title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2018-12 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Identification and characterization of miRNA169 family members in banana (Musa acuminata L.) that respond to fusarium oxysporum f. sp. cubense infection in banana cultivars link: https://peerj.com/articles/6209 last-modified: 2018-12-21 description: MicroRNAs (miRNAs) play an important role in plant resistance to pathogen infections. However, little is known about the role of miRNAs in banana Fusarium wilt, which is the most economically devastating disease in banana production. In the present study, we identified and characterized a total of 18 miR169 family members in banana (Musa acuminata L.) based on small RNA sequencing. The banana miR169 family clustered into two groups based on miRNA evolutionary analysis. Multiple sequence alignment indicated a high degree of sequence conservation in miRNA169 family members across 28 plant species. Computational target prediction algorithms were used to identify 25 targets of miR169 family members in banana. These targets were enriched in various metabolic pathways that include the following molecules: glycine, serine, threonine, pentose, glycerolipids, nucleotide sugars, starch, and sucrose. Through miRNA transcriptomic analysis, we found that ma-miR169a and ma-miR169b displayed high expression levels, whereas the other 16 ma-miR169 members exhibited low expression in the HG and Baxi banana cultivars. Further experiments indicate that there were negative relationships between ma-miR169a, ma-miR169b and their targets basing on their expression levels to Foc4 (Fusarium oxysporum f. sp. cubense tropical race 4) infection in resistant cultivars. But they were low expressed in susceptive cultivars. These results suggested that the expression levels of ma-miR169a and ma-miR169b were consistent with the resistance degree of the banana cultivars to Foc4. The analysis presented here constitutes a starting point to understand ma-miR169-mediated Fusarium wilt resistance at the transcriptional level in banana and predicts possible candidate targets for the genetic improvement of banana resistance to Foc4. creator: Shun Song creator: Yi Xu creator: Dongmei Huang creator: Muhammad Aleem Ashraf creator: Jingyang Li creator: Wei Hu creator: Zhiqiang Jin creator: Changying Zeng creator: Fenling Tang creator: Biyu Xu creator: Huicai Zeng creator: Yujia Li creator: Jianghui Xie uri: https://doi.org/10.7717/peerj.6209 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Song et al. title: In vivo antioxidant activity of mackerel (Scomber japonicus) muscle protein hydrolysate link: https://peerj.com/articles/6181 last-modified: 2018-12-21 description: Pacific chub mackerel (Scomber japonicus) is an important fish throughout the world, especially in East Asian countries, including Korea, China, and Japan. Protein hydrolysates from marine sources are commonly used as nutritional supplements, functional ingredients, and flavor enhancers in the food, beverage, and pharmaceutical industries. Antioxidants isolated from fish are relatively easy to prepare, are cost effective, and have no reported side effects. Hence, the present study aimed to investigate the in vivo antioxidant activities of mackerel muscle protein hydrolysate (MMPH) prepared using Protamex. The in vivo bioactivities of MMPH were investigated in alcoholic fatty liver mice (C57BL/6). Serum alanine aminotransferase and aspartate aminotransferase levels were comparable in test and control mice, whereas serum triglyceride and lipid peroxidation levels significantly (p < 0.05; p < 0.001) decreased after administration of MMPH (100–500 mg kg−1), especially at a concentration of 100 mg kg−1. A significant (p < 0.05) reduction in xanthine oxidase activity was observed in all groups treated with MMPH (100–500 mg kg−1), as compared with the control group. Significantly (p < 0.05) higher superoxide dismutase (SOD) activity/protein expression and regulated catalase (CAT) activity/protein expression levels were observed in groups administered MMPH (100–500 mg kg−1), especially at a concentration of 100 mg kg−1. These results show that the abundant amino acids of S. japonicus play an important role in the cytosol of the liver cells by directly participating in the expression of xanthine oxidase and the detoxifying SOD and CAT proteins, thereby enhancing antioxidant ability and ultimately, inhibiting lipid peroxidation. This study demonstrated that muscle protein hydrolysate from S. japonicus has strong antioxidant activities. creator: Khawaja Muhammad Imran Bashir creator: Md. Mohibbullah creator: Jeong Hyeon An creator: Ji-Yeon Choi creator: Yong-Ki Hong creator: Jae Hak Sohn creator: Jin-Soo Kim creator: Jae-Suk Choi uri: https://doi.org/10.7717/peerj.6181 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Bashir et al. title: Modulation of corticomotor excitability in response to distal focal cooling link: https://peerj.com/articles/6163 last-modified: 2018-12-21 description: BackgroundThermal stimulation has been proposed as a modality to facilitate motor recovery in neurological populations, such as stroke. Recently (Ansari, Remaud & Tremblay, 2018), we showed that application of cold or warm stimuli distally to a single digit produced a variable and short lasting modulation in corticomotor excitability. Here, our goal was to extend these observations to determine whether an increase in stimulation area could elicit more consistent modulation.MethodsParticipants (n = 22) consisted of a subset who participated in our initial study. Participants were asked to come for a second testing session where the thermal protocol was repeated but with extending the stimulation area from single-digit (SD) to multi-digits (MD, four fingers, no thumb). As in the first session, skin temperature and motor evoked potentials (MEPs) elicited with transcranial magnetic stimulation were measured at baseline (BL, neutral gel pack at 22 °C), at 1 min during the cooling application (pre-cooled 10 °C gel pack) and 5 and 10 min post-cooling (PC5 and PC10). The analysis combined the data obtained previously with single-SD cooling (Ansari, Remaud & Tremblay, 2018) with those obtained here for MD cooling.ResultsAt BL, participants exhibited comparable measures of resting corticomotor excitability between testing sessions. MD cooling induced similar reductions in skin temperature as those recorded with SD cooling with a peak decline at C1 of respectively, −11.0 and −10.3 °C. For MEPs, the primary analysis revealed no main effect attributable to the stimulation area. A secondary analysis of individual responses to MD cooling revealed that half of the participants exhibited delayed MEP facilitation (11/22), while the other half showed delayed inhibition (10/22); which was sustained in the post-cooling phase. More importantly, a correlation between variations in MEP amplitude recorded during the SD cooling session with those recorded in the second session with MD cooling, revealed a very good degree of correspondence between the two at the individual level.ConclusionThese results indicate that increasing the cooling area in the distal hand, while still eliciting variable responses, did produce more sustained modulation in MEP amplitude in the post-cooling phase. Our results also highlight that responses to cooling in terms of either depression or facilitation of corticomotor excitability tend to be fairly consistent in a given individual with repeated applications. creator: Yekta Ansari creator: Anthony Remaud creator: François Tremblay uri: https://doi.org/10.7717/peerj.6163 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Ansari et al. title: Species turnover in plants does not predict turnover in flower-visiting insects link: https://peerj.com/articles/6139 last-modified: 2018-12-21 description: Congruence between plant and insect diversity is considered possibly useful in conservation planning, as the better known plants could be surrogates for the lesser known insects. There has been little quantification of congruence across space, especially in biodiversity rich areas. We compare here species richness, and turnover relationships between plants and flower-visiting insects across space (0.5–80 km) in natural areas of a biodiversity hotspot, the Greater Cape Floristic Region, South Africa. A total of 22,352 anthophile individuals in 198 species and 348 plant species were sampled. A comparison between the plants and anthophiles suggest significant concordance between the two assemblages. However, turnover was weaker in plants than in anthophiles. Plant turnover decreased with greater geographical distance between plot pairs. In contrast, insect turnover remained high with increasing geographical distance between plot pairs. These findings suggest that while patterns of plant diversity and distribution shape flower-visiting insect assemblages, they are not reliable surrogates. The conservation significance of these results is that specialist mutualisms are at greatest risk, and that set-asides on farms would help improve the functional connectivity leading to the maintenance of the full range of mutualisms. creator: John P. Simaika creator: Michael Samways creator: Sven M. Vrdoljak uri: https://doi.org/10.7717/peerj.6139 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Simaika et al. title: Application of insect-proof nets in pesticide-free rice creates an altered microclimate and differential agronomic performance link: https://peerj.com/articles/6135 last-modified: 2018-12-21 description: BackgroundInsect-proof nets are commonly used in crop production and scientific research because of their environmental, economic, and agronomic benefits. However, insect-proof nets can unintentionally alter the microclimate inside the screenhouse and therefore greatly affect plant growth and yield. To examine the microclimate and agronomic performance of pesticide-free rice under insect-proof nets, two-year field experiments were carried out in 2011 and 2012.MethodsIn the present study, the experiment was conducted by using a split-plot design considering the cultivation environment (open field cultivation (OFC) and insect-proof nets cultivation (IPNC)) as the main plot and the varieties as the subplot (Suxiangjing3 and Nanjing44).ResultsIPNC significantly reduced the air speed and solar radiation, and slightly increased the daytime soil temperature, daytime air temperature, and nighttime relative humidity. By contrast, the nighttime soil temperature, nighttime air temperature, and daytime relative humidity were relatively unaffected. The grain yield of both rice cultivars decreased significantly under IPNC, which was largely attributed to the reduced panicle number. The reduced panicle number was largely associated with the decreased maximum tiller number, which was positively correlated with the tillering rate, time of tillering onset, and tillering cessation for both rice cultivars under IPNC. In addition, dry matter accumulation significantly decreased for both rice cultivars under IPNC, which was mainly caused by the decreased leaf area duration resulting from the reduced leaf area index. By contrast, the mean net assimilation rate was relatively unaffected by IPNC.DiscussionInsect-proof nets altered the microclimate in comparison with OFC by reducing the air speed and changing the radiation regime, which significantly affected dry matter production and yield of both japonica rice cultivars. Our results indicated that cultivation measures that could increase the tillering rate and the maximum tiller number under IPNC would lead to a significant increase in panicle number, ultimately increasing grain yield. In addition, maintaining a high leaf area duration by increasing the leaf area index would be important to compensate for the dry matter accumulation losses under IPNC. These findings are critical to provide a theoretical basis for improving agronomic performance of pesticide-free rice under IPNC. creator: Guoying Yang creator: Zhi Guo creator: Hongting Ji creator: Jing Sheng creator: Liugen Chen creator: Yanwen Zhao uri: https://doi.org/10.7717/peerj.6135 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Yang et al. title: Shell variability in the stem turtles Proterochersis spp. link: https://peerj.com/articles/6134 last-modified: 2018-12-21 description: BackgroundTurtle shells tend to exhibit frequent and substantial variability, both in bone and scute layout. Aside from secondary changes, caused by diseases, parasites, and trauma, this variability appears to be inherent and result from stochastic or externally induced flaws of developmental programs. It is, thus, expected to be present in fossil turtle species at least as prominently, as in modern populations. Descriptions of variability and ontogeny are, however, rare for fossil turtles, mainly due to rarity, incompleteness, damage, and post-mortem deformation of their remains. This paper is an attempt at description and interpretation of external shell variability in representatives of the oldest true turtles, Proterochersis robusta and Proterochersis porebensis (Proterochersidae, the sister group to all other known testudinatans) from the Late Triassic (Norian) of Germany and Poland.MethodsAll the available shell remains of Proterochersis robusta (13 specimens) and Proterochersis porebensis (275 specimens) were studied morphologically in order to identify any ontogenetic changes, intraspecific variability, sexual dimorphism, and shell abnormalities. To test the inferred sexual dimorphism, shape analyses were performed for two regions (gular and anal) of the plastron.ResultsProterochersis spp. exhibits large shell variability, and at least some of the observed changes seem to be correlated with ontogeny (growth of gulars, extragulars, caudals, and marginals, disappearance of middorsal keel on the carapace). Several specimens show abnormal layout of scute sulci, several others unusual morphologies of vertebral scute areas, one has an additional pair of plastral scutes, and one extraordinarily pronounced, likely pathological, growth rings on the carapace. Both species are represented in a wide spectrum of sizes, from hatchlings to old, mature individuals. The largest fragmentary specimens of Proterochersis porebensis allow estimation of its maximal carapace length at approximately 80 cm, while Proterochersis robusta appears to have reached lower maximal sizes.DiscussionThis is the second contribution describing variability among numerous specimens of Triassic turtles, and the first to show evidence of unambiguous shell abnormalities. Presented data supplement the sparse knowledge of shell scute development in the earliest turtles and suggest that at least some aspects of the developmental programs governing scute development were already similar in the Late Triassic to these of modern forms. creator: Tomasz Szczygielski creator: Justyna Słowiak creator: Dawid Dróżdż uri: https://doi.org/10.7717/peerj.6134 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Szczygielski et al. title: Non-invasive monitoring of glucocorticoid metabolite concentrations in urine and faeces of the Sungazer (Smaug giganteus) link: https://peerj.com/articles/6132 last-modified: 2018-12-21 description: Developing non-invasive techniques for monitoring physiological stress responses has been conducted in a number of mammal and bird species, revolutionizing field-based endocrinology and conservation practices. However, studies validating and monitoring glucocorticoid concentrations in reptiles are still limited. The aim of the study was to validate a method for monitoring glucocorticoid metabolite concentrations in urine (uGCM) and faeces (fGCM) of the cordylid lizard, the Sungazer (Smaug giganteus). An adrenocorticotropic hormone (ACTH) challenge was conducted on one male and two females with both urine and faecal material being collected during baseline and post-injection periods. Steroid extracts were analysed with four enzyme immunoassays (EIAs)namely: 11-oxoaetiocholanolone, 5α-pregnane-3β-11β-21-triol-20-one, tetrahydrocorticosterone, and corticosterone. A considerable response in fGCM and uGCM concentrations following ACTH administration was observed in all subjects, with the 5α-pregnane-3β-11β-21-triol-20-one and tetrahydrocorticosterone EIAs appearing to be the most suited for monitoring alterations in glucocorticoid metabolite concentrations in S. giganteus using faeces or urine as hormone matrix. Both EIAs showed a significantly higher concentration of glucocorticoid metabolites in faeces compared to urine for both sexes. Collectively, the findings of this study confirmed that both urine and faeces can be used to non-invasively assess adrenocortical function in S. giganteus. creator: Juan Scheun creator: Dominique Greeff creator: Andre Ganswindt uri: https://doi.org/10.7717/peerj.6132 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Scheun et al. title: Characterization of the mitochondrial genome of Arge bella Wei & Du sp. nov. (Hymenoptera: Argidae) link: https://peerj.com/articles/6131 last-modified: 2018-12-21 description: We describe Arge bella Wei & Du sp. nov., a large and beautiful species of Argidae from south China, and report its mitochondrial genome based on high-throughput sequencing data. We present the gene order, nucleotide composition of protein-coding genes (PCGs), and the secondary structures of RNA genes. The nearly complete mitochondrial genome of A. bella has a length of 15,576 bp and a typical set of 37 genes (22 tRNAs, 13 PCGs, and 2 rRNAs). Three tRNAs are rearranged in the A. bella mitochondrial genome as compared to the ancestral type in insects: trnM and trnQ are shuffled, while trnW is translocated from the trnW-trnC-trnY cluster to a location downstream of trnI. All PCGs are initiated by ATN codons, and terminated with TAA, TA or T as stop codons. All tRNAs have a typical cloverleaf secondary structure, except for trnS1. H821 of rrnS and H976 of rrnL are redundant. A phylogenetic analysis based on mitochondrial genome sequences of A. bella, 21 other symphytan species, two apocritan representatives, and four outgroup taxa supports the placement of Argidae as sister to the Pergidae within the symphytan superfamily Tenthredinoidea. creator: Shiyu Du creator: Gengyun Niu creator: Tommi Nyman creator: Meicai Wei uri: https://doi.org/10.7717/peerj.6131 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Du et al. title: Biochemical and growth responses of silver maple (Acer saccharinum L.) to sodium chloride and calcium chloride link: https://peerj.com/articles/5958 last-modified: 2018-12-21 description: The present research investigated the response of silver maple (Acer saccharinum L.) to salt treatment. The short- and long-term effects of NaCl and CaCl2 treatments on plant fitness characteristics (growth parameters, leaf chlorophyll content) and biochemical stress-coping mechanisms (proline accumulation as well as enzymatic activities) were examined. We found that the silver maple response to salt stress strictly depended on salt type and dose—calcium chloride was less toxic than sodium chloride, but high concentrations of both salts negatively influenced plant growth. The accumulation of proline, slight changes in the activity of superoxide dismutase and marked changes in catalase and peroxidase activities in the roots and leaves indicated complexity of the plant response. It was also shown that after one year, enzymatic parameters were restabilized, which indicates plant recovery, but the reduced mass of seedlings suggests that one year is not enough to cope with the prolonged cyclic salt stress, both resulting from NaCl and CaCl2 application. Therefore, seedlings of silver maple should be considered as moderately susceptible to salinity. Hence, it is recommended to use silver maple on non-de-iced urban areas, while planting on often de-iced roads should be avoided. creator: Jacek Patykowski creator: Jeremi Kołodziejek creator: Mateusz Wala uri: https://doi.org/10.7717/peerj.5958 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Patykowski et al. title: Factors affecting the distribution and abundance of autumn vagrant New World warblers in northwestern California and southern Oregon link: https://peerj.com/articles/5881 last-modified: 2018-12-21 description: Birds found outside their typical range, or vagrants, have fascinated naturalists for decades. Despite broad interest in vagrancy, few attempts have been made to statistically examine the explanatory variables potentially responsible for the phenomenon. In this study, we used multiple linear regression to model the occurrence of 28 rare warbler species (family Parulidae) in autumn in northern California and southern Oregon as a function of migration distance, continental population size, distance, and bearing to both closest breeding population and breeding population center. In addition to our predictive model, we used capture data from the California coast to 300 km inland to examine relationships between the presence of vagrant warblers, regional warbler species richness and age class distribution. Our study yielded three important results: (1) vagrancy is strongly correlated with larger North American population size; (2) vagrants are more common at some coastal sites; and (3) where young birds are over-represented, vagrants tend to occur—such as on the coast and at far inland sites. Of the many explanations of rare and vagrant individuals, we feel that the most likely is that these birds represent the ends of the distributions of a normal curve of migration direction, bringing some few migrants to locations out of their normal migratory range as vagrants. We also examine the underrepresented species that, according to our model, are overdue for being recorded in our study area. creator: C. John Ralph creator: Jared D. Wolfe uri: https://doi.org/10.7717/peerj.5881 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Ralph and Wolfe title: Work stress and health problems of professional drivers: a hazardous formula for their safety outcomes link: https://peerj.com/articles/6249 last-modified: 2018-12-20 description: BackgroundSeveral empirical studies have shown that professional drivers are a vulnerable occupational group, usually exposed to environmental stressors and adverse work conditions. Furthermore, recent studies have associated work-related stress with negative job performances and adverse health outcomes within this occupational group, including cardiovascular diseases and unsafe vehicle operation.ObjectiveThe aim of this study was to describe the working conditions and the health status of this occupational group, and to evaluate the association between the Demand–Control model of job stress and their self-reported health and safety outcomes.MethodsA pooled sample of 3,665 Colombian professional drivers was drawn from five different studies. The Job Content Questionnaire and the General Health Questionnaire were used to measure work stress and self-reported mental health, respectively. Additionally, professional drivers self-reported health problems (hypertension, dyslipidemia, diabetes and overweight) and health-related risky behaviors (smoking and sedentary behavior).ResultsRegarding the Job Demands–Control (JDC) model, it was found that approximately a third part of Colombian professional drivers suffer from high job strain (29.1%). Correlational and multivariate analyses suggest that de JDC model of stress is associated with the professional drivers’ mental health, traffic accidents and fines, but not with other physical and behavioral health-related outcomes, which are highly prevalent among this occupational group, such as hypertension, dyslipidemia, diabetes, overweight, smoking and sedentary behavior.ConclusionThe results of this study suggest that (a) stressful working conditions are associated with health and lifestyle-related outcomes among professional drivers, and (b) that evidence-based interventions are needed in order to reduce hazardous working conditions, job stress rates and their negative impact on the health of this occupational group. creator: Sergio A. Useche creator: Boris Cendales creator: Luis Montoro creator: Cristina Esteban uri: https://doi.org/10.7717/peerj.6249 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Useche et al. title: Optimal control of irrupting pest populations in a climate-driven ecosystem link: https://peerj.com/articles/6146 last-modified: 2018-12-20 description: Irruptions of small consumer populations, driven by pulsed resources, can lead to adverse effects including the decline of indigenous species or increased disease spread. Broad-scale pest management to combat such effects benefits from forecasting of irruptions and an assessment of the optimal control conditions for minimising consumer abundance. We use a climate-based consumer-resource model to predict irruptions of a pest species (Mus musculus) population in response to masting (episodic synchronous seed production) and extend this model to account for broad-scale pest control of mice using toxic bait. The extended model is used to forecast the magnitude and frequency of pest irruptions under low, moderate and high control levels, and for different timings of control operations. In particular, we assess the optimal control timing required to minimise the frequency with which pests reach ‘plague’ levels, whilst avoiding excessive toxin use. Model predictions suggest the optimal timing for mouse control in beech forest, with respect to minimising plague time, is mid-September. Of the control regimes considered, a seedfall driven biannual-biennial regime gave the greatest reduction in plague time and plague years for low and moderate control levels. Although inspired by a model validated using house mouse populations in New Zealand forests, our modelling approach is easily adapted for application to other climate-driven systems where broad-scale control is conducted on irrupting pest populations. creator: E Penelope Holland creator: Rachelle N. Binny creator: Alex James uri: https://doi.org/10.7717/peerj.6146 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Holland et al. title: Spatial distributions, feeding ecologies, and behavioral interactions of four rabbitfish species (Siganus unimaculatus, S. virgatus, S. corallinus, and S. puellus) link: https://peerj.com/articles/6145 last-modified: 2018-12-20 description: Clarifying the underlying mechanisms that enable closely related species to coexist in a particular environment is a fundamental aspect of ecology. Coral reefs support a high diversity of marine organisms, among which rabbitfishes (family Siganidae) are a major component The present study aimed to reveal the mechanism that allows rabbitfishes to coexist on coral reefs in Okinawa, Japan, by investigating the spatial distributions, feeding ecologies, and behavioral interactions of four species: Siganus unimaculatus, S. virgatus, S. corallinus, and S. puellus. All four species had a size-specific spatial distribution, whereby small individuals were found in sheltered areas that were covered by branching and bottlebrush Acropora spp. and large individuals were found in both sheltered and exposed rocky areas. However, no clear species-specific spatial distribution was observed. There was some variation in the food items taken, with S. unimaculatus primarily feeding on brown foliose algae, red foliose algae, and red styloid algae, and S. virgatus and S. puellus preferring brown foliose algae and sponges, respectively. However, S. corallinus did not show any clear differences in food preferences from S. virgatus or S. unimaculatus, mainly feeding on brown foliose algae and red styloid algae. The four species exhibited differences in foraging substrate use, which was probably related to differences in their body shape characteristics: S. unimaculatus has a slender body with a remarkably protruding snout and mainly used concave substrates for feeding, whereas S. virgatus has a deeper body with a low degree of snout protrusion and mainly used convex substrates. The other two species have a low degree of snout protrusion combined with a deeper body in the case of S. corallinus and a slender body in the case of S. puellus and used concave, flat, and convex substrates to an equal degree for feeding. Behavioral interactions were categorized into “agonistic behaviors” (attack and agonistic displays) and “no interactions.” For all four species, a greater frequency of agonistic behaviors was observed when two conspecific pairs approached each other than when two heterospecific individuals encountered each other. Together, these results suggest that food item partitioning is one of the main factors enabling the coexistence of these four syntopic rabbitfish species, which is enhanced by species-specific differences in feeding substrates as a result of their different body shape and behavioral characteristics. creator: Atsushi Nanami uri: https://doi.org/10.7717/peerj.6145 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Nanami title: Effects of artemisinin on ventricular arrhythmias in response to left ventricular afterload increase and microRNA expression profiles in Wistar rats link: https://peerj.com/articles/6110 last-modified: 2018-12-20 description: BackgroundPatients with dilated cardiomyopathy, increased ventricular volume, pressure overload or dysynergistic ventricular contraction and relaxation are susceptible to develop serious ventricular arrhythmias (VA). These phenomena are primarily based on a theory of mechanoelectric feedback, which reflects mechanical changes that produce alterations in electrical activity. However, very few systematic studies have provided evidence of the preventive effects of artemisinin (ART) on VA in response to left ventricle (LV) afterload increases. MicroRNAs (miRNAs) are endogenous small non-coding RNAs that regulate expression of multiple genes by suppressing mRNAs post-transcriptionally.AimsThe aims of this study were to investigate preventive effects of ART on mechanical VA and the underling molecular mechanisms of differentially expressed miRNAs (DEMs).MethodsFor the study, 70 male Wistar rats were randomly divided into seven groups: group 1 was a control group (sham surgery); group 2 was a model group that underwent transverse aortic constriction (TAC) surgery; groups 3, 4, 5 and 6 were administered ART 75, 150, 300 and 600 mg/kg before TAC surgery, respectively; and group 7 was administered verapamil (VER) 1 mg/kg before TAC surgery. A ventricular arrhythmia score (VAS) was calculated to evaluate preventive effects of ART and VER on mechanical VA. The high throughput sequencing-based approach provided DEMs that were altered by ART pretreatment between group 2 and group 4. All predicted mRNAs of DEMs were enriched by gene ontology (GO) and Kyoto Encyclopedia annotation of Genes and Genomes (KEGG) databases. These DEMs were validated by a real time quantitative polymerase chain reaction (RT-qPCR).ResultsThe average VASs of groups 3, 4, 5, 6 and 7 were significantly reduced compared with those of group 2 (2.70 ± 0.48, 1.70 ± 0.95, 2.80 ± 0.79, 2.60 ± 0.97, 1.40 ± 0.52, vs 3.70 ± 0.67, p < 0.01, respectively). The three top GO terms were neuron projection, organ morphogenesis and protein domain specific binding. KEGG enrichment of the 16 DEMs revealed that MAPK, Wnt and Hippo signaling pathways were likely to play a substantial role in the preventive effects of ART on mechanical VA in response to LV afterload increases. All candidate DEMs with the exception of rno-miR-370-3p, rno-miR-6319, rno-miR-21-3p and rno-miR-204-5p showed high expression levels validated by RT-qPCR.ConclusionsArtemisinin could prevent mechanical VA in response to LV afterload increases. Validated DEMs could be biomarkers and therapeutic targets of ART regarding its prevention of VA induced by pressure overload. The KEGG pathway and GO annotation analyses of the target mRNAs could indicate the potential functions of candidate DEMs. These results will help to elucidate the functional and regulatory roles of candidate DEMs associated with antiarrhythmic effects of ART. creator: Xue Xu creator: Qiang Zhang creator: Huanqiu Song creator: Zhuo Ao creator: Xiang Li creator: Cheng Cheng creator: Maojing Shi creator: Fengying Fu creator: Chengtao Sun creator: Yuansheng Liu creator: Dong Han uri: https://doi.org/10.7717/peerj.6110 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Xu et al. title: Climatic niche shift and possible future spread of the invasive South African Orchid Disa bracteata in Australia and adjacent areas link: https://peerj.com/articles/6107 last-modified: 2018-12-20 description: Orchids are generally regarded as plants with an insignificant invasive potential and so far only one species has proved to be harmful for native flora. However, previous studies on Epipactis helleborine and Arundina graminifolia indicate that the ecological aspects of range extension in their non-native geographical range are not the same for all species of orchids. Disa bracteata in its native range, South Africa, is categorized as of little concern in terms of conservation whereas in Australia it is naturalized and considered to be an environmental weed. The aim of this research was to determine the ecological preferences enabling the spread of Disa bracteata in Western and South Australia, Victoria and Tasmania and to evaluate the effect of future climate change on its potential range. The ecological niche modeling approach indicates that most of the accessible areas are already occupied by this species but future expansion will continue based on four climate change scenarios (rcp26, rcp45, rcp60, rcp85). Further expansion is predicted especially in eastern Australia and eastern Tasmania. Moreover, there are some unpopulated but suitable habitats in New Zealand, which according to climate change scenarios will become even more suitable in the future. The most striking result of this study is the significant difference between the environmental conditions recorded in the areas which D. bracteata