roots in response to osmotic stress, providing firmer foundation to further study the mechanism of osmotic resistance in wheat. creator: Jianhui Ma creator: Wen Dong creator: Daijing Zhang creator: Xiaolong Gao creator: Lina Jiang creator: Yun Shao creator: Doudou Tong creator: Chunxi Li uri: https://doi.org/10.7717/peerj.2334 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Ma et al. title: Effects of origin, seasons and storage under different temperatures on germination of Senecio vulgaris (Asteraceae) seeds link: https://peerj.com/articles/2346 last-modified: 2016-08-17 description: Invasive plants colonize new environments, become pests and cause biodiversity loss, economic loss and health damage. Senecio vulgaris L. (Common groundsel, Asteraceae), a widely distributing cosmopolitan weed in the temperate area, is reported with large populations in the north–eastern and south–western part, but not in southern, central, or north-western parts of China. We studied the germination behavior of S. vulgaris to explain the distribution and the biological invasion of this species in China. We used seeds originating from six native and six invasive populations to conduct germination experiments in a climate chamber and under outdoor condition. When incubated in a climate chamber (15 °C), seeds from the majority of the populations showed >90% germination percentage (GP) and the GP was equal for seeds with a native and invasive origin. The mean germination time (MGT) was significantly different among the populations. Under outdoor conditions, significant effects of origin, storage conditions (stored at 4 °C or ambient room temperature, ca. 27 °C) and seasons (in summer or autumn) were observed on the GP while the MGT was only affected by the season. In autumn, the GP (38.6%) was higher and the MGT was slightly longer than that in summer. In autumn, seeds stored at 4 °C showed higher GP than those stored at ambient room temperature (ca.27 °C), and seeds from invasive populations revealed higher GP than those from native populations. The results implied that the high temperature in summer has a negative impact on the germination and might cause viability loss or secondary dormancy to S. vulgaris seeds. Our study offers a clue to exploring what factor limits the distribution of S. vulgaris in China by explaining why, in the cities in South-East China and central China such as Wuhan, S. vulgaris cannot establish natural and viable populations. creator: Noel Ndihokubwayo creator: Viet-Thang Nguyen creator: Dandan Cheng uri: https://doi.org/10.7717/peerj.2346 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Ndihokubwayo et al. title: Selection of a marker gene to construct a reference library for wetland plants, and the application of metabarcoding to analyze the diet of wintering herbivorous waterbirds link: https://peerj.com/articles/2345 last-modified: 2016-08-17 description: Food availability and diet selection are important factors influencing the abundance and distribution of wild waterbirds. In order to better understand changes in waterbird population, it is essential to figure out what they feed on. However, analyzing their diet could be difficult and inefficient using traditional methods such as microhistologic observation. Here, we addressed this gap of knowledge by investigating the diet of greater white-fronted goose Anser albifrons and bean goose Anser fabalis, which are obligate herbivores wintering in China, mostly in the Middle and Lower Yangtze River floodplain. First, we selected a suitable and high-resolution marker gene for wetland plants that these geese would consume during the wintering period. Eight candidate genes were included: rbcL, rpoC1, rpoB, matK, trnH-psbA, trnL (UAA), atpF-atpH, and psbK-psbI. The selection was performed via analysis of representative sequences from NCBI and comparison of amplification efficiency and resolution power of plant samples collected from the wintering area. The trnL gene was chosen at last with c/h primers, and a local plant reference library was constructed with this gene. Then, utilizing DNA metabarcoding, we discovered 15 food items in total from the feces of these birds. Of the 15 unique dietary sequences, 10 could be identified at specie level. As for greater white-fronted goose, 73% of sequences belonged to Poaceae spp., and 26% belonged to Carex spp. In contrast, almost all sequences of bean goose belonged to Carex spp. (99%). Using the same samples, microhistology provided consistent food composition with metabarcoding results for greater white-fronted goose, while 13% of Poaceae was recovered for bean goose. In addition, two other taxa were discovered only through microhistologic analysis. Although most of the identified taxa matched relatively well between the two methods, DNA metabarcoding gave taxonomically more detailed information. Discrepancies were likely due to biased PCR amplification in metabarcoding, low discriminating power of current marker genes for monocots, and biases in microhistologic analysis. The diet differences between two geese species might indicate deeper ecological significance beyond the scope of this study. We concluded that DNA metabarcoding provides new perspectives for studies of herbivorous waterbird diets and inter-specific interactions, as well as new possibilities to investigate interactions between herbivores and plants. In addition, microhistologic analysis should be used together with metabarcoding methods to integrate this information. creator: Yuzhan Yang creator: Aibin Zhan creator: Lei Cao creator: Fanjuan Meng creator: Wenbin Xu uri: https://doi.org/10.7717/peerj.2345 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Yang et al. title: MOST: a modified MLST typing tool based on short read sequencing link: https://peerj.com/articles/2308 last-modified: 2016-08-17 description: Multilocus sequence typing (MLST) is an effective method to describe bacterial populations. Conventionally, MLST involves Polymerase Chain Reaction (PCR) amplification of housekeeping genes followed by Sanger DNA sequencing. Public Health England (PHE) is in the process of replacing the conventional MLST methodology with a method based on short read sequence data derived from Whole Genome Sequencing (WGS). This paper reports the comparison of the reliability of MLST results derived from WGS data, comparing mapping and assembly-based approaches to conventional methods using 323 bacterial genomes of diverse species. The sensitivity of the two WGS based methods were further investigated with 26 mixed and 29 low coverage genomic data sets from Salmonella enteridis and Streptococcus pneumoniae. Of the 323 samples, 92.9% (n = 300), 97.5% (n = 315) and 99.7% (n = 322) full MLST profiles were derived by the conventional method, assembly- and mapping-based approaches, respectively. The concordance between samples that were typed by conventional (92.9%) and both WGS methods was 100%. From the 55 mixed and low coverage genomes, 89.1% (n = 49) and 67.3% (n = 37) full MLST profiles were derived from the mapping and assembly based approaches, respectively. In conclusion, deriving MLST from WGS data is more sensitive than the conventional method. When comparing WGS based methods, the mapping based approach was the most sensitive. In addition, the mapping based approach described here derives quality metrics, which are difficult to determine quantitatively using conventional and WGS-assembly based approaches. creator: Rediat Tewolde creator: Timothy Dallman creator: Ulf Schaefer creator: Carmen L. Sheppard creator: Philip Ashton creator: Bruno Pichon creator: Matthew Ellington creator: Craig Swift creator: Jonathan Green creator: Anthony Underwood uri: https://doi.org/10.7717/peerj.2308 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Tewolde et al. title: Detection of a Yersinia pestis gene homologue in rodent samples link: https://peerj.com/articles/2216 last-modified: 2016-08-17 description: A homologue to a widely used genetic marker, pla, for Yersinia pestis has been identified in tissue samples of two species of rat (Rattus rattus and Rattus norvegicus) and of mice (Mus musculus and Apodemus sylvaticus) using a microarray based platform to screen for zoonotic pathogens of interest. Samples were from urban locations in the UK (Liverpool) and Canada (Vancouver). The results indicate the presence of an unknown bacterium that shares a homologue for the pla gene of Yersinia pestis, so caution should be taken when using this gene as a diagnostic marker. creator: Timothy A. Giles creator: Alex D. Greenwood creator: Kyriakos Tsangaras creator: Tom C. Giles creator: Paul A. Barrow creator: Duncan Hannant creator: Abu-Bakr Abu-Median creator: Lisa Yon uri: https://doi.org/10.7717/peerj.2216 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Giles et al. title: Arktocara yakataga, a new fossil odontocete (Mammalia, Cetacea) from the Oligocene of Alaska and the antiquity of Platanistoidea link: https://peerj.com/articles/2321 last-modified: 2016-08-16 description: The diversification of crown cetacean lineages (i.e., crown Odontoceti and crown Mysticeti) occurred throughout the Oligocene, but it remains an ongoing challenge to resolve the phylogenetic pattern of their origins, especially with respect to stem lineages. One extant monotypic lineage, Platanista gangetica (the Ganges and Indus river dolphin), is the sole surviving member of the broader group Platanistoidea, with many fossil relatives that range from Oligocene to Miocene in age. Curiously, the highly threatened Platanista is restricted today to freshwater river systems of South Asia, yet nearly all fossil platanistoids are known globally from marine rocks, suggesting a marine ancestry for this group. In recent years, studies on the phylogenetic relationships in Platanistoidea have reached a general consensus about the membership of different sub-clades and putative extinct groups, although the position of some platanistoid groups (e.g., Waipatiidae) has been contested. Here we describe a new genus and species of fossil platanistoid, Arktocara yakataga, gen. et sp. nov. from the Oligocene of Alaska, USA. The type and only known specimen was collected from the marine Poul Creek Formation, a unit known to include Oligocene strata, exposed in the Yakutat City and Borough of Southeast Alaska. In our phylogenetic analysis of stem and node-based Platanistoidea, Arktocara falls within the node-based sub-clade Allodelphinidae as the sister taxon to Allodelphis pratti. With a geochronologic age between ∼29–24 million years old, Arktocara is among the oldest crown Odontoceti, reinforcing the long-standing view that the diversification for crown lineages must have occurred no later than the early Oligocene. creator: Alexandra T. Boersma creator: Nicholas D. Pyenson uri: https://doi.org/10.7717/peerj.2321 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Boersma and Pyenson title: Ancient phylogenetic divergence of the enigmatic African rodent Zenkerella and the origin of anomalurid gliding link: https://peerj.com/articles/2320 last-modified: 2016-08-16 description: The “scaly-tailed squirrels” of the rodent family Anomaluridae have a long evolutionary history in Africa, and are now represented by two gliding genera (Anomalurus and Idiurus) and a rare and obscure genus (Zenkerella) that has never been observed alive by mammalogists. Zenkerella shows no anatomical adaptations for gliding, but has traditionally been grouped with the glider Idiurus on the basis of craniodental similarities, implying that either the Zenkerella lineage lost its gliding adaptations, or that Anomalurus and Idiurus evolved theirs independently. Here we present the first nuclear and mitochondrial DNA sequences of Zenkerella, based on recently recovered whole-body specimens from Bioko Island (Equatorial Guinea), which show unambiguously that Zenkerella is the sister taxon of Anomalurus and Idiurus. These data indicate that gliding likely evolved only once within Anomaluridae, and that there were no subsequent evolutionary reversals. We combine this new molecular evidence with morphological data from living and extinct anomaluromorph rodents and estimate that the lineage leading to Zenkerella has been evolving independently in Africa since the early Eocene, approximately 49 million years ago. Recently discovered fossils further attest to the antiquity of the lineage leading to Zenkerella, which can now be recognized as a classic example of a “living fossil,” about which we know remarkably little. The osteological markers of gliding are estimated to have evolved along the stem lineage of the Anomalurus–Idiurus clade by the early Oligocene, potentially indicating that this adaptation evolved in response to climatic perturbations at the Eocene–Oligocene boundary (∼34 million years ago). creator: Steven Heritage creator: David Fernández creator: Hesham M. Sallam creator: Drew T. Cronin creator: José Manuel Esara Echube creator: Erik R. Seiffert uri: https://doi.org/10.7717/peerj.2320 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Heritage et al. title: The adder (Vipera berus) in Southern Altay Mountains: population characteristics, distribution, morphology and phylogenetic position link: https://peerj.com/articles/2342 last-modified: 2016-08-16 description: As the most widely distributed snake in Eurasia, the adder (Vipera berus) has been extensively investigated in Europe but poorly understood in