naturally inhabits and invasive sites—that indicates a possible niche shift. In Australia the studied species continues to populate a new niche or exploit habitats that are only moderately represented in South Africa. creator: Kamil Konowalik creator: Marta Kolanowska uri: https://doi.org/10.7717/peerj.6107 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Konowalik and Kolanowska title: The feasibility of predicting ground reaction forces during running from a trunk accelerometry driven mass-spring-damper model link: https://peerj.com/articles/6105 last-modified: 2018-12-20 description: BackgroundMonitoring the external ground reaction forces (GRF) acting on the human body during running could help to understand how external loads influence tissue adaptation over time. Although mass-spring-damper (MSD) models have the potential to simulate the complex multi-segmental mechanics of the human body and predict GRF, these models currently require input from measured GRF limiting their application in field settings. Based on the hypothesis that the acceleration of the MSD-model’s upper mass primarily represents the acceleration of the trunk segment, this paper explored the feasibility of using measured trunk accelerometry to estimate the MSD-model parameters required to predict resultant GRF during running.MethodsTwenty male athletes ran at approach speeds between 2–5 m s−1. Resultant trunk accelerometry was used as a surrogate of the MSD-model upper mass acceleration to estimate the MSD-model parameters (ACCparam) required to predict resultant GRF. A purpose-built gradient descent optimisation routine was used where the MSD-model’s upper mass acceleration was fitted to the measured trunk accelerometer signal. Root mean squared errors (RMSE) were calculated to evaluate the accuracy of the trunk accelerometry fitting and GRF predictions. In addition, MSD-model parameters were estimated from fitting measured resultant GRF (GRFparam), to explore the difference between ACCparam and GRFparam.ResultsDespite a good match between the measured trunk accelerometry and the MSD-model’s upper mass acceleration (median RMSE between 0.16 and 0.22 g), poor GRF predictions (median RMSE between 6.68 and 12.77 N kg−1) were observed. In contrast, the MSD-model was able to replicate the measured GRF with high accuracy (median RMSE between 0.45 and 0.59 N kg−1) across running speeds from GRFparam. The ACCparam from measured trunk accelerometry under- or overestimated the GRFparam obtained from measured GRF, and generally demonstrated larger within parameter variations.DiscussionDespite the potential of obtaining a close fit between the MSD-model’s upper mass acceleration and the measured trunk accelerometry, the ACCparam estimated from this process were inadequate to predict resultant GRF waveforms during slow to moderate speed running. We therefore conclude that trunk-mounted accelerometry alone is inappropriate as input for the MSD-model to predict meaningful GRF waveforms. Further investigations are needed to continue to explore the feasibility of using body-worn micro sensor technology to drive simple human body models that would allow practitioners and researchers to estimate and monitor GRF waveforms in field settings. creator: Niels J. Nedergaard creator: Jasper Verheul creator: Barry Drust creator: Terence Etchells creator: Paulo Lisboa creator: Mark A. Robinson creator: Jos Vanrenterghem uri: https://doi.org/10.7717/peerj.6105 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Nedergaard et al. title: Early swelling response to phytohemagglutinin is lower in older toads link: https://peerj.com/articles/6104 last-modified: 2018-12-20 description: The effects of age on performance of life-history traits are diverse, but a common outcome is senescence, an irreversible deterioration of physical and physiological capabilities of older individuals. Immune response is potentially bound to senescence. However, little is known about immune response ageing in amphibians. In this work, we test the hypothesis that amphibian early immune response is reduced in older individuals. To this end, we captured adult natterjack toads (Epidalea calamita) and inoculated them with phytohemagglutinin, an innocuous protein that triggers a skin-swelling immune response whose magnitude is directly proportional to the ability of the individual to mount an immune response. We measured early swelling immune response (corresponding to an innate-response stage) hourly, for six hours, and we calculated the area under the curve (AUC) for each individual’s time series, as a measure of immune response magnitude incorporating time. We estimated toad age by means of phalanx skeletochronology. Swelling and AUC decreased with age. Therefore, in accordance with our predictions, early immune response seems subject to senescence in these toads. Reduced ability to get over infections due to senescence of immune respose might be—together with a worse functioning of other organs and systems—among the causes of lower survival of older specimens. creator: Francisco Javier Zamora-Camacho creator: Mar Comas uri: https://doi.org/10.7717/peerj.6104 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Zamora-Camacho and Comas title: Chemical composition, antioxidant and antitumor activities of sub-fractions of wild and cultivated Pleurotus ferulae ethanol extracts link: https://peerj.com/articles/6097 last-modified: 2018-12-20 description: Pleurotus ferulae is an edible and medicinal mushroom with various bioactivities. Here, the ethanol extracts of wild and cultivated P. ferulae (PFEE-W and PFEE-C) and their subfractions including petroleum ether (Pe-W/Pe-C), ethyl acetate (Ea-W/Ea-C) and n-butanol (Ba-W/Ba-C) were prepared to evaluate their antioxidant and antitumor activities. Both PFEE-W and PFEE-C show the antioxidant activity and PFEE-W is stronger than PFEE-C. The antioxidant activities of their subfractions are in the following order: Ea > Ba > Pe. Moreover, PFEE-W and PFEE-C significantly inhibit the proliferation of murine melanoma B16 cells, human esophageal cancer Eca-109 cells, human gastric cancer BGC823 cells and human cervical cancer HeLa cells through induction of apoptosis, which partially mediated by reactive oxygen species. The antitumor activities of their subfractions are in the following order: Ea ≥ Pe > Ba. Pe-W shows higher antitumor activity compared with Pe-C, which might be correlated with the difference of their components identified by gas chromatography-mass spectrometry. These results suggest that both wild and cultivated P. ferulae have antioxidant and antitumor activities, and cultivated P. ferulae could be used to replace wild one in some functions. creator: Yi Yang creator: Changshuang Fu creator: Fangfang Zhou creator: Xiaoyu Luo creator: Jinyu Li creator: Jun Zhao creator: Jiang He creator: Xiaoqin Li creator: Jinyao Li uri: https://doi.org/10.7717/peerj.6097 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Yang et al. title: Undocumented translocations spawn taxonomic inflation in Sri Lankan fire rasboras (Actinopterygii, Cyprinidae) link: https://peerj.com/articles/6084 last-modified: 2018-12-20 description: A recent (2013) taxonomic review of the freshwater-fish genus Rasboroides, which is endemic to Sri Lanka, showed it to comprise four species: R. vaterifloris, R. nigromarginatus, R. pallidus and R. rohani. Here, using an integrative-taxonomic analysis of morphometry, meristics and mitochondrial DNA sequences of cytochrome b (cytb) and cytochrome oxidase subunit 1 (coi), we show that R. nigromarginatus is a synonym of R. vaterifloris, and that R. rohani is a synonym of R. pallidus. The creation and recognition of unnecessary taxa (‘taxonomic inflation’) was in this case a result of selective sampling confounded by a disregard of allometry. The population referred to R. rohani in the Walawe river basin represents an undocumented trans-basin translocation of R. pallidus, and a translocation into the Mahaweli river of R. vaterifloris, documented to have occurred ca 1980, in fact involves R. pallidus. A shared haplotype suggests the latter introduction was likely made from the Bentara river basin and not from the Kelani, as claimed. To stabilize the taxonomy of these fishes, the two valid species, R. vaterifloris and R. pallidus, are diagnosed and redescribed, and their distributions delineated. We draw attention to the wasteful diversion of conservation resources to populations resulting from undocumented translocations and to taxa resulting from taxonomic inflation. We argue against translocations except where mandated by a conservation emergency, and even then, only when supported by accurate documentation. creator: Hiranya Sudasinghe creator: Jayampathi Herath creator: Rohan Pethiyagoda creator: Madhava Meegaskumbura uri: https://doi.org/10.7717/peerj.6084 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Sudasinghe et al. title: Fuyuanichthys wangi gen. et sp. nov. from the Middle Triassic (Ladinian) of China highlights the early diversification of ginglymodian fishes link: https://peerj.com/articles/6054 last-modified: 2018-12-20 description: A series of well-preserved fossil assemblages from the Middle Triassic marine rock succession in Southwest China provide unique evidences for studying the early evolution of holostean fishes, including Halecomorphi (e.g., bownfin) and Ginglymodi (e.g., gars). Ginglymodi have the earliest record in the early Middle Triassic (Anisian, ∼244 Ma) of China, represented by Kyphosichthys and Sangiorgioichthys sui from Yunnan and S. yangjuanensis from Guizhou. Here, we report the discovery of a new ginglymodian, Fuyuanichthys wangi gen. et sp. nov., based on 22 well-preserved specimens from the lower part of the Zhuganpo member of the Falang Formation in eastern Yunnan and western Guizhou, which documents the first discovery of convincing ginglymodians from the late Middle Triassic (Ladinian, ∼240 Ma) Xingyi biota in China. Fuyuanichthys possesses a unique combination of features that easily distinguishes it from other ginglymodians, such as presence of a median gular and short and edentulous maxillae, and absence of a supramaxilla and supraorbitals. As one of the smallest known ginglymodians with a maximum standard length of ∼75 mm, the new finding further supports that the Middle Triassic Ginglymodi have a relatively small range of body sizes compared with the Halecomorphi from the same ecosystems in China. Results of a phylogenetic analysis recover Fuyuanichthys as a sister taxon to Kyphosichthys at the ginglymodian stem, and provide new insights into the early evolution of this clade. creator: Guang-Hui Xu creator: Xin-Ying Ma creator: Yi Ren uri: https://doi.org/10.7717/peerj.6054 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Xu et al. title: An exploration of the effect of proprioceptive knee bracing on biomechanics during a badminton lunge to the net, and the implications to injury mechanisms link: https://peerj.com/articles/6033 last-modified: 2018-12-20 description: The aim of this study was to determine changes in knee biomechanics during badminton lunges due to fatigue, lunge strategy and knee bracing. Kinetic and kinematic data were collected from 16 experienced right-handed badminton players. Three factor repeated measures ANOVAs (lunge direction—fatigue—brace) were performed with Least Significant Difference pairwise comparisons. In addition, clinical assessments including; Y-balance test, one leg hop distance and ankle dorsiflexion range of motion were performed pre- and postfatigue. The knee showed significantly greater flexion during the forehand lunge compared to backhand. In contrast, the internal rotation velocity and the knee extension moment were greater during backhand. Knee angular velocity in the sagittal plane, peak knee moment and range of moment in the coronal plane and stance time showed significantly lower values postfatigue. In addition, the peak knee adduction moment showed significantly lower values in the braced condition in both the fatigued and nonfatigues states, and no significant differences were seen for peak vertical force, loading rate, approach velocity, or in any of the clinical assessment scores. There appears to be greater risk factors when performing a backhand lunge to the net compared to a forehand lunge, and proprioceptive bracing appears to reduce the loading at the knee. creator: Raúl Valldecabres creator: Ana María de Benito creator: Greg Littler creator: Jim Richards uri: https://doi.org/10.7717/peerj.6033 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Valldecabres et al. title: Morphology and genome size of Epipactis helleborine (L.) Crantz (Orchidaceae) growing in anthropogenic and natural habitats link: https://peerj.com/articles/5992 last-modified: 2018-12-20 description: BackgroundThe process of apophytism or spreading native species to human-made habitats is one of the main elements in the creation of plant cover in anthropogenic areas. Lately, an increase of anthropogenic localities with valuable flora has been observed. Apophytes are also members of the family Orchidaceae, especially from the genus Epipactis. The aim of the study was to (i) determine and compare the phenotypic variation of E. helleborine (L.) Crantz plants in anthropogenic and natural habitats, (ii) compare the genome size of plants growing in natural and anthropogenic habitats. The results reported in this study may indicate that a habitat influences morphological characteristics of plant species.MethodsField studies were conducted on four native stands and four stands in anthropogenic areas of E. helleborine in Poland in years 2011–2013. Biometrical analyses were performed on shoots and flowers. The flowers were characterised by 25 biometric features and measured using a Nikon SMZ 800 binocular, microscopic Moticam-1SP cameras and the MIPlus07 programme (Conbest Co.). The nuclear DNA content was determined in fresh and young leaves of E. helleborine, collected from four natural and four anthropogenic populations.ResultsWe observed that in anthropogenic populations: (i) shoots were higher than shoots from natural populations, (ii) flowers differed significantly in terms of ten biometric features between habitats, (iii) the genome size of some population differed significantly between plants growing in natural and anthropogenic habitats.DiscussionAccording to some researchers, the presence of phenotypic variability and the occurrence of ecotypes are adaptation strategies of plants to environmental changes. In our opinion, in the case of the studied anthropogenic habitats (roadside) in which the E. helleborine populations grew, we can talk about ecofen due to the often repeated set of characteristic features, i.e., high shoots, long inflorescence and long, broad leaves. We agree, however, that it is difficult to isolate a taxonomic unit for ecofen due to the lack of experimental research. creator: Agnieszka Rewicz creator: Monika Rewers creator: Iwona Jędrzejczyk creator: Tomasz Rewicz creator: Jeremi Kołodziejek creator: Anna Jakubska-Busse uri: https://doi.org/10.7717/peerj.5992 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Rewicz et al. title: The oldest ceratosaurian (Dinosauria: Theropoda), from the Lower Jurassic of Italy, sheds light on the evolution of the three-fingered hand of birds link: https://peerj.com/articles/5976 last-modified: 2018-12-19 description: The homology of the tridactyl hand of birds is a still debated subject, with both paleontological and developmental evidence used in support of alternative identity patterns in the avian fingers. With its simplified phalangeal morphology, the Late Jurassic ceratosaurian Limusaurus has been argued to support a II–III–IV digital identity in birds and a complex pattern of homeotic transformations in three-fingered (tetanuran) theropods. We report a new large-bodied theropod, Saltriovenator zanellai gen. et sp. nov., based on a partial skeleton from the marine Saltrio Formation (Sinemurian, lowermost Jurassic) of Lombardy (Northern Italy). Taphonomical analyses show bone bioerosion by marine invertebrates (first record for dinosaurian remains) and suggest a complex history for the carcass before being deposited on a well-oxygenated and well-illuminated sea bottom. Saltriovenator shows a mosaic of features seen in four-fingered theropods and in basal tetanurans. Phylogenetic analysis supports sister taxon relationships between the new Italian theropod and the younger Early Jurassic Berberosaurus from Morocco, in a lineage which is the basalmost of Ceratosauria. Compared to the atrophied hand of later members of Ceratosauria, Saltriovenator demonstrates that a fully functional hand, well-adapted for struggling and grasping, was primitively present in ceratosaurians. Ancestral state reconstruction along the avian stem supports 2-3-4-1-X and 2-3-4-0-X as the manual phalangeal formulae at the roots of Ceratosauria and Tetanurae, confirming the I–II–III pattern in the homology of the avian fingers. Accordingly, the peculiar hand of Limusaurus represents a derived condition restricted to late-diverging ceratosaurians and cannot help in elucidating the origin of the three-fingered condition of tetanurans. The evolution of the tridactyl hand of birds is explained by step-wise lateral simplification among non-tetanuran theropod dinosaurs, followed by a single primary axis shift from digit position 4 to 3 at the root of Tetanurae once the fourth finger was completely lost, which allowed independent losses of the vestigial fourth metacarpal among allosaurians, tyrannosauroids, and maniraptoromorphs. With an estimated body length of 7.5 m, Saltriovenator is the largest and most robust theropod from the Early Jurassic, pre-dating the occurrence in theropods of a body mass approaching 1,000 Kg by over 25 My. The radiation of larger and relatively stockier averostran theropods earlier than previously known may represent one of the factors that ignited the trend toward gigantism in Early Jurassic sauropods. creator: Cristiano Dal Sasso creator: Simone Maganuco creator: Andrea Cau uri: https://doi.org/10.7717/peerj.5976 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Dal Sasso et al. title: Feeding response of the tropical copepod Acartia erythraea to short-term thermal stress: more animal-derived food was consumed link: https://peerj.com/articles/6129 last-modified: 2018-12-19 description: The objective of this study was to explore the feeding response of tropical copepods to short-term thermal shock and provide insight into the potential impact of coastal power plants on the trophic dynamics of tropical coastal ecosystems. Feeding experiments were conducted at three different temperatures (29 °C, 33 °C, and 35 °C) using the copepod Acartia erythraea, collected from Sanya Bay, China. The grazing rate of A. erythraea decreased dramatically in the high temperature treatment. Analysis of 18S rDNA clone libraries revealed that the diet of copepods from different treatments was mainly comprised of diatoms, metazoans, and protozoans; A. erythraea exhibited an obvious feeding preference shift with temperature, with a change from a diatom-dominated diet at 29 °C to a metazoan-dominated diet at 35 °C, and the omnivory index shifted from 0.1 to 2.84 correspondingly. Furthermore, A. erythraea showed a positive feeding response to plant food (i.e., phytoplankton and land plants) in the control treatment (29 °C), but a positive response to animal prey (i.e., metazoans and protozoans) at temperatures exceeding 33 °C, as evaluated by the Ivlev’s selectivity index. Our results suggest that copepods could regulate their food intake by considering their energy demands when exposed to short-term thermal stress, which might influence the pathway of materials moving up the trophic system. However, further studies are required to elucidate the effects of elevated temperature on feeding of different organisms in order to predict the influence of thermal pollution on the food web of tropical coastal ecosystems. creator: Simin Hu creator: Sheng Liu creator: Lingli Wang creator: Tao Li creator: Hui Huang uri: https://doi.org/10.7717/peerj.6129 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Hu et al. title: Transposons and pathogenicity in Xanthomonas: acquisition of murein lytic transglycosylases by TnXax1 enhances Xanthomonas citri subsp. citri 306 virulence and fitness link: https://peerj.com/articles/6111 last-modified: 2018-12-19 description: Xanthomonas citri subsp. citri 306 (XccA) is the causal agent of type A citrus canker (CC), one of the most significant citriculture diseases. Murein lytic transglycosylases (LT), potentially involved in XccA pathogenicity, are enzymes responsible for peptidoglycan structure assembly, remodeling and degradation. They directly impact cell wall expansion during bacterial growth, septum division allowing cell separation, cell wall remodeling allowing flagellar assembly, bacterial conjugation, muropeptide recycling, and secretion system assembly, in particular the Type 3 Secretion System involved in bacterial virulence, which play a fundamental role in XccA pathogenicity. Information about the XccA LT arsenal is patchy: little is known about family diversity, their exact role or their connection to virulence in this bacterium. Among the LTs with possible involvement in virulence, two paralogue open reading frames (ORFs) (one on the chromosome and one in plasmid pXAC64) are passenger genes of the Tn3 family transposon TnXax1, known to play a significant role in the evolution and emergence of pathogenicity in Xanthomonadales and to carry a variety of virulence determinants. This study addresses LT diversity in the XccA genome and examines the role of plasmid and chromosomal TnXax1 LT passenger genes using site-directed deletion mutagenesis and functional characterization. We identified 13 XccA LTs: 12 belong to families 1A, 1B, 1C, 1D (two copies), 1F, 1G, 3A, 3B (two copies), 5A, 6A and one which is non-categorized. The non-categorized LT is exclusive to the Xanthomonas genus and related to the 3B family but contains an additional domain linked to carbohydrate metabolism. The categorized LTs are probably involved in cell wall remodeling to allow insertion of type 3, 4 and 6 secretion systems, flagellum assembly, division and recycling of cell wall and degradation and control of peptidoglycan production. The TnXax1 passenger LT genes (3B family) are not essential to XccA or for CC development but are implicated in peptidoglycan metabolism, directly impacting bacterial fitness and CC symptom enhancement in susceptible hosts (e.g., Citrus sinensis). This underlines the role of TnXax1 as a virulence and pathogenicity-propagating agent in XccA and suggests that LT acquisition by horizontal gene transfer mediated by TnXax1 may improve bacterial fitness, conferring adaptive advantages to the plant-pathogen interaction process. creator: Amanda C.P. Oliveira creator: Rafael M. Ferreira creator: Maria Inês T. Ferro creator: Jesus A. Ferro creator: Mick Chandler creator: Alessandro M. Varani uri: https://doi.org/10.7717/peerj.6111 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Oliveira et al. title: First steps towards mitochondrial pan-genomics: detailed analysis of Fusarium graminearum mitogenomes link: https://peerj.com/articles/5963 last-modified: 2018-12-19 description: There is a gradual shift from representing a species’ genome by a single reference genome sequence to a pan-genome representation. Pan-genomes are the abstract representations of the genomes of all the strains that are present in the population or species. In this study, we employed a pan-genomic approach to analyze the intraspecific mitochondrial genome diversity of Fusarium graminearum. We present an improved reference mitochondrial genome for F. graminearum with an intron-exon annotation that was verified using RNA-seq data. Each of the 24 studied isolates had a distinct mitochondrial sequence. Length variation in the F. graminearum mitogenome was found to be largely due to variation of intron regions (99.98%). The “intronless” mitogenome length was found to be quite stable and could be informative when comparing species. The coding regions showed high conservation, while the variability of intergenic regions was highest. However, the most important variable parts are the intron regions, because they contain approximately half of the variable sites, make up more than half of the mitogenome, and show presence/absence variation. Furthermore, our analyses show that the mitogenome of F. graminearum is recombining, as was previously shown in F. oxysporum, indicating that mitogenome recombination is a common phenomenon in Fusarium. The majority of mitochondrial introns in F. graminearum belongs to group I introns, which are associated with homing endonuclease genes (HEGs). Mitochondrial introns containing HE genes may spread within populations through homing, where the endonuclease recognizes and cleaves the recognition site in the target gene. After cleavage of the “host” gene, it is replaced by the gene copy containing the intron with HEG. We propose to use introns unique to a population for tracking the spread of the given population, because introns can spread through vertical inheritance, recombination as well as via horizontal transfer. We demonstrate how pooled sequencing of strains can be used for mining mitogenome data. The usage of pooled sequencing offers a scalable solution for population analysis and for species level comparisons studies. This study may serve as a basis for future mitochondrial genome variability studies and representations. creator: Balázs Brankovics creator: Tomasz Kulik creator: Jakub Sawicki creator: Katarzyna Bilska creator: Hao Zhang creator: G Sybren de Hoog creator: Theo AJ van der Lee creator: Cees Waalwijk creator: Anne D. van Diepeningen uri: https://doi.org/10.7717/peerj.5963 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Brankovics et al. title: Iberian pig adaptation to acorn consumption: II. Net portal appearance of amino acids link: https://peerj.com/articles/6137 last-modified: 2018-12-18 description: In Iberian pig outdoor production, pigs are fed equilibrated diets until the final fattening period when grazing pigs consume mainly acorns from oak trees. Acorns are rich in energy but poor in crude protein where lysine is the first limiting amino acid (AA). Net portal appearance (NPA) is very useful to ascertain AA available for liver and peripheral tissues. The aim of this study was to determine NPA of AA in Iberian gilts fed with acorns and to ascertain if there was an effect of acorn feeding over time. Two sampling periods were carried out (after one day and after one week of acorn feeding) with six gilts (34 kg average BW) set up with three catheters: in carotid artery and portal vein for blood sampling, and ileal vein for a marker infusion to measure portal plasma flow (PPF). Pigs were fed at 2.5 × ME for maintenance a standard diet in two meals, at 09:00 (0.25) and 15:00 h (the remaining 0.75). The day previous to first sampling, pig diet was replaced by 2.4 kg of acorn. A serial blood collection was done at −5 min, 0.5, 1, 1.5, 2, 2.5, 3, 3.5, 4, 5 and 6 h after feeding 0.25 of total daily acorn ration. Following identical protocol, one week later the second sampling was done. NPA of sum of essential AA (EAA) was poor. Although increased NPA of histidine (P < 0.001), leucine, phenylalanine and valine (0.05 < P < 0.08) was found after one week of acorn consumption, the sum of EAA did not change. Furthermore, fractional absorption (NPA/AA intake) of EAA, non-essential AA (NEAA) and total AA was 97, 44 and 49% lower, respectively, at the beginning of eating acorn than a week later. Supplementation, with some of the EAA and NEAA to Iberian pigs during the grazing period would be beneficial to overcome the increased portal-drained viscera (PDV) utilization of AA observed in the present study. creator: Manuel Lachica creator: Jose Miguel Rodríguez-López creator: Lucrecia González-Valero creator: Ignacio Fernández-Fígares uri: https://doi.org/10.7717/peerj.6137 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Lachica et al. title: ScanFold: an approach for genome-wide discovery of local RNA structural elements—applications to Zika virus and HIV link: https://peerj.com/articles/6136 last-modified: 2018-12-18 description: In addition to encoding RNA primary structures, genomes also encode RNA secondary and tertiary structures that play roles in gene regulation and, in the case of RNA viruses, genome replication. Methods for the identification of functional RNA structures in genomes typically rely on scanning analysis windows, where multiple partially-overlapping windows are used to predict RNA structures and folding metrics to deduce regions likely to form functional structure. Separate structural models are produced for each window, where the step size can greatly affect the returned model. This makes deducing unique local structures challenging, as the same nucleotides in each window can be alternatively base paired. We are presenting here a new approach where all base pairs from analysis windows are considered and weighted by favorable folding. This results in unique base pairing throughout the genome and the generation of local regions/structures that can be ranked by their propensity to form unusually thermodynamically stable folds. We applied this approach to the Zika virus (ZIKV) and HIV-1 genomes. ZIKV is linked to a variety of neurological ailments including microcephaly and Guillain–Barré syndrome and its (+)-sense RNA genome encodes two, previously described, functionally essential structured RNA regions. HIV, the cause of AIDS, contains multiple functional RNA motifs in its genome, which have been extensively studied. Our approach is able to successfully identify and model the structures of known functional motifs in both viruses, while also finding additional regions likely to form functional structures. All data have been archived at the RNAStructuromeDB (www.structurome.bb.iastate.edu), a repository of RNA folding data for humans and their pathogens. creator: Ryan J. Andrews creator: Julien Roche creator: Walter N. Moss uri: https://doi.org/10.7717/peerj.6136 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Andrews et al. title: Effects of ultraviolet radiation on metabolic rate and fitness of Aedes albopictus and Culex pipiens mosquitoes link: https://peerj.com/articles/6133 last-modified: 2018-12-18 description: Natural and anthropogenic changes (e.g., land use change, pollution) will alter many environmental factors in the coming years, including the amount of solar radiation reaching the earth’s surface. Alterations in solar radiation exposure is likely to impact the ecologies of many living organisms, including invertebrates that inhabit aquatic habitats. In this study, we assessed the effect of UV-B radiation on the metabolic rates and fitness (survival, development time, body size) of Aedes albopictus and Culex pipiens mosquitoes and the activity of their microbial food resources in experimental aquatic microcosms. We exposed single-species cohorts of newly hatched Ae. albopictus and Cx. pipiens larvae and a control treatment with no larvae to three UV-B conditions that mimicked those in full-sun and shade in the field and to a control condition with no UV-B radiation. Our results indicated that UV-B radiation affected the metabolic rates of both Ae. albopictus and Cx. pipiens larvae, with significantly higher rates found in full-sun compared to shade and no-UV conditions, 8 and 15 days after exposure began. Ae. albopictus and Cx. pipiens survival was also affected by UV-B radiation condition, with significantly lower survival in full-sun compared to shade and no UV-B conditions. Microbial metabolic rates were consistently significantly lower in full-sun compared to shade and no-UV conditions, especially at 8 days of exposure. These results show that UV-B radiation at levels found in open spaces showed strong and important impacts on the metabolic rates and survival of Ae. albopictus and Cx. pipiens larvae. Decreased survival of Ae. albopictus and Cx. pipiens with higher UV-B radiation levels may be caused by both direct exposure to radiation as well as the indirect effects of reduced microbial food, resulting in greater metabolic demands and stress. Negative impacts of UV-B radiation on the survival of Ae. albopictus and Cx. pipiens are likely to have important implications for the distribution and abundance of these mosquitoes, and the transmission of pathogens that these two broadly distributed mosquitoes vector. creator: Oswaldo C. Villena creator: Bahram Momen creator: Joseph Sullivan creator: Paul T. Leisnham uri: https://doi.org/10.7717/peerj.6133 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Villena et al. title: Local persistence of Mann’s soft-haired mouse Abrothrix manni (Rodentia, Sigmodontinae) during Quaternary glaciations in southern Chile link: https://peerj.com/articles/6130 last-modified: 2018-12-18 description: Quaternary climatic oscillations have impacted Patagonian sigmodontine fauna, leaving traceable genetic footprints. In southern Chile, changes in the landscape included transitions to different vegetation formations as well as the extension of ice sheets. In this study, we focus on the Valdivian forest endemic and recently described sigmodontine species Abrothrix manni. We aim to assess the genetic structure of this species, testing for the existence of intraspecific lineages, and inferring the recent demographic history of the species. Analyses were based on the first 801 bp of the mitochondrial gene Cytocrhome-b from 49 individuals of A. manni collected at 10 localities that covers most part of its geographic distribution. Genealogical analyses recovered two main intraspecific lineages that are geographically segregated and present an intermediate site of secondary contact. Historical demography shows signal of recent population decrease. Based on these results, we proposed that current genetic diversity of A. manni