Asia. The Southern Altay Mountains represent the adder’s southern distribution limit in Central Asia, whereas its population status has never been assessed. We conducted, for the first time, field surveys for the adder at two areas of Southern Altay Mountains using a combination of line transects and random searches. We also described the morphological characteristics of the collected specimens and conducted analyses of external morphology and molecular phylogeny. The results showed that the adder distributed in both survey sites and we recorded a total of 34 sightings. In Kanas river valley, the estimated encounter rate over a total of 137 km transects was 0.15 ± 0.05 sightings/km. The occurrence of melanism was only 17%. The small size was typical for the adders in Southern Altay Mountains in contrast to other geographic populations of the nominate subspecies. A phylogenetic tree obtained by Bayesian Inference based on DNA sequences of the mitochondrial cytochrome b (1,023 bp) grouped them within the Northern clade of the species but failed to separate them from the subspecies V. b. sachalinensis. Our discovery extends the distribution range of V. berus and provides a basis for further researches. We discuss the hypothesis that the adder expands its distribution border to the southwest along the mountains’ elevation gradient, but the population abundance declines gradually due to a drying climate. creator: Shaopeng Cui creator: Xiao Luo creator: Daiqiang Chen creator: Jizhou Sun creator: Hongjun Chu creator: Chunwang Li creator: Zhigang Jiang uri: https://doi.org/10.7717/peerj.2342 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Cui et al. title: Evolution of morphological and climatic adaptations in Veronica L. (Plantaginaceae) link: https://peerj.com/articles/2333 last-modified: 2016-08-16 description: Perennials and annuals apply different strategies to adapt to the adverse environment, based on ‘tolerance’ and ‘avoidance’, respectively. To understand lifespan evolution and its impact on plant adaptability, we carried out a comparative study of perennials and annuals in the genus Veronica from a phylogenetic perspective. The results showed that ancestors of the genus Veronicawere likely to be perennial plants. Annual life history of Veronica has evolved multiple times and subtrees with more annual species have a higher substitution rate. Annuals can adapt to more xeric habitats than perennials. This indicates that annuals are more drought-resistant than their perennial relatives. Due to adaptation to similar selective pressures, parallel evolution occurs in morphological characters among annual species of Veronica. creator: Jian-Cheng Wang creator: Bo-Rong Pan creator: Dirk C. Albach uri: https://doi.org/10.7717/peerj.2333 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Wang et al. title: The health care and life sciences community profile for dataset descriptions link: https://peerj.com/articles/2331 last-modified: 2016-08-16 description: Access to consistent, high-quality metadata is critical to finding, understanding, and reusing scientific data. However, while there are many relevant vocabularies for the annotation of a dataset, none sufficiently captures all the necessary metadata. This prevents uniform indexing and querying of dataset repositories. Towards providing a practical guide for producing a high quality description of biomedical datasets, the W3C Semantic Web for Health Care and the Life Sciences Interest Group (HCLSIG) identified Resource Description Framework (RDF) vocabularies that could be used to specify common metadata elements and their value sets. The resulting guideline covers elements of description, identification, attribution, versioning, provenance, and content summarization. This guideline reuses existing vocabularies, and is intended to meet key functional requirements including indexing, discovery, exchange, query, and retrieval of datasets, thereby enabling the publication of FAIR data. The resulting metadata profile is generic and could be used by other domains with an interest in providing machine readable descriptions of versioned datasets. creator: Michel Dumontier creator: Alasdair J.G. Gray creator: M. Scott Marshall creator: Vladimir Alexiev creator: Peter Ansell creator: Gary Bader creator: Joachim Baran creator: Jerven T. Bolleman creator: Alison Callahan creator: José Cruz-Toledo creator: Pascale Gaudet creator: Erich A. Gombocz creator: Alejandra N. Gonzalez-Beltran creator: Paul Groth creator: Melissa Haendel creator: Maori Ito creator: Simon Jupp creator: Nick Juty creator: Toshiaki Katayama creator: Norio Kobayashi creator: Kalpana Krishnaswami creator: Camille Laibe creator: Nicolas Le Novère creator: Simon Lin creator: James Malone creator: Michael Miller creator: Christopher J. Mungall creator: Laurens Rietveld creator: Sarala M. Wimalaratne creator: Atsuko Yamaguchi uri: https://doi.org/10.7717/peerj.2331 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Dumontier et al. title: Moderate evidence for a Lombard effect in a phylogenetically basal primate link: https://peerj.com/articles/2328 last-modified: 2016-08-16 description: When exposed to enhanced background noise, humans avoid signal masking by increasing the amplitude of the voice, a phenomenon termed the Lombard effect. This auditory feedback-mediated voice control has also been found in monkeys, bats, cetaceans, fish and some frogs and birds. We studied the Lombard effect for the first time in a phylogenetically basal primate, the grey mouse lemur, Microcebus murinus. When background noise was increased, mouse lemurs were able to raise the amplitude of the voice, comparable to monkeys, but they did not show this effect consistently across context/individuals. The Lombard effect, even if representing a generic vocal communication system property of mammals, may thus be affected by more complex mechanisms. The present findings emphasize an effect of context, and individual, and the need for further standardized approaches to disentangle the multiple system properties of mammalian vocal communication, important for understanding the evolution of the unique human faculty of speech and language. creator: Christian Schopf creator: Sabine Schmidt creator: Elke Zimmermann uri: https://doi.org/10.7717/peerj.2328 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Schopf et al. title: On the diversity of the SE Indo-Pacific species of Terebellides (Annelida; Trichobranchidae), with the description of a new species link: https://peerj.com/articles/2313 last-modified: 2016-08-16 description: The study of material collected during routine monitoring surveys dealing with oil extraction and aquaculture in waters off Myanmar (North Andaman Sea) and in the Gulf of Thailand, respectively, allowed us to analyse the taxonomy and diversity of the polychaete genus Terebellides (Annelida). Three species were found, namely Terebellides cf. woolawa, Terebellides hutchingsaespec. nov. (a new species fully described and illustrated), and Terebellides sp. (likely a new species, but with only one available specimen). The new species is characterised by the combination of some branchial (number, fusion and relative length of lobes and papillation of lamellae), and thoracic (lateral lobes and relative length of notopodia) characters and is compared with all species described or reported in the SW Indo-Pacific area, as well as with those sharing similar morphological characteristics all around the world. The taxonomic relevance of the relative length of branchial lobes and different types of ciliature in branchial lamellae for species discrimination in the genus is discussed. A key to all Terebellides species described in SE Indo-Pacific waters is presented. creator: Julio Parapar creator: Juan Moreira creator: Daniel Martin uri: https://doi.org/10.7717/peerj.2313 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Parapar et al. title: An energetics-based honeybee nectar-foraging model used to assess the potential for landscape-level pesticide exposure dilution link: https://peerj.com/articles/2293 last-modified: 2016-08-16 description: Estimating the exposure of honeybees to pesticides on a landscape scale requires models of their spatial foraging behaviour. For this purpose, we developed a mechanistic, energetics-based model for a single day of nectar foraging in complex landscape mosaics. Net energetic efficiency determined resource patch choice. In one version of the model a single optimal patch was selected each hour. In another version, recruitment of foragers was simulated and several patches could be exploited simultaneously. Resource availability changed during the day due to depletion and/or intrinsic properties of the resource (anthesis). The model accounted for the impact of patch distance and size, resource depletion and replenishment, competition with other nectar foragers, and seasonal and diurnal patterns in availability of nectar-providing crops and wild flowers. From the model we derived simple rules for resource patch selection, e.g., for landscapes with mass-flowering crops only, net energetic efficiency would be proportional to the ratio of the energetic content of the nectar divided by distance to the hive. We also determined maximum distances at which resources like oilseed rape and clover were still energetically attractive. We used the model to assess the potential for pesticide exposure dilution in landscapes of different composition and complexity. Dilution means a lower concentration in nectar arriving at the hive compared to the concentration in nectar at a treated field and can result from foraging effort being diverted away from treated fields. Applying the model for all possible hive locations over a large area, distributions of dilution factors were obtained that were characterised by their 90-percentile value. For an area for which detailed spatial data on crops and off-field semi-natural habitats were available, we tested three landscape management scenarios that were expected to lead to exposure dilution: providing alternative resources than the target crop (oilseed rape) in the form of (i) other untreated crop fields, (ii) flower strips of different widths at field edges (off-crop in-field resources), and (iii) resources on off-field (semi-natural) habitats. For both model versions, significant dilution occurred only when alternative resource patches were equal or more attractive than oilseed rape, nearby and numerous and only in case of flower strips and off-field habitats. On an area-base, flower strips were more than one order of magnitude more effective than off-field habitats, the main reason being that flower strips had an optimal location. The two model versions differed in the predicted number of resource patches exploited over the day, but mainly in landscapes with numerous small resource patches. In landscapes consisting of few large resource patches (crop fields) both versions predicted the use of a small number of patches. creator: Johannes M. Baveco creator: Andreas Focks creator: Dick Belgers creator: Jozef J.M. van der Steen creator: Jos J.T.I. Boesten creator: Ivo Roessink uri: https://doi.org/10.7717/peerj.2293 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Baveco et al. title: Experimental exposure to urban and pink noise affects brain development and song learning in zebra finches (Taenopygia guttata) link: https://peerj.com/articles/2287 last-modified: 2016-08-16 description: Recently, numerous studies have observed changes in bird vocalizations—especially song—in urban habitats. These changes are often interpreted as adaptive, since they increase the active space of the signal in its environment. However, the proximate mechanisms driving cross-generational changes in song are still unknown. We performed a captive experiment to identify whether noise experienced during development affects song learning and the development of song-control brain regions. Zebra finches (Taeniopygia guttata) were bred while exposed, or not exposed, to recorded traffic urban noise (Study 1) or pink noise (Study 2). We recorded the songs of male offspring and compared these to fathers’ songs. We also measured baseline corticosterone and measured the size of song-control brain regions when the males reached adulthood (Study 1 only). While male zebra finches tended to copy syllables accurately from tutors regardless of noise environment, syntax (the ordering of syllables within songs) was incorrectly copied affected by juveniles exposed to noise. Noise did not affect baseline corticosterone, but did affect the size of brain regions associated with song learning: these regions were smaller in males that had been had been exposed to recorded traffic urban noise in early development. These findings provide a possible mechanism by which noise affects behaviour, leading to potential population differences between wild animals occupying noisier urban environments compared with those in quieter habitats. creator: Dominique A. Potvin creator: Michael T. Curcio creator: John P. Swaddle creator: Scott A. MacDougall-Shackleton uri: https://doi.org/10.7717/peerj.2287 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Potvin et al. title: Effect of wetland management: are lentic wetlands refuges of plant-species diversity in the Andean–Orinoco Piedmont of Colombia? link: https://peerj.com/articles/2267 last-modified: 2016-08-16 description: Accelerated degradation of the