differentiated in at least two distinct refugial areas in southern Chile. This scenario, in addition to be unique among those uncovered for the so far studied Valdivian forest rodents, is noteworthy because of the reduced geographic scale inhabited by the species. creator: Lourdes Valdez creator: Guilermo D’Elía uri: https://doi.org/10.7717/peerj.6130 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Valdez and D’Elía title: Elevated CD3low double negative T lymphocyte is associated with pneumonia and its severity in pediatric patients link: https://peerj.com/articles/6114 last-modified: 2018-12-18 description: BackgroundPrevious studies have shown that the adaptive immunity function of T cells in disease states correlates with CD3 surface expression closely. During routine assessment of TBNK subsets in peripheral blood of pediatric patients by flow cytometry, we noticed that variable expression levels of CD3 on CD3+CD4−CD8− double-negative T (DNT) lymphocytes in different patients. The objective of this study was to assess the relationship of CD3 expression levels on DNT cells with disease severity.MethodsIn this prospective study, we investigated the frequencies of circulating CD4−CD8− DNT cell subsets with CD3low or CD3high phenotype by flow cytometry in 76 pediatric patients with pneumonia, 55 patients with severe pneumonia (SP), and 29 healthy controls (Con).ResultsThe numbers of circulating DNT cells were similar in all groups; however, the frequency of CD3low DNT cell subsets was significantly increased in patients with pneumonia (p < 0.001) and SP (p < 0.001). The elevated CD3low DNT cell frequency showed a positive correlation with the clinical severity of pneumonia. On sub-group analysis, the frequency of CD3low DNT cells was only elevated in children with pneumonia aged <5 years, while no association was observed with the causative pathogen of pneumonia.ConclusionsThese findings suggest that CD3 expression levels on DNT cell subsets of peripheral lymphocytes may be a valuable biomarker for evaluation of immune response in pediatric infectious disease. CD3low DNT cells were elevated in children with pneumonia aged <5 years, which indicates that it may be an important research target in pediatric infectious diseases. creator: Ying Wang creator: Wenting Lu creator: Aipeng Li creator: Zhengyi Sun creator: Liying Wang uri: https://doi.org/10.7717/peerj.6114 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Wang et al. title: Morphological characterization and staging of bumble bee pupae link: https://peerj.com/articles/6089 last-modified: 2018-12-18 description: Bumble bees (Hymenoptera: Apidae, Bombus) are important pollinators and models for studying mechanisms underlying developmental plasticity, such as factors influencing size, immunity, and social behaviors. Research on such processes, as well as expanding use of gene-manipulation and gene expression technologies, requires a detailed understanding of how these bees develop. Developmental research often uses time-staging of pupae, however dramatic size differences in these bees can generate variation in developmental timing. To study developmental mechanisms in bumble bees, appropriate staging of developing bees using morphology is necessary. In this study, we describe morphological changes across development in several bumble bee species and use this to establish morphology-based staging criteria, establishing 20 distinct illustrated stages. These criteria, defined largely by eye and cuticle pigmentation patterns, are generalizable across members of the subgenus Pyrobombus, and can be used as a framework for study of other bumble bee subgenera. We examine the effects of temperature, caste, size, and species on pupal development, revealing that pupal duration shifts with each of these factors, confirming the importance of staging pupae based on morphology rather than age and the need for standardizing sampling. creator: Li Tian creator: Heather M. Hines uri: https://doi.org/10.7717/peerj.6089 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Tian and Hines title: Nanocontainer designed from an infectious hypodermal and hematopoietic necrosis virus (IHHNV) has excellent physical stability and ability to deliver shrimp tissues link: https://peerj.com/articles/6079 last-modified: 2018-12-18 description: BackgroundA virus-like particle (VLP) is an excellent tool for a compound delivery system due to its simple composition, symmetrical structure and self-assembly. Its surface modification both chemically and genetically is established, leading to the target-specific delivery and improved encapsulation efficiency. However, its physical stabilities against many harsh conditions that guarantee long term storage and oral administration have been much less studied.MethodsIHHNV-VLPs were reconstructed from recombinant IHHNV capsid protein in E. coli. Their physical properties against three strong physical conditions including long term storage (0–30 days) in 4 °C, physical stabilities against broad ranged pH (4–9) and against three types of digestive enzymes were tested. Disassembly and reassembly of VLPs for encapsidating an enhanced green fluorescent protein tagged plasmid DNA (EGFP-VLPs) were controlled by the use of reducing agent (DTT) and calcium specific chelating agent (EGTA). Lastly, delivering ability of EGFP-VLPs was performed in vivo by intramuscular injection and traced the expression of GFP in the shrimp tissues 24 hr post-injection.ResultsUpon its purification, IHHNV-VLPs were able to be kept at 4 °C up to 30 days with only slight degradation. They were very stable in basic condition (pH 8–9) and to a lesser extent in acidic condition (pH 4–6) while they could stand digestions of trypsin and chymotrypsin better than pepsin. As similar with many other non-enveloped viruses, the assembly of IHHNV-VLPs was dependent on both disulfide bridging and calcium ions which allowed us to control disassembly and reassembly of these VLPs to pack EGFP plasmid DNA. IHHNV-VLPs could deliver EGFP plasmids into shrimp muscles and gills as evident by RT-PCR and confocal microscopy demonstrating the expression of GFP in the targeted tissues.DiscussionThere are extensive data in which capsid proteins of the non-enveloped viruses in the form of VLPs are constructed and used as nano-containers for therapeutic compound delivery. However, the bottleneck of its application as an excellent delivery container for oral administration would rely solely on physical stability and interacting ability of VLPs to the host cells. These properties are retained for IHHNV-VLPs reported herein. Thus, IHHNV-VLPs would stand as a good applicable nanocontainer to carry therapeutic agents towards the targeting tissues against ionic and digestive conditions via oral administration in aquaculture field. creator: Pauline Kiatmetha creator: Charoonroj Chotwiwatthanakun creator: Pitchanee Jariyapong creator: Wanida Santimanawong creator: Puey Ounjai creator: Wattana Weerachatyanukul uri: https://doi.org/10.7717/peerj.6079 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Kiatmetha et al. title: Effects of dietary supplementation with Lactobacillus acidophilus on the performance, intestinal physical barrier function, and the expression of NOD-like receptors in weaned piglets link: https://peerj.com/articles/6060 last-modified: 2018-12-18 description: Lactobacillus supplementation is beneficial to the barrier function of the intestinal physical barrier in piglets. However, the mechanisms underlying this beneficial function remain largely unknown. Here, we investigated the effects of dietary supplementation with Lactobacillus acidophilus on the performance, intestinal physical barrier functioning, and NOD-like receptors (NLRs) expression in weaned piglets. Sixteen weaned piglets were randomly allocated to two groups. The control group received a corn-soybean basal diet, while the treatment group received the same diet adding 0.1% L. acidophilus, for 14 days. As a result, dietary L. acidophilus supplementation was found to increase the average daily gain (ADG) (P < 0.05), reduced serum diamine oxidase (DAO) activity (P < 0.05), increased the mRNA expression and protein abundance of occludin in the jejunum and ileum (P < 0.01), reduced the mRNA levels of NOD1 (P < 0.01), receptor interacting serine/threonine kinase 2 (RIPK2) (P < 0.05), nuclear factor κB (NF-κB) (P < 0.01), NLR family pyrin domain containing 3 (NLRP3) (P < 0.01), caspase-1 (P < 0.01), interleukin 1β (IL-1β) (P < 0.05) and IL-18 (P < 0.01) in the jejunum tissues of the weaned pigs. The expression of NLRP3 (P < 0.05), caspase-1 (P < 0.01), IL-1β (P < 0.05) and IL-18 (P < 0.05) was also reduced in the ileum tissues of the weaned pigs. These results showed that L. acidophilus supplementation improves the growth performance, enhances the intestinal physical barrier function, and inhibits the expression of NOD1 and NLRP3 signaling-pathway-related genes in jejunum and ileum tissues. They also suggest that L. acidophilus enhances the intestinal physical barrier functioning by inhibiting IL-1β and IL-18 pro-inflammatory cytokines via the NOD1/NLRP3 signaling pathway in weaned piglets. creator: Shiqiong Wang creator: Haihua Li creator: Chenhong Du creator: Qian Liu creator: Dongji Yang creator: Longbin Chen creator: Qi Zhu creator: Zhixiang Wang uri: https://doi.org/10.7717/peerj.6060 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Wang et al. title: Systematic review and meta-analysis of age-related differences in instructed emotion regulation success link: https://peerj.com/articles/6051 last-modified: 2018-12-18 description: The process model of emotion regulation (ER) is based on stages in the emotion generative process at which regulation may occur. This meta-analysis examines age-related differences in the subjective, behavioral, and physiological outcomes of instructed ER strategies that may be initiated after an emotional event has occurred; attentional deployment, cognitive change, and response modulation. Within-process strategy, stimulus type, and valence were also tested as potential moderators of the effect of age on ER. A systematic search of the literature identified 156 relevant comparisons from 11 studies. Few age-related differences were found. In our analysis of the subjective outcome of response modulation strategies, young adults used expressive enhancement successfully (g = 0.48), but not expressive suppression (g = 0.04). Response modulation strategies had a small positive effect among older adults, and enhancement vs suppression did not moderate this success (g = 0.31 and g = 0.10, respectively). Young adults effectively used response modulation to regulate subjective emotion in response to pictures (g = 0.41) but not films (g = 0.01). Older adults were able to regulate in response to both pictures (g = 0.26) and films (g = 0.11). Interestingly, both age groups effectively used detached reappraisal, but not positive reappraisal to regulate emotional behavior. We conclude that, in line with well-established theories of socioemotional aging, there is a lack of evidence for age differences in the effects of instructed ER strategies, with some moderators suggesting more consistent effectiveness for older compared to younger adults. creator: Brooke Brady creator: Ian I. Kneebone creator: Nida Denson creator: Phoebe E. Bailey uri: https://doi.org/10.7717/peerj.6051 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Brady et al. title: Niche modeling for the genus Pogona (Squamata: Agamidae) in Australia: predicting past (late Quaternary) and future (2070) areas of suitable habitat link: https://peerj.com/articles/6128 last-modified: 2018-12-17 description: BackgroundAs the climate warms, many species of reptiles are at risk of habitat loss and ultimately extinction. Locations of suitable habitat in the past, present, and future were modeled for several lizard species using MaxEnt, incorporating climatic variables related to temperature and precipitation. In this study, we predict where there is currently suitable habitat for the genus Pogona and potential shifts in habitat suitability in the past and future.MethodsGeoreferenced occurrence records were obtained from the Global Biodiversity Information Facility, climate variables (describing temperature and precipitation) were obtained from WorldClim, and a vegetation index was obtained from AVHRR satellite data. Matching climate variables were downloaded for three different past time periods (mid-Holocene, Last Glacial Maximum, and Last Interglacial) and two different future projections representative concentration pathways (RCPs 2.6 and 8.5). MaxEnt produced accuracy metrics, response curves, and probability surfaces. For each species, parameters were adjusted for the best possible output that was biologically informative.ResultsModel results predicted that in the past, there was little suitable habitat for P. henrylawsoni and P. microlepidota within the areas of their current range. Past areas of suitable habitat for P. barbata were predicted to be similar to the current prediction. Pogona minor and P. nullarbor were predicted to have had a more expansive range of suitable habitat in the past, which has reduced over time. P. vitticeps was predicted to have less suitable habitat in the past when examining the region of their known occurrence; however, there was predicted growth in suitable habitat in Western Australia. Both 2070 models predict a similar distribution of habitat; however, the model produced using the 2070 RCP 8.5 climate change projection showed a larger change, both in areas of suitable habitat gain and loss. In the future, P. henrylawsoni and P. microlepidota might gain suitable habitat, while the other four species could possibly suffer habitat loss.DiscussionBased on the model results, P. henrylawsoni and P. microlepidota had minimal areas of suitable habitat during the Last Glacial Maximum, possibly due to changes in tolerance or data/model limitations, especially since genetic analyses for these species suggest a much earlier emergence. The predicted late Quaternary habitat results for all species of Pogona are conservative and should be compared to the fossil record which is not possible at the moment due to the current inability to identify fossil Pogona to the species level. P. nullarbor and P. vitticeps future models predict substantial habitat loss. P. nullarbor could potentially be considered vulnerable in the present since it already has a restricted range, and a conservation plan may need to be considered. creator: Julie E. Rej creator: T. Andrew Joyner uri: https://doi.org/10.7717/peerj.6128 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Rej and Joyner title: Remains of Leatherback turtles, Dermochelys coriacea, at Mid-Late Holocene archaeological sites in coastal Oman: clues of past worlds link: https://peerj.com/articles/6123 last-modified: 2018-12-17 description: Small, irregular isolated bones identified as remains of leatherback turtles (Dermochelys coriacea) were recovered from Mid to Late Holocene sites at Ra’s al-Hamra and Ra’s al-Hadd, coastal Oman. These provide the third instance of this animal being documented from any prehistoric site anywhere, and the records provide one of the oldest, if not the oldest, dates for this distinctive chelonian—even though they do not refer to fossils. Decades of research in this region has yielded vast amounts of archeological information, including abundant evidence of intense exploitation and utilization of marine turtles from about 6,500 to 4,000 BP. During part of this period, turtle remains in human burials have been extraordinary; the turtle involved, Chelonia mydas, has been abundant in the region during modern times. Yet despite intense and varied forms of prehistoric marine resource exploitation, and major, long-term archeological work, no other turtle species has been previously authenticated from these, or other coastal sites. The documentation of remains of the largest and most distinctive of living marine turtles, D. coriacea, at Ra’s al-Hamra and Ra’s al-Hadd, presented herein, provide detailed information that serves as the basis for future interpretations and discussions regarding incomplete, disarticulated remains from the Mid to Late Holocene, particularly in reference to taphonomic questions and diverse environmental conditions. creator: John G. Frazier creator: Valentina Azzarà creator: Olivia Munoz creator: Lapo Gianni Marcucci creator: Emilie Badel creator: Francesco Genchi creator: Maurizio Cattani creator: Maurizio Tosi creator: Massimo Delfino uri: https://doi.org/10.7717/peerj.6123 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Frazier et al. title: Dogs can be trained to find a bar magnet link: https://peerj.com/articles/6117 last-modified: 2018-12-17 description: Magnetoreception, the ability to sense the Earth’s magnetic field (MF), is a widespread phenomenon in the animal kingdom. In 1966, the first report on a magnetosensitive vertebrate, the European robin (Erithacus rubecula), was published. After that, numerous further species of different taxa have been identified to be magnetosensitive as well. Recently, it has been demonstrated that domestic dogs (Canis lupus familiaris) prefer to align their body axis along the North–South axis during territorial marking under calm MF conditions and that they abandon this preference when the Earth’s MF is unstable. In a further study conducting a directional two-choice-test, dogs showed a spontaneous preference for the northern direction. Being designated as putatively magnetosensitive and being also known as trainable for diverse choice and search tests, dogs seem to be suitable model animals for a direct test of magnetoreception: learning to find a magnet. Using operant conditioning dogs were trained to identify the MF of a bar magnet in a three-alternative forced-choice experiment. We excluded visual cues and used control trials with food treats to test for the role of olfaction in finding the magnet. While 13 out of 16 dogs detected the magnet significantly above chance level (53–73% success rate), none of the dogs managed to do so in finding the food treat (23–40% success rate). In a replication of the experiment under strictly blinded conditions five out of six dogs detected the magnet above chance level (53–63% success rate). These experiments support the existence of a magnetic sense in domestic dogs. Whether the sense enables dogs to perceive MFs as weak as the Earth’s MF, if they use it for orientation, and by which mechanism the fields are perceived remain open questions. creator: Sabine Martini creator: Sabine Begall creator: Tanja Findeklee creator: Marcus Schmitt creator: E. Pascal Malkemper creator: Hynek Burda uri: https://doi.org/10.7717/peerj.6117 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Martini et al. title: Synthesis, characterization and antibacterial activity of silver nanoparticles using Rhazya stricta link: https://peerj.com/articles/6086 last-modified: 2018-12-17 description: BackgroundGreen synthesis of metallic nanoparticles has gained significant attention in the field of nanomedicine as an environment-friendly and cost-effective alternative in comparison with other physical and chemical methods. Several metals such as silver, gold, iron, titanium, zinc, magnesium and copper have been subjected to nanoformulation for a wide range of useful applications. Silver nanoparticles (AgNPs) are playing a major role in the field of nanomedicine and nanotechnology. They are widely used in diagnostics, therapeutic and pharmaceutical industries. Studies have shown potential inhibitory antimicrobial, anti-inflammatory and antiangiogenesis activities of AgNPs.MethodsAgNPs have been synthesized using silver nitrate and methanolic root extract of Rhazya stricta that belongs to the Apocynaceae family. Stability and dispersion of nanoparticles were improved by adding xylitol. Synthesized nanoparticles were characterized by UV–Vis spectroscopy, scanning electron microscopy, energy dispersive spectroscopy, X-ray diffractometer and Fourier transforms infrared spectroscopy. Furthermore, the antibacterial effect of the plant extract and the nanoparticles were evaluated against gram-positive (Bacillus subtilis) and gram-negative (Escherichia coli) bacteria.ResultsThe average size of AgNPs synthesized, was 20 nm with the spherical shape. Rhazya stricta based nanoparticles exhibited improved antibacterial activity against both gram-positive and negative strains. creator: Adeeb Shehzad creator: Munibah Qureshi creator: Saima Jabeen creator: Rizwan Ahmad creator: Amira H. Alabdalall creator: Meneerah Abdulrahman Aljafary creator: Ebtesam Al-Suhaimi uri: https://doi.org/10.7717/peerj.6086 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Shehzad et al. title: In silico engineering of Pseudomonas metabolism reveals new biomarkers for increased biosurfactant production link: https://peerj.com/articles/6046 last-modified: 2018-12-17 description: BackgroundRhamnolipids, biosurfactants with a wide range of biomedical applications, are amphiphilic molecules produced on the surfaces of or excreted extracellularly by bacteria including Pseudomonas aeruginosa. However, Pseudomonas putida is a non-pathogenic model organism with greater metabolic versatility and potential for industrial applications.MethodsWe investigate in silico the metabolic capabilities of P. putida for rhamnolipids biosynthesis using statistical, metabolic and synthetic engineering approaches after introducing key genes (RhlA and RhlB) from P. aeruginosa into a genome-scale model of P. putida. This pipeline combines machine learning methods with multi-omic modelling, and drives the engineered P. putida model toward an optimal production and export of rhamnolipids out of the membrane.ResultsWe identify a substantial increase in synthesis of rhamnolipids by the engineered model compared to the control model. We apply statistical and machine learning techniques on the metabolic reaction rates to identify distinct features on the structure of the variables and individual components driving the variation of growth and rhamnolipids production. We finally provide a computational framework for integrating multi-omics data and identifying latent pathways and genes for the production of rhamnolipids in P. putida.ConclusionsWe anticipate that our results will provide a versatile methodology for integrating multi-omics data for topological and functional analysis of P. putida toward maximization of biosurfactant production. creator: Annalisa Occhipinti creator: Filmon Eyassu creator: Thahira J. Rahman creator: Pattanathu K. S. M. Rahman creator: Claudio Angione uri: https://doi.org/10.7717/peerj.6046 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Occhipinti et al. title: Transcriptome analysis of oil palm inflorescences revealed candidate genes for an auxin signaling pathway involved in parthenocarpy link: https://peerj.com/articles/5975 last-modified: 2018-12-17 description: Oil palm parthenocarpic fruits, which are produced without fertilization, can be targeted to increase oil content because the majority of the fruit is occupied by mesocarp, the part in which palm oil is stored. Consequently, gaining an understanding of the parthenocarpic mechanism would be instrumental for producing parthenocarpic oil palm. This study aims to determine effects of auxin treatment and analyze differentially expressed genes in oil palm pistils at the pollination/anthesis stage, using an RNA sequencing (RNA seq) approach. The auxin treatment caused 100% parthenocarpy when auxin was sprayed before stigmas opened. The parthenocarpy decreased to 55%, 8% and 5% when the auxin was sprayed 1, 2 and 3 days after the opening of stigmas, respectively. Oil palm plants used for RNA seq were plants untreated with auxin as controls and auxin-treated plants on the day before pollination and 1 day after pollination. The number of raw reads ranged from 8,425,859 to 11,811,166 reads, with an average size ranging from 99 to 137 base pairs (bp). When compared with the oil palm transcriptome, the mapped reads ranged from 8,179,948 to 11,320,799 reads, representing 95.85–98.01% of the oil palm matching. Based on five comparisons between RNA seq of treatments and controls, and confirmation using reverse transcription polymerase chain reaction and quantitative real-time RT-PCR expression, five candidate genes, including probable indole-3-acetic acid (IAA)-amido synthetase GH3.8 (EgGH3.8), IAA-amido synthetase GH3.1 (EgGH3.1), IAA induced ARG7 like (EgARG7), tryptophan amino transferase-related protein 3-like (EgTAA3) and flavin-containing monooxygenase 1 (EgFMO1), were differentially expressed between auxin-treated and untreated samples. This evidence suggests a pathway of parthenocarpic fruit development at the beginning of fruit development. However, more research is needed to identify which genes are definitely involved in parthenocarpy. creator: Suthasinee Somyong creator: Kitti Walayaporn creator: Nukoon Jomchai creator: Chaiwat Naktang creator: Tanapong Yodyingyong creator: Chalermpol Phumichai creator: Wirulda Pootakham creator: Sithichoke Tangphatsornruang uri: https://doi.org/10.7717/peerj.5975 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Somyong et al. title: Do longer sequences improve the accuracy of identification of forensically important Calliphoridae species? link: https://peerj.com/articles/5962 last-modified: 2018-12-17 description: Species identification is a crucial step in forensic entomology. In several cases the calculation of the larval age allows the estimation of the minimum Post-Mortem Interval (mPMI). A correct identification of the species is the first step for a correct mPMI estimation. To overcome the difficulties due to the morphological identification especially of the immature stages, a molecular approach can be applied. However, difficulties in separation of closely related species are still an unsolved problem. Sequences of 4 different genes (COI, ND5, EF-1α, PER) of 13 different fly species collected during forensic experiments (Calliphora vicina, Calliphora vomitoria, Lucilia sericata, Lucilia illustris, Lucilia caesar, Chrysomya albiceps, Phormia regina, Cynomya mortuorum, Sarcophaga sp., Hydrotaea sp., Fannia scalaris, Piophila sp., Megaselia scalaris) were evaluated for their capability to identify correctly the species. Three concatenated sequences were obtained combining the four genes in order to verify if longer sequences increase the probability of a correct identification. The obtained results showed that this rule does not work for the species L. caesar and L. illustris. Future works on other DNA regions are suggested to solve this taxonomic issue. creator: Sara Bortolini creator: Giorgia Giordani creator: Fabiola Tuccia creator: Lara Maistrello creator: Stefano Vanin uri: https://doi.org/10.7717/peerj.5962 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Bortolini et al. title: Influenced but not determined by historical events: genetic, demographic and morphological differentiation in Heleobia ascotanensis from the Chilean Altiplano link: https://peerj.com/articles/5802 last-modified: 2018-12-17 description: In the present study, we focus on the phylogeographic pattern, demographic history and morphological differentiation of Heleobia ascotanensis, a freshwater gastropod restricted to the Ascotán saltpan in the Chilean Altiplano. The current distribution of the species is limited to twelve isolated or partially isolated springs that were affected by transitions between humid and arid periods during last glaciations. The genetic analysis of 322 specimens showed that H. ascotanensis is subdivided into three genetically divergent populations, with low and moderate degrees of historical gene flow among them and incipient morphological differentiation as a consequence of genetic and geographical isolation. Molecular analyses revealed different demographic histories among populations which seem to respond independently to climatic events, probably due to an environmental imposition and idiosyncratic strategies developed to cope with water availability. The results of this study and co-distributed taxa support the hypothesis that contemporary and historical events have influenced microevolutionary differentiation of these snails, although there is a need to complement further information to predict genetic or morphological divergence at microgeographic scale. creator: Moisés A. Valladares creator: Marco A. Méndez creator: Gonzalo A. Collado uri: https://doi.org/10.7717/peerj.5802 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Valladares et al. title: The Plasmodium knowlesi Pk41 surface protein diversity, natural selection, sub population and geographical clustering: a 6-cysteine protein family member link: https://peerj.com/articles/6141 last-modified: 2018-12-14 description: IntroductionThe zoonotic malaria parasite Plasmodium knowlesi has currently become the most dominant form of infection in humans in Malaysia and is an emerging infectious disease in most Southeast Asian countries. The P41 is a merozoite surface protein belonging to the 6-cysteine family and is a well-characterized vaccine candidate in P. vivax and P. falciparum; however, no study has been done in the orthologous gene of P. knowlesi. This study investigates the level of polymorphism, haplotypes and natural selection of pk41 genes in clinical isolates from Malaysia.MethodThirty-five full-length pk41 sequences from clinical isolates of Malaysia along with four laboratory lines (along with H-strain) were downloaded from public databases. For comparative analysis between species, orthologous P41 genes from P. falciparum, P. vivax, P. coatneyi and P. cynomolgi were also downloaded. Genetic diversity, polymorphism, haplotype and natural selection were determined using DnaSP 5.10 software. Phylogenetic relationships between Pk41 genes were determined using MEGA 5.0 software.ResultsAnalysis of 39 full-length pk41 sequences along with the H-strain identified 36 SNPs (20 non-synonymous and 16 synonymous substitutions) resulting in 31 haplotypes. Nucleotide diversity across the full-length gene was low and was similar to its ortholog in P. vivax; pv41. Domain-wise amino acid analysis of the two s48/45 domains indicated low level of polymorphisms for both the domains, and the glutamic acid rich region had extensive size variations. In the central domain, upstream to the glutamate rich region, a unique two to six (K-E)n repeat region was identified within the clinical isolates. Overall, the pk41 genes were indicative of negative/purifying selection due to functional constraints. Domain-wise analysis of the s48/45 domains also indicated purifying selection. However, analysis of Tajima’s D across the genes identified non-synonymous SNPs in the s48/45 domain II with high positive values indicating possible epitope binding regions. All the 6-cysteine residues within the s48/45 domains were conserved within the clinical isolates indicating functional conservation of these regions. Phylogenetic analysis of full-length pk41 genes indicated geographical clustering and identified three subpopulations of P. knowlesi; one originating in the laboratory lines and two originating from Sarawak, Malaysian Borneo.ConclusionThis is the first study to report on the polymorphism and natural selection of pk41 genes from clinical isolates of Malaysia. The results reveal that there is low level of polymorphism in both s48/45 domains, indicating that this antigen could be a potential vaccine target. However, genetic and molecular immunology studies involving higher number of samples from various parts of Malaysia would be necessary to validate this antigen’s candidacy as a vaccine target for P. knowlesi. creator: Md Atique Ahmed creator: Ki-Back Chu creator: Fu-Shi Quan uri: https://doi.org/10.7717/peerj.6141 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Ahmed et al. title: Shaping ability of the profile 25/0.06 and protaper F2 in rotary motion, and reciproc in simulated canals link: https://peerj.com/articles/6109 last-modified: 2018-12-14 description: BackgroundSince the introduction of nickel–titanium (Ni–Ti) instruments to dentistry, a wide variety of Ni–Ti instruments have become commercially available. These Ni–Ti instruments are expensive, which limits their usage in developing countries and forces practitioners to use instruments repeatedly. Another problem is the possible prion cross-contamination associated with the multiple usage of endodontic instruments. In addition, the use of these instruments requires new skills and experience. In this article, the shaping capacities of two conventional rotary file systems, ProFile 25/0.06 and ProTaper F2, were reviewed and compared with the Reciproc single-file system.MethodsA total of 45 simulated canals with 40° curvature, in clear resin blocks, were prepared using conventional rotary systems consisting of ProFile orifice shaping (OS) #3 and final flaring #25/.06, Reciproc R25, and ProTaper shaping file SX and finishing file F2. Pre-and post-instrumentation images were analyzed at ten different levels, using AutoCAD 2007 software. The measurement positions were defined in 1-mm intervals: positions 0–3 established the apical part, positions 4–6 constituted the middle part, and positions 7–10 established the coronal part of the canal. The amount of removed resin, the transportation, instrumentation time, change in working length (WL), instrumentation fractures, and the presence of ledge were evaluated. Data were analyzed using ANOVA, Kruskal–Wallis and independent t-test (p < 0.001).ResultsProFile removed the least resin (p < 0.001) and caused less transportation than Reciproc and ProTaper, in total (p < 0.001). ProTaper caused more transportation ProFile and Reciproc in the apical part (p < 0.000). Reciproc caused more transportation than ProTaper and ProFile (p < 0.001), and the transportation tendency toward the inner aspect of the curvature in the middle part. Reciproc caused the less transportation than ProFile and ProTaper in