wetlands and fragmentation of surrounding vegetation in the Andean–Orinoco Piedmont are the main threats to diversity and ecological integrity of these ecosystems; however, information on this topic is of limited availability. In this region, we evaluated the value of 37 lentic wetlands as reservoirs of woody and aquatic plants and analyzed diversity and changes in species composition within and among groups defined according to management given by: (1) type (swamps, heronries, rice fields, semi-natural lakes, constructed lakes and fish farms) and (2) origins (natural, mixed and artificial). A total of 506 plant species were recorded: 80% woody and 20% aquatic. Of these, 411 species (81%) were considered species typical of the area (Meta Piedmont distribution). Diversity patterns seem to be driven by high landscape heterogeneity and wetland management. The fish farms presented the highest diversity of woody plants, while swamps ranked highest for aquatic plant diversity. Regarding wetland origin, the artificial systems were the most diverse, but natural wetlands presented the highest diversity of typical species and can therefore be considered representative ecosystems at the regional scale. Our results suggest that lentic wetlands act as refuges for native vegetation of Meta Piedmont forest, hosting 55% of the woody of Piedmont species and 29% of the aquatic species of Orinoco basin. The wetlands showed a high species turnover and the results indicated that small wetlands (mean ± SD: size = 11 ± 18.7 ha), with a small area of surrounding forest (10 ± 8.6 ha) supported high local and regional plant diversity. To ensure long-term conservation of lentic wetlands, it is necessary to develop management and conservation strategies that take both natural and created wetlands into account. creator: Johanna I. Murillo-Pacheco creator: Matthias Rös creator: Federico Escobar creator: Francisco Castro-Lima creator: José R. Verdú creator: Germán M. López-Iborra uri: https://doi.org/10.7717/peerj.2267 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Murillo-Pacheco et al. title: Pseudorhabdosynochus sulamericanus (Monogenea, Diplectanidae), a parasite of deep-sea groupers (Serranidae) occurs transatlantically on three congeneric hosts (Hyporthodus spp.), one from the Mediterranean Sea and two from the western Atlantic link: https://peerj.com/articles/2233 last-modified: 2016-08-16 description: Little is known of the diversity of the monogenean parasites infesting deep-sea groupers, and there is even less information available about their geographic distributions within the ranges of their hosts. To improve our understanding of these host-parasite relationships we conducted parasitological evaluations of the deep-water Haifa grouper Hyporthodus haifensis from the southern Mediterranean off Tunisia and Libya. We collected more than one species of diplectanid monogeneans from this host, but among these only one dominant species was abundant. This proved to be morphologically very similar to Pseudorhabdosynochus sulamericanus Santos, Buchmann & Gibson, 2000, a species originally described from the congeneric host H. niveatus off Brazil and also recorded from H. niveatus and H. nigritus off Florida. Here, we conducted a morphological comparison between newly collected specimens and those previously deposited in museum collections by other authors. Further, we used COI barcoding to ascertain the specific identity of the three host species to better elucidate the circumstances that might explain the unexpectedly broad distribution of P. sulamericanus. We assigned our specimens from H. haifensis to P. sulamericanus primarily on the basis of morphological characteristics of the sclerotized vagina. We also noted morphological characteristics of eastern and western Atlantic specimens that are not clearly described or not given in previous descriptions and so prepared a redescription of the species. We confirmed, by COI barcoding, that no sister-species relationships were evident among the three hosts of P. sulamericanus. Our observation that P. sulamericanus infects unrelated host species with putatively allopatric distributions was unexpected given the very limited dispersive capabilities and the high degree of host specificity common to members of Pseudorhabdosynochus. This transatlantic distribution raises questions with regard to phylogeography and assumptions about the allopatry of Atlantic grouper species from the Americas and Afro-Eurasia. Here, we propose some hypothetical explanations for our findings. creator: Amira Chaabane creator: Jean-Lou Justine creator: Delphine Gey creator: Micah D. Bakenhaster creator: Lassad Neifar uri: https://doi.org/10.7717/peerj.2233 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Chaabane et al. title: Delivering a medical school elective with massive open online course (MOOC) technology link: https://peerj.com/articles/2343 last-modified: 2016-08-11 description: Introduction: The educational technology of massive open online courses (MOOCs) has been successfully applied in a wide variety of disciplines and are an intense focus of educational research at this time. Educators are now looking to MOOC technology as a means to improve professional medical education, but very little is known about how medical MOOCs compare with traditional content delivery.Methods: A retrospective analysis of the course evaluations for the Medicine as a Business elective by fourth-year medical students at Southern Illinois University School of Medicine (SIU-SOM) for the 2012–2015 academic years was conducted. This course was delivered by small group flipped classroom discussions for 2012–2014 and delivered via MOOC technology in 2015. Learner ratings were compared between the two course delivery methods using routinely collected course evaluations.Results: Course enrollment has ranged from 6–19 students per year in the 2012–2015 academic years. Student evaluations of the course are favorable in the areas of effective teaching, accurate course objectives, meeting personal learning objectives, recommending the course to other students, and overall when rated on a 5-point Likert scale. The majority of all student ratings (76–95%) of this elective course are for the highest possible choice (Strongly agree or Excellent) for any criteria, regardless if the course was delivered via a traditional or MOOC format. Statistical analysis of these ratings suggests that the Effective Teacher and Overall Evaluations did not statistically differ between the two delivery formats.Discussion: Student ratings of this elective course were highly similar when delivered in a flipped classroom format or by using MOOC technology. The primary advantage of this new course format is flexibility of time and place for learners, allowing them to complete the course objectives when convenient for them. The course evaluations suggest this is a change that is acceptable to the target audience.Conclusions: This study suggests that learner evaluations of a fourth-year medical school elective course do not significantly differ when delivered by flipped classroom group discussions or via MOOC technology in a very small single center observational study. Further investigation is required to determine if this delivery method is an acceptable and effective means of teaching in the medical school environment. creator: Robert Robinson uri: https://doi.org/10.7717/peerj.2343 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Robinson title: Prediction of pKa values using the PM6 semiempirical method link: https://peerj.com/articles/2335 last-modified: 2016-08-11 description: The PM6 semiempirical method and the dispersion and hydrogen bond-corrected PM6-D3H+ method are used together with the SMD and COSMO continuum solvation models to predict pKa values of pyridines, alcohols, phenols, benzoic acids, carboxylic acids, and phenols using isodesmic reactions and compared to published ab initio results. The pKa values of pyridines, alcohols, phenols, and benzoic acids considered in this study can generally be predicted with PM6 and ab initio methods to within the same overall accuracy, with average mean absolute differences (MADs) of 0.6–0.7 pH units. For carboxylic acids, the accuracy (0.7–1.0 pH units) is also comparable to ab initio results if a single outlier is removed. For primary, secondary, and tertiary amines the accuracy is, respectively, similar (0.5–0.6), slightly worse (0.5–1.0), and worse (1.0–2.5), provided that di- and tri-ethylamine are used as reference molecules for secondary and tertiary amines. When applied to a drug-like molecule where an empirical pKa predictor exhibits a large (4.9 pH unit) error, we find that the errors for PM6-based predictions are roughly the same in magnitude but opposite in sign. As a result, most of the PM6-based methods predict the correct protonation state at physiological pH, while the empirical predictor does not. The computational cost is around 2–5 min per conformer per core processor, making PM6-based pKa prediction computationally efficient enough to be used for high-throughput screening using on the order of 100 core processors. creator: Jimmy C. Kromann creator: Frej Larsen creator: Hadeel Moustafa creator: Jan H. Jensen uri: https://doi.org/10.7717/peerj.2335 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Kromann et al. title: The modified Thomas test is not a valid measure of hip extension unless pelvic tilt is controlled link: https://peerj.com/articles/2325 last-modified: 2016-08-11 description: The modified Thomas test was developed to assess the presence of hip flexion contracture and to measure hip extensibility. Despite its widespread use, to the authors’ knowledge, its criterion reference validity has not yet been investigated. The purpose of this study was to assess the criterion reference validity of the modified Thomas test for measuring peak hip extension angle and hip extension deficits, as defined by the hip not being able to extend to 0º, or neutral. Twenty-nine healthy college students (age = 22.00 ± 3.80 years; height = 1.71 ± 0.09 m; body mass = 70.00 ± 15.60 kg) were recruited for this study. Bland–Altman plots revealed poor validity for the modified Thomas test’s ability to measure hip extension, which could not be explained by differences in hip flexion ability alone. The modified Thomas test displayed a sensitivity of 31.82% (95% CI [13.86–54.87]) and a specificity of 57.14% (95% CI [18.41–90.10]) for testing hip extension deficits. It appears, however, that by controlling pelvic tilt, much of this variance can be accounted for (r = 0.98). When pelvic tilt is not controlled, the modified Thomas test displays poor criterion reference validity and, as per previous studies, poor reliability. However, when pelvic tilt is controlled, the modified Thomas test appears to be a valid test for evaluating peak hip extension angle. creator: Andrew D. Vigotsky creator: Gregory J. Lehman creator: Chris Beardsley creator: Bret Contreras creator: Bryan Chung creator: Erin H. Feser uri: https://doi.org/10.7717/peerj.2325 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Vigotsky et al. title: Bunyaviruses are common in male and female Ixodes scapularis ticks in central Pennsylvania link: https://peerj.com/articles/2324 last-modified: 2016-08-11 description: The blacklegged tick Ixodes scapularis is widely distributed in the United States and transmits multiple pathogens to humans, wildlife and domestic animals. Recently, several novel viruses in the family Bunyaviridae (South Bay virus (SBV) and Blacklegged tick phlebovirus (BTPV)) were identified infecting female I. scapularis ticks collected in New York State. We used metagenomic sequencing to investigate the distribution of viruses infecting male and female I. scapularis ticks collected in Centre County, Pennsylvania. We identified both SBV and BTPV in both male and female ticks from all collection locations. The role of male I. scapularis in pathogen epidemiology has been overlooked because they rarely bite and are not considered important pathogen vectors. However, males may act as reservoirs for pathogens that can then be transmitted to females during mating. Our data highlight the importance of examining all potential avenues of pathogen maintenance and transmission throughout the vector-pathogen life cycle in order to understand the epidemiology of tick-borne pathogens. creator: Joyce M. Sakamoto creator: Terry Fei Fan Ng creator: Yasutsugu Suzuki creator: Hitoshi Tsujimoto creator: Xutao Deng creator: Eric Delwart creator: Jason L. Rasgon uri: https://doi.org/10.7717/peerj.2324 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Sakamoto et al. title: Transcriptional activation of muscle atrophy promotes cardiac muscle remodeling during mammalian hibernation link: https://peerj.com/articles/2317 last-modified: 2016-08-11 description: Background. Mammalian hibernation in thirteen-lined ground squirrels (Ictidomys tridecemlineatus) is characterized by dramatic changes on a physiological and molecular level. During hibernation, mammalian hearts show a propensity to hypertrophy due to the need for increasing contractility to pump colder and more viscous blood. While cardiac hypertrophy is quite often a process characterized by decompensation, the ground squirrel studied is an excellent model of cardiac plasticity and cardioprotection under conditions of hypothermia and ischemia. The forkhead box O (Foxo) family of proteins and myogenin (MyoG) are transcription factors that control protein degradation and muscle atrophy by regulating the expression of the E3 ubiquitin ligases, MAFbx and MuRF1. These ligases are part of the ubiquitin proteasome system by transferring ubiquitin to proteins and targeting these proteins for degradation. Regulation of Foxo1 and 3a occurs through phosphorylation at different residues. The threonine-24 (Thr-24) and serine-319 (Ser-319) residues on Foxo1, and the Thr-32 residue on Foxo3a are phosphorylated by Akt, leading to cytoplasmic localization of Foxo. We propose that the described mechanism contributes to the changes taking place in cardiac muscle throughout hibernation.Methods. Total and phosphorylated protein levels of Foxo1 and Foxo3a, as well as total protein levels of MyoG, MAFbx, and MuRF1, were studied using immunoblotting.Results. Immunoblotting results demonstrated upregulations in Foxo1 and Foxo3a total protein levels (1.3- and 4.5-fold increases relative to euthermic control, for Foxo1 and 3a respectively) during late torpor, and protein levels remained elevated throughout the rest of torpor and at interbout arousal. We also observed decreases in inactive, phosphorylated Foxo1 and 3a proteins during throughout torpor, where levels of p-Foxo1 Ser319 and Thr24, as well as p-Foxo3a Thr32 decreased by at least 45% throughout torpor. MyoG was upregulated only during late torpor by 2.4-fold. Protein levels of MAFbx and MuRF1 increased in late torpor as well as during early arousal by as much as 2.8-fold, and MAFbx levels remained elevated during interbout arousal, whereas MuRF1 levels returned to control levels.Discussion. The present results indicate that upregulation and activation of Foxo1 and 3a, in addition to the increase in MyoG levels at late torpor, may be upregulating the expression of MAFbx and MuRF1. These findings suggest that there is activation of the ubiquitin proteasome system (UPS) as ground squirrels arouse from torpor. Therefore, the signalling pathway involving MyoG, and the E3 ligases MAFbx and MuRF1, plays a significant role in cardiac muscle remodelling during hibernation. These findings provide insights into the regulation of protein degradation and turnover in the cardiac muscle of a hibernator model. creator: Yichi Zhang creator: Oscar A. Aguilar creator: Kenneth B. Storey uri: https://doi.org/10.7717/peerj.2317 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Zhang et al. title: Stereotactically-navigated percutaneous Irreversible Electroporation (IRE) compared to conventional IRE: a prospective trial link: https://peerj.com/articles/2277 last-modified: 2016-08-11 description: Purpose. The purpose of this study was to compare CT-navigated stereotactic IRE (SIRE) needle placement to non-navigated conventional IRE (CIRE) for percutaneous ablation of liver malignancies.Materials and Methods. A prospective trial including a total of 20 patients was conducted with 10 patients in each arm of the study. IRE procedures were guided using either CT fluoroscopy (CIRE) or a stereotactic planning and navigation system (SIRE). Primary endpoint was procedure time. Secondary endpoints were accuracy of needle placement, technical success rate, complication rate and dose-length product (DLP).Results. A total of 20 IRE procedures were performed to ablate hepatic malignancies (16 HCC, 4 liver metastases), 10 procedures in each arm. Mean time for placement of IRE electrodes in SIRE was significantly shorter with 27 ± 8 min compared to 87 ± 30 min for CIRE (p < 0.001). Accuracy of needle placement for SIRE was higher than CIRE (2.2 mm vs. 3.3 mm mean deviation, p < 0.001). The total DLP and the fluoroscopy DLP were significantly lower in SIRE compared to CIRE. Technical success rate and complication rates were equal in both arms.Conclusion. SIRE demonstrated a significant reduction of procedure length and higher accuracy compared to CIRE. Stereotactic navigation has the potential to reduce radiation dose for the patient and the radiologist without increasing the risk of complications or impaired technical success compared to CIRE. creator: Lukas P. Beyer creator: Benedikt Pregler creator: Christoph Nießen creator: Andreas Schicho creator: Michael Haimerl creator: Ernst Michael Jung creator: Christian Stroszczynski creator: Philipp Wiggermann uri: https://doi.org/10.7717/peerj.2277 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Beyer et al. title: Metabolomics of pulmonary exacerbations reveals the personalized nature of cystic fibrosis disease link: https://peerj.com/articles/2174 last-modified: 2016-08-11 description: Background. Cystic fibrosis (CF) is a genetic disease that results in chronic infections of the lungs. CF patients experience intermittent pulmonary exacerbations (CFPE) that are associated with poor clinical outcomes. CFPE involves an increase in disease symptoms requiring more aggressive therapy.Methods. Longitudinal sputum samples were collected from 11 patients (n = 44 samples) to assess the effect of exacerbations on the sputum metabolome using liquid chromatography-tandem mass spectrometry (LC-MS/MS). The data was analyzed with MS/MS molecular networking and multivariate statistics.Results. The individual patient source had a larger influence on the metabolome of sputum than the clinical state (exacerbation, treatment, post-treatment, or stable). Of the 4,369 metabolites detected, 12% were unique to CFPE samples; however, the only known metabolites significantly elevated at exacerbation across the dataset were platelet activating factor (PAF) and a related monacylglycerophosphocholine lipid. Due to the personalized nature of the sputum metabolome, a single patient was followed for 4.2 years (capturing four separate exacerbation events) as a case study for the detection of personalized biomarkers with metabolomics. PAF and related lipids were significantly elevated during CFPEs of this patient and ceramide was elevated during CFPE treatment. Correlating the abundance of bacterial 16S rRNA gene amplicons to metabolomics data from the same samples during a CFPE demonstrated that antibiotics were positively correlated to Stenotrophomonas and Pseudomonas, while ceramides and other lipids were correlated with Streptococcus, Rothia, and anaerobes.Conclusions. This study identified PAF and other inflammatory lipids as potential biomarkers of CFPE, but overall, the metabolome of CF sputum was patient specific, supporting a personalized approach to molecular detection of CFPE onset. creator: Robert A. Quinn creator: Yan Wei Lim creator: Tytus D. Mak creator: Katrine Whiteson creator: Mike Furlan creator: Douglas Conrad creator: Forest Rohwer creator: Pieter Dorrestein uri: https://doi.org/10.7717/peerj.2174 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Quinn et al. title: Changes in segmentation and setation along the anterior/posterior axis of the homonomous trunk limbs of a remipede (Crustacea, Arthropoda) link: https://peerj.com/articles/2305 last-modified: 2016-08-10 description: This study describes the segmentation and setation at different developmental stages of the homonomous trunk limbs of the remipede Speleonectes tulumensisYager, 1987 collected in anchialine caves of the Yucatan Peninsula. Most homonomous trunk limbs originate ventrolaterally and are composed of two protopodal segments, three exopodal segments and four endopodal segments; contralateral limb pairs are united by a sternal bar. However, the last few posterior limbs originate ventrally, are smaller sized, and have regressively fewer segments, suggesting that limb development passes through several intermediate steps beginning with a limb bud. A terminal stage of development is proposed for specimens on which the posterior somite bears a simple bilobate limb bud, and the adjacent somite bears a limb with a protopod comprised of a coxapod and basipod, and with three exopodal and four endopodal segments. On each trunk limb there are 20 serially homologous groups of setae, and the numbers of setae on different limbs usually varies. These groups of setae are arranged linearly and are identified based on the morphology of the setae and their position on the segments. The number of setae in these groups increases gradually from the anterior homonomous limb to a maximum between limbs 8–12; the number then decreases sharply on the more posterior limbs. Changes in the number of setae, which reach a maximum between trunk limbs 8–12, differ from changes in segmentation which vary only over the last few posterior trunk limbs. Following a vector analysis that identified a spatial pattern for these 20 groups of setae among the different homonomous limbs, the hypothesis was confirmed that the number of setae in any given group and any given limb is correlated with the group, with the position of the somite along the body axis, and with the number of somites present on the specimens. This is the first vector analysis used to analyze a pattern of developmental changes in serially homologs of an arthropod. Development of remipede limbs are compared and contrasted with similar copepod limbs. Architecture, particularly the sternal bar uniting contralateral limb pairs, proposed as homologous, and development of trunk limb segmentation of the remipede is generally similar to that of copepods, but the remipede limb differs in several ways including an additional endopodal segment, the proximal, that appears simultaneously with the protopod during development. creator: Viacheslav N. Ivanenko creator: Ekaterina A. Antonenko creator: Mikhail S. Gelfand creator: Jill Yager creator: Frank D. Ferrari uri: https://doi.org/10.7717/peerj.2305 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Ivanenko et al. title: Vegemite Beer: yeast extract spreads as nutrient supplements to promote fermentation link: https://peerj.com/articles/2271 last-modified: 2016-08-10 description: Vegemite is an iconic Australian food spread made from spent brewers’ yeast extract, which has been reported to be used as an ingredient in illegal home brewing. In this study, we tested the utility of Vegemite and the similar spread Marmite in promoting fermentation. We could not culture microorganisms from either Vegemite or Marmite, consistent with these food-grade spreads being essentially sterile. To test if the addition of Vegemite or Marmite could assist in fermentation when additional viable yeast was also present, solutions containing glucose and a range of concentrations of either Vegemite or Marmite were inoculated with brewers’ yeast. No fermentation occurred in any condition without addition of extra brewer’s yeast. Fermentation did not occur when yeast was inoculated into solutions containing only glucose, but progressed efficiently with when Vegemite or Marmite was also added. Gas Chromatography confirmed that ethanol was present at ∼3% v/v post-fermentation in all samples which contained glucose, Vegemite or Marmite, and brewers’ yeast. Trace amounts of methanol were also detected. Mass spectrometry proteomics identified abundant intracellular yeast proteins and barley proteins in Vegemite and Marmite, and abundant secreted yeast proteins from actively growing yeast in those samples to which extra brewers’ yeast had been added. We estimate that the real-world cost of home brewed “Vegemite Beer” would be very low. Our results show that Vegemite or other yeast extract spreads could provide cheap and readily available sources of nutrient supplementation to increase the efficiency of fermentation in home brewing or other settings. creator: Edward D. Kerr creator: Benjamin L. Schulz uri: https://doi.org/10.7717/peerj.2271 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Kerr and Schulz title: Is it safe to nest near conspicuous neighbours? Spatial patterns in predation risk associated with the density of American Golden-Plover nests link: https://peerj.com/articles/2193 last-modified: 2016-08-10 description: Predation is one of the main factors explaining nesting mortality in most bird species. Birds can avoid nest predation or reduce predation pressure by breeding at higher latitude, showing anti-predator behaviour, selecting nest sites protected from predators, and nesting in association with protective species. American Golden-Plovers (Pluvialis dominica) defend their territory by using various warning and distraction behaviours displayed at varying levels of intensity (hereafter “conspicuous behaviour”), as well as more aggressive behaviours such as aerial attacks, but only in some populations. Such antipredator behaviour has the potential to repel predators and thus benefit the neighbouring nests by decreasing their predation risk. Yet, conspicuous behaviour could also attract predators by signalling the presence of a nest. To test for the existence of a protective effect associated with the conspicuous antipredator behaviour of American Golden-Plovers, we studied the influence of proximity to plover nests on predation risk of artificial nests on Igloolik Island (Nunavut, Canada) in July 2014. We predicted that the predation risk of artificial nests would decrease with proximity to and density of plover nests. We monitored 18 plover nests and set 35 artificial nests at 30, 50, 100, 200, and 500 m from seven of those plover nests. We found that the predation risk of artificial nests increases with the density of active plover nests. We also found a significant negative effect of the distance