the coronal part. The transportations tended to occur toward the outside of the curvature, except the middle part with Reciproc and at points 5 and 6 with ProTaper. There were no significant differences among the groups in terms of maintaining the original WL. Reciproc was significantly faster than the others group (p < 0.001). Only one instrument fracture (25/0.06 ProFile) was noted. All groups showed one ledge each.DiscussionThe results of the present study showed that both ProFile 25/06 and ProTaper F2, combined with a file used for coronal enlargement (OS3 and SX), have the potential to create satisfactory canal shape in the curved root canals. Further studies using real human teeth are needed to confirm our results. creator: Gül Çelik creator: Murat Maden creator: Ahmet Savgat creator: Hikmet Orhan uri: https://doi.org/10.7717/peerj.6109 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Çelik et al. title: Comparing enzyme activity modifier equations through the development of global data fitting templates in Excel link: https://peerj.com/articles/6082 last-modified: 2018-12-14 description: The classical way of defining enzyme inhibition has obscured the distinction between inhibitory effect and the inhibitor binding constant. This article examines the relationship between the simple binding curve used to define biomolecular interactions and the standard inhibitory term (1 + ([I]∕Ki)). By understanding how this term relates to binding curves which are ubiquitously used to describe biological processes, a modifier equation which distinguishes between inhibitor binding and the inhibitory effect, is examined. This modifier equation which can describe both activation and inhibition is compared to standard inhibitory equations with the development of global data fitting templates in Excel and via the global fitting of these equations to simulated and previously published datasets. In both cases, this modifier equation was able to match or outperform the other equations by providing superior fits to the datasets. The ability of this single equation to outperform the other equations suggests an over-complication of the field. This equation and the template developed in this article should prove to be useful tools in the study of enzyme inhibition and activation. creator: Ryan Walsh uri: https://doi.org/10.7717/peerj.6082 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Walsh title: Detection of bacterial endosymbionts in freshwater crustaceans: the applicability of non-degenerate primers to amplify the bacterial 16S rRNA gene link: https://peerj.com/articles/6039 last-modified: 2018-12-14 description: Bacterial endosymbionts of aquatic invertebrates remain poorly studied. This is at least partly due to a lack of suitable techniques and primers for their identification. We designed a pair of non-degenerate primers which enabled us to amplify a fragment of ca. 500 bp of the 16S rRNA gene from various known bacterial endosymbiont species. By using this approach, we identified four bacterial endosymbionts, two endoparasites and one uncultured bacterium in seven, taxonomically diverse, freshwater crustacean hosts from temporary waters across a wide geographical area. The overall efficiency of our new WOLBSL and WOLBSR primers for amplification of the bacterial 16S rRNA gene was 100%. However, if different bacterial species from one sample were amplified simultaneously, sequences were illegible, despite a good quality of PCR products. Therefore, we suggest using our primers at the first stage of bacterial endosymbiont identification. Subsequently, genus specific primers are recommended. Overall, in the era of next-generation sequencing our method can be used as a first simple and low-cost approach to identify potential microbial symbionts associated with freshwater crustaceans using simple Sanger sequencing. The potential to detected bacterial symbionts in various invertebrate hosts in such a way will facilitate studies on host-symbiont interactions and coevolution. creator: Monika Mioduchowska creator: Michał Jan Czyż creator: Bartłomiej Gołdyn creator: Adrianna Kilikowska creator: Tadeusz Namiotko creator: Tom Pinceel creator: Małgorzata Łaciak creator: Jerzy Sell uri: https://doi.org/10.7717/peerj.6039 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Mioduchowska et al. title: Evidence for the Cretaceous shark Cretoxyrhina mantelli feeding on the pterosaur Pteranodon from the Niobrara Formation link: https://peerj.com/articles/6031 last-modified: 2018-12-14 description: A cervical vertebra of the large, pelagic pterodactyloid pterosaur Pteranodon sp. from the Late Cretaceous Niobrara Formation of Kansas, USA is significant for its association with a tooth from the large lamniform shark, Cretoxyrhina mantelli. Though the tooth does not pierce the vertebral periosteum, the intimate association of the fossils—in which the tooth is wedged below the left prezygapophysis—suggests their preservation together was not mere chance, and the specimen is evidence of Cretoxyrhina biting Pteranodon. It is not possible to infer whether the bite reflects predatory or scavenging behaviour from the preserved material. There are several records of Pteranodon having been consumed by other fish, including other sharks (specifically, the anacoracid Squalicorax kaupi), and multiple records of Cretoxyrhina biting other vertebrates of the Western Interior Seaway, but until now interactions between Cretoxyrhina and Pteranodon have remained elusive. The specimen increases the known interactions between large, pelagic, vertebrate carnivores of the Western Interior Seaway of North America during the Late Cretaceous, in addition to bolstering the relatively small fossil record representing pterosaurian interactions with other species. creator: David W.E. Hone creator: Mark P. Witton creator: Michael B. Habib uri: https://doi.org/10.7717/peerj.6031 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Hone et al. title: Exploring the mechanistic link between corticosterone and insulin-like growth factor-1 in a wild passerine bird link: https://peerj.com/articles/5936 last-modified: 2018-12-14 description: BackgroundPhysiological regulators of life history trade-offs need to be responsive to sudden changes of resource availability. When homeostasis is challenged by unpredictable stressors, vertebrates respond through a set of physiological reactions, which can promote organismal survival. Glucocorticoids have been traditionally recognized as one of the main regulators of the physiological stress response, but the role of an evolutionarily more conserved pathway, the hypothalamic-pituitary-somatotropic (HPS) axis producing insulin-like growth factor-1 (IGF-1) has received much less attention. Although IGF-1 is known to affect several life history traits, little is known about its role in the physiological stress response and it has never been studied directly in adult wild animals.MethodsIn this study, we combined field observations with a controlled experiment to investigate how circulating levels of IGF-1 change in response to stress and whether this change is due to concomitant change in glucocorticoids in a free-living songbird, the bearded reedling Panurus biarmicus. We used a standard capture-restraint protocol in field observation, in which we took first and second (stress induced: 15 minutes later) samples. In a follow-up experiment, we used a minimally invasive oral corticosterone manipulation.ResultsWe showed that corticosterone levels significantly increased while IGF-1 levels significantly decreased during capture and handling stress. However, change in corticosterone levels were not related to change in IGF-1 levels. We found that experimentally elevated corticosterone levels did not affect IGF-1 levels.DiscussionOur results are the first to highlight that circulating IGF-1 levels are responsive to stress independently from glucocorticoids and suggest that the HPS axis is an autonomous physiological pathway that may play an important role as regulator of life-history decisions. creator: Zsófia Tóth creator: Jenny Q. Ouyang creator: Ádám Z. Lendvai uri: https://doi.org/10.7717/peerj.5936 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Tóth et al. title: Populations and assemblages living on the edge: dung beetles responses to forests-pasture ecotones link: https://peerj.com/articles/6148 last-modified: 2018-12-13 description: Edge effects alter insect biodiversity in several ways. However, we still have a limited understanding on simultaneous responses of ecological populations and assemblages to ecotones, especially in human modified landscapes. We analyze edge effects on dung beetle populations and assemblages between livestock pastures and native temperate forests (Juniperus and pine-oak forests (POFs)) to describe how species abundances and assemblage parameters respond to edge effects through gradients in forest-pasture ecotones. In Juniperus forest 13 species avoided the ecotones: six species showed greater abundance in forest interior and seven in pasturelands, while the other two species had a neutral response to the edge. In a different way, in POF we found five species avoiding the edge (four with greater abundance in pastures and only one in forest), two species had a neutral response, and two showed a unimodal pattern of abundance near to the edge. At the assemblage level edge effects are masked, as species richness, diversity, functional richness, functional evenness, and compositional incidence dissimilarity did not vary along forest-pasture ecotones. However, total abundance and functional divergence showed higher values in pastures in one of the two sampling localities. Also, assemblage similarity based on species’ abundance showed a peak near to the edge in POF. We propose that conservation efforts in human-managed landscapes should focus on mitigating current and delayed edge effects. Ecotone management will be crucial in livestock dominated landscapes to conserve regional biodiversity and the environmental services carried out by dung beetles. creator: Ana Paola Martínez-Falcón creator: Gustavo A. Zurita creator: Ilse J. Ortega-Martínez creator: Claudia E. Moreno uri: https://doi.org/10.7717/peerj.6148 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Martínez-Falcón et al. title: Characterization of five complete Cyrtodactylus mitogenome structures reveals low structural diversity and conservation of repeated sequences in the lineage link: https://peerj.com/articles/6121 last-modified: 2018-12-13 description: Mitochondrial genomes (mitogenomes) of five Cyrtodactylus were determined. Their compositions and structures were similar to most of the available gecko lizard mitogenomes as 13 protein-coding, two rRNA and 22 tRNA genes. The non-coding control region (CR) of almost all Cyrtodactylus mitogenome structures contained a repeated sequence named the 75-bp box family, except for C. auribalteatus which contained the 225-bp box. Sequence similarities indicated that the 225-bp box resulted from the duplication event of 75-bp boxes, followed by homogenization and fixation in C. auribalteatus. The 75-bp box family was found in most gecko lizards with high conservation (55–75% similarities) and could form secondary structures, suggesting that this repeated sequence family played an important role under selective pressure and might involve mitogenome replication and the likelihood of rearrangements in CR. The 75-bp box family was acquired in the common ancestral genome of the gecko lizard, evolving gradually through each lineage by independent nucleotide mutation. Comparison of gecko lizard mitogenomes revealed low structural diversity with at least six types of mitochondrial gene rearrangements. Cyrtodactylus mitogenome structure showed the same gene rearrangement as found in most gecko lizards. Advanced mitogenome information will enable a better understanding of structure evolution mechanisms. creator: Prapatsorn Areesirisuk creator: Narongrit Muangmai creator: Kirati Kunya creator: Worapong Singchat creator: Siwapech Sillapaprayoon creator: Sorravis Lapbenjakul creator: Watcharaporn Thapana creator: Attachai Kantachumpoo creator: Sudarath Baicharoen creator: Budsaba Rerkamnuaychoke creator: Surin Peyachoknagul creator: Kyudong Han creator: Kornsorn Srikulnath uri: https://doi.org/10.7717/peerj.6121 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Areesirisuk et al. title: Acute effects of contract-relax proprioceptive neuromuscular facilitation stretching of hip abductors and adductors on dynamic balance link: https://peerj.com/articles/6108 last-modified: 2018-12-13 description: BackgroundBalance control has been shown to play a fundamental role both in everyday life and many athletic activities. An important component of balance control is the somatosensory information gained from muscle spindles and Golgi tendon organs. The changes in the muscle-tendon unit stiffness could alter the ability to detect and respond promptly to changes of an unstable environment. One of the procedures affecting muscle stiffness is stretching, and contract-relax PNF stretching (CRS) is considered as one of the safest and most effective techniques. So far, there are no studies on the impact of CRS of hip adductor and abductor muscles on body balance. These muscle groups are responsible for maintaining mediolateral balance which is of particular interest, since it is more affected by ageing and disease and since its deterioration has been associated with an increased risk of falling. In light of the above, the aim of the present study was to investigate the effects of a single dose of contract-relax proprioceptive neuromuscular facilitation stretching of hip adductors and abductors on mediolateral dynamic balance.MethodsThe study involved 45 healthy individuals (age 19–23 years) assigned to the intervention group (IG) or the control group (CG). Balance testing was carried out before (Pre) and immediately after CRS in the intervention group or after 5-minute rest in the control group (Post). There were performed three repetitions of the CRS targeting the adductor and abductor muscles of the hip.ResultsStatistically significant differences between Pre and Post condition were observed only in the intervention group. The values of all measured variables defining the body’s dynamic balance were significantly lower immediately after the applied CRS, which indicates an improved body balance: Global Index (p = 0.0001), total area of sway (p = 0.0001), external area of sway (p = 0.00004), external time (p = 0.0004) and reaction time (p = 0.0003).ConclusionsA single dose of contract-relax proprioceptive neuromuscular facilitation stretching of the hip adductor and abductor muscles improved mediolateral dynamic balance. creator: Rafał Szafraniec creator: Krystyna Chromik creator: Amanda Poborska creator: Adam Kawczyński uri: https://doi.org/10.7717/peerj.6108 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Szafraniec et al. title: The influence of maternal body mass index and physical activity on select cardiovascular risk factors of preadolescent Hispanic children link: https://peerj.com/articles/6100 last-modified: 2018-12-13 description: BackgroundMaternal obesity and physical inactivity have been identified as correlates of overweight and obesity and physical inactivity in older preadolescents; however, no study has explored this relationship in Hispanic preadolescents. Furthermore, the relation between maternal physical activity (PA) and blood pressure (BP) in Hispanic preadolescents has not been examined.PurposeThis study aimed to assess the associations between Hispanic mothers’ PA and body mass index (BMI) and their preadolescents’ PA, screen time, BP, and BMI.MethodsData of 118 mother-child (aged 2–10 years) dyads enrolled in a cross-sectional study of metabolic syndrome in Hispanic preadolescents at a community health center in Johnson City, TN were used. Parent and child questionnaires were used to ascertain mothers’ BMI and PA and preadolescents’ PA and screen time. Preadolescents’ height, weight, and BP were measured. Multiple logistic regression was used to examine the association between child and maternal variables, adjusting for mother’s education and the child’s sex and age.ResultsPradolescents of obese mothers were more likely than preadolescents of mothers with normal weight to engage in less than three days of at least 60 min of vigorous PA per week (OR: 6.47, 95% CI [1.61–26.0]). Preadolescents whose mothers did not engage in moderate PA were more likely to engage in less than three days of at least 60 min of vigorous PA per week (OR: 2.92, CI [1.18–7.24]); and have elevated BP (OR: 2.50, 95% CI [1.02–4.53]) than preadolescents whose mothers engaged in moderate PA.DiscussionOur results show a negative relationship between maternal obesity and preadolescent PA, and a positive relationship between lower maternal PA and elevated BP and lower PA in Hispanic preadolescents. This suggests that interventions aimed at improving Hispanic preadolescents’ PA and BP may use maternal PA and maternal BMI (for preadolescent PA) as a modification strategy to improve health in Hispanic preadolescents. creator: Basil A. Alhassan creator: Ying Liu creator: Deborah Slawson creator: Jonathan M. Peterson creator: Jo-Ann Marrs creator: William A. Clark creator: Arsham Alamian uri: https://doi.org/10.7717/peerj.6100 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Alhassan et al. title: Isolation and identification of pathogenic fungi and oomycetes associated with beans and cowpea root diseases in Oman link: https://peerj.com/articles/6064 last-modified: 2018-12-13 description: The purpose of this study was to characterize fungal and oomycete species associated with root diseases of Phaseolus vulgaris, Vigna unguiculata, V. radiata and Vicia faba in Oman. Root samples were collected from plants suffering from weakened growth and yellowing symptoms. Fungal species were isolated on 2.5% potato dextrose agar amended with 10 mg l−1 rifampicin and 200 mg l−1 of ampicillin and identification was based on sequences of the internal transcribed spacer region of the ribosomal RNA gene (ITS rRNA), glycerol-3-phosphate dehydrogenase (GPDH), translation elongation factor-1 alpha (TEF), beta-tubulin (TUB), calmodulin (CMD), actin (ACT). Isolations yielded 204 fungal isolates belonging to nine different genera, with most isolates belonging to Alternaria and Fusarium. Molecular identification revealed that the isolates belong to 20 fungal species, the most dominant of which was Alternaria alternata. Pathogenicity tests were conducted on each plant species. The inoculations on P. vulgaris revealed that Pythium aphanidermatum induced rotting, damping-off and wilt symptoms while Fusarium equiseti induced yellowing symptoms on the leaves. Rhizoctonia solani produced lesions and root rot on Vigna unguiculata while Curvularia muehlenbeckiae and Curvularia caricae-papayae produced root lesions on the roots of V. unguiculata and V. radiata, respectively. Alternaria alternata produced brown symptoms on the tap root of Vicia faba. P. aphanidermatum resulted in a significant reduction in the fresh weight, dry weight and shoot length of Phaseolus vulgaris. The study shows that several fungal species can be found associated with the roots of beans and Vigna unguiculata in Oman and can result in varying disease symptoms. This is the first report of root lesions produced by Curvularia muehlenbeckiae on the roots of V. unguiculata and by C. caricae-papayae on V. radiata worldwide. creator: Asma Al-Jaradi creator: Issa Al-Mahmooli creator: Rhonda Janke creator: Sajeewa Maharachchikumbura creator: Nadiya Al-Saady creator: Abdullah M. Al-Sadi uri: https://doi.org/10.7717/peerj.6064 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Al-Jaradi et al. title: Rapid increases in soil pH solubilise organic matter, dramatically increase denitrification potential and strongly stimulate microorganisms from the Firmicutes phylum link: https://peerj.com/articles/6090 last-modified: 2018-12-12 description: Rapid and transient changes in pH frequently occur in soil, impacting dissolved organic matter (DOM) and other chemical attributes such as redox and oxygen conditions. Although we have detailed knowledge on microbial adaptation to long-term pH changes, little is known about the response of soil microbial communities to rapid pH change, nor how excess DOM might affect key aspects of microbial N processing. We used potassium hydroxide (KOH) to induce a range of soil pH changes likely to be observed after livestock urine or urea fertilizer application to soil. We also focus on nitrate reductive processes by incubating microcosms under anaerobic conditions for up to 48 h. Soil pH was elevated from 4.7 to 6.7, 8.3 or 8.8, and up to 240-fold higher DOM was mobilized by KOH compared to the controls. This increased microbial metabolism but there was no correlation between DOM concentrations and CO2 respiration nor N-metabolism rates. Microbial communities became dominated by Firmicutes bacteria within 16 h, while few changes were observed in the fungal communities. Changes in N-biogeochemistry were rapid and denitrification enzyme activity (DEA) increased up to 25-fold with the highest rates occurring in microcosms at pH 8.3 that had been incubated for 24-hour prior to measuring DEA. Nitrous oxide reductase was inactive in the pH 4.7 controls but at pH 8.3 the reduction rates exceeded 3,000 ng N2–N g−1 h−1 in the presence of native DOM. Evidence for dissimilatory nitrate reduction to ammonium and/or organic matter mineralisation was observed with ammonium increasing to concentrations up to 10 times the original native soil concentrations while significant concentrations of nitrate were utilised. Pure isolates from the microcosms were dominated by Bacillus spp. and exhibited varying nitrate reductive potential. creator: Craig R. Anderson creator: Michelle E. Peterson creator: Rebekah A. Frampton creator: Simon R. Bulman creator: Sandi Keenan creator: Denis Curtin uri: https://doi.org/10.7717/peerj.6090 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Anderson et al. title: The impact of pneumococcal vaccination on pneumonia mortality among the elderly in Japan: a difference-in-difference study link: https://peerj.com/articles/6085 last-modified: 2018-12-12 description: BackgroundIt is plausible that the routine immunization among infants using pneumococcal conjugate vaccine 13 (PCV13) from 2013 and among the elderly using pneumococcal polysaccharide vaccine 23 (PPV23) from 2014 contributed to reducing the pneumonia mortality among the elderly in Japan. The present study aimed to estimate the causal effect of this vaccination on pneumonia mortality, using the available cause-of-death data and employing a difference-in-difference (DID) design.MethodsTwo types of mortality data, that is, prefecture-dependent and age- and gender-specific mortality data, from 2003 to 2017 were retrieved. We used mortality due to malignant neoplasm and heart disease as control groups and employed a DID design with an assumed parallel mortality trend between pneumonia and control group mortality since 2013 to estimate the causal effect of pneumococcal vaccination from 2014.ResultsOur estimation based on malignant neoplasm and heart disease as controls indicated that the reduced pneumonia mortality in 2017 owing to pneumococcal vaccination was as large as 41.9 (33.2, 50.6) and 31.2 (23.8, 38.6) per 100,000 individuals, respectively. The largest mortality reduction was observed for the oldest group (aged ≥90 years), especially among men.DiscussionThe pneumococcal vaccination program, perhaps mainly represented by high vaccination coverage of PCV13 among children and partly by PPV23 administration with low coverage among the elderly in Japan, was shown to have reduced the pneumonia mortality in the elderly at the population level. creator: Sung-mok Jung creator: Hyojung Lee creator: Hiroshi Nishiura uri: https://doi.org/10.7717/peerj.6085 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Jung et al. title: Ranaviruses and reptiles link: https://peerj.com/articles/6083 last-modified: 2018-12-12 description: Ranaviruses can infect many vertebrate classes including fish, amphibians and reptiles, but for the most part, research has been focused on non-reptilian hosts, amphibians in particular. More recently, reports of ranaviral infections of reptiles are increasing with over 12 families of reptiles currently susceptible to ranaviral infection. Reptiles are infected by ranaviruses that are genetically similar to, or the same as, the viruses that infect amphibians and fish; however, physiological and ecological differences result in differences in study designs. Although ranaviral disease in reptiles is often influenced by host species, viral strain and environmental differences, general trends in pathogenesis are emerging. More experimental studies using a variety of reptile species, life stages and routes of transmission are required to unravel the complexity of wild ranavirus transmission. Further, our understanding of the reptilian immune response to ranaviral infection is still lacking, although the considerable amount of work conducted in amphibians will serve as a useful guide for future studies in reptiles. creator: Wytamma Wirth creator: Lin Schwarzkopf creator: Lee F. Skerratt creator: Ellen Ariel uri: https://doi.org/10.7717/peerj.6083 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Wirth et al. title: Short-term interval aerobic exercise training does not improve memory functioning in relapsing-remitting multiple sclerosis—a randomized controlled trial link: https://peerj.com/articles/6037 last-modified: 2018-12-12 description: BackgroundOnly few aerobic exercise intervention trials specifically targeting cognitive functioning have been performed in multiple sclerosis.Objective and MethodsThis randomized controlled trial with 34 patients in the intervention group (IG) (mean: 38.2 years (±9.6)) and 34 patients in the control group (CG) (mean: 39.6 years (±9.7)) aimed to determine the effects of aerobic exercise on cognition in relapsing-remitting multiple sclerosis (RRMS). The primary outcome was verbal learning assessed by the verbal learning and memory test (VLMT). Patients were randomized to an IG or a waitlist CG. Patients in the IG exercised according to an individually tailored training schedule (with two to three sessions per week for 12 weeks). The primary analysis was carried out using the intention-to-treat (ITT) sample with ANCOVA adjusting for baseline scores.ResultsA total of 77 patients with RRMS were screened and 68 participants randomized (CG n = 34; IG n = 34). The sample comprised 68% females, had a mean age of 39 years, a mean disease duration of 6.3 years, and a mean expanded disability status scale of 1.8. No significant effects were detected in the ITT analysis for the primary endpoint VLMT or any other cognitive measures. Moreover, no significant treatment effects were observed for quality of life, fatigue, or depressive symptoms.ConclusionThis study failed to demonstrate beneficial effects of aerobic exercise on cognition in RRMS. The trial was prospectively registered at clinicaltrials.gov (NCT02005237). creator: Lisa Baquet creator: Helge Hasselmann creator: Stefan Patra creator: Jan-Patrick Stellmann creator: Eik Vettorazzi creator: Andreas K. Engel creator: Sina Cathérine Rosenkranz creator: Jana Poettgen creator: Stefan Michael Gold creator: Karl-Heinz Schulz creator: Christoph Heesen uri: https://doi.org/10.7717/peerj.6037 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Baquet et al. title: Founder effects drive the genetic structure of passively dispersed aquatic invertebrates link: https://peerj.com/articles/6094 last-modified: 2018-12-11 description: Populations of passively dispersed organisms in continental aquatic habitats typically show high levels of neutral genetic differentiation despite their high dispersal capabilities. Several evolutionary factors, including founder events, local adaptation, and life cycle features such as high population growth rates and the presence of propagule banks, have been proposed to be responsible for this paradox. Here, we have modeled the colonization process to assess the impact of migration rate, population growth rate, population size, local adaptation and life-cycle features on the population genetic structure in these organisms. Our simulations show that the strongest effect on population structure are persistent founder effects, resulting from the interaction of a few population founders, high population growth rates, large population sizes and the presence of diapausing egg banks. In contrast, the role of local adaptation, genetic hitchhiking and migration is limited to small populations in these organisms. Our results indicate that local adaptation could have different impact on genetic structure in different groups of zooplankters. creator: Javier Montero-Pau creator: Africa Gómez creator: Manuel Serra uri: https://doi.org/10.7717/peerj.6094 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Montero-Pau et al. title: Four tyrosine residues of the rice immune receptor XA21 are not required for interaction with the co-receptor OsSERK2 or resistance to Xanthomonas oryzae pv. oryzae link: https://peerj.com/articles/6074 last-modified: 2018-12-11 description: Tyrosine phosphorylation has emerged as an important regulator of plasma membrane-localized immune receptors activity. Here, we investigate the role of tyrosine phosphorylation in the regulation of rice XANTHOMONAS RESISTANCE 21 (XA21)-mediated immunity. We demonstrate that the juxtamembrane and kinase domain of Escherichia coli–expressed XA21 (XA21JK) autophosphorylates on tyrosine residues. Directed mutagenesis of four out of the nine tyrosine residues in XA21JK reduced autophosphorylation. These sites include Tyr698 in the juxtamembrane domain, and Tyr786, Tyr907, and Tyr909 in the kinase domain. Rice plants expressing XA21-GFP fusion proteins or proteins with these tyrosine residues individually mutated to phenylalanine (XA21YF-GFP), which prevents phosphorylation at these sites, maintain resistance to Xanthomonas oryzae pv. oryzae. In contrast, plants expressing phosphomimetic XA21 variants with tyrosine mutated to aspartate (XA21YD-GFP) were susceptible. In vitro purified XA21JKY698F, XA21JKY907F, and XA21JKY909F variants are catalytically active, whereas activity was not detected in XA21JKY768F and the four XA21JKYD variants. We previously demonstrated that interaction of XA21 with the co-receptor OsSERK2 is critical for biological function. Four of the XA21JKYF variants maintain interaction with OsSERK2 as well as the XA21 binding (XB) proteins XB3 and XB15 in yeast, suggesting that these four tyrosine residues are not required for their interaction. Taken together, these results suggest that XA21 is capable of tyrosine autophosphorylation, but the identified tyrosine residues are not required for activation of XA21-mediated immunity or interaction with predicted XA21 signaling proteins. creator: Daniel F. Caddell creator: Tong Wei creator: Sweta Sharma creator: Man-Ho Oh creator: Chang-Jin Park creator: Patrick Canlas creator: Steven C. Huber creator: Pamela C. Ronald uri: https://doi.org/10.7717/peerj.6074 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Caddell et al. title: A tuber mustard AP2/ERF transcription factor gene, BjABR1, functioning in abscisic acid and abiotic stress responses, and evolutionary trajectory of the ABR1 homologous genes in Brassica species link: https://peerj.com/articles/6071 last-modified: 2018-12-11 description: The AP2/ERF superfamily of transcription factors is one of the largest transcription factor families in plants and plays an important role in plant development processes and stress responses. In this study, BjABR1, an AP2/ERF superfamily gene, from tuber mustard (Brassica juncea var. tumida Tsen et Lee), sharing high amino acid sequence similarity with the AtABR1 (Arabidopsis thaliana AP2-like abscisic acid repressor 1) gene, were performed functional research, and the ABR1 homologous genes in Brassica species were identified and performed phylogenetic analysis. The promoter sequence of BjABR1 contained many phytohormone- and stress-related cis-elements; ABA (abscisic acid) and abiotic stresses can induce BjABR1 expression in tuber mustard; overexpression of BjABR1 in Arabidopsis can alleviate plant sensitivity to ABA and salt and osmotic stresses, and the alleviation may be due to changes in stress/ABA-induced gene expression. These results indicated that BjABR1 functions in ABA and abiotic stress responses. By BLAST searches against the genome database of five Brassica species (three diploids, B. rapa, B. nigra, and B. oleracea, and two allotetraploid, B. juncea and B. napus) using the protein sequence of AtABR1, 3, 3, 3, 6, and 5 ABR1 homologous genes in B. nigra, B. rapa, B. oleracea, B. juncea, and B. napus were identified, respectively, and they shared high sequence similarity. By sequence analysis, annotation mistakes of the protein-coding regions of two ABR1 homologous genes, GSBRNA2T00134741001 and BjuB007684, were found and corrected. Then, the evolution analysis of these ABR1 homologous genes showed that the ancestor of the three diploid species had three ABR1 homologous genes and each diploid inherited all the three genes from their ancestor; then, allotetraploid B. juncea inherited all the six genes from B. rapa and B. nigra with no gene lost, while allotetraploid B. napus inherited all the three genes from B. oleracea and two genes from B. rapa with one gene lost, indicating that ABR1 homologous genes possessed greater hereditary conservation in Brassica species. The ABR1 homologous genes between B. rapa and B. oleracea shared much higher sequence similarity compared to that of B. nigra in diploid species, indicating that ABR1 homologous genes in B. nigra had experienced more rapid evolution, and B. rapa and B. oleracea may share closer relationship compared to B. nigra. Moreover, the spatial