to the nearest active protector nest on predation risk of artificial nests. Understanding how the composition and structure of shorebird communities generate spatial patterns in predation risks represents a key step to better understand the importance of these species of conservation concern in tundra food webs. creator: Marie-Andrée Giroux creator: Myriam Trottier-Paquet creator: Joël Bêty creator: Vincent Lamarre creator: Nicolas Lecomte uri: https://doi.org/10.7717/peerj.2193 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Giroux et al. title: A horizon scan of future threats and opportunities for pollinators and pollination link: https://peerj.com/articles/2249 last-modified: 2016-08-09 description: Background. Pollinators, which provide the agriculturally and ecologically essential service of pollination, are under threat at a global scale. Habitat loss and homogenisation, pesticides, parasites and pathogens, invasive species, and climate change have been identified as past and current threats to pollinators. Actions to mitigate these threats, e.g., agri-environment schemes and pesticide-use moratoriums, exist, but have largely been applied post-hoc. However, future sustainability of pollinators and the service they provide requires anticipation of potential threats and opportunities before they occur, enabling timely implementation of policy and practice to prevent, rather than mitigate, further pollinator declines.Methods.Using a horizon scanning approach we identified issues that are likely to impact pollinators, either positively or negatively, over the coming three decades.Results.Our analysis highlights six high priority, and nine secondary issues. High priorities are: (1) corporate control of global agriculture, (2) novel systemic pesticides, (3) novel RNA viruses, (4) the development of new managed pollinators, (5) more frequent heatwaves and drought under climate change, and (6) the potential positive impact of reduced chemical use on pollinators in non-agricultural settings.Discussion. While current pollinator management approaches are largely driven by mitigating past impacts, we present opportunities for pre-emptive practice, legislation, and policy to sustainably manage pollinators for future generations. creator: Mark J.F. Brown creator: Lynn V. Dicks creator: Robert J. Paxton creator: Katherine C.R. Baldock creator: Andrew B. Barron creator: Marie-Pierre Chauzat creator: Breno M. Freitas creator: Dave Goulson creator: Sarina Jepsen creator: Claire Kremen creator: Jilian Li creator: Peter Neumann creator: David E. Pattemore creator: Simon G. Potts creator: Oliver Schweiger creator: Colleen L. Seymour creator: Jane C. Stout uri: https://doi.org/10.7717/peerj.2249 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Brown et al. title: A study of institutional spending on open access publication fees in Germany link: https://peerj.com/articles/2323 last-modified: 2016-08-09 description: Publication fees as a revenue source for open access publishing hold a prominent place on the agendas of researchers, policy makers, and academic publishers. This study contributes to the evolving empirical basis for funding these charges and examines how much German universities and research organisations spent on open access publication fees. Using self-reported cost data from the Open APC initiative, the analysis focused on the amount that was being spent on publication fees, and compared these expenditure with data from related Austrian (FWF) and UK (Wellcome Trust, Jisc) initiatives, in terms of both size and the proportion of articles being published in fully and hybrid open access journals. We also investigated how thoroughly self-reported articles were indexed in Crossref, a DOI minting agency for scholarly literature, and analysed how the institutional spending was distributed across publishers and journal titles. According to self-reported data from 30 German universities and research organisations between 2005 and 2015, expenditures on open access publication fees increased over the years in Germany and amounted to € 9,627,537 for 7,417 open access journal articles. The average payment was € 1,298, and the median was € 1,231. A total of 94% of the total article volume included in the study was supported in accordance with the price cap of € 2,000, a limit imposed by the Deutsche Forschungsgemeinschaft (DFG) as part of its funding activities for open access funding at German universities. Expenditures varied considerably at the institutional level. There were also differences in how much the institutions spent per journal and publisher. These differences reflect, at least in part, the varying pricing schemes in place including discounted publication fees. With an indexing coverage of 99%, Crossref thoroughly indexed the open access journals articles included in the study. A comparison with the related openly available cost data from Austria and the UK revealed that German universities and research organisations primarily funded articles in fully open access journals. By contrast, articles in hybrid journal accounted for the largest share of spending according to the Austrian and UK data. Fees paid for hybrid journals were on average more expensive than those paid for fully open access journals. creator: Najko Jahn creator: Marco Tullney uri: https://doi.org/10.7717/peerj.2323 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Jahn et al. title: Probing the origins of human acetylcholinesterase inhibition via QSAR modeling and molecular docking link: https://peerj.com/articles/2322 last-modified: 2016-08-09 description: Alzheimer’s disease (AD) is a chronic neurodegenerative disease which leads to the gradual loss of neuronal cells. Several hypotheses for AD exists (e.g., cholinergic, amyloid, tau hypotheses, etc.). As per the cholinergic hypothesis, the deficiency of choline is responsible for AD; therefore, the inhibition of AChE is a lucrative therapeutic strategy for the treatment of AD. Acetylcholinesterase (AChE) is an enzyme that catalyzes the breakdown of the neurotransmitter acetylcholine that is essential for cognition and memory. A large non-redundant data set of 2,570 compounds with reported IC50 values against AChE was obtained from ChEMBL and employed in quantitative structure-activity relationship (QSAR) study so as to gain insights on their origin of bioactivity. AChE inhibitors were described by a set of 12 fingerprint descriptors and predictive models were constructed from 100 different data splits using random forest. Generated models afforded R2, ${Q}_{\mathrm{CV }}^{2}$QCV2 and ${Q}_{\mathrm{Ext}}^{2}$QExt2 values in ranges of 0.66–0.93, 0.55–0.79 and 0.56–0.81 for the training set, 10-fold cross-validated set and external set, respectively. The best model built using the substructure count was selected according to the OECD guidelines and it afforded R2, ${Q}_{\mathrm{CV }}^{2}$QCV2 and ${Q}_{\mathrm{Ext}}^{2}$QExt2 values of 0.92 ± 0.01, 0.78 ± 0.06 and 0.78 ± 0.05, respectively. Furthermore, Y-scrambling was applied to evaluate the possibility of chance correlation of the predictive model. Subsequently, a thorough analysis of the substructure fingerprint count was conducted to provide informative insights on the inhibitory activity of AChE inhibitors. Moreover, Kennard–Stone sampling of the actives were applied to select 30 diverse compounds for further molecular docking studies in order to gain structural insights on the origin of AChE inhibition. Site-moiety mapping of compounds from the diversity set revealed three binding anchors encompassing both hydrogen bonding and van der Waals interaction. Molecular docking revealed that compounds 13, 5 and 28 exhibited the lowest binding energies of −12.2, −12.0 and −12.0 kcal/mol, respectively, against human AChE, which is modulated by hydrogen bonding, π–π stacking and hydrophobic interaction inside the binding pocket. These information may be used as guidelines for the design of novel and robust AChE inhibitors. creator: Saw Simeon creator: Nuttapat Anuwongcharoen creator: Watshara Shoombuatong creator: Aijaz Ahmad Malik creator: Virapong Prachayasittikul creator: Jarl E.S. Wikberg creator: Chanin Nantasenamat uri: https://doi.org/10.7717/peerj.2322 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Simeon et al. title: Temporal dynamics of the developing lung transcriptome in three common inbred strains of laboratory mice reveals multiple stages of postnatal alveolar development link: https://peerj.com/articles/2318 last-modified: 2016-08-09 description: To characterize temporal patterns of transcriptional activity during normal lung development, we generated genome wide gene expression data for 26 pre- and post-natal time points in three common inbred strains of laboratory mice (C57BL/6J, A/J, and C3H/HeJ). Using Principal Component Analysis and least squares regression modeling, we identified both strain-independent and strain-dependent patterns of gene expression. The 4,683 genes contributing to the strain-independent expression patterns were used to define a murine Developing Lung Characteristic Subtranscriptome (mDLCS). Regression modeling of the Principal Components supported the four canonical stages of mammalian embryonic lung development (embryonic, pseudoglandular, canalicular, saccular) defined previously by morphology and histology. For postnatal alveolar development, the regression model was consistent with four stages of alveolarization characterized by episodic transcriptional activity of genes related to pulmonary vascularization. Genes expressed in a strain-dependent manner were enriched for annotations related to neurogenesis, extracellular matrix organization, and Wnt signaling. Finally, a comparison of mouse and human transcriptomics from pre-natal stages of lung development revealed conservation of pathways associated with cell cycle, axon guidance, immune function, and metabolism as well as organism-specific expression of genes associated with extracellular matrix organization and protein modification. The mouse lung development transcriptome data generated for this study serves as a unique reference set to identify genes and pathways essential for normal mammalian lung development and for investigations into the developmental origins of respiratory disease and cancer. The gene expression data are available from the Gene Expression Omnibus (GEO) archive (GSE74243). Temporal expression patterns of mouse genes can be investigated using a study specific web resource (http://lungdevelopment.jax.org). creator: Kyle J. Beauchemin creator: Julie M. Wells creator: Alvin T. Kho creator: Vivek M. Philip creator: Daniela Kamir creator: Isaac S. Kohane creator: Joel H. Graber creator: Carol J. Bult uri: https://doi.org/10.7717/peerj.2318 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Beauchemin et al. title: An optimized approach to germ-free rearing in the jewel wasp Nasonia link: https://peerj.com/articles/2316 last-modified: 2016-08-09 description: Development of a Nasonia in vitrogerm-free rearing system in 2012 enabled investigation of Nasonia-microbiota interactions and real-time visualization of parasitoid metamorphosis. However, the use of antibiotics, bleach, and fetal bovine serum introduced artifacts relative to conventional rearing of Nasonia. Here, we optimize the germ-free rearing procedure by using filter sterilization in lieu of antibiotics and by removing residual bleach and fetal bovine serum. Comparison of these methods reveals no influence on larval survival or growth, and a 52% improvement in adult production. Additionally, adult males produced in the new germ-free system are similar in size to conventionally reared males. Experimental implications of these changes are discussed. creator: J. Dylan Shropshire creator: Edward J. van Opstal creator: Seth R. Bordenstein uri: https://doi.org/10.7717/peerj.2316 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Shropshire et al. title: An investigation into the bilateral functional differences of the lower limb muscles in standing and walking link: https://peerj.com/articles/2315 last-modified: 2016-08-09 description: To date, most studies use surface electromyographic (sEMG) signals as the control source on active rehabilitation robots, and unilateral data are collected based on the gait symmetry hypothesis, which has caused much controversy. The purpose of this study is to quantitatively evaluate the sEMG activity asymmetry of bilateral muscles in lower extremities during functional tasks. Nine participants were instructed to perform static and dynamic steady state tests. sEMG signals from the tibialis anterior, soleus, medial gastrocnemius and lateral gastrocnemius muscles of bilateral lower extremities were recorded in the experiments. Muscle activities are quantified in terms of sEMG amplitude. We investigated whether characteristics of left limb and the one of the right limb have the same statistical characteristics during functional tasks using The Wilcoxon rank-sum test, and studied dynamic signal irregularity degree for sEMG activities via sample entropy. The total of muscle activities showed significant differences between left limb and right limb during the static steady state (p = 0.000). For dynamic steady states, there were significant differences for most muscle activities between left limb and right limb at different speeds (p = 0.000). Nevertheless, there was no difference between the lateral gastrocnemius