and temporal expression analysis of six ABR1 homologous genes of tuber mustard showed that they possessed different expression models. These results imply that ABR1 homologous genes are important to Brassica plants, and they may possess similar function in ABA and abiotic stress responses but play a role in different tissues and growing stages of plant. This study will provide the foundation to the functional research of ABR1 homologous genes in the Brassica species and help to reveal and understand the evolution mechanisms of Brassica species. creator: Liuxin Xiang creator: Chao Liu creator: Jingzhi Luo creator: Lin He creator: Yushan Deng creator: Jie Yuan creator: Chaofeng Wu creator: Yingfan Cai uri: https://doi.org/10.7717/peerj.6071 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Xiang et al. title: Changes in intentional binding effect during a novel perceptual-motor task link: https://peerj.com/articles/6066 last-modified: 2018-12-11 description: Perceptual-motor learning describes the process of improving the smoothness and accuracy of movements. Intentional binding (IB) is a phenomenon whereby the length of time between performing a voluntary action and the production of a sensory outcome during perceptual-motor control is perceived as being shorter than the reality. How IB may change over the course of perceptual-motor learning, however, has not been explicitly investigated. Here, we developed a set of IB tasks during perceptual-motor learning. Participants were instructed to stop a circular moving object by key press when it reached the center of a target circle on the display screen. The distance between the center of the target circle and the center of the moving object was measured, and the error was used to approximate the perceptual-motor performance index. This task also included an additional exercise that was unrelated to the perceptual-motor task: after pressing the key, a sound was presented after a randomly chosen delay of 200, 500, or 700 ms and the participant had to estimate the delay interval. The difference between the estimated and actual delay was used as the IB value. A cluster analysis was then performed using the error values from the first and last task to group the participants based on their perceptual-motor performance. Participants showing a very small change in error value, and thus demonstrating a small effect of perceptual-motor learning, were classified into cluster 1. Those who exhibited a large decrease in error value from the first to the last set, and thus demonstrated a strong improvement in perceptual-motor performance, were classified into cluster 2. Those who exhibited perceptual-motor learning also showed improvements in the IB value. Our data suggest that IB is elevated when perceptual-motor learning occurs. creator: Shu Morioka creator: Kazuki Hayashida creator: Yuki Nishi creator: Sayaka Negi creator: Yuki Nishi creator: Michihiro Osumi creator: Satoshi Nobusako uri: https://doi.org/10.7717/peerj.6066 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Morioka et al. title: Combining ultraconserved elements and mtDNA data to uncover lineage diversity in a Mexican highland frog (Sarcohyla; Hylidae) link: https://peerj.com/articles/6045 last-modified: 2018-12-11 description: Molecular studies have uncovered significant diversity in the Mexican Highlands, leading to the description of many new endemic species. DNA approaches to this kind of species discovery have included both mitochondrial DNA (mtDNA) sequencing and multilocus genomic methods. While these marker types have often been pitted against one another, there are benefits to deploying them together, as linked mtDNA data can provide the bridge between uncovering lineages through rigorous multilocus genomic analysis and identifying lineages through comparison to existing mtDNA databases. Here, we apply one class of multilocus genomic marker, ultraconserved elements (UCEs), and linked mtDNA data to a species complex of frogs (Sarcohyla bistincta, Hylidae) found in the Mexican Highlands. We generated data from 1,891 UCEs, which contained 1,742 informative SNPs for S. bistincta and closely related species and captured mitochondrial genomes for most samples. Genetic analyses based on both whole loci and SNPs agree there are six to seven distinct lineages within what is currently described as S. bistincta. Phylogenies from UCEs and mtDNA mostly agreed in their topologies, and the few differences suggested a more complex evolutionary history of the mtDNA marker. Our study demonstrates that the Mexican Highlands still hold substantial undescribed diversity, making their conservation a particularly urgent goal. The Trans-Mexican Volcanic Range stands out as a significant geographic feature in Sarcohyla and may have acted as a dispersal corridor for S. bistincta to spread to the north. Combining multilocus genomic data with linked mtDNA data is a useful approach for identifying potential new species and associating them with already described taxa, which will be especially important in groups with undescribed subadult phenotypes and cryptic species. creator: Eugenia Zarza creator: Elizabeth M. Connors creator: James M. Maley creator: Whitney L.E. Tsai creator: Peter Heimes creator: Moises Kaplan creator: John E. McCormack uri: https://doi.org/10.7717/peerj.6045 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Zarza et al. title: Effects of crude oil on survival and development in embryonated eggs in Callinectes sapidus Rathbun, 1896 (Decapoda, Portunidae) link: https://peerj.com/articles/5985 last-modified: 2018-12-11 description: Blue crabs, Callinectes sapidus Rathbun, 1896, are ubiquitous along the Atlantic and Gulf coasts of the USA. These organisms play an integral role in the ecosystems of the Gulf of Mexico (GOM), where not only are they a keystone species, but are also socioeconomically important. The survival of embryonated eggs is necessary to ensure adequate recruitment into the next generation. Because the 2010 Deepwater Horizon oil spill (DWH) occurred during the peak of the blue crab spawning season, the incident likely impacted blue crab embryos. In order to assess the effect of oil on embryonic growth and development, we collected embryonated eggs from seven different female blue crabs from the GOM throughout the spawning season and exposed them to an oil concentration of 500 ppb (the approximate concentration of oil at the surface water near the site of the Deepwater Horizon oil rig). Exposure to oil at this concentration caused a significantly larger proportion of prezoeae vs. zoeae to hatch from embryonated eggs in experiments lasting longer than 4 days. Exposure to oil did not significantly affect overall survival or development rate. The prezoeal stage is a little-studied stage of blue crab development. Though it may or may not be a normal stage of development, this stage has been found to occur in suboptimal conditions and has lower survival than zoeal stages. The larger proportion of prezoeae following prolonged exposure to oil thus indicates that crude oil at concentrations likely to be experienced by crabs after the DWH spill negatively impacted the development of blue crab embryos. In addition to providing insight into the effects of the DWH, this study sheds light on embryonic development in blue crabs, a critical, but poorly investigated phase of this important species’ life cycle. creator: Kelsie L. Kelly creator: Caz M. Taylor uri: https://doi.org/10.7717/peerj.5985 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Kelly and Taylor title: Stress among on-duty firefighters: an ambulatory assessment study link: https://peerj.com/articles/5967 last-modified: 2018-12-11 description: BackgroundStress at work has been broadly acknowledged as a worldwide problem and has been the focus of concern for many researchers. Firefighting, in particular, is frequently reported as a highly stressful occupation. In order to investigate firefighters’ occupational health in terms of stress events, perceptions, symptoms, and physiological reactions under real-world conditions, an ambulatory assessment protocol was developed.MethodsSeventeen firefighters’ cardiac signal was continuously monitored during an average of three shifts within a working week with medical clinically certified equipment (VitalJacket®), which allows for continuous electrocardiogram (ECG) and actigraphy measurement. Psychological data were collected with a software application running on smartphones, collecting potential stressful events, stress symptoms, and stress appraisal.ResultsA total of 450.56 h of medical-quality ECG were collected, and heart rate variability (HRV) analysis was performed. Findings suggest that although ‘fire’ situations are more common, ‘accidents’ are more stressful. Additionally, firefighters showed high levels of physiological stress (based on AVNN and LF/HF HRV metrics) when compared to normative healthy population values that may not be diagnosed using merely self-reports.DiscussionThe proposed ambulatory study seems to be useful for the monitoring of stress levels and its potential impact on health of first responders. Additionally, it could also be an important tool for the design and implementation of efficient interventions and informed management resolutions in real time. Potential applications of this research include the development of quantified occupational health (qOHealth) devices for real life monitoring of emergency personnel stress reactions. creator: Susana Rodrigues creator: Joana S. Paiva creator: Duarte Dias creator: João Paulo S. Cunha uri: https://doi.org/10.7717/peerj.5967 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Rodrigues et al. title: Plant-derived chimeric antibodies inhibit the invasion of human fibroblasts by Toxoplasma gondii link: https://peerj.com/articles/5780 last-modified: 2018-12-11 description: The parasite Toxoplasma gondii causes an opportunistic infection, that is, particularly severe in immunocompromised patients, infants, and neonates. Current antiparasitic drugs are teratogenic and cause hypersensitivity-based toxic side effects especially during prolonged treatment. Furthermore, the recent emergence of drug-resistant toxoplasmosis has reduced the therapeutic impact of such drugs. In an effort to develop recombinant antibodies as a therapeutic alternative, a panel of affinity-matured, T. gondii tachyzoite-specific single-chain variable fragment (scFv) antibodies was selected by phage display and bioinformatic analysis. Further affinity optimization was attempted by introducing point mutations at hotspots within light chain complementarity-determining region 2. This strategy yielded four mutated scFv sequences and a parental scFv that were used to produce five mouse–human chimeric IgGs in Nicotiana benthamiana plants, with yields of 33–72 mg/kg of plant tissue. Immunological analysis confirmed the specific binding of these plant-derived antibodies to T. gondii tachyzoites, and in vitro efficacy was demonstrated by their ability to inhibit the invasion of human fibroblasts and impair parasite infectivity. These novel recombinant antibodies could therefore be suitable for the development of plant-derived immunotherapeutic interventions against toxoplasmosis. creator: Sherene Swee Yin Lim creator: Kek Heng Chua creator: Greta Nölke creator: Holger Spiegel creator: Wai Leong Goh creator: Sek Chuen Chow creator: Boon Pin Kee creator: Rainer Fischer creator: Stefan Schillberg creator: Rofina Yasmin Othman uri: https://doi.org/10.7717/peerj.5780 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Lim et al. title: Behavior problems and personality in Korean high school students link: https://peerj.com/articles/6106 last-modified: 2018-12-10 description: IntroductionExtant studies have examined the effect of psychological characteristics on clinical features that define behavior problems. The purpose of this study was to analyze the effects of temperament and character as both individual factors and complex profiles on behavior problems in a community sample of adolescents.MethodsBehavior problems and personality of 670 Korean high school students were measured with the Youth Self-Report (YSR) and Junior version of the Temperament and Character Inventory (JTCI). Stepwise regression analysis analyzed the effects of JTCI character and temperament traits on YSR Total, Internalizing and Externalizing subscale scores, and Profile Analysis examined differences of JTCI personality profiles among three latent YSR subscale profiles acquired from Latent Profile Analysis.ResultsSeven subscales of the JTCI explained 38% of the YSR total degree of behavior problems, and JTCI Novelty-Seeking and Harm-Avoidance were found to account for vulnerability while JTCI Reward-Dependence and Self-Directedness explained resilience to behavior problems. There were three distinct latent YSR profile groups based on nine YSR subscales, and low behavior problem group showed a resilient personality profile characterized by low Novelty-Seeking and Harm-Avoidance and high Reward-Dependence, Persistence, Self-Directedness and Cooperativeness while high behavior problem group exhibited a vulnerable personality profile of the opposite tendency.DiscussionTemperament and character explained behavior problems of Korean high school students as both individual personality traits and a complex personality profile. The results and implications of this study were examined in regard to mental health of adolescents, and the importance of education in the development of mature personality are discussed. creator: Soo Jin Lee creator: Soo Hyun Park creator: C Robert Cloninger creator: Han Chae uri: https://doi.org/10.7717/peerj.6106 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Lee et al. title: Effects of gelsemine on oxidative stress and DNA damage responses of Tetrahymena thermophila link: https://peerj.com/articles/6093 last-modified: 2018-12-10 description: Gelsemine is an important toxic substance extracted from Gelsemium elegans, which has a lot of biological functions in cells and organisms, but its toxicity has been rarely reported in Tetrahymena thermophila. In this study, we used the protozoan T. thermophila as an experimental model to investigate the potential toxicity-induced mechanism of gelsemine in the unicellular eukaryote. Our results clearly showed gelsemine inhibited T. thermophila growth in a dose-dependent manner. This exposure also resulted in oxidative stress on T. thermophila cells and antioxidant enzyme levels were significantly altered at high gelsemine levels (p < 0.05). Gelsemine produced a slight apoptotic effect at the highest (0.8 mg/mL) gelsemine level used here (p < 0.05). Furthermore, the toxin-induced DNA damage in a dose-dependent manner. The ultrastructural analysis also revealed mitophagic vacuoles at 0.4 and 0.8 mg/mL levels of gelsemine exposure. Moreover, expressions of oxidative stress-related and MAP kinase genes were significantly changed after exposure to 0.8 mg/mL level of gelsemine (p < 0.05). Altogether, our results clearly show that gelsemine from G. elegans can inhibit the growth via inducing oxidative stress and DNA damage in T. thermophila cells. creator: Qiao Ye creator: Yongyong Feng creator: Zhenlu Wang creator: Wenzhao Jiang creator: Yuexin Qu creator: Chaonan Zhang creator: Aiguo Zhou creator: Shaolin Xie creator: Jixing Zou uri: https://doi.org/10.7717/peerj.6093 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Ye et al. title: Screening of prognostic biomarkers for endometrial carcinoma based on a ceRNA network link: https://peerj.com/articles/6091 last-modified: 2018-12-10 description: ObjectiveThis study aims to reveal the regulation network of lncRNAs-miRNAs-mRNA in endometrial carcinoma (EC), to investigate the underlying mechanisms of EC occurrence and progression, to screen prognostic biomarkers.MethodsRNA-seq and miRNA-seq data of endometrial carcinoma were downloaded from the TCGA database. Edge.R package was used to screen differentially expressed genes. A database was searched to determine differentially expressed lncRNA-miRNA and miRNA-mRNA pairs, to construct the topological network of ceRNA, and to elucidate the key RNAs that are for a prognosis of survival.ResultsWe screened out 2632 mRNAs, 1178 lncRNAs and 189 miRNAs that were differentially expressed. The constructed ceRNA network included 97 lncRNAs, 20 miRNAs and 73 mRNAs. Analyzing network genes for associations with prognosies revealed 169 prognosis-associated RNAs, including 92 lncRNAs, 16miRNAs and 61 mRNAs.ConclusionOur results reveal new potential mechanisms underlying the carcinogenesis and progression of endometrial carcinoma. creator: Ming-Jun Zheng creator: Rui Gou creator: Wen-Chao Zhang creator: Xin Nie creator: Jing Wang creator: Ling-Ling Gao creator: Juan-Juan Liu creator: Xiao Li creator: Bei Lin uri: https://doi.org/10.7717/peerj.6091 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Zheng et al. title: The recent expansion of Fox Sparrow (Passerella iliaca iliaca) breeding range into the northeastern United States link: https://peerj.com/articles/6087 last-modified: 2018-12-10 description: The breeding range of the Eastern Fox Sparrow (Passerella iliaca iliaca) is generally recognized as comprising the boreal forest of Canada. However, recent observations suggest that the species is present during the summer months throughout much of the northeastern US, unexpected for a species characterized as a passage migrant in the region. To clarify, I conducted a literature review to document the historical status of the species in the northeastern US and then analyzed observations submitted to eBird to describe its recent and current status in the region. Historical accounts consistently identify Fox Sparrow as a passage migrant through the region during early spring and late fall. Beginning in the early 1980s, observers began noting regular extralimital records of Fox Sparrow in northern Maine. A single nest was discovered in the state in 1983, and another in northern New Hampshire in 1997. Despite the paucity of breeding records, observations submitted to eBird suggest that the southern limit of the breeding range of Fox Sparrow has expanded rapidly to the south and west in recent years. The proportion of complete checklists submitted to eBird that contained at least one observation of Fox Sparrow grew at an annual rate of 18% from 2003–2016 and was independent of observer effort. Fox Sparrow now occurs regularly on mountaintops and in young stands of spruce (Picea spp.) and balsam fir (Abies balsamea) during the breeding season throughout northern and western Maine and northern New Hampshire, with occasional records from the Green Mountains of Vermont and the Adirondack Mountains of New York. The cause of this rapid expansion of its breeding range is unknown, but may be related to an increase in the amount of young conifer forest in the northeastern US created by commercial timber harvest. creator: John D. Lloyd uri: https://doi.org/10.7717/peerj.6087 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Lloyd title: Posture similarity index: a method to compare hand postures in synergy space link: https://peerj.com/articles/6078 last-modified: 2018-12-10 description: BackgroundThe human hand can perform a range of manipulation tasks, from holding a pen to holding a hammer. The central nervous system (CNS) uses different strategies in different manipulation tasks based on task requirements. Attempts to compare postures of the hand have been made for use in robotics and animation industries. In this study, we developed an index called the posture similarity index to quantify the similarity between two human hand postures.MethodsTwelve right-handed volunteers performed 70 postures, and lifted and held 30 objects (total of 100 different postures, each performed five times). A 16-sensor electromagnetic tracking system captured the kinematics of individual finger phalanges (segments). We modeled the hand as a 21-DoF system and computed the corresponding joint angles. We used principal component analysis to extract kinematic synergies from this 21-DoF data. We developed a posture similarity index (PSI), that represents the similarity between posture in the synergy (Principal component) space. First, we tested the performance of this index using a synthetic dataset. After confirming that it performs well with the synthetic dataset, we used it to analyze the experimental data. Further, we used PSI to identify postures that are “representative” in the sense that they have a greater overlap (in synergy space) with a large number of postures.ResultsOur results confirmed that PSI is a relatively accurate index of similarity in synergy space both with synthetic data and real experimental data. Also, more special postures than common postures were found among “representative” postures.ConclusionWe developed an index for comparing posture similarity in synergy space and demonstrated its utility by using synthetic dataset and experimental dataset. Besides, we found that “special” postures are actually “special” in the sense that there are more of them in the “representative” postures as identified by our posture similarity index. creator: Nayan Bhatt creator: Varadhan SKM uri: https://doi.org/10.7717/peerj.6078 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Bhatt and SKM title: Freshwater carbon and nutrient cycles revealed through reconstructed population genomes link: https://peerj.com/articles/6075 last-modified: 2018-12-10 description: Although microbes mediate much of the biogeochemical cycling in freshwater, the categories of carbon and nutrients currently used in models of freshwater biogeochemical cycling are too broad to be relevant on a microbial scale. One way to improve these models is to incorporate microbial data. Here, we analyze both genes and genomes from three metagenomic time series and propose specific roles for microbial taxa in freshwater biogeochemical cycles. Our metagenomic time series span multiple years and originate from a eutrophic lake (Lake Mendota) and a humic lake (Trout Bog Lake) with contrasting water chemistry. Our analysis highlights the role of polyamines in the nitrogen cycle, the diversity of diazotrophs between lake types, the balance of assimilatory vs. dissimilatory sulfate reduction in freshwater, the various associations between types of phototrophy and carbon fixation, and the density and diversity of glycoside hydrolases in freshwater microbes. We also investigated aspects of central metabolism such as hydrogen metabolism, oxidative phosphorylation, methylotrophy, and sugar degradation. Finally, by analyzing the dynamics over time in nitrogen fixation genes and Cyanobacteria genomes, we show that the potential for nitrogen fixation is linked to specific populations in Lake Mendota. This work represents an important step towards incorporating microbial data into ecosystem models and provides a better understanding of how microbes may participate in freshwater biogeochemical cycling. creator: Alexandra M. Linz creator: Shaomei He creator: Sarah L.R. Stevens creator: Karthik Anantharaman creator: Robin R. Rohwer creator: Rex R. Malmstrom creator: Stefan Bertilsson creator: Katherine D. McMahon uri: https://doi.org/10.7717/peerj.6075 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Linz et al. title: Technology-assisted white cane: evaluation and future directions link: https://peerj.com/articles/6058 last-modified: 2018-12-10 description: BackgroundSeveral technology-assisted aids are available to help blind and visually impaired people perform their daily activities. The current research uses the state-of-the-art technology to enhance the utility of traditional navigational aids to produce solutions that are more reliable. In this regard, a white cane is no exception, which is supplemented with the existing technologies to design Electronic Travel Aids (ETAs), Electronic Orientation Aids (EOAs), and Position Locator Devices (PLDs). Although several review articles uncover the strengths and limitations of research contributions that extend traditional navigational aids, we find no review article that covers research contributions on a technology-assisted white cane. The authors attempt to fill this literature gap by reviewing the most relevant research articles published during 2010–2017 with the common objective of enhancing the utility of white cane with the existing technology.MethodsThe authors have collected the relevant literature published during 2010–17 by searching and browsing all the major digital libraries and publishers’ websites. The inclusion/exclusion criteria were applied to select the research articles that are relevant to the topic of this review article, and all other irrelevant papers were excluded. Among the 577 (534 through database searching and 43 through other sources) initially screened papers, the authors collected 228 full-text articles, which after applying exclusion/inclusion criteria resulted in 36 papers that were included in the evaluation, comparison, and discussion. This also includes research articles of commercially available aids published before the specified range.ResultsThe findings show that the research trend is shifting towards developing a technology-assisted white cane solution that is applicable in both indoor and outdoor environments to aid blind users in navigation. In this regard, exploiting smartphones to develop low-cost and user-friendly navigation solution is among the best research opportunities to explore. In addition, the authors contribute a theoretical evaluation framework to compare and evaluate the state-of-the-art solutions, identify research trends and future directions.DiscussionResearchers have been in the quest to find out ways of enhancing the utility of white cane using existing technology. However, for a more reliable enhancement, the design should have user-centric characteristics. It should be portable, reliable, trust-worthy, lightweight, less costly, less power hungry, and require minimal training with special emphasis on its ergonomics and social acceptance. Smartphones, which are the ubiquitous and general-purpose portable devices, should be considered to exploit its capabilities in making technology-assisted white cane smarter and reliable. creator: Izaz Khan creator: Shah Khusro creator: Irfan Ullah uri: https://doi.org/10.7717/peerj.6058 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Khan et al. title: The relationship between carbon and nitrogen metabolism in cucumber leaves acclimated to salt stress link: https://peerj.com/articles/6043 last-modified: 2018-12-10 description: The study examines the effect of acclimation on carbon and nitrogen metabolism in cucumber leaves subjected to moderate and severe NaCl stress. The levels of glucose, sucrose, NADH/NAD+-GDH, AspAT, AlaAT, NADP+-ICDH, G6PDH and 6GPDH activity were determined after 24 and 72 hour periods of salt stress in acclimated and non-acclimated plants. Although both groups of plants showed high Glc and Suc accumulation, they differed with regard to the range and time of accumulation. Acclimation to salinity decreased the activities of NADP+-ICDH and deaminating NAD+-GDH compared to controls; however, these enzymes, together with the other examined parameters, showed elevated values in the stressed plants. The acclimated plants showed higher G6PDH activity than the non-acclimated plants, whereas both groups demonstrated similar 6PGDH activity. The high activities of NADH-GDH, AlaAT and AspAT observed in the examined plants could be attributed to a high demand for glutamate. The observed changes may be required for the maintenance of correct TCA cycle activity, and acclimation appeared to positively influence these adaptive processes. creator: Marcin Robert Naliwajski creator: Maria Skłodowska uri: https://doi.org/10.7717/peerj.6043 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Naliwajski and Skłodowska title: A direct approach to estimating false discovery rates conditional on covariates link: https://peerj.com/articles/6035 last-modified: 2018-12-10 description: Modern scientific studies from many diverse areas of research abound with multiple hypothesis testing concerns. The false discovery rate (FDR) is one of the most commonly used approaches for measuring and controlling error rates when performing multiple tests. Adaptive FDRs rely on an estimate of the proportion of null hypotheses among all the hypotheses being tested. This proportion is typically estimated once for each collection of hypotheses. Here, we propose a regression framework to estimate the proportion of null hypotheses conditional on observed covariates. This may then be used as a multiplication factor with the Benjamini–Hochberg adjusted p-values, leading to a plug-in FDR estimator. We apply our method to a genome-wise association meta-analysis for body mass index. In our framework, we are able to use the sample sizes for the individual genomic loci and the minor allele frequencies as covariates. We further evaluate our approach via a number of simulation scenarios. We provide an implementation of this novel method for estimating the proportion of null hypotheses in a regression framework as part of the Bioconductor package swfdr. creator: Simina M. Boca creator: Jeffrey T. Leek uri: https://doi.org/10.7717/peerj.6035 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Boca and Leek title: A new phylogenetic analysis of Phytosauria (Archosauria: Pseudosuchia) with the application of continuous and geometric morphometric character coding link: https://peerj.com/articles/5901 last-modified: 2018-12-10 description: Phytosauria is a clade of large, carnivorous, semi-aquatic archosauromorphs which reached its peak diversity and an almost global distribution in the Late Triassic (c. 230–201 Mya). Previous phylogenetic analyses of Phytosauria have either focused primarily on the relationships of specific subclades, or were limited in taxonomic scope, and no taxonomically comprehensive dataset is currently available. We here present the most taxonomically comprehensive cladistic dataset of phytosaurs to date, based on extensive first-hand study, identification of novel characters and synthesis of previous matrices. This results in an almost twofold increase in phylogenetic information scored per taxon over previous analyses. Alongside a traditional discrete character matrix, three variant matrices were analysed in which selected characters were coded using continuous and landmarking methods, to more rigorously explore phytosaur relationships. Based on these four data matrices, four tree topologies were recovered. Relationships among non-leptosuchomorph phytosaurs are largely consistent between these four topologies, whereas those of more derived taxa are more variable. Rutiodon carolinensis consistently forms a sister relationship with Angistorhinus. In three topologies Nicrosaurus nests deeply within a group of traditionally non-Mystriosuchini taxa, leading us to redefine Mystriosuchini by excluding Nicrosaurus as an internal specifier. Two distinct patterns of relationships within Mystriosuchini are present in the four topologies, distinguished largely by the variable position of Mystriosuchus. In two topologies Mystriosuchus forms the most basal clade in Mystriosuchini, whilst in the others it occupies a highly derived position within the Machaeroprosopus clade. ‘Redondasaurus’ is consistently recovered as monophyletic; however, it also nests within the Machaeroprosopus clade. The greatest impact on tree topology was associated with the incorporation of continuous data into our matrices, with landmark characters exerting a relatively modest influence. All topologies correlated significantly with stratigraphic range estimates. Topological variability in our results highlights clades in which further investigation may better elucidate phytosaur relationships. creator: Andrew S. Jones creator: Richard J. Butler uri: https://doi.org/10.7717/peerj.5901 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Jones and Butler title: Characterization and comparative genomic analysis of virulent and temperate Bacillus megaterium bacteriophages link: https://peerj.com/articles/5687 last-modified: 2018-12-10 description: Next-Generation Sequencing (NGS) technologies provide unique possibilities for the comprehensive assessment of the environmental diversity of bacteriophages. Several Bacillus bacteriophages have been isolated, but very few Bacillus megaterium bacteriophages have been characterized. In this study, we describe the biological characteristics, whole genome sequences, and annotations for two new isolates of the B. megaterium bacteriophages (BM5 and BM10), which were isolated from Egyptian soil samples. Growth analyses indicated that the phages BM5 and BM10 have a shorter latent period (25 and 30 min, respectively) and a smaller burst size (103 and 117 PFU, respectively), in comparison to what is typical for Bacillus phages. The genome sizes of the phages BM5 and BM10 were 165,031 bp and 165,213 bp, respectively, with modular organization. Bioinformatic analyses of these genomes enabled the assignment of putative functions to 97 and 65 putative ORFs, respectively. Comparative analysis of the BM5 and BM10 genome structures, in conjunction with other B. megaterium bacteriophages, revealed relatively high levels of sequence and organizational identity. Both genomic comparisons and phylogenetic analyses support the conclusion that the sequenced phages (BM5 and BM10) belong to different sub-clusters (L5 and L7, respectively), within the L-cluster, and display different lifestyles (lysogenic and lytic, respectively). Moreover, sequenced phages encode proteins associated with Bacillus pathogenesis. In addition, BM5 does not contain any tRNA sequences, whereas BM10 genome codes for 17 tRNAs. creator: Abdoallah Sharaf creator: Miroslav Oborník creator: Adel Hammad creator: Sohair El-Afifi creator: Eman Marei uri: https://doi.org/10.7717/peerj.5687 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Sharaf et al. title: Enriched environment improves working memory impairment of mice with traumatic brain injury by enhancing histone acetylation in the prefrontal cortex link: https://peerj.com/articles/6113 last-modified: 2018-12-07 description: Working memory impairment is a common cognitive dysfunction after traumatic brain injury (TBI), which severely affects the quality of life of patients. Acetylcholine is a neurotransmitter which is closely related to cognitive functions. In addition, epigenetic modifications are also related to cognitive functions. A neurorehabilitation strategy, enriched environment (EE) intervention, has been widely used to improve cognitive impairment. However, studies of the mechanism of EE on cholinergic system and epigenetic modifications in mouse with TBI have not been reported yet. In this paper, a mouse model with traumatic frontal lobe injury was established, and the mechanism on EE for the mice with TBI was explored. It was found that EE could improve Y-maze performance of mice with TBI, the function of cholinergic system, and the imbalance of acetylation homeostasis in the prefrontal cortex of contralateral side of TBI. In addition, EE also could increase the level of CREB binding protein and histones H3 acetylation at ChAT gene promoter region in the prefrontal cortex of contralateral side of TBI. These indicate that EE has an important effect on the improvement of working memory impairment and the underlying mechanism may involve in histones H3 acetylation at ChAT gene promoter regions in the prefrontal cortex. creator: Xin Wang creator: Zhaoxiang Meng creator: Jibing Wang creator: Hongyu Zhou creator: Yi Wu creator: Junfa Wu uri: https://doi.org/10.7717/peerj.6113 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Wang et al. title: Symmetry breaking of the cellular lobes closely relates to phylogenetic structure within green microalgae of the Micrasterias lineage (Zygnematophyceae) link: https://peerj.com/articles/6098 last-modified: 2018-12-07 description: Green microalgae of the Micrasterias lineage are unicellular microorganisms with modular morphology consisting of successively differentiated lobes. Due to their morphological diversity and peculiar morphogenesis, these species are important model systems for studies of cytomorphogenesis and cellular plasticity. Interestingly, the phylogenetic structure of the Micrasterias lineage and most other Desmidiales is poorly related to the traditional morphological characters used for delimitation of taxa. In this study, we focused on symmetry breaking between adjacent cellular lobes in relation to phylogeny of the studied species. While pronounced morphological asymmetry between the adjacent lobes is typical for some species, others have been characterized by the almost identical morphologies of these structures. We asked whether there is any detectable average shape asymmetry between the pairs of lobes and terminal lobules in 19 Micrasterias species representing all major clades of this desmidiacean lineage. Then, we evaluated whether the asymmetric patterns among species are phylogenetically structured. The analyses showed that the phylogeny was in fact strongly related to the patterns of morphological asymmetry between the adjacent cellular lobes. Thus, evolution of the asymmetric development between the adjacent lobes proved to be the key event differentiating cellular shape patterns of Micrasterias. Conversely, the phylogeny was only weakly related to asymmetry between the pairs of terminal lobules. The subsequent analyses of the phylogenetic morphological integration showed that individual hierarchical levels of cellular morphology were only weakly coordinated with regard to asymmetric variation among species. This finding indicates that evolutionary differentiation of morphogenetic processes leading to symmetry breaking may be relatively independent at different branching levels. Such modularity is probably the key to the evolvability of cellular shapes, leading to the extraordinary morphological diversity of these intriguing microalgae. creator: Jiri Neustupa creator: Jan Stastny uri: https://doi.org/10.7717/peerj.6098 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Neustupa and Stastny title: In silico analyses for potential key genes associated with gastric cancer link: https://peerj.com/articles/6092 last-modified: 2018-12-07 description: BackgroundUnderstanding hub genes involved in gastric cancer (GC) metastasis could lead to effective approaches to diagnose and treat cancer. In this study, we aim to identify the hub genes and investigate the underlying molecular mechanisms of GC.MethodsTo explore potential therapeutic targets for GC,three expression profiles (GSE54129, GSE33651, GSE81948) of the genes were extracted from the Gene Expression Omnibus (GEO) database. The GEO2R online tool was applied to screen out differentially expressed genes (DEGs) between GC and normal gastric samples. Database for Annotation, Visualization and Integrated Discovery was applied to perform Gene Ontology (GO) and KEGG pathway enrichment analysis. The protein-protein interaction (PPI) network of these DEGs was constructed using a STRING online software. The hub genes were identified by the CytoHubba plugin of Cytoscape software. Then, the prognostic value of these identified genes was verified by gastric cancer database derived from Kaplan-Meier plotter platform.ResultsA total of 85 overlapped upregulated genes and 44 downregulated genes were identified. The majority of the DEGs were enriched in extracellular matrix organization, endodermal cell differentiation, and endoderm formation. Moreover, five KEGG pathways were significantly enriched, including ECM-receptor interaction, amoebiasis, AGE-RAGE signaling pathway in diabetic complications, focal adhesion, protein digestion and absorption. By combining the results of PPI network and CytoHubba, a total of nine hub genes including COL1A1, THBS1, MMP2, CXCL8, FN1, TIMP1, SPARC, COL4A1, and ITGA5 were selected. The Kaplan-Meier plotter database confirmed that overexpression levels of these genes were associated with reduced overall survival, except for THBS1 and CXCL8.ConclusionsOur study suggests that COL1A1, MMP2, FN1, TIMP1, SPARC, COL4A1, and ITGA5 may be potential biomarkers and therapeutic targets for GC. Further study is needed to assess the effect of THBS1 and CXCL8 on GC. creator: Ping Yan creator: Yingchun He creator: Kexin Xie creator: Shan Kong creator: Weidong Zhao uri: https://doi.org/10.7717/peerj.6092 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Yan et al. title: Dopamine and eye movement control in Parkinson’s disease: deficits in corollary discharge signals? link: https://peerj.com/articles/6038 last-modified: 2018-12-07 description: Movement in Parkinson’s disease (PD) is fragmented, and the patients depend on visual information in their behavior. This suggests that the patients may have deficits in internally monitoring their own movements. Internal monitoring of movements is assumed to rely on corollary discharge signals that enable the brain to predict the sensory consequences of actions. We studied early-stage PD patients (N = 14), and age-matched healthy control participants (N = 14) to examine whether PD patients reveal deficits in updating their sensory representations after eye movements. The participants performed a double-saccade task where, in order to accurately fixate a second target, the participant must correct for the displacement caused by the first saccade. In line with previous reports, the patients had difficulties in fixating the second target when the eye movement was performed without visual guidance. Furthermore, the patients had difficulties in taking into account the error in the first saccade when making a saccade toward the second target, especially when eye movements were made toward the side with dominant motor symptoms. Across PD patients, the impairments in saccadic eye movements correlated with the integrity of the dopaminergic system as measured with [123I]FP-CIT SPECT: Patients with lower striatal (caudate, anterior putamen, and posterior putamen) dopamine transporter binding made larger errors in saccades. This effect was strongest when patients made memory-guided saccades toward the second target. Our results provide tentative evidence that the motor deficits in PD may be partly due to deficits in internal monitoring of movements. creator: Henry Railo creator: Henri Olkoniemi creator: Enni Eeronheimo creator: Oona Pääkkönen creator: Juho Joutsa creator: Valtteri Kaasinen uri: https://doi.org/10.7717/peerj.6038 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Railo et al. title: RIP-MD: a tool to study residue interaction networks in protein molecular dynamics link: https://peerj.com/articles/5998 last-modified: 2018-12-07 description: Protein structure is not static; residues undergo conformational rearrangements and, in doing so, create, stabilize or break non-covalent interactions. Molecular dynamics (MD) is a technique used to simulate these movements with atomic resolution. However, given the data-intensive nature of the technique, gathering relevant information from MD simulations is a complex and time consuming process requiring several computational tools to perform these analyses. Among different approaches, the study of residue interaction networks (RINs) has proven to facilitate the study of protein structures. In a RIN, nodes represent amino-acid residues and the connections between them depict non-covalent interactions. Here, we describe residue interaction networks in protein molecular dynamics (RIP-MD), a visual molecular dynamics (VMD) plugin to facilitate the study of RINs using trajectories obtained from MD simulations of proteins. Our software generates RINs from MD trajectory files. The non-covalent interactions defined by RIP-MD include H-bonds, salt bridges, VdWs, cation-π, π–π, Arginine–Arginine, and Coulomb interactions. In addition, RIP-MD also computes interactions based on distances between Cαs and disulfide bridges. The results of the analysis are shown in an user friendly interface. Moreover, the user can take advantage of the VMD visualization capacities, whereby through some effortless steps, it is possible to select and visualize interactions described for a single, several or all residues in a MD trajectory. Network and descriptive table files are also generated, allowing their further study in other specialized platforms. Our method was written in python in a parallelized fashion. This characteristic allows the analysis of large systems impossible to handle otherwise. RIP-MD is available at http://www.dlab.cl/ripmd. creator: Sebastián Contreras-Riquelme creator: Jose-Antonio Garate creator: Tomas Perez-Acle creator: Alberto J.M. Martin uri: https://doi.org/10.7717/peerj.5998 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Contreras-Riquelme et al. title: Bait-attending amphipods of the Tonga Trench and depth-stratified population structure in the scavenging amphipod Hirondellea dubia Dahl, 1959 link: https://peerj.com/articles/5994 last-modified: 2018-12-07 description: BackgroundThe hadal zone encompasses the deepest parts of the world’s ocean trenches from depths of ∼6,000–11,000 m. The communities observed at these depths are dominated by scavenging amphipods that rapidly intercept and consume carrion as it falls to the deepest parts of the trenches. New samples collected in the Tonga Trench provide an opportunity to compare the amphipod assemblages and the population structure of a dominant species, Hirondellea dubiaDahl, 1959, between trenches and with earlier data presented for the Tonga Trench, and other trenches in the South Pacific.MethodsOver 3,600 individual scavenging amphipods across 10 species were collected in seven baited traps at two sites; in the Horizon Deep site, the deepest part of the Tonga Trench (10,800 m) and a site directly up-slope at the trench edge (6,250 m). The composition of the bait-attending amphipods is described and a morphometric analysis of H. dubia examines the bathymetric distribution of the different life stages encountered.ResultsThe amphipod assemblage was more diverse than previously reported, seven species were recorded for the first time from the Tonga Trench. The species diversity was highest at the shallower depth, with H. dubia the only species captured at the deepest site. At the same time, the abundance of amphipods collected at 10,800 m was around sevenfold higher than at the shallower site. H. dubia showed clear ontogenetic vertical structuring, with juveniles dominant at the shallow site and adults dominant at the deep site. The amphipods of the deeper site were always larger at comparable life stage.DiscussionThe numbers of species encountered in the Tonga Trench is less than reported from the New Hebrides and Kermadec trenches, and six species encountered are shared across trenches. These findings support the previous suggestion that the fauna of the New Hebrides, Tonga and Kermadec Trenches may represent a single biogeographic province. The ontogenetic shift in H. dubia between the two Tonga Trench sites supports the hypothesis of interspecific competition at the shallower bathymetric range of the species, and the presence of competitive physiological advantages that allow the adults at the trench axis to exploit the more labile organic material that reaches the bottom of the trench. creator: James P.A. Wilson creator: Kareen E. Schnabel creator: Ashley A. Rowden creator: Rachael A. Peart creator: Hiroshi Kitazato creator: Ken G. Ryan uri: https://doi.org/10.7717/peerj.5994 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Wilson et al. title: Abstract, emotional and concrete concepts and the activation of mouth-hand effectors link: https://peerj.com/articles/5987 last-modified: 2018-12-07 description: According to embodied and grounded theories, concepts are grounded in sensorimotor systems. The majority of evidence supporting these views concerns concepts referring to objects or actions, while evidence on abstract concepts is more scarce. Explaining how abstract concepts such as “freedom” are represented would thus be pivotal for grounded theories. According to some recent proposals, abstract concepts are grounded in both sensorimotor and linguistic experience, thus they activate the mouth motor system more than concrete concepts. Two experiments are reported, aimed at verifying whether abstract, concrete and emotional words activate the mouth and the hand effectors. In both experiments participants performed first a lexical decision, then a recognition task. In Experiment 1 participants responded by pressing a button either with the mouth or with the hand, in Experiment 2 responses were given with the foot, while a button held either in the mouth or in the hand was used to respond to catch-trials. Abstract words were slower to process in both tasks (concreteness effect). Across the tasks and experiments, emotional concepts had instead a fluctuating pattern, different from those of both concrete and abstract concepts, suggesting that they cannot be considered as a subset of abstract concepts. The interaction between type of concept (abstract, concrete and emotional) and effector (mouth, hand) was not significant in the lexical decision task, likely because it emerged only with tasks implying a deeper processing level. It reached significance, instead, in the recognition tasks. In both experiments abstract concepts were facilitated in the mouth condition compared to the hand condition, supporting our main prediction. Emotional concepts instead had a more variable pattern. Overall, our findings indicate that various kinds of concepts differently activate the mouth and hand effectors, but they also suggest that concepts activate effectors in a flexible and task-dependent way. creator: Claudia Mazzuca creator: Luisa Lugli creator: Mariagrazia Benassi creator: Roberto Nicoletti creator: Anna M. Borghi uri: https://doi.org/10.7717/peerj.5987 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Mazzuca et al. title: Comparative cranial morphology of the Late Cretaceous protostegid sea turtle Desmatochelys lowii link: https://peerj.com/articles/5964 last-modified: 2018-12-07 description: BackgroundThe phylogenetic placement of Cretaceous marine turtles, especially Protostegidae, is still under debate among paleontologists. Whereas protostegids were traditionally thought to be situated within the clade of recent marine turtles (Chelonioidea), some recent morphological and molecular studies suggest placement along the stem of Cryptodira. The main reason why the evolution of marine turtles is still poorly understood, is in part due to a lack of insights into the cranial anatomy of protostegids. However, a general availability of high-quality fossil material, combined with modern analysis techniques, such as X-ray microtomography, provide ample opportunity to improve this situation. The scope of this study is to help resolve its phylogenetic relationships by providing a detailed description of the external and internal cranial morphology of the extinct protostegid sea turtle Desmatochelys lowiiWilliston, 1894.Material and MethodsThis study is based on the well-preserved holotype of Desmatochelys lowii from the Late Cretaceous (middle Cenomanian to early Turonian) Greenhorn Limestone of Jefferson County, Nebraska. The skulls of two recent marine turtles, Eretmochelys imbricata (Linnaeus, 1766) (Cheloniidae) and Dermochelys coriaceaLydekker, 1889 (Dermochelyidae), as well as the snapping turtle Chelydra serpentina (Linnaeus, 1758) (Chelydridae) provide a comparative basis. All skulls were scanned using regular or micro CT scanners and the scans were then processed with the software program Amira to create 3D isosurface models. In total, 81 bones are virtually isolated, figured, and described, including the nature of their contacts. The novel bone contact data is compiled and utilized in a preliminary phenetic study. In addition, an update phylogenetic analysis is conduced that utilizes newly obtained anatomical insights.ResultsThe detailed examination of the morphology of the herein used specimens allowed to explore some features of the skull, to refine the scoring of Desmatochelys lowii in the recent global matrix of turtles, and develop five new characters. The alleged pineal foramen in the type skull of Desmatochelys lowii is shown to be the result of damage. Instead, it appears that the pineal gland only approached the skull surface, as it is in Dermochelys coriacea. Whereas the parasphenoid in confirmed to be absent in hard-shelled sea turtles, ist possible presence in Desmatochelys lowii is unclear. The results of the phenetic study show that Desmatochelys lowii is least similar to the other examined taxa in regards to the nature of its bone contacts, and therefore suggests a placement outside Americhelydia for this protostegid sea turtle. The phylogenetic study results in a placement of Protostegidae along the stem of Chelonioidea, which is a novel position for the group. creator: Irena Raselli uri: https://doi.org/10.7717/peerj.5964 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Raselli title: Achieving the impossible: a review of magic-based interventions and their effects on wellbeing link: https://peerj.com/articles/6081 last-modified: 2018-12-06 description: Research has demonstrated that involvement with mainstream performing arts, such as music and dance, can boost wellbeing. This article extends this work by reviewing little-known research on whether learning magic tricks can have an equally beneficial effect. We first present an historic overview of several magic-based interventions created by magicians, psychologists and occupational therapists. We then identify the potential benefits of such interventions, and review studies that have attempted to systematically assess these interventions. The studies have mostly revealed beneficial outcomes, but much of the work is of poor methodological quality (involving small numbers of participants and no control group), and has tended to focus on clinical populations. Finally, we present guidelines for future research in the area, emphasizing the need for more systematic and better-controlled studies. creator: Richard Wiseman creator: Caroline Watt uri: https://doi.org/10.7717/peerj.6081 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Wiseman and Watt title: Bacterial communities in the digester bed and liquid effluent of a microflush composting toilet system link: https://peerj.com/articles/6077 last-modified: 2018-12-06 description: Lack of access to clean water and sanitation is a major factor impacting public health in communities worldwide. To address this, the S-Lab at Providence College and the Global Sustainable Aid Project developed a microflush composting toilet system to isolate and treat human waste. Solid waste is composted within a filter-digester bed via an aerobic process involving microbes and invertebrates. Liquid waste may be sanitized by solar disinfection (SODIS) or slow sand filtration (SSF). Here, we used 16S rRNA amplicon sequencing of samples from a scaled-down test version of the system to better understand the bacterial component of the toilet system. Immediately after fecal matter was deposited in the test system, the bacterial community of the filter-digester bed at the site of deposition resembled that of the human gut at both the phylum and genus level, which was expected. Genus-level analysis of filter-digester bed samples collected over the next 30 days from the site of deposition showed reduced or undetectable levels of fecal-associated taxa, with the exception of Clostridium XI, which persisted at low abundance throughout the sampling period. Starting with the sample collected on day 4, the bacterial community of the filter-digester bed at the site of deposition was dominated by bacterial taxa commonly associated with environmental sources, reflecting a major shift in bacterial community composition. These data support the toilet system’s capacity for processing solid human waste. We also analyzed how SODIS and SSF sanitization methods affected the bacterial community composition of liquid effluent collected on day 15 from the test system. Untreated and treated liquid effluent samples were dominated by Proteobacteria. At the genus level, the bacterial community of the untreated effluent included taxa commonly associated with environmental sources. In the SODIS-treated effluent, these genera increased in abundance, whereas in the SSF-treated effluent, they were greatly reduced or undetectable. By analyzing operational taxonomic units that were unclassified at the genus level, we observed that SSF appears to introduce new taxa into the treated effluent, likely from the biological film of microbes and small animals that constitutes the key element of SSF. These data will inform continued development of liquid waste handling strategies for the toilet system. Using the test system as an indicator of the performance of the full-scale version, we have shown the effectiveness of the microflush composting toilet system for containing and eliminating gut-associated bacteria, thereby improving sanitation and contributing to better public health in rural and peri-urban communities. creator: Laura E. Williams creator: Claire E. Kleinschmidt creator: Stephen Mecca uri: https://doi.org/10.7717/peerj.6077 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Williams et al. title: Modelling of the SDF-1/CXCR4 regulated in vivo homing of therapeutic mesenchymal stem/stromal cells in mice link: https://peerj.com/articles/6072 last-modified: 2018-12-06 description: BackgroundMesenchymal stem/stromal cells (MSCs) are a promising tool for cell-based therapies in the treatment of tissue injury. The stromal cell-derived factor-1 (SDF-1)/CXC chemokine receptor 4 (CXCR4) axis plays a significant role in directing MSC homing to sites of injury. However in vivo MSC distribution following intravenous transplantation remains poorly understood, potentially hampering the precise prediction and evaluation of therapeutic efficacy.MethodsA murine model of partial ischemia/reperfusion (I/R) is used to induce liver injury, increase the hepatic levels of SDF-1, and study in vivo MSC distribution. Hypoxia-preconditioning increases the expression of CXCR4 in human bone marrow-derived MSCs. Quantitative assays for human DNA using droplet digital PCR (ddPCR) allow us to examine the in vivo kinetics of intravenously infused human MSCs in mouse blood and liver. A mathematical model-based system is developed to characterize in vivo homing of human MSCs in mouse models with SDF-1 levels in liver and CXCR4 expression on the transfused MSCs. The model is calibrated to experimental data to provide novel estimates of relevant parameter values.ResultsImages of immunohistochemistry for SDF-1 in the mouse liver with I/R injury show a significantly higher SDF-1 level in the I/R injured liver than that in the control. Correspondingly, the ddPCR results illustrate a higher MSC concentration in the I/R injured liver than the normal liver. CXCR4 is overexpressed in hypoxia-preconditioned MSCs. An increased number of hypoxia-preconditioned MSCs in the I/R injured liver is observed from the ddPCR results. The model simulations align with the experimental data of control and hypoxia-preconditioned human MSC distribution in normal and injured mouse livers, and accurately predict the experimental outcomes with different MSC doses.DiscussionThe modelling results suggest that SDF-1 in organs is an effective in vivo attractant for MSCs through the SDF-1/CXCR4 axis and reveal the significance of the SDF-1/CXCR4 chemotaxis on in vivo homing of MSCs. This in vivo modelling approach allows qualitative characterization and prediction of the MSC homing to normal and injured organs on the basis of clinically accessible variables, such as the MSC dose and SDF-1 concentration in blood. This model could also be adapted to abnormal conditions and/or other types of circulating cells to predict in vivo homing patterns. creator: Wang Jin creator: Xiaowen Liang creator: Anastasia Brooks creator: Kathryn Futrega creator: Xin Liu creator: Michael R. Doran creator: Matthew J. Simpson creator: Michael S. Roberts creator: Haolu Wang uri: https://doi.org/10.7717/peerj.6072 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Jin et al. title: Conservation implications of primate trade in China over 18 years based on web news reports of confiscations link: https://peerj.com/articles/6069 last-modified: 2018-12-06 description: Primate species have been increasingly threatened by legal and illegal trade in China, mainly for biomedical research or as pets and traditional medicine, yet most reports on trade from China regard international trade. To assess a proxy for amount of national primate trades, we quantified the number of reports of native primate species featuring in unique web news reports from 2000 to 2017, including accuracy of their identification, location where they were confiscated or rescued, and their condition upon rescue. To measure temporal trends across these categories, the time span was divided into three sections: 2000–2005, 2006–2011 and 2012–2017. A total of 735 individuals of 14 species were reported in 372 news reports, mostly rhesus macaques (n = 165, 22.5%, Macaca mulatta) and two species of slow lorises (n = 487, 66.3%, Nycticebus spp.). During the same period, live individuals of rhesus macaques were recorded 206 times (70,949 individuals) in the Convention on International Trade in Endangered Species of Wild Fauna and Flora Trade Database, whereas slow lorises were only recorded four times (nine individuals), indicating that the species originated illegally from China or were illegally imported into China. Due to their rescued locations in residential areas (n = 211, 56.7%), most primates appeared to be housed privately as pets. A higher proportion of ‘market’ rescues during 2006–2011 (χ2 = 8.485, df = 2, p = 0.014), could be partly attributed to an intensive management on wildlife markets since the outbreak of severe acute respiratory syndrome (SARS) in 2003. More than half (68.3%, 502 individuals) of the primate individuals were unhealthy, injured or dead when rescued. Thus, identification and welfare training and capacity-building should be provided to husbandry and veterinary professionals, as well as education to the public through awareness initiatives. The increase in presence of some species, especially slow lorises, with a declining population in restricted areas, also suggests the urgent need for public awareness about the illegal nature of keeping these taxa as pets. creator: Qingyong Ni creator: Yu Wang creator: Ariana Weldon creator: Meng Xie creator: Huailiang Xu creator: Yongfang Yao creator: Mingwang Zhang creator: Ying Li creator: Yan Li creator: Bo Zeng creator: K.A.I. Nekaris uri: https://doi.org/10.7717/peerj.6069 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Ni et al. title: Association of urinary activity of MMP-9 with renal impairment in Mexican patients with type 2 diabetes mellitus link: https://peerj.com/articles/6067 last-modified: 2018-12-06 description: BackgroundDiabetic kidney disease is the most common cause of chronic kidney disease (CKD). An early event in diabetic kidney disease is alteration of the glomerular basement membrane and the mesangial expansion. Matrix metalloproteinases (MMP) are a family of endopeptidases responsible for controlling the pathophysiological remodeling of tissues, including renal tissues. MMP-9 in human urine has been proposed as a marker of diabetic nephropathy and urinary tract infections (UTI).MethodsA cross-sectional study was conducted in type 2 diabetes mellitus (T2DM) patients who receive first level medical attention in Mexico. We used ELISA to measure MMP-9 levels in the urine of subjects with T2DM ≥ 18 years of age, who fulfilled the clinical requirements for calculation of glomerular filtration rate (GFR), according to the K/DOQI guide, in an attempt to identify whether MMP-9 levels in T2DM differ in patients with and without renal impairment. Univariate and multivariable analyses were performed in order to identify the association between MMP-9 and renal impairment.ResultsIncluded in the study were 34 (45%) subjects with renal impairment and 42 (55%) without. In the group with renal impairment, 10 subjects corresponded to stages 1–2 and 24 subjects corresponded to stage 3, according to their values of GFR and urinary albumin, following that proposed by the K/DOQI. No differences were found relating to sex, age, having or not having a partner, education, being able to read and write a message and duration of T2DM. Moreover, no differences were found between the groups in terms of weight, height, body mass index, waist size in general and frequency of UTI. In contrast, serum creatinine and urinary albumin were higher in the group with renal impairment, while GFR was greater in the group without renal impairment. Levels of MMP-9 were greater in women compared to men. Through univariate analysis in the general population, the presence of MMP-9 and that of its percentile 90 (P90) P90 were associated with the renal impairment group; however, in patients without UTI, only the presence of MMP-9 was associated with the renal impairment group, and no association was found with its P90. Multivariate analysis revealed an association between MMP-9 and its P90 with renal impairment.DiscussionIt is necessary to validate sensitive and non-invasive biological markers of CKD. We demonstrate that the presence and P90 of urinary MMP-9 are associated with renal impairment in Mexican patients with T2DM. While high levels of MMP-9 were associated to females and UTI, the presence of UTI was not associated with the incidence of renal impairment. creator: Alan Uriel García-Tejeda creator: Clara Luz Sampieri creator: Irene Suárez-Torres creator: Jaime Morales-Romero creator: Verónica Patricia Demeneghi-Marini creator: Magda Elena Hernández-Hernández creator: Arturo Rodríguez-Hernández uri: https://doi.org/10.7717/peerj.6067 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 García-Tejeda et al. title: Development and internal validation of a nine-lncRNA prognostic signature for prediction of overall survival in colorectal cancer patients link: https://peerj.com/articles/6061 last-modified: 2018-12-06 description: BackgroundColorectal cancer remains a serious public health problem due to the poor prognosis. In the present study, we attempted to develop and validate a prognostic signature to predict the individual mortality risk in colorectal cancer patients.Materials and MethodsThe original study datasets were downloaded from The Cancer Genome Atlas database. The present study finally included 424 colorectal cancer patients with wholly gene expression information and overall survival information.ResultsA nine-lncRNA prognostic signature was built through univariate and multivariate Cox proportional regression model. Time-dependent receiver operating characteristic curves in model cohort demonstrated that the Harrell’s concordance indexes of nine-lncRNA prognostic signature were 0.768 (95% CI [0.717–0.819]), 0.778 (95% CI [0.727–0.829]) and 0.870 (95% CI [0.819–0.921]) for 1-year, 3-year and 5-year overall survival respectively. In validation cohort, the Harrell’s concordance indexes of nine-lncRNA prognostic signature were 0.761 (95% CI [0.710–0.812]), 0.801 (95% CI [0.750–0.852]) and 0.883 (95% CI [0.832–0.934]) for 1-year, 3-year and 5-year overall survival respectively. According to the median of nine-lncRNA prognostic signature score in model cohort, 424 CRC patients could be stratified into high risk group (n = 212) and low risk group (n = 212). Kaplan–Meier survival curves showed that the overall survival rate of high risk group was significantly lower than that of low risk group (P < 0.001).DiscussionThe present study developed and validated a nine-lncRNA prognostic signature for individual mortality risk assessment in colorectal cancer