for bilateral limb at 2.0 kilometers per hour (p = 0.060). For medial gastrocnemius, differences were not found between left limb and right limb at 1.0 and 3.0 kilometers per hours (p = 0.390 and p = 0.085, respectively). Similarly, there was no difference for soleus at 3.0 kilometers per hour (p = 0.115). The importance of the differences in muscle activities between left limb and right limb were found. These results can potentially be used for evaluating lower limb extremity function of special populations (elderly people or stroke patients) in an objective and simple method. creator: Shengyun Liang creator: Jiali Xu creator: Lei wang creator: Guoru Zhao uri: https://doi.org/10.7717/peerj.2315 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Liang et al. title: The core clock gene Per1 phases molecular and electrical circadian rhythms in SCN neurons link: https://peerj.com/articles/2297 last-modified: 2016-08-09 description: The brain’s biological clock, the suprachiasmatic nucleus (SCN), exhibits endogenous 24-hour rhythms in gene expression and spontaneous firing rate; however, the functional relationship between these neuronal rhythms is not fully understood. Here, we used a Per1::GFP transgenic mouse line that allows for the simultaneous quantification of molecular clock state and firing rate in SCN neurons to examine the relationship between these key components of the circadian clock. We find that there is a stable, phased relationship between E-box-driven clock gene expression and spontaneous firing rate in SCN neurons and that these relationships are independent of light input onto the system or of GABAA receptor-mediated synaptic activity. Importantly, the concordant phasing of gene and neural rhythms is disrupted in the absence of the homologous clock gene Per1, but persists in the absence of the core clock gene Per2. These results suggest that Per1 plays a unique, non-redundant role in phasing gene expression and firing rate rhythms in SCN neurons to increase the robustness of cellular timekeeping. creator: Jeff R. Jones creator: Douglas G. McMahon uri: https://doi.org/10.7717/peerj.2297 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Jones and McMahon title: A comparison of blood gases, biochemistry, and hematology to ecomorphology in a health assessment of pinfish (Lagodon rhomboides) link: https://peerj.com/articles/2262 last-modified: 2016-08-09 description: Despite the promise of hematological parameters and blood chemistry in monitoring the health of marine fishes, baseline data is often lacking for small fishes that comprise central roles in marine food webs. This study establishes blood chemistry and hematological baseline parameters for the pinfish Lagodon rhomboides, a small marine teleost that is among the most dominant members of near-shore estuarine communities of the Atlantic Ocean and Gulf of Mexico. Given their prominence, pinfishes are an ideal candidate species to use as a model for monitoring changes across a wide range of near-shore marine communities. However, pinfishes exhibit substantial morphological differences associated with a preference for feeding in primarily sea-grass or sand dominated habitats, suggesting that differences in the foraging ecology of individuals could confound health assessments. Here we collect baseline data on the blood physiology of pinfish while assessing the relationship between blood parameters and measured aspects of feeding morphology using data collected from 37 individual fish. Our findings provide new baseline health data for this important near shore fish species and find no evidence for a strong linkage between blood physiology and either sex or measured aspects of feeding morphology. Comparing our hematological and biochemical data to published results from other marine teleost species suggests that analyses of trends in blood value variation correlated with major evolutionary transitions in ecology will shed new light on the physiological changes that underlie the successful diversification of fishes. creator: Sara Collins creator: Alex Dornburg creator: Joseph M. Flores creator: Daniel S. Dombrowski creator: Gregory A. Lewbart uri: https://doi.org/10.7717/peerj.2262 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Collins et al. title: Systematic relationships of five newly sequenced cervid species link: https://peerj.com/articles/2307 last-modified: 2016-08-04 description: Cervid phylogenetics has been puzzling researchers for over 150 years. In recent decades, molecular systematics has provided new input for both the support and revision of the previous results from comparative anatomy but has led to only partial consensus. Despite all of the efforts to reach taxon-wide species sampling over the last two decades, a number of cervid species still lack molecular data because they are difficult to access in the wild. By extracting ancient DNA from museum specimens, in this study, we obtained partial mitochondrial cytochrome b gene sequences for Mazama bricenii, Mazama chunyi, Muntiacus atherodes, Pudu mephistophiles, and Rusa marianna, including three holotypes. These new sequences were used to enrich the existing mitochondrial DNA alignments and yielded the most taxonomically complete data set for cervids to date. Phylogenetic analyses provide new insights into the evolutionary history of these five species. However, systematic uncertainties within Muntiacus persist and resolving phylogenetic relationships within Pudu and Mazama remain challenging. creator: Nicola S. Heckeberg creator: Dirk Erpenbeck creator: Gert Wörheide creator: Gertrud E. Rössner uri: https://doi.org/10.7717/peerj.2307 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Heckeberg et al. title: Short-term exposure to predation affects body elemental composition, climbing speed and survival ability in Drosophila melanogaster link: https://peerj.com/articles/2314 last-modified: 2016-08-04 description: Factors such as temperature, habitat, larval density, food availability and food quality substantially affect organismal development. In addition, risk of predation has a complex impact on the behavioural and morphological life history responses of prey. Responses to predation risk seem to be mediated by physiological stress, which is an adaptation for maintaining homeostasis and improving survivorship during life-threatening situations. We tested whether predator exposure during the larval phase of development has any influence on body elemental composition, energy reserves, body size, climbing speed and survival ability of adult Drosophila melanogaster. Fruit fly larvae were exposed to predation by jumping spiders (Phidippus apacheanus), and the percentage of carbon (C) and nitrogen (N) content, extracted lipids, escape response and survival were measured from predator-exposed and control adult flies. The results revealed predation as an important determinant of adult phenotype formation and survival ability. D. melanogaster reared together with spiders had a higher concentration of body N (but equal body C), a lower body mass and lipid reserves, a higher climbing speed and improved adult survival ability. The results suggest that the potential of predators to affect the development and the adult phenotype of D. melanogaster is high enough to use predators as a more natural stimulus in laboratory experiments when testing, for example, fruit fly memory and learning ability, or when comparing natural populations living under different predation pressures. creator: Indrikis Krams creator: Sarah Eichler Inwood creator: Giedrius Trakimas creator: Ronalds Krams creator: Gordon M. Burghardt creator: David M. Butler creator: Severi Luoto creator: Tatjana Krama uri: https://doi.org/10.7717/peerj.2314 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Krams et al. title: Familiar face + novel face = familiar face? Representational bias in the perception of morphed faces in chimpanzees link: https://peerj.com/articles/2304 last-modified: 2016-08-04 description: Highly social animals possess a well-developed ability to distinguish the faces of familiar from novel conspecifics to induce distinct behaviors for maintaining society. However, the behaviors of animals when they encounter ambiguous faces of familiar yet novel conspecifics, e.g., strangers with faces resembling known individuals, have not been well characterised. Using a morphing technique and preferential-looking paradigm, we address this question via the chimpanzee’s facial–recognition abilities. We presented eight subjects with three types of stimuli: (1) familiar faces, (2) novel faces and (3) intermediate morphed faces that were 50% familiar and 50% novel faces of conspecifics. We found that chimpanzees spent more time looking at novel faces and scanned novel faces more extensively than familiar or intermediate faces. Interestingly, chimpanzees looked at intermediate faces in a manner similar to familiar faces with regards to the fixation duration, fixation count, and saccade length for facial scanning, even though the participant was encountering the intermediate faces for the first time. We excluded the possibility that subjects merely detected and avoided traces of morphing in the intermediate faces. These findings suggest a bias for a feeling-of-familiarity that chimpanzees perceive familiarity with an intermediate face by detecting traces of a known individual, as 50% alternation is sufficient to perceive familiarity. creator: Yoshi-Taka Matsuda creator: Masako Myowa-Yamakoshi creator: Satoshi Hirata uri: https://doi.org/10.7717/peerj.2304 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Matsuda et al. title: Novel fermented chickpea milk with enhanced level of γ-aminobutyric acid and neuroprotective effect on PC12 cells link: https://peerj.com/articles/2292 last-modified: 2016-08-04 description: In this study, novel fermented chickpea milk with high γ -aminobutyric acid (GABA) content and potential neuroprotective activity was developed. Fermentation starter that can produce GABA was selected from 377 strains of lactic acid bacteria isolated from traditional Chinese fermented foods. Among the screened strains, strain M-6 showed the highest GABA-producing capacity in De Man–Rogosa and Sharp (MRS) broth and chickpea milk. M-6 was identified as Lactobacillus plantarum based on Gram staining, API carbohydrate fermentation pattern testing, and 16s rDNA sequencing. The complete gene encoding glutamate decarboxylase was cloned to confirm the presence of the gene in L. plantarum M-6. The fermentation condition was optimized by response surface methodology. Results demonstrated that L. plantarum M-6 produced the highest GABA content of 537.23 mg/L. The optimal condition included an inoculum concentration of 7%, presence of 0.2% (m/v) monosodium glutamate and 55 µ M pyridoxal-5-phosphate, incubation temperature of 39 °C and fermentation time of 48 h . GABA-enriched chickpea milk exerted protective effects on PC12 cells against MnCl2 -induced injury. GABA-enriched chickpea milk improved cell viability and markedly attenuated the release of lactate dehydrogenase compared with the impaired cells. creator: Wen Li creator: Mingming Wei creator: Junjun Wu creator: Xin Rui creator: Mingsheng Dong uri: https://doi.org/10.7717/peerj.2292 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Li et al. title: Use of the melting curve assay as a means for high-throughput quantification of Illumina sequencing libraries link: https://peerj.com/articles/2281 last-modified: 2016-08-04 description: Background. Multiplexed sequencing is commonly performed on massively parallel short-read sequencing platforms such as Illumina, and the efficiency of library normalisation can affect the quality of the output dataset. Although several library normalisation approaches have been established, none are ideal for highly multiplexed sequencing due to issues of cost and/or processing time.Methods. An inexpensive and high-throughput library quantification method has been developed, based on an adaptation of the melting curve assay. Sequencing libraries were subjected to the assay using the Bio-Rad Laboratories CFX ConnectTM Real-Time PCR Detection System. The library quantity was calculated through summation of reduction of relative fluorescence units between 86 and 95 °C.Results.PCR-enriched sequencing libraries are suitable for this quantification without pre-purification of DNA. Short DNA molecules, which ideally should be eliminated from the library for subsequent processing, were differentiated from the target DNA in a mixture on the basis of differences in melting temperature. Quantification results for long sequences targeted using the melting curve assay were correlated with those from existing methods (R2 > 0.77), and that observed from MiSeq sequencing (R2 = 0.82).Discussion.The results of multiplexed sequencing suggested that the normalisation performance of the described method is equivalent to that of another recently reported high-throughput bead-based method, BeNUS. However, costs for the melting curve assay are considerably lower and processing times shorter than those of other existing methods, suggesting greater suitability for highly multiplexed sequencing applications. creator: Hiroshi Shinozuka creator: John W. Forster uri: https://doi.org/10.7717/peerj.2281 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Shinozuka and Forster title: The antioxidative properties of S-allyl cysteine not only influence somatic cells but also improve early embryo cleavage in pigs link: https://peerj.com/articles/2280 last-modified: 2016-08-04 description: In vitro cultivation systems for oocytes and embryos are characterised by increased levels of reactive oxygen species (ROS), which can be balanced by the addition of suitable antioxidants. S-allyl cysteine (SAC) is a sulfur compound naturally occurring in garlic (Allium sativum), which is responsible for its high antioxidant properties. In this study, we demonstrated the capacity of SAC (0.1, 0.5 and 1.0 mM) to reduce levels of ROS in maturing oocytes significantly after 24 (reduced by 90.33, 82.87 and 91.62%, respectively) and 48 h (reduced by 86.35, 94.42 and 99.05%, respectively) cultivation, without leading to a disturbance of the standard course of meiotic maturation. Oocytes matured in the presence of SAC furthermore maintained reduced levels of ROS even 22 h after parthenogenic activation (reduced by 66.33, 61.64 and 57.80%, respectively). In these oocytes we also demonstrated a growth of early embryo cleavage rate (increased by 33.34, 35.00 and 35.00%, respectively). SAC may be a valuable supplement to cultivation media. creator: Markéta Dvořáková creator: Ivona Heroutová creator: David Němeček creator: Kateřina Adámková creator: Tereza Krejčová creator: Jan Nevoral creator: Veronika Kučerová Chrpová creator: Jaroslav Petr creator: Markéta Sedmíková uri: https://doi.org/10.7717/peerj.2280 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Dvořáková et al. title: The pes of Australovenator wintonensis (Theropoda: Megaraptoridae): analysis of the pedal range of motion and biological restoration link: https://peerj.com/articles/2312 last-modified: 2016-08-03 description: The pedal range of motion in Australovenator wintonensis is investigated to determine what influence soft tissue had on range of motion in the foot. Fortunately, the theropod pes shares a close morphology with extant large cursorial birds. Therefore, to better understand the pedal range of motion of Australovenator, the pedal range of motion of Dromaius novaehollandiae (commonly known as the emu) was analysed with and without soft tissue. We used a variety of innovative digital techniques to analyse the range of motion and biologically restore the Australovenator pes. Computed tomography scans of Dromaius pes in fully flexed and fully extended positions provided the soft tissue range of motion limits. The bone on bone range of motion of the same specimen was replicated following the removal of soft tissue. It was identified that there was an increase in range of motion potential with the removal of soft tissue. This variation provided a guide to develop the potential range of motion of a fully fleshed Australovenator pes. Additionally, the dissection of the Dromaius pes provided a guide enabling the replication of the corresponding soft tissue and keratin sheaths of the Australovenator pes. creator: Matt A. White creator: Alex G. Cook creator: Ada J. Klinkhamer creator: David A. Elliott uri: https://doi.org/10.7717/peerj.2312 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 White et al. title: Cafeteria diet induce changes in blood flow that are more related with heat dissipation than energy accretion link: https://peerj.com/articles/2302 last-modified: 2016-08-03 description: Background. A “cafeteria” diet is a self-selected high-fat diet, providing an excess of energy, which can induce obesity. Excess of lipids in the diet hampers glucose utilization eliciting insulin resistance, which, further limits amino acid oxidation for energy.Methods. Male Wistar rats were exposed for a month to “cafeteria” diet. Rats were cannulated and fluorescent microspheres were used to determine blood flow.Results. Exposure to the cafeteria diet did not change cardiac output, but there was a marked shift in organ irrigation. Skin blood flow decreased to compensate increases in lungs and heart. Blood flow through adipose tissue tended to increase in relation to controls, but was considerably increased in brown adipose tissue (on a weight basis).Discussion. The results suggest that the cafeteria diet-induced changes were related to heat transfer and disposal. creator: David Sabater creator: Silvia Agnelli creator: Sofía Arriarán creator: María del Mar Romero creator: José Antonio Fernández-López creator: Marià Alemany creator: Xavier Remesar uri: https://doi.org/10.7717/peerj.2302 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Sabater et al. title: A multifunctional GH39 glycoside hydrolase from the anaerobic gut fungus Orpinomyces sp. strain C1A link: https://peerj.com/articles/2289 last-modified: 2016-08-03 description: Background. The anaerobic gut fungi (phylum Neocallimastigomycota) represent a promising source of novel lignocellulolytic enzymes. Here, we report on the cloning, expression, and characterization of a glycoside hydrolase family 39 (GH39) enzyme (Bgxg1) that is highly transcribed by the anaerobic fungus Orpinomycessp. strain C1A under different growth conditions. This represents the first study of a GH39-family enzyme from the anaerobic fungi.Methods. Using enzyme activity assays, we performed a biochemical characterization of Bgxg1 on a variety of substrates over a wide range of pH and temperature values to identify the optimal enzyme conditions and the specificity of the enzyme. In addition, substrate competition studies and comparative modeling efforts were completed.Results. Contrary to the narrow range of activities (β-xylosidase or α-L-iduronidase) observed in previously characterized GH39 enzymes, Bgxg1 is unique in that it is multifunctional, exhibiting strong β-xylosidase, β-glucosidase, β-galactosidase activities (11.5 ± 1.2, 73.4 ± 7.15, and 54.6 ± 2.26 U/mg, respectively) and a weak xylanase activity (10.8 ± 1.25 U/mg), as compared to previously characterized enzymes. Further, Bgxg1 possesses extremely high affinity (as evident by the lowest Km values), compared to all previously characterized β-glucosidases, β-galactosidases, and xylanases. Physiological characterization revealed that Bgxg1 is active over a wide range of pH (3–8, optimum 6) and temperatures (25–60 °C, optimum 39 °C), and possesses excellent temperature and thermal stability. Substrate competition assays suggest that all observed activities occur at a single active site. Using comparative modeling and bioinformatics approaches, we putatively identified ten amino acid differences between Bgxg1 and previously biochemically characterized GH39 β-xylosidases that we speculate could impact active site architecture, size, charge, and/or polarity.Discussion. Collectively, the unique capabilities and multi-functionality of Bgxg1 render it an excellent candidate for inclusion in enzyme cocktails mediating cellulose and hemicellulose saccharification from lignocellulosic biomass. creator: Jessica M. Morrison creator: Mostafa S. Elshahed creator: Noha Youssef uri: https://doi.org/10.7717/peerj.2289 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Morrison et al. title: Imbalance between subsets of CD8+ peripheral blood T cells in patients with chronic obstructive pulmonary disease link: https://peerj.com/articles/2301 last-modified: 2016-08-02 description: Background. CD8+ T lymphocytes are known to play a critical role in the pathogenesis of chronic obstructive pulmonary disease (COPD). However, systematic analyses of CD8+ T cell (Cytotoxic T cells, Tc) subsets in COPD patients have yet to be well conducted.Methods. The whole Tc subsets, including Tc1/2/10/17, CD8+ regulatory T cells (Tregs) and CD8+α7+ T cells, were quantified by flow cytometry in peripheral blood from 24 stable COPD subjects (SCOPD), 14 patients during acute exacerbations (AECOPD), and 14 healthy nonsmokers (HN).Results. Acute exacerbations of COPD were accompanied by elevated levels of circulating CD8+ T cells. Tc1 cells were increased in both SCOPD and AECOPD patients, whereas the percentage of Tc2 cells was decreased in SCOPD patients but remained normal in AECOPD patients. Tc17 cells were increased only in AECOPD patients, and the percentage of Tc10 cells was reduced in both SCOPD and AECOPD patients. The imbalances of pro/anti-inflammatory Tc subsets observed in COPD may be caused by the lack of Tc10 cells and the impaired anti-inflammatory capacity of CD8+ Tregs.Conclusions. The imbalances between subsets of CD8+ peripheral blood T cells contribute to the immune response dysfunction in COPD pathogenesis. creator: Long Chen creator: Gang Chen creator: Ming-Qiang Zhang creator: Xian-Zhi Xiong creator: Hong-Ju Liu creator: Jian-Bao Xin creator: Jian-Chu Zhang creator: Jiang-Hua Wu creator: Zhao-Ji Meng creator: Sheng-Wen Sun uri: https://doi.org/10.7717/peerj.2301 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Chen et al. title: Bone lesions in Chinese POEMS syndrome patients: imaging characteristics and clinical implications link: https://peerj.com/articles/2294 last-modified: 2016-08-02 description: Objective. Bone lesion is crucial for diagnosing and management of polyneuropathy, organomegaly, endocrinopathy, monoclonal protein, and skin change (POEMS) syndrome, a rare plasma cell disorder. This study is to compare the effectiveness of X-ray skeletal survey (SS) and computed tomography (CT) for detecting bone lesions in Chinese POEMS syndrome patients, and to investigate the relationship between bone lesion features and serum markers.Methods. SS and chest/abdomen/pelvic CT images of 38 Chinese patients (26 males, 12 females, aged 21–70 years) with POEMS syndrome recruited at our medical center between January 2013 and January 2015 were retrospectively analyzed. Bone lesions identified by CT were further categorized according to the size (<5 mm, 5–10 mm, >10 mm) and appearance (osteosclerotic, lytic, mixed). The percentage of plasma cells in bone marrow smears, type of immunoglobulin, platelet (Plt), and levels of serum bone metabolic markers and inflammatory factors including alkaline phosphatase (ALP), calcium, phosphate, parathyroid hormone (PTH), beta-isomerized C-telopeptide (β-CTx), vascular endothelial growth factor (VEGF), and interleukin (IL)-6 levels were also recorded.Results. Of the 38 POEMS syndrome patients, the immunoglobulin heavy chain isotypes were IgA in 25 patients (65.8%; 25/38) and IgG in 13 patients (34.2%; 13/38), and the light chain isotypes were λ in 35 patients (92.1%; 35/38) and κ in 3 patients (7.9%; 3/38). There were 23 patients with thrombocytosis. More patients with bone lesions were detected by CT than by SS (97.4% vs. 86.8%). The most commonly affected location was the pelvis (89.5%), followed by the spine, clavicle/scapula/sternum/ribs, skull, and long bones. Of the 38 POEMS syndrome patients, 35 (94.6%) had osteosclerotic and 32 (86.5%) had mixed lesions. Osteosclerotic lesions were typically scattered, variable in size, and plaque-like, whereas mixed lesions were pouch-shaped or soup bubble-like with a clear sclerotic margin and were generally larger. Although the majority of bone lesions were small in size, 23 (62.2%) had at least one lesion >10 mm. There was no correlation between serum marker levels and bone lesion patterns after Bonferroni correction (all P > 0.001).Conclusions. CT is more sensitive and accurate than SS in detecting bone lesions in POEMS syndrome. creator: Fengdan Wang creator: Xufei Huang creator: Yan Zhang creator: Jian Li creator: Daobin Zhou creator: Zhengyu Jin uri: https://doi.org/10.7717/peerj.2294 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Wang et al. title: Microbial production and characterization of poly-3-hydroxybutyrate by Neptunomonas antarctica link: https://peerj.com/articles/2291 last-modified: 2016-08-02 description: Considering the industrial interest of biodegradable polymer poly-3-hydroxybutyrate (PHB), the marine bacteria Neptunomonas antarctica was studied for its ability to accumulate PHB. The extracted polymer was confirmed to be PHB by nuclear magnetic resonance analysis. In shake flask cultures using natural seawater as medium components, PHB was produced up to 2.12 g/L with a yield of 0.18 g PHB/g fructose. In the presence of artificial seawater, the PHB titer and yield reached 2.13 g/L and 0.13 g PHB/g fructose, respectively. The accumulated polymer gradually decreased when fructose was exhausted, indicating that intracellular PHB was degraded by N. antarctica. The weight-average and number-average molecular weights of PHB produced within natural seawater were 2.4 × 105 g/mol and 1.7 × 105 g/mol, respectively. Our results highlight the potential of N. antarctica for PHB production with seawater as a nutrient source. creator: Xiao-Jie Liu creator: Jie Zhang creator: Peng-Hui Hong creator: Zheng-Jun Li uri: https://doi.org/10.7717/peerj.2291 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Liu et al. title: The physiological consequences of varied heat exposure events in adult Myzus persicae: a single prolonged exposure compared to repeated shorter exposures link: https://peerj.com/articles/2290 last-modified: 2016-08-02 description: The study of environmental stress tolerance in aphids has primarily been at low temperatures. In these cases, and in the rare cases of high temperature tolerance assessments, all exposures had been during a single stress event. In the present study, we examined the physiological consequences of repeated high temperature exposure with recovery periods between these stress events in