patients. This nine-lncRNA prognostic signature is helpful to evaluate the individual mortality risk and to improve the decision making of individualized treatments in colorectal cancer patients. creator: Zhiqiao Zhang creator: Qingbo Liu creator: Peng Wang creator: Jing Li creator: Tingshan He creator: Yanling Ouyang creator: Yiyan Huang creator: Weidong Wang uri: https://doi.org/10.7717/peerj.6061 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Zhang et al. title: Diversity of social-genetic relationships in the socially monogamous pied flycatcher (Ficedula hypoleuca) breeding in Western Siberia link: https://peerj.com/articles/6059 last-modified: 2018-12-06 description: We explored the genetic background of social interactions in two breeding metapopulations of the pied flycatcher (Ficedula hypoleuca) in Western Siberia. In 2005, we sampled blood from birds breeding in study areas located in the city of Tomsk and in a natural forest 13 km southward of Tomsk (Western Siberia, Russia). We sampled 30 males, 46 females, 268 nestlings (46 nests) in the urban settlement of pied flycatcher, and 232 males, 250 females, 1,485 nestlings (250 nests) in the woodland plot. DNA fingerprinting was carried out using eight microsatellite loci, which were amplified by two multiplex-PCRs and analyzed by capillary electrophoresis. About 50–58% of all couples were socially and genetically monogamous in both study plots. However, almost all possible social and genetic interactions were detected for non-monogamous couples: polygamy, polyandry, helping, adoption, and egg dumping. Differences in the rate of polygyny and the rate of extra-pair paternity between both study sites could be explained by differences in environmental heterogeneity and breeding density. Our findings suggest that egg dumping, adoption, polygamy, extra pair copulation, and other types of social-genetic interactions are modifications of the monogamous social system caused by patchy environment, breeding density, and birds’ breeding status. creator: Vladimir G. Grinkov creator: Andreas Bauer creator: Sergey I. Gashkov creator: Helmut Sternberg creator: Michael Wink uri: https://doi.org/10.7717/peerj.6059 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Grinkov et al. title: Urbanization, environmental stabilization and temporal persistence of bird species: a view from Latin America link: https://peerj.com/articles/6056 last-modified: 2018-12-06 description: BackgroundA scarcely studied consequence of urbanization is the effect of temporal stabilization of the environment on bird communities. This alteration is thought to dampen environmental variations between day and night, seasons and years, promoting a temporal persistence of bird composition in urban areas. The aim of this study was to review current evidence of temporal stabilization of biotic and abiotic factors in urban environments and the potential effects of such stabilization on temporal variation of bird species presence at different temporal scales.MethodsI selected the literature by searching published articles and book chapters using Scopus and Google scholar. I only included articles that compared the temporal variation of bird composition or resources between different levels of urbanization.ResultsIn general, there is evidence of temporal stabilization of abiotic and biotic factors at the three time scales considered. At the diurnal scale, the main factor considered was artificial light in the context of light pollution. At the seasonal and interannual scales, several case studies found a smaller temporal variation of primary productivity in urban than in natural and rural areas. Bird species composition showed more stabilization in urban environments at the three temporal scales: (1) several case studies reported bird activity at night, associated with artificial light; (2) studies in urban parks and along urbanization gradients showed smaller seasonal variation of bird composition in the more urbanized areas; and (3) in general, case studies along urbanization gradients showed smaller interannual variation of bird composition in the more urbanized areas, although some studies showed no relationships or opposite trends than expected.DiscussionThe published evidence suggests that urban areas dampen the natural cycles at several temporal scales. The stabilization of biotic and abiotic factors, such as light, temperature, food and habitat structure, is desynchronized from natural diurnal, seasonal and interannual cycles. However, there is a dearth of long-term comparisons of bird composition and studies that simultaneously analyze the relationship between resources and bird composition stabilization at the seasonal and interannual scales. More research is needed in the Southern hemisphere, where there is a lack of studies dealing with the seasonal and interannual variations of primary productivity along urbanization gradients and nocturnal activity of bird species. A future research agenda should include differentiation of spatial and temporal homogenization of avifaunas. creator: Lucas Matías Leveau uri: https://doi.org/10.7717/peerj.6056 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Leveau title: JacLy: a Jacobian-based method for the inference of metabolic interactions from the covariance of steady-state metabolome data link: https://peerj.com/articles/6034 last-modified: 2018-12-06 description: Reverse engineering metabolome data to infer metabolic interactions is a challenging research topic. Here we introduce JacLy, a Jacobian-based method to infer metabolic interactions of small networks (<20 metabolites) from the covariance of steady-state metabolome data. The approach was applied to two different in silico small-scale metabolome datasets. The power of JacLy lies on the use of steady-state metabolome data to predict the Jacobian matrix of the system, which is a source of information on structure and dynamic characteristics of the system. Besides its advantage of inferring directed interactions, its superiority over correlation-based network inference was especially clear in terms of the required number of replicates and the effect of the use of priori knowledge in the inference. Additionally, we showed the use of standard deviation of the replicate data as a suitable approximation for the magnitudes of metabolite fluctuations inherent in the system. creator: Mohammad Jafar Khatibipour creator: Furkan Kurtoğlu creator: Tunahan Çakır uri: https://doi.org/10.7717/peerj.6034 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Khatibipour et al. title: An integrative taxonomic approach reveals Octopus insularis as the dominant species in the Veracruz Reef System (southwestern Gulf of Mexico) link: https://peerj.com/articles/6015 last-modified: 2018-12-06 description: The common octopus of the Veracruz Reef System (VRS, southwestern Gulf of Mexico) has historically been considered as Octopus vulgaris, and yet, to date, no study including both morphological and genetic data has tested that assumption. To assess this matter, 52 octopuses were sampled in different reefs within the VRS to determine the taxonomic identity of this commercially valuable species using an integrative taxonomic approach through both morphological and genetic analyses. Morphological and genetic data confirmed that the common octopus of the VRS is not O. vulgaris and determined that it is, in fact, the recently described O. insularis. Morphological measurements, counts, indices, and other characteristics such as specific colour patterns, closely matched what had been reported for O. insularis in Brazil. In addition, sequences from cytochrome oxidase I (COI) and 16S ribosomal RNA (r16S) mitochondrial genes confirmed that the common octopus from the VRS is in the same highly supported clade as O. insularis from Brazil. Genetic distances of both mitochondrial genes as well as of cytochrome oxidase subunit III (COIII) and novel nuclear rhodopsin sequences for the species, also confirmed this finding (0–0.8%). We discuss our findings in the light of the recent reports of octopus species misidentifications involving the members of the ‘O. vulgaris species complex’ and underscore the need for more morphological studies regarding this group to properly address the management of these commercially valuable and similar taxa. creator: Roberto González-Gómez creator: Irene de los Angeles Barriga-Sosa creator: Ricardo Pliego-Cárdenas creator: Lourdes Jiménez-Badillo creator: Unai Markaida creator: César Meiners-Mandujano creator: Piedad S. Morillo-Velarde uri: https://doi.org/10.7717/peerj.6015 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 González-Gómez et al. title: Genetic analysis reveals Finnish Formica fennica populations do not form a separate genetic entity from F. exsecta link: https://peerj.com/articles/6013 last-modified: 2018-12-06 description: Coptoformica Müller, 1923 is a subgenus of Formica Linnaeus, 1758 that consists of c. a dozen species of ants that typically inhabit open grassy habitats and build small nest mounds. The most recent addition to the group is Formica fennica Seifert, 2000. The description was based on morphological characters, but the species status has not been confirmed by molecular methods. In this study, we use thirteen DNA microsatellite markers and a partial mitochondrial COI gene sequence to assess the species status of F. fennica, by comparing the genetic variation among samples identified as F. fennica and six other boreal Formica (Coptoformica) species. Most of the species studied form separate, discontinuous clusters in phylogenetic and spatial analyses with only little intraspecific genetic variation. However, both nuclear and mitochondrial markers fail to separate the species pair F. exsecta Nylander, 1846 and F. fennica despite established morphological differences. The genetic variation within the F. exsecta/fennica group is extensive, but reflects spatial rather than morphological differences. Finnish F. fennica populations studied so far should not be considered a separate species, but merely a morph of F. exsecta. creator: Sanja Maria Hakala creator: Perttu Seppä creator: Maria Heikkilä creator: Pekka Punttila creator: Jouni Sorvari creator: Heikki Helanterä uri: https://doi.org/10.7717/peerj.6013 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Hakala et al. title: From morphology to molecules: a combined source approach to untangle the taxonomy of Clessinia (Gastropoda, Odontostomidae), endemic land snails from the Dry Chaco ecoregion link: https://peerj.com/articles/5986 last-modified: 2018-12-06 description: BackgroundLand gastropods of the Dry Chaco merit special attention because they comprise a highly diverse but barely studied group. Clessinia Doering, 1875 are typical inhabitants of this ecoregion. The inclusion of their distribution areas into Spixia range, their shell shape similarities, and a former molecular study raised doubts on the monophyly of this genus. The present study review the species of Clessinia, under a morphological, geometric morphometrics, and molecular combined approach.MethodsAdults were collected, photographed, measured, and dissected for anatomical studies. Shell ultrastructure was studied with scanning electron microscope. Geometric morphometric analyses on shells were performed testing if they gave complementary information to anatomy. Two mitochondrial genes, and a nuclear region were studied. Phylogenetic reconstructions to explore the relationships of DNA sequences here obtained to those of Clessinia and Spixia species from GenBank were performed.ResultsSpecies description on shell, periostracal ornamentation and anatomy is provided. We raised former Clessinia cordovana striata to species rank, naming it as Clessinia tulumbensis sp. nov. The periostracum, consisting of hairs and lamellae, has taxonomic importance for species identification. Shell morphometric analyses, inner sculpture of penis and proportion of the epiphallus and penis, were useful tools to species identification. Nuclear markers do not exhibit enough genetic variation to determine species relationships. Based on the mitochondrial markers, genetic distances among Clessinia species were greater than 10%, and while C. cordovana, C. nattkemperi, and C. pagoda were recognized as distinct evolutionary genetic species, the distinction between C. stelzneri and C. tulumbensis sp. nov. was not evident. Clessinia and Spixia were paraphyletic in the molecular phylogenetic analyses. Species of Clessinia here treated have narrow distributional areas and are endemic to the Chaco Serrano subecoregion, restricted to small patches within the Dry Chaco. Clessinia and Spixia are synonymous, and the valid name of the taxon should be Clessinia Doering, 1875 which has priority over Spixia Pilsbry & Vanatta, 1894.DiscussionOur results support the composition of C. cordovana complex by three species, C. cordovana, C. stelzneri, and C. tulumbensis sp. nov. The low genetic divergence between C. stelzneri and C. tulumbensis sp. nov. suggests that they have evolved relatively recently. The former Spixia and Clessinia are externally distinguished because Clessinia has a detached aperture from the body whorl forming a cornet, periostracal microsculpture extended over dorsal portion of the peristome, five inner teeth on the shell aperture instead of three–four found in Spixia. Morphological similarities exists between both genera in shell shape, type of periostracum microsculpture, reproductive anatomy, besides the overlap in geographic ranges. creator: Maria Gabriela Cuezzo creator: Maria Jose Miranda creator: Roberto Eugenio Vogler creator: Ariel Anibal Beltramino uri: https://doi.org/10.7717/peerj.5986 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Cuezzo et al. title: Density-dependent changes in the distribution of Southern Right Whales (Eubalaena australis) in the breeding ground Peninsula Valdés link: https://peerj.com/articles/5957 last-modified: 2018-12-06 description: BackgroundThe Southern Right Whale (Eubalaena australis) population of the South–western Atlantic Ocean is recovering. In the breeding ground of Peninsula Valdés, as a consequence of the population growth, expansion to new areas by some types of groups and a change in the habitat use patterns at the coastal area were recorded.MethodsWe analysed information gathered from aerial surveys conducted along the coast of Peninsula Valdés in 15 years of effective sampling in a 19-year span. These surveys were divided into four periods (1999–2000; 2004–2007; 2008–2012 and 2013–2016) and estimated the density of whales in a 620 km of coast divided into segments of five km.ResultsThe density of the whales increased to near three whales per km2 (averaged over each period) in the high-density areas. When this mean number was reached, the significant changes in density in the adjacent areas were detected in the following period. These changes were a decrease in density in the high-density areas and an increase of density in the low-density areas.DiscussionWe propose that a threshold in density elicits a response in habitat use, with the Mother-calf pairs remaining in the area, while the other groups are displaced to new areas. creator: Nicolas Sueyro creator: Enrique Alberto Crespo creator: Magdalena Arias creator: Mariano Alberto Coscarella uri: https://doi.org/10.7717/peerj.5957 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Sueyro et al. title: Micro-remediation of chromium contaminated soils link: https://peerj.com/articles/6076 last-modified: 2018-12-05 description: Bacteria are tiny organisms which are ubiquitously found in the environment. These microscopic living bodies are responsible for the flow of nutrients in biogeochemical cycles and fertility imparted to the soil. Release of excessive chromium in agricultural soils due to rapid growth of industries may result in minimizing the fertility of soil in future, which will lead to reduction in crop production. Plant growth promoting bacteria (PGPB) are beneficial to the environment, some of which can tolerate chromium and protect plants against heavy metal stress. The current study aims to identify such chromium-tolerant auxin-producing rhizobacteria and to investigate their inoculation effects on the growth characteristics of Lens culinaris in chromium polluted soils by using two different chromium salts i.e., K2Cr2O7 and K2CrO4 in varying concentrations (0, 50, 100, 200, 400 and 500 µgml−1). The results revealed that Bacillus species are efficient in significantly reducing the deleterious effects of Cr. These effective bacterial strains were able to stimulate the growth of metal effected plants of Lens culinaris which were grown in chromium contaminated environment. Therefore, these plant growth promoting rhizobacteria PGPRs, having both auxin production potential and chromium-resistance ability, are considered as efficient micro-factories against chromium pollution. creator: Hadia -e- Fatima creator: Ambreen Ahmed uri: https://doi.org/10.7717/peerj.6076 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Fatima and Ahmed title: Importance of biotic predictors in estimation of potential invasive areas: the example of the tortoise beetle Eurypedus nigrosignatus, in Hispaniola link: https://peerj.com/articles/6052 last-modified: 2018-12-05 description: Climatic variables have been the main predictors employed in ecological niche modeling and species distribution modeling, although biotic interactions are known to affect species’ spatial distributions via mechanisms such as predation, competition, and mutualism. Biotic interactions can affect species’ responses to abiotic environmental changes differently along environmental gradients, and abiotic environmental changes can likewise influence the nature of biotic interactions. Understanding whether and how to integrate variables at different scales in ecological niche models is essential to better estimate spatial distributions of species on macroecological scales and their responses to change. We report the leaf beetle Eurypedus nigrosignatus as an alien species in the Dominican Republic and investigate whether biotic factors played a meaningful role in the distributional expansion of the species into the Caribbean. We evaluate ecological niche models built with an additive gradient of unlinked biotic predictors—host plants, using likelihood-based model evaluation criteria (Akaike information criterion and Bayesian information criterion) within a range of regularization multiplier parameter values. Our results support the argument that ecological niche models should be more inclusive, as selected biotic predictors can improve the performance of models, despite the increased model complexity, and show that biotic interactions matter at macroecological scales. Moreover, we provide an alternative approach to select optimal combination of relevant variables, to improve estimation of potential invasive areas using global minimum model likelihood scores. creator: Marianna V.P. Simões creator: A. Townsend Peterson uri: https://doi.org/10.7717/peerj.6052 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Simões and Peterson title: Simultaneous preservation of the DNA quality, the community composition and the density of freshwater oligochaetes for the development of genetically based biological indices link: https://peerj.com/articles/6050 last-modified: 2018-12-05 description: IntroductionOligochaetes are recognized as valuable bioindicators of sediment quality in streams and lakes. The development of an oligochaete index based on the identification of specimens using DNA barcodes requires a method for simultaneously preserving the DNA quality and information on the specimen density and oligochaete community composition. Absolute ethanol optimally preserves DNA but fixation of freshwater oligochaetes with this medium can cause disintegration and fragmentation of specimens. Here, we investigated the possibility to preserve oligochaete specimens in low-pH formalin and in neutral buffered formalin for up to four weeks before genetic analyses and tested if the addition of absolute ethanol to formalin-fixed oligochaetes resulted in a loss of specimens and/or species.MethodsWe performed guanidine extraction and polymerase chain reaction (PCR) amplification/sequencing of a fragment of the cytochrome c oxidase I (COI) gene on tissue fragments preserved in low-pH formalin for up to 3 weeks and in neutral buffered formalin for up to 4 weeks. In addition, we compared the density and taxonomic composition of formalin-fixed oligochaetes of several sieved sediment samples before and after the addition of absolute ethanol.ResultsThe COI fragment of all oligochaete specimens preserved in neutral buffered formalin for up to 28 days was successfully amplified by PCR and obtained sequences were complete and of high quality. The amplification success rate for low-pH formalin fixed specimens declined after 7 days of storage. The addition of absolute ethanol to formalin-fixed oligochaete communities did not alter density or diversity estimates.DiscussionOur results indicate that sediment samples can be stored in neutral buffered formalin for up to 4 weeks and the sieved material can then be transferred to absolute ethanol, without affecting DNA quality, density and community composition of oligochaetes. Based on these results, a protocol for preserving freshwater oligochaetes, describing all the steps from collection of sediments to preservation of the biological material in absolute ethanol, is proposed. This method of fixation/preservation is of relevance for establishing DNA barcode reference databases, inventories of genetic diversity and developing genetically based biological indices. creator: Régis Vivien creator: Inge Werner creator: Benoit J.D. Ferrari uri: https://doi.org/10.7717/peerj.6050 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Vivien et al. title: Bacterial diversity and community in Qula from the Qinghai–Tibetan Plateau in China link: https://peerj.com/articles/6044 last-modified: 2018-12-05 description: Qula is a cheese-like product usually prepared with unpasteurized yak milk under open conditions, with both endogenous and exogenous microorganisms involved in the fermentation process. In the present study, 15 Qula samples were collected from five different regions in China to investigate the diversity of microbial communities using high-throughput sequencing targeting the V3–V4 region of 16S rRNA gene. The bacterial diversity significantly differed among samples of different origins, indicating a possible effect of geography. The result also showed that microbial communities significantly differed in samples of different origin and these differences were greater at the genus than the phylum level. A total of six phyla were identified in the samples, and Firmicutes and Proteobacteria had a relative abundance >20%. A total of 73 bacterial genera were identified in the samples. Two dominant genera (Lactobacillus and Acetobacter) were common to all samples, and a total of 47 operational taxonomic units at different levels significantly differed between samples of different origin. The predicted functional genes of the bacteria present in samples also indicated differences in bacterial communities between the samples of different origin. The network analysis showed that microbial interactions between bacterial communities in Qula were very complex. This study lays a foundation for further investigations into its food ecology. creator: Yan Zhu creator: Yingying Cao creator: Min Yang creator: Pengchen Wen creator: Lei Cao creator: Jiang Ma creator: Zhongmin Zhang creator: Weibing Zhang uri: https://doi.org/10.7717/peerj.6044 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Zhu et al. title: Drivers and assemblies of soil eukaryotic microbes among different soil habitat types in a semi-arid mountain in China link: https://peerj.com/articles/6042 last-modified: 2018-12-05 description: The effects of environmental and species structure on soil eukaryotic microbes inhabiting semi-arid mountains remain unclear. Furthermore, whether community assembly differs in a variety of soil habitat types, for example, artificial forest, artificial bush, farmland, and natural grassland, is not well understood. Here, we explored species diversity and composition of soil eukaryotic microbes south of the Taihang Mountains (mid-western region of China) using Illumina sequencing of the 18S rRNA gene (V4) region on the MiSeq platform. The results suggest that the forest soil habitat type improved the diversity and abundance of soil eukaryotic microbes that will benefit the restoration of degraded soil. The SAR (Stramenopiles, Alveolates, Rhizaria) supergroup and Metazoa were the dominant soil eukaryotic microbial groups at the phylum level. About 26% of all operational taxonomic units were common among the different soil habitat types. The O-elements, water content, soil organic matter, and elevation significantly influenced the abundance of soil eukaryote communities (P < 0.05). Our findings provide some reference for the effectiveness of local ecological restoration and the establishment of a soil eukaryotic microbe resource databases in a semi-arid area. creator: He Zhao creator: Xuanzhen Li creator: Zhiming Zhang creator: Yong Zhao creator: Peng Chen creator: Yiwei Zhu uri: https://doi.org/10.7717/peerj.6042 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Zhao et al. title: Aberrant repair initiated by the adenine-DNA glycosylase does not play a role in UV-induced mutagenesis in Escherichia coli link: https://peerj.com/articles/6029 last-modified: 2018-12-05 description: BackgroundDNA repair is essential to counteract damage to DNA induced by endo- and exogenous factors, to maintain genome stability. However, challenges to the faithful discrimination between damaged and non-damaged DNA strands do exist, such as mismatched pairs between two regular bases resulting from spontaneous deamination of 5-methylcytosine or DNA polymerase errors during replication. To counteract these mutagenic threats to genome stability, cells evolved the mismatch-specific DNA glycosylases that can recognize and remove regular DNA bases in the mismatched DNA duplexes. The Escherichia coli adenine-DNA glycosylase (MutY/MicA) protects cells against oxidative stress-induced mutagenesis by removing adenine which is mispaired with 7,8-dihydro-8-oxoguanine (8oxoG) in the base excision repair pathway. However, MutY does not discriminate between template and newly synthesized DNA strands. Therefore the ability to remove A from 8oxoG•A mispair, which is generated via misincorporation of an 8-oxo-2′-deoxyguanosine-5′-triphosphate precursor during DNA replication and in which A is the template base, can induce A•T→C•G transversions. Furthermore, it has been demonstrated that human MUTYH, homologous to the bacterial MutY, might be involved in the aberrant processing of ultraviolet (UV) induced DNA damage.MethodsHere, we investigated the role of MutY in UV-induced mutagenesis in E. coli. MutY was probed on DNA duplexes containing cyclobutane pyrimidine dimers (CPD) and pyrimidine (6–4) pyrimidone photoproduct (6–4PP). UV irradiation of E. coli induces Save Our Souls (SOS) response characterized by increased production of DNA repair enzymes and mutagenesis. To study the role of MutY in vivo, the mutation frequencies to rifampicin-resistant (RifR) after UV irradiation of wild type and mutant E. coli strains were measured.ResultsWe demonstrated that MutY does not excise Adenine when it is paired with CPD and 6–4PP adducts in duplex DNA. At the same time, MutY excises Adenine in A•G and A•8oxoG mispairs. Interestingly, E. coli mutY strains, which have elevated spontaneous mutation rate, exhibited low mutational induction after UV exposure as compared to MutY-proficient strains. However, sequence analysis of RifR mutants revealed that the frequencies of C→T transitions dramatically increased after UV irradiation in both MutY-proficient and -deficient E. coli strains.DiscussionThese findings indicate that the bacterial MutY is not involved in the aberrant DNA repair of UV-induced DNA damage. creator: Caroline Zutterling creator: Aibek Mursalimov creator: Ibtissam Talhaoui creator: Zhanat Koshenov creator: Zhiger Akishev creator: Amangeldy K. Bissenbaev creator: Gerard Mazon creator: Nicolas E. Geacintov creator: Didier Gasparutto creator: Regina Groisman creator: Dmitry O. Zharkov creator: Bakhyt T. Matkarimov creator: Murat Saparbaev uri: https://doi.org/10.7717/peerj.6029 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Zutterling et al. title: Association between dry eye disease and asthma: a nationwide population-based study link: https://peerj.com/articles/5941 last-modified: 2018-12-05 description: BackgroundDry eye disease (DED), a chronic ocular disease, is associated with numerous medical issues, including asthma. However, studies on these associations are limited. In this study, we investigated the incidence of DED among patients with asthma and its correlation with other allergic comorbidities.MethodsWe retrospectively analyzed data from the National Health Insurance Research Database of Taiwan. We compared the data of 41,229 patients with asthma with those of 164,916 sex- and age-matched non-asthma controls. We followed up the patient and control groups from 1998 to 2010, and compared the rate of DED in these two groups. We further analyzed the allergic comorbidities and asthma-related medication use among the patients with asthma to verify whether these factors were associated with DED.ResultsThe patients in the asthma group were more likely to have DED than were the controls (6.35% vs. 4.92%, p < 0.0001). In the asthma group, female had a higher risk of DED (odds ratio (OR) = 1.70, 95% confidence interval (CI) [1.57–1.85]) than males did. After adjustment for sex, age, income, urbanization, and the other two allergic comorbidities, patients with allergic rhinitis (adjusted OR = 1.58, 95% CI [1.46–1.72]) and urticaria (adjusted OR = 1.25, 95% CI [1.12–1.38]) were more likely to have DED, but not patients with atopic dermatitis (adjusted OR = 1.17, 95% CI [0.98–1.40]). Patients with asthma who had prescriptions of leukotriene receptor antagonists (LTRAs) (adjusted OR = 1.29, 95% CI [1.01–1.64]), oral antihistamines (adjusted OR = 2.02, 95% CI [1.84–2.21]), and inhaled corticosteroids (adjusted OR = 1.19, 95% CI [1.04–1.36]) exhibited association with DED.DiscussionOur findings reveal that patients with asthma—particularly females—were more likely to have DED, with comorbidities such as allergic rhinitis and urticaria, and prescriptions including LTRAs, antihistamines, and inhaled corticosteroids. The results suggest that in clinical practice, physicians should pay attention to DED, particularly in patients with a high risk of DED. creator: Yung-Chieh Huang creator: Wei-Cheng Chan creator: Jiaan-Der Wang creator: Lin-Shien Fu creator: Yu-Tse Tsan uri: https://doi.org/10.7717/peerj.5941 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Huang et al. title: An experimental comparison of composite and grab sampling of stream water for metagenetic analysis of environmental DNA link: https://peerj.com/articles/5871 last-modified: 2018-12-05 description: Use of environmental DNA (eDNA) to assess distributions of aquatic and semi-aquatic macroorganisms is promising, but sampling schemes may need to be tailored to specific objectives. Given the potentially high variance in aquatic eDNA among replicate grab samples, compositing smaller water volumes collected over a period of time may be more effective for some applications. In this study, we compared eDNA profiles from composite water samples aggregated over three hours with grab water samples. Both sampling patterns were performed with identical autosamplers paired at two different sites in a headwater stream environment, augmented with exogenous fish eDNA from an upstream rearing facility. Samples were filtered through 0.8 μm cellulose nitrate filters and DNA was extracted with a cetyl trimethylammonium bromide procedure. Eukaryotic and bacterial community profiles were derived by amplicon sequencing of 12S ribosomal, 16S ribosomal, and cytochrome oxidase I loci. Operational taxa were assigned to genus with a lowest common ancestor approach for eukaryotes and to family with the RDP Classifier software for prokaryotes. Eukaryotic community profiles were more consistent with composite sampling than grab sampling. Downstream, rarefaction curves suggested faster taxon accumulation for composite samples, and estimated richness was higher for composite samples as a set than for grab samples. Upstream, composite sampling produced lower estimated richness than grab samples, but with overlapping standard errors. Furthermore, a bimodal pattern of richness as a function of sequence counts suggested the impact of clumped particles on upstream samples. Bacterial profiles were insensitive to sample method, consistent with the more even dispersion expected for bacteria compared with eukaryotic eDNA. Overall, samples composited over 3 h performed equal to or better than triplicate grab sampling for quantitative community metrics, despite the higher total sequencing effort provided to grab replicates. On the other hand, taxon-specific detection rates did not differ appreciably and the two methods gave similar estimates of the ratio of the common fish genera Salmo and Coregonus at each site. Unexpectedly, Salmo eDNA dropped out substantially faster than Coregonus eDNA between the two sites regardless of sampling method, suggesting that differential settling affects the estimation of relative abundance. We identified bacterial patterns that were associated with eukaryotic diversity, suggesting potential roles as biomarkers of sample representativeness. creator: Robert S. Cornman creator: James E. McKenna creator: Jennifer Fike creator: Sara J. Oyler-McCance creator: Robin Johnson uri: https://doi.org/10.7717/peerj.5871 license: http://creativecommons.org/publicdomain/zero/1.0/ rights: title: Ornithopod diversity in the Griman Creek