Myzus persicae. We subjected individuals to either a single prolonged three hour heating event, or three one hour heating events with a recovery time of 24 h between bouts. Aphids exposed to repeated bouts of high temperatures had more glucose and higher expression of proteins and osmolyte compounds, such as glycerol, compared to the prolonged exposure group. However, aphids exposed to the repeated high temperature treatment had reduced sources of energy such as trehalose and triglyceride compounds than the prolonged exposure group. Recovery time had more physiological costs (based on production of more protein and consumption of more trehalose and triglyceride) and benefits (based on production of more osmolytes) in repeated high temperature treatments. As aphids are known to respond differently to constant versus ‘natural’ fluctuating temperature regimes, conclusions drawn from constant temperature data sets may be problematic. We suggest future experiments assessing insect responses to thermal stress incorporate a repeated stress and recovery pattern into their methodologies. creator: Behnaz Ghaedi creator: Nigel R. Andrew uri: https://doi.org/10.7717/peerj.2290 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Ghaedi and Andrew title: A framework for smartphone-enabled, patient-generated health data analysis link: https://peerj.com/articles/2284 last-modified: 2016-08-02 description: Background: Digital medicine and smartphone-enabled health technologies provide a novel source of human health and human biology data. However, in part due to its intricacies, few methods have been established to analyze and interpret data in this domain. We previously conducted a six-month interventional trial examining the efficacy of a comprehensive smartphone-based health monitoring program for individuals with chronic disease. This included 38 individuals with hypertension who recorded 6,290 blood pressure readings over the trial.Methods: In the present study, we provide a hypothesis testing framework for unstructured time series data, typical of patient-generated mobile device data. We used a mixed model approach for unequally spaced repeated measures using autoregressive and generalized autoregressive models, and applied this to the blood pressure data generated in this trial.Results: We were able to detect, roughly, a 2 mmHg decrease in both systolic and diastolic blood pressure over the course of the trial despite considerable intra- and inter-individual variation. Furthermore, by supplementing this finding by using a sequential analysis approach, we observed this result over three months prior to the official study end—highlighting the effectiveness of leveraging the digital nature of this data source to form timely conclusions.Conclusions: Health data generated through the use of smartphones and other mobile devices allow individuals the opportunity to make informed health decisions, and provide researchers the opportunity to address innovative health and biology questions. The hypothesis testing framework we present can be applied in future studies utilizing digital medicine technology or implemented in the technology itself to support the quantified self. creator: Shreya S. Gollamudi creator: Eric J. Topol creator: Nathan E. Wineinger uri: https://doi.org/10.7717/peerj.2284 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Gollamudi et al. title: Stable isotopes in bivalves as indicators of nutrient source in coastal waters in the Bocas del Toro Archipelago, Panama link: https://peerj.com/articles/2278 last-modified: 2016-08-02 description: To examine N-isotope ratios (15N/14N) in tissues and shell organic matrix of bivalves as a proxy for natural and anthropogenic nutrient fluxes in coastal environments, Pinctada imbricata, Isognomon alatus, and Brachidontes exustusbivalves were live-collected and analyzed from eight sites in Bocas del Toro, Panama. Sites represent a variety of coastal environments, including more urbanized, uninhabited, riverine, and oceanic sites. Growth under differing environmental conditions is confirmed by δ18O values, with open ocean Escudo de Veraguas shells yielding the highest average δ18O (−1.0‰) value and freshwater endmember Rio Guarumo the lowest (−1.7‰). At all sites there is no single dominant source of organic matter contributing to bivalve δ15N and δ13C values. Bivalve δ15N and δ13C values likely represent a mixture of mangrove and seagrass N and C, although terrestrial sources cannot be ruled out. Despite hydrographic differences between end-members, we see minimal δ15N and δ13C difference between bivalves from the river-influenced Rio Guarumo site and those from the oceanic Escudo de Veraguas site, with no evidence for N from open-ocean phytoplankton in the latter. Populated sites yield relative 15N enrichments suggestive of anthropogenic nutrient input, but low δ15N values overall make this interpretation equivocal. Lastly, δ15N values of tissue and shell organic matrix correlate significantly for pterioideans P. imbricata and I. alatus. Thus for these species, N isotope studies of historical and fossil shells should provide records of ecology of past environments. creator: Lauren E. Graniero creator: Ethan L. Grossman creator: Aaron O’Dea uri: https://doi.org/10.7717/peerj.2278 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Graniero et al. title: Competition and fixation of cohorts of adaptive mutations under Fisher geometrical model link: https://peerj.com/articles/2256 last-modified: 2016-08-02 description: One of the simplest models of adaptation to a new environment is Fisher’s Geometric Model (FGM), in which populations move on a multidimensional landscape defined by the traits under selection. The predictions of this model have been found to be consistent with current observations of patterns of fitness increase in experimentally evolved populations. Recent studies investigated the dynamics of allele frequency change along adaptation of microbes to simple laboratory conditions and unveiled a dramatic pattern of competition between cohorts of mutations, i.e., multiple mutations simultaneously segregating and ultimately reaching fixation. Here, using simulations, we study the dynamics of phenotypic and genetic change as asexual populations under clonal interference climb a Fisherian landscape, and ask about the conditions under which FGM can display the simultaneous increase and fixation of multiple mutations—mutation cohorts—along the adaptive walk. We find that FGM under clonal interference, and with varying levels of pleiotropy, can reproduce the experimentally observed competition between different cohorts of mutations, some of which have a high probability of fixation along the adaptive walk. Overall, our results show that the surprising dynamics of mutation cohorts recently observed during experimental adaptation of microbial populations can be expected under one of the oldest and simplest theoretical models of adaptation—FGM. creator: Jorge A. Moura de Sousa creator: João Alpedrinha creator: Paulo R.A. Campos creator: Isabel Gordo uri: https://doi.org/10.7717/peerj.2256 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Moura de Sousa et al. title: Decoupling the response of an estuarine shrimp to architectural components of habitat structure link: https://peerj.com/articles/2244 last-modified: 2016-08-02 description: In order to explore biotic attraction to structure, we examined how the amount and arrangement of artificial biotic stalks affected responses of a shrimp, Palaemon macrodactylus, absent other proximate factors such as predation or interspecific competition. In aquaria, we tested the effect of differing densities of both un-branched and branched stalks, where the amount of material in the branched stalk equaled four-times that of the un-branched. The results clearly showed that it was the amount of material, not how it was arranged, that elicited responses from shrimp. Also, although stalks were not purposefully designed to mimic structural elements found in nature, they did resemble biogenic structure such as hydroids, algae, or plants. In order to test shrimp attraction to a different, perhaps more unfamiliar habitat type, we examined responses to plastic “army men.” These structural elements elicited similar attraction of shrimp, and, in general, shrimp response correlated well with the fractal dimension of both stalks and army men. Overall, these results indicate that attraction to physical structure, regardless of its nature, may be an important driver of high abundances often associated with complex habitats. creator: Jeffrey A. Crooks creator: Andrew L. Chang creator: Gregory M. Ruiz uri: https://doi.org/10.7717/peerj.2244 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Crooks et al. title: Effects of salinity change on two superoxide dismutases (SODs) in juvenile marbled eel Anguilla marmorata link: https://peerj.com/articles/2149 last-modified: 2016-08-02 description: Salinity is one of the most important factors that affect the fish growth and survival. Superoxide dismutases (SODs), as the primary antioxidant enzymes, play a first role in the process of preventing oxidative stress caused by excessive superoxide anion (O${}_{2}^{-}$2−) in living organisms. In the present study, we investigated the effects of salinity on the gene expressions as well as enzymatic activities of MnSOD and Cu/ZnSOD in gill, intestine, kidney, liver and muscle tissues of the marbled eel Anguilla marmorata. We found that the liver might possess stronger redox capacity compared with other tissues. Furthermore, the gene expressions and enzymatic activities of SODs in juvenile marbled eels could be effectively enhanced by low salinity but inhibited when the salinity was higher than the body tolerance. Our findings indicated that MnSOD and Cu/ZnSOD played vital roles in the adaptation of marbled eels to salinity variation, which contributed to the elucidation of physiological adaptation and regulatory mechanism of SODs in eels. creator: Li Wang creator: Xiaolu Wang creator: Shaowu Yin uri: https://doi.org/10.7717/peerj.2149 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Wang et al. title: The masquerade game: marine mimicry adaptation between egg-cowries and octocorals link: https://peerj.com/articles/2051 last-modified: 2016-08-02 description: Background. Background matching, as a camouflage strategy, is one of the most outstanding examples of adaptation, where little error or mismatch means high vulnerability to predation. It is assumed that the interplay of natural selection and adaptation are the main evolutionary forces shaping the great diversity of phenotypes observed in mimicry; however, there may be other significant processes that intervene in the development of mimicry such as phenotypic plasticity. Based on observations of background mismatching during reproduction events of egg-cowries, sea snails of the family Ovulidae that mimic the octocoral where they inhabit, we wondered if they match the host species diversity. Using observations in the field and molecular systematics, we set out to establish whether the different egg-cowrie color/shape polymorphisms correspond to distinct lineages restricted to specific octocoral species.Methods. Collection and observations of egg-cowries and their octocoral hosts were done using SCUBA diving between 2009 and 2012 at two localities in the Tropical Eastern Pacific (TEP), Malpelo Island and Cabo Corrientes (Colombia). Detailed host preference observations were done bi-annually at Malpelo Island. We analyzed the DNA sequence of the mitochondrial genes COIand 16S rDNA, extensively used in phylogenetic and DNA barcoding studies, to assess the evolutionary relationship among different egg-cowrie colorations and morphologies.Results. No genetic divergence among egg-cowries associated to different species of the same octocoral genus was observed based on the two mitochondrial genes analyzed. For instance, all egg-cowrie individuals from the two sampled localities observed on 8 different Pacifigorgia-Eugorgia species showed negligible mitochondrial divergence yet large morphologic divergence, which suggests that morphologies belonging to at least two sea snail species, Simnia avena(=S. aequalis) and Simnialena rufa, can cross-fertilize.Discussion. Our study system comprised background-matching mimicry, of the masquerade type, between egg-cowries (Simnia/Simnialena) and octocorals (Pacifigorgia/Eugorgia/Leptogorgia). We observed mimicry mismatches related to fitness trade-offs, such as reproductive aggregations vs. vulnerability against predators. Despite the general assumption that coevolution of mimicry involves speciation, egg-cowries with different hosts and colorations comprise the same lineages. Consequently, we infer that there would be significant tradeoffs between mimicry and the pursuit of reproductive aggregations in egg-cowries. The findings of this study not only contribute to the understanding of the evolution of mimicry in egg-cowries, a poorly studied group of marine gastropods, but also to the development of a new biologically meaningful board game that could be implemented as a learning tool. creator: Juan A. Sánchez creator: Angela P. Fuentes-Pardo creator: Íde Ní Almhain creator: Néstor E. Ardila-Espitia creator: Jaime Cantera-Kintz creator: Manu Forero-Shelton uri: https://doi.org/10.7717/peerj.2051 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Sánchez et al.