Formation (Cenomanian), New South Wales, Australia link: https://peerj.com/articles/6008 last-modified: 2018-12-04 description: During the Early Cretaceous, dinosaur communities of the Australian-Antarctic rift system (Eumeralla and Wonthaggi formations) cropping out in Victoria were apparently dominated by a diverse small-bodied ‘basal ornithopod’ fauna. Further north, in Queensland (Winton and Mackunda formations), poorly-represented small-bodied ornithopods coexisted with large-bodied iguanodontians. Our understanding of the ornithopod diversity from the region between the Australian-Antarctic rift and Queensland, represented by Lightning Ridge in central-northern New South Wales (Griman Creek Formation), has been superficial. Here, we re-investigate the ornithopod diversity at Lightning Ridge based on new craniodental remains. Our findings indicate a diverse ornithopod fauna consisting of two-to-three small-bodied non-iguanodontian ornithopods (including Weewarrasaurus pobeni gen. et sp. nov.), at least one indeterminate iguanodontian, and a possible ankylopollexian. These results support those of previous studies that favour a general abundance of small-bodied basal ornithopods in Early to mid-Cretaceous high-latitude localities of southeastern Australia. Although these localities are not necessarily time-equivalent, increasing evidence indicates that Lightning Ridge formed a ‘meeting point’ between the basal ornithopod-dominated localities in Victoria and the sauropod-iguanodontian faunas in Queensland to the north. creator: Phil R. Bell creator: Matthew C. Herne creator: Sienna A. Birch creator: Elizabeth T. Smith uri: https://doi.org/10.7717/peerj.6008 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Bell et al. title: COI barcoding of plant bugs (Insecta: Hemiptera: Miridae) link: https://peerj.com/articles/6070 last-modified: 2018-12-04 description: The family Miridae is the most diverse and one of the most economically important groups in Heteroptera. However, identification of mirid species on the basis of morphology is difficult and time-consuming. In the present study, we evaluated the effectiveness of COI barcoding for 123 species of plant bugs in seven subfamilies. With the exception of three Apolygus species—A. lucorum, A. spinolae, and A. watajii (subfamily Mirinae)—each of the investigated species possessed a unique COI sequence. The average minimum interspecific genetic distance of congeners was approximately 37 times higher than the average maximum intraspecific genetic distance, indicating a significant barcoding gap. Despite having distinct morphological characters, A. lucorum, A. spinolae, and A. watajii mixed and clustered together, suggesting taxonomic revision. Our findings indicate that COI barcoding represents a valuable identification tool for Miridae and can be economically viable in a variety of scientific research fields. creator: Junggon Kim creator: Sunghoon Jung uri: https://doi.org/10.7717/peerj.6070 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Kim and Jung title: Mesquite bugs, other insects, and a bat in the diet of pallid bats in southeastern Arizona link: https://peerj.com/articles/6065 last-modified: 2018-12-04 description: The pallid bat (Antrozous pallidus) is a species of western North America, inhabiting ecoregions ranging from desert to oak and pine forest. They are primarily insectivorous predators on large arthropods that occasionally take small vertebrate prey, and are at least seasonally omnivorous in certain parts of their geographic range where they take nectar from cactus flowers and eat cactus fruit pulp and seeds. Until recently, mesquite bugs were primarily tropical-subtropical inhabitants of Mexico and Central America but have since occupied the southwestern United States where mesquite trees occur. Using a noninvasive method, we investigated the bats’ diet at the Cienega Creek Natural Preserve, Arizona, by collecting food parts discarded beneath three night roosts in soil-piping cavities in a mesquite bosque. We also made phenological and behavioral observations of mesquite bugs, Thasus neocalifornicus, and their interactions with the mesquite trees. We determined that the bats discarded inedible parts of 36 species in 8 orders of mainly large-bodied and nocturnal insects below the night-roosts. In addition, one partial bat wing represents probable predation upon a phyllostomid bat, Choeronycteris mexicana. About 17 of the insect taxa are newly reported as prey for pallid bats, as is the bat C. mexicana. The majority of culled insect parts (88%) were from adult mesquite bugs. Mesquite bug nymphs did not appear in the culled insect parts. After breeding in late summer, when nighttime low temperatures dropped below 21 °C, the adult bugs became immobile on the periphery of trees where they probably make easy prey for opportunistic foliage-gleaning pallid bats. Proximity of night-roosts to mesquite bug habitat probably also enhances the bats’ exploitation of these insects in this location. creator: Nicholas J. Czaplewski creator: Katrina L. Menard creator: William D. Peachey uri: https://doi.org/10.7717/peerj.6065 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Czaplewski et al. title: Increased presence of mammal-eating killer whales in the Salish Sea with implications for predator-prey dynamics link: https://peerj.com/articles/6062 last-modified: 2018-12-04 description: The inland waters of Washington State and southern British Columbia, collectively known as the Salish Sea, comprise key habitat for two regional populations of killer whales (Orcinus orca): the mammal-eating West Coast Transients and the endangered fish-eating Southern Residents. These two populations are genetically distinct and may avoid each other. Transient killer whale usage of the Salish Sea has been previously assessed over two seven-year time periods, showing an increase from 1987 to 2010. We documented a continued significant increase in mammal-eating killer whale presence in the Salish Sea from 2011 to 2017, with intra- and inter-annual variability and with record sightings in 2017. This continued increase, likely in response to abundant marine mammal prey, is related to both a growing population and an increase in the number of West Coast Transients visiting the area. Additionally, a negative binomial regression shows that absence of Southern Residents is correlated to transient presence. Finally, both populations of killer whales have been linked to regional harbor seal populations; harbor seals are salmonid-eating competitors of the Southern Residents and are prey for the mammal-eating transients. With Southern Residents listed as endangered, culling harbor seals has been proposed as a measure to help in their recovery. With this in mind, we developed an energetic model to assess the minimum number of harbor seals consumed by transient killer whales. Using the actual number of whales present in each age-sex class for each day of the year, we estimate that, at a minimum, transients in the Salish Sea consumed 1090 seals in 2017. This is more than 2% of the 2014 estimated harbor seal population the Salish Sea. The population controlling effects of transient killer whale predation on harbor seals should be considered when evaluating any pinniped management actions in the Salish Sea. creator: Monika W. Shields creator: Sara Hysong-Shimazu creator: Jason C. Shields creator: Julie Woodruff uri: https://doi.org/10.7717/peerj.6062 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Shields et al. title: Reducing protected lands in a hotspot of bee biodiversity: bees of Grand Staircase-Escalante National Monument link: https://peerj.com/articles/6057 last-modified: 2018-12-04 description: Grand Staircase-Escalante National Monument is a federally protected area found in central southern Utah. Designated in 1996 by President William J. Clinton, it was recently reduced in size by President Donald J. Trump in a proclamation that turned the one large monument into three smaller ones. A long-term, standardized study of the bees had been conducted from 2000–2003, revealing 660 species. The bee communities of the area are characterized by being spatially heterogeneous; most of the bees occur in isolated areas, with only a few being both abundant and widespread. Here we examine what affect the recent resizing of the monument has on the number, and ecology, of the bees now excluded from monument boundaries. Using the new monument boundaries and the geographic coordinates associated with each bee, we derived new species lists for each of the three monuments, and compared them to each other, and to the excluded lands. All three monuments now protect unique faunas, with Bray–Curtis similarity values not exceeding 0.59%. Each monument now harbors species not found in the other two monuments. We found that 84 bee species are no longer protected by any of the three monuments. These 84 species were not concentrated in one area that is now excluded, but were scattered throughout the newly excluded lands. For some of the excluded bee species, there is no evidence that they are rare or imperiled, being widespread throughout the west. However, there is a concentration of bees in the southern and eastern former monument lands that represent range extensions from nearby hot deserts. In addition to numerous range extensions, the list of excluded bees also contains several undescribed species (newly discovered species that have not yet been named and described by taxonomists) and morphospecies (individuals that are morphologically distinct, but that require additional research before species designations can be made). This indicates that the bee communities housed in these excluded areas would benefit from additional scientific inquiry. The areas now excluded from monument protections house a greater proportion of the original GSENM bee community than any of the three new monument units. We conclude this paper by discussing what the smaller monuments might mean for bee conservation in this hot spot of bee biodiversity and suggest that bee communities here and elsewhere should be taken into account when conservation decisions are being made. creator: Joseph S. Wilson creator: Matt Kelly creator: Olivia Messinger Carril uri: https://doi.org/10.7717/peerj.6057 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Wilson et al. title: Diversity of NC10 bacteria associated with sediments of submerged Potamogeton crispus (Alismatales: Potmogetonaceae) link: https://peerj.com/articles/6041 last-modified: 2018-12-04 description: BackgroundThe nitrite-dependent anaerobic methane oxidation (N-DAMO) pathway, which plays an important role in carbon and nitrogen cycling in aquatic ecosystems, is mediated by “Candidatus Methylomirabilis oxyfera” (M. oxyfera) of the NC10 phylum. M. oxyfera-like bacteria are widespread in nature, however, the presence, spatial heterogeneity and genetic diversity of M. oxyfera in the rhizosphere of aquatic plants has not been widely reported.MethodIn order to simulate the rhizosphere microenvironment of submerged plants, Potamogeton crispus was cultivated using the rhizobox approach. Sediments from three compartments of the rhizobox: root (R), near-rhizosphere (including five sub-compartments of one mm width, N1–N5) and non-rhizosphere (>5 mm, Non), were sampled. The 16S rRNA gene library was used to investigate the diversity of M. oxyfera-like bacteria in these sediments.ResultsMethylomirabilis oxyfera-like bacteria were found in all three sections, with all 16S rRNA gene sequences belonging to 16 operational taxonomic units (OTUs). A maximum of six OTUs was found in the N1 sub-compartment of the near-rhizosphere compartment and a minimum of four in the root compartment (R) and N5 near-rhizosphere sub-compartment. Indices of bacterial community diversity (Shannon) and richness (Chao1) were 0.73–1.16 and 4–9, respectively. Phylogenetic analysis showed that OTU1-11 were classified into group b, while OTU12 was in a new cluster of NC10.DiscussionOur results confirmed the existence of M. oxyfera-like bacteria in the rhizosphere microenvironment of the submerged plant P. crispus. Group b of M. oxyfera-like bacteria was the dominant group in this study as opposed to previous findings that both group a and b coexist in most other environments. Our results indicate that understanding the ecophysiology of M. oxyfera-like bacteria group b may help to explain their existence in the rhizosphere sediment of aquatic plant. creator: Binghan Wang creator: Shanshan Huang creator: Liangmao Zhang creator: Jianwei Zhao creator: Guanglong Liu creator: Yumei Hua creator: Wenbing Zhou creator: Duanwei Zhu uri: https://doi.org/10.7717/peerj.6041 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Wang et al. title: Identification of key candidate genes and biological pathways in bladder cancer link: https://peerj.com/articles/6036 last-modified: 2018-12-04 description: BackgroundBladder cancer is a malignant tumor in the urinary system with high mortality and recurrence rates. However, the causes and recurrence mechanism of bladder cancer are not fully understood. In this study, we used integrated bioinformatics to screen for key genes associated with the development of bladder cancer and reveal their potential molecular mechanisms.MethodsThe GSE7476, GSE13507, GSE37815 and GSE65635 expression profiles were downloaded from the Gene Expression Omnibus database, and these datasets contain 304 tissue samples, including 81 normal bladder tissue samples and 223 bladder cancer samples. The RobustRankAggreg (RRA) method was utilized to integrate and analyze the four datasets to obtain integrated differentially expressed genes (DEGs), and the gene ontology (GO) functional annotation and Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis were performed. Protein-protein interaction (PPI) network and module analyses were performed using Cytoscape software. The OncoLnc online tool was utilized to analyze the relationship between the expression of hub genes and the prognosis of bladder cancer.ResultsIn total, 343 DEGs, including 111 upregulated and 232 downregulated genes, were identified from the four datasets. GO analysis showed that the upregulated genes were mainly involved in mitotic nuclear division, the spindle and protein binding. The downregulated genes were mainly involved in cell adhesion, extracellular exosomes and calcium ion binding. The top five enriched pathways obtained in the KEGG pathway analysis were focal adhesion (FA), PI3K-Akt signaling pathway, proteoglycans in cancer, extracellular matrix (ECM)-receptor interaction and vascular smooth muscle contraction. The top 10 hub genes identified from the PPI network were vascular endothelial growth factor A (VEGFA), TOP2A, CCNB1, Cell division cycle 20 (CDC20), aurora kinase B, ACTA2, Aurora kinase A, UBE2C, CEP55 and CCNB2. Survival analysis revealed that the expression levels of ACTA2, CCNB1, CDC20 and VEGFA were related to the prognosis of patients with bladder cancer. In addition, a KEGG pathway analysis of the top 2 modules identified from the PPI network revealed that Module 1 mainly involved the cell cycle and oocyte meiosis, while the analysis in Module 2 mainly involved the complement and coagulation cascades, vascular smooth muscle contraction and FA.ConclusionsThis study identified key genes and pathways in bladder cancer, which will improve our understanding of the molecular mechanisms underlying the development and progression of bladder cancer. These key genes might be potential therapeutic targets and biomarkers for the treatment of bladder cancer. creator: Xin Gao creator: Yinyi Chen creator: Mei Chen creator: Shunlan Wang creator: Xiaohong Wen creator: Shufang Zhang uri: https://doi.org/10.7717/peerj.6036 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Gao et al. title: Complete chloroplast genome sequences of Dioscorea: Characterization, genomic resources, and phylogenetic analyses link: https://peerj.com/articles/6032 last-modified: 2018-12-04 description: Dioscorea L., the largest genus of the family Dioscoreaceae with over 600 species, is not only an important food but also a medicinal plant. The identification and classification of Dioscorea L. is a rather difficult task. In this study, we sequenced five Dioscorea chloroplast genomes, and analyzed with four other chloroplast genomes of Dioscorea species from GenBank. The Dioscorea chloroplast genomes displayed the typical quadripartite structure of angiosperms, which consisted of a pair of inverted repeats separated by a large single-copy region, and a small single-copy region. The location and distribution of repeat sequences and microsatellites were determined, and the rapidly evolving chloroplast genome regions (trnK-trnQ, trnS-trnG, trnC-petN, trnE-trnT, petG-trnW-trnP, ndhF, trnL-rpl32, and ycf1) were detected. Phylogenetic relationships of Dioscorea inferred from chloroplast genomes obtained high support even in shortest internodes. Thus, chloroplast genome sequences provide potential molecular markers and genomic resources for phylogeny and species identification. creator: Zhenyu Zhao creator: Xin Wang creator: Yi Yu creator: Subo Yuan creator: Dan Jiang creator: Yujun Zhang creator: Teng Zhang creator: Wenhao Zhong creator: Qingjun Yuan creator: Luqi Huang uri: https://doi.org/10.7717/peerj.6032 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Zhao et al. title: Structural plasticity in root-fungal symbioses: diverse interactions lead to improved plant fitness link: https://peerj.com/articles/6030 last-modified: 2018-12-04 description: Root-fungal symbioses such as mycorrhizas and endophytes are key components of terrestrial ecosystems. Diverse in trophy habits (obligate, facultative or hemi-biotrophs) and symbiotic relations (from mutualism to parasitism), these associations also show great variability in their root colonization and nutritional strategies. Specialized interface structures such as arbuscules and Hartig nets are formed by certain associations while others are restricted to non-specialized intercellular or intracellular hyphae in roots. In either case, there are documented examples of active nutrient exchange, reinforcing the fact that specialized structures used to define specific mycorrhizal associations are not essential for reciprocal exchange of nutrients and plant growth promotion. In feremycorrhiza (with Austroboletus occidentalis and eucalypts), the fungal partner markedly enhances plant growth and nutrient acquisition without colonizing roots, emphasizing that a conventional focus on structural form of associations may have resulted in important functional components of rhizospheres being overlooked. In support of this viewpoint, mycobiome studies using the state-of-the-art DNA sequencing technologies have unearthed much more complexity in root-fungal relationships than those discovered using the traditional morphology-based approaches. In this review, we explore the existing literature and most recent findings surrounding structure, functioning, and ecology of root-fungal symbiosis, which highlight the fact that plant fitness can be altered by taxonomically/ecologically diverse fungal symbionts regardless of root colonization and interface specialization. Furthermore, transition from saprotrophy to biotrophy seems to be a common event that occurs in diverse fungal lineages (consisting of root endophytes, soil saprotrophs, wood decayers etc.), and which may be accompanied by development of specialized interface structures and/or mycorrhiza-like effects on plant growth and nutrition. creator: Khalil Kariman creator: Susan Jane Barker creator: Mark Tibbett uri: https://doi.org/10.7717/peerj.6030 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Kariman et al. title: Comprehensive tissue-specific transcriptome profiling of pineapple (Ananas comosus) and building an eFP-browser for further study link: https://peerj.com/articles/6028 last-modified: 2018-12-04 description: Pineapple is one of the most economically important tropical or subtropical fruit trees. However, few studies focus on the development of its unique collective fruit. In this study, we generated a genome-wide developmental transcriptomic profile of 14 different tissues of the collective fruit of the pineapple covering each of the three major fruit developmental stages. In total, 273 tissue-specific and 1,051 constitutively expressed genes were detected. We also performed gene co-expression analysis and 18 gene modules were classified. Among these, we found three interesting gene modules; one was preferentially expressed in bracts and sepals and was likely involved in plant defense; one was highly expressed at the beginning of fruit expansion and faded afterward and was probably involved in endocytosis; Another gene module increased expression level with pineapple fruit development and was involved in terpenoid and polyketide metabolism. In addition, we built a pineapple electronic fluorescent pictograph (eFP) browser to facilitate exploration of gene expression during pineapple fruit development. With this tool, users can visualize expression data in this study in an intuitive way. Together, the transcriptome profile generated in this work and the corresponding eFP browser will facilitate further study of fruit development in pineapple. creator: Qi Mao creator: Chengjie Chen creator: Tao Xie creator: Aiping Luan creator: Chaoyang Liu creator: Yehua He uri: https://doi.org/10.7717/peerj.6028 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Mao et al. title: Saproxylic Diptera assemblages in a temperate deciduous forest: implications for community assembly link: https://peerj.com/articles/6027 last-modified: 2018-12-04 description: Saproxylic insects, those associated directly or indirectly with decaying wood for all or part of their life cycle, compose a large proportion of forest organisms. Flies (Diptera) are often the most abundant and species-rich group of insects in forest microhabitats, yet most work to date on saproxylic insect diversity and ecology has focused on beetles (Coleoptera). We compared saproxylic Diptera assemblages reared from two tree species (sugar maple and American beech) at two stages of decay (early/young and advanced/old) for a total of 20 logs in an eastern Canadian Nearctic old-growth forest. We found that communities are distinct within both species type and decay stage of wood. Early decay stage wood is more variable in community composition than later decay stage; however, as the age of the decaying wood increases, the abundance of Diptera increases significantly. Most indicator species are discernible in later decay stage and wood type. We venture to suggest that stochastic and deterministic processes may play a role in driving Diptera communities in temperate deciduous forests. To retain the highest saproxylic Diptera diversity in a forest, a variety of decaying wood types at different stages of decomposition is necessary. creator: Julia J. Mlynarek creator: Amélie Grégoire Taillefer creator: Terry A. Wheeler uri: https://doi.org/10.7717/peerj.6027 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Mlynarek et al. title: Molecular evolution and expression divergence of three key Met biosynthetic genes in plants: CGS, HMT and MMT link: https://peerj.com/articles/6023 last-modified: 2018-12-04 description: Methionine (Met) is an essential sulfur-containing amino acid in animals. Cereal and legume crops with limiting levels of Met represent the major food and feed sources for animals. In plants, cystathionine gamma-synthase (CGS), methionine methyltransferase (MMT) and homocysteine methyltransferase (HMT) are committing enzymes synergistically synthesizing Met through the aspartate (Asp) family pathway and the S-methylmethionine (SMM) cycle. The biological functions of CGS, MMT and HMT genes have been respectively studied, whereas their evolution patterns and their contribution to the evolution of Met biosynthetic pathway in plants are unknown. In the present study, to reveal their evolution patterns and contribution, the evolutionary relationship of CGS, MMT and HMT gene families were reconstructed. The results showed that MMTs began in the ancestor of the land plants and kept conserved during evolution, while the CGSs and HMTs had diverged. The CGS genes were divided into two branches in the angiosperms, Class 1 and Class 2, of which Class 2 only contained the grasses. However, the HMT genes diverged into Class 1 and Class 2 in all of the seed plants. Further, the gene structure analysis revealed that the CGSs, MMTs and HMTs were relatively conserved except for the CGSs in Class 2. According to the expression of CGS, HMT and MMT genes in soybeans, as well as in the database of soybean, rice and Arabidopsis, the expression patterns of the MMTs were shown to be consistently higher in leaves than in seeds. However, the expression of CGSs and HMTs had diverged, either expressed higher in leaves or seeds, or showing fluctuated expression. Additionally, the functions of HMT genes had diverged into the repair of S-adenosylmethionine and SMM catabolism during the evolution. The results indicated that the CGS and HMT genes have experienced partial subfunctionalization. Finally, given the evolution and expression of the CGS, HMT and MMT gene families, we built the evolutionary model of the Met biosynthetic pathways in plants. The model proposed that the Asp family pathway existed in all the plant lineages, while the SMM cycle began in the ancestor of land plants and then began to diverge in the ancestor of seed plants. The model suggested that the evolution of Met biosynthetic pathway is basically consistent with that of plants, which might be vital to the growth and development of different botanical lineages during evolution. creator: Man Zhao creator: Wenyi Wang creator: Lei Wei creator: Peng Chen creator: Fengjie Yuan creator: Zhao Wang creator: Xiangxian Ying uri: https://doi.org/10.7717/peerj.6023 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Zhao et al. title: Coming out in a harsh environment: a new genus and species for a land flatworm (Platyhelminthes: Tricladida) occurring in a ferruginous cave from the Brazilian savanna link: https://peerj.com/articles/6007 last-modified: 2018-12-04 description: Faunal inventories in ferruginous caves from an area belonging to the Brazilian savanna (Cerrado phytophysiognomy), on the eastern margin of the Serra do Espinhaço Plateau, in southeastern Brazil, have revealed the occurrence of land flatworms. Herein, a flatworm sampled in such subterranean environment is described as a new genus and species of the Neotropical subfamily Geoplaninae, Difroehlichia elenae gen. nov., sp. nov. The new genus shows rare features within Geoplaninae, namely sub-cylindrical body, poorly developed sub-epidermal musculature and a narrow creeping sole. Some features, such as a small body and a broad sensory margin in the anterior region of the body, as well as the fact that the holotype showed signs of recent copula, may indicate an adaptation to the subterranean environment, probably representing a troglophile. Difroehlichia elenae is characterized by an almost homogeneous dark brown pigmentation over dorsal surface and body margins, a short cylindrical pharynx, and a tubular and unforked intrabulbar prostatic vesicle, among other features. The holotype shows a secondary male copulatory organ located immediately behind the primary one, both communicating with the female atrium and gonopore canal. Since the species seems to have low abundance and restricted distribution and its type-locality is affected by mining activities, major concern arises regarding its conservation. creator: Ana M. Leal-Zanchet creator: Alessandro Damasceno Marques uri: https://doi.org/10.7717/peerj.6007 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Leal-Zanchet and Marques title: A retrospective study of surgical treatment and outcome among women with adnexal torsion in eastern Taiwan from 2010 to 2015 link: https://peerj.com/articles/5995 last-modified: 2018-12-04 description: BackgroundAdnexal torsion is a gynecologic emergency that requires surgical treatment. In this study, we reviewed the surgical outcomes of women with adnexal torsion in eastern Taiwan (Hualien county, area 4,629 km2, 330,000 residents).MethodsThis retrospective study included 42 women diagnosed with surgically-proven adnexal torsion from January 1, 2010, to September 31, 2015. We compared the symptoms, objective findings, and surgical outcomes of patients who underwent laparotomy or laparoscopy.ResultsThe laparoscopy and laparotomy groups included 27 and 15 patients, respectively. The most common symptom and sign was abdominal pain, followed by nausea and vomiting. In all patients, an adnexal tumor was detected through ultrasound. The median and range of time from admission to surgery was 1.5 (1–11.5) and 1.0 (1–11) hours in the laparotomy and laparoscopy groups, respectively. Compared with those undergoing laparotomy, the smaller tumor size [7 (4.2–10) vs. 10 (7–17) cm] and shorter hospital stay [4 (2–8) vs. 6 (3–9) days] in patients undergoing laparoscopy were significantly noted, respectively (P < 0.01). No differences were observed in age, operative time, and blood loss between both groups. The surgeries performed were mostly detorsion with cystectomy and adnexectomy. The most common pathology was a simple ovarian cyst, followed by teratoma. Regarding the surgical types, older age is the only risk factor for radical surgery.DiscussionAcute onset of abdominal pain with a presenting ovarian tumor is the most common feature of adnexal torsion. Laparoscopic surgical group showed a small tumor size and a short ER hospital stay than laparotomy. Older age is the risk factor for radical surgery. creator: Ci Huang creator: Mun-Kun Hong creator: Tang-Yuan Chu creator: Dah-Ching Ding uri: https://doi.org/10.7717/peerj.5995 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Huang et al. title: Real-time loop-mediated isothermal amplification for rapid detection of Enterocytozoon hepatopenaei link: https://peerj.com/articles/5993 last-modified: 2018-12-04 description: BackgroundEnterocytozoon hepatopenaei (EHP) is a newly emerged microsporidian parasite that causes retarded shrimp growth in many countries. But there are no effective approaches to control this disease to date. The EHP could be an immune risk factor for increased dissemination of other diseases. Further, EHP infection involves the absence of obvious clinical signs and it is difficult to identify the pathogen through visual examination, increasing the risk of disease dissemination. It is urgent and necessary to develop a specific, rapid and sensitive EHP-infected shrimp diagnostic method to detect this parasite. In the present study, we developed and evaluated a rapid real-time loop-mediated isothermal amplification (real-time LAMP) for detection of EHP.MethodsA rapid and efficient real-time LAMP method for the detection of EHP has been developed. Newly emerged EHP pathogens in China were collected and used as the sample, and three sets of specificity and sensitivity primers were designed. Three other aquatic pathogens were used as templates to test the specificity of the real-time LAMP assay. Also, we compared the real-time LAMP with the conventional LAMP by the serial dilutions of EHP DNA and their amplification curves. Application of real-time LAMP was carried out with clinical samples.ResultsPositive products were amplified only from EHP, but not from other tested species, EHP was detected from the clinical samples, suggesting a high specificity of this method. The final results of this assay were available within less than 45 min, and the initial amplification curve was observed at about 6 min. We found that the amplification with an exponential of sixfold dilutions of EHP DNA demonstrated a specific positive signal by the real-time LAMP, but not for the LAMP amplicons from the visual inspection. The real-time LAMP amplification curves demonstrated a higher slope than the conventional LAMP.DiscussionIn this study, pathogen virulence impacts have been increased in aquaculture and continuous observation was predominantly focused on EHP. The present study confirmed that the real-time LAMP assay is a promising and convenient method for the rapid identification of EHP in less time and cost. Its application greatly aids in the detection, surveillance, and prevention of EHP. creator: Shao-Xin Cai creator: Fan-De Kong creator: Shu-Fei Xu creator: Cui-Luan Yao uri: https://doi.org/10.7717/peerj.5993 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Cai et al. title: NCR3 polymorphism, haematological parameters, and severe malaria in Senegalese patients link: https://peerj.com/articles/6048 last-modified: 2018-12-03 description: BackgroundHost factors, including host genetic variation, have been shown to influence the outcome of Plasmodium falciparum infection. Genome-wide linkage studies have mapped mild malaria resistance genes on chromosome 6p21, whereas NCR3-412 polymorphism (rs2736191) lying within this region was found to be associated with mild malaria.MethodsBlood samples were taken from 188 Plasmodium falciparum malaria patients (76 mild malaria patients, 85 cerebral malaria patients, and 27 severe non-cerebral malaria patients). NCR3-412 (rs2736191) was analysed by sequencing, and haematological parameters were measured. Finally, their association with clinical phenotypes was assessed.ResultsWe evidenced an association of thrombocytopenia with both cerebral malaria and severe non-cerebral malaria, and of an association of high leukocyte count with cerebral malaria. Additionally, we found no association of NCR3-412 with either cerebral malaria, severe non-cerebral malaria, or severe malaria after grouping cerebral malaria and severe non-cerebral malaria patients.ConclusionsOur results suggest that NCR3 genetic variation has no effect, or only a small effect on the occurrence of severe malaria, although it has been strongly associated with mild malaria. We discuss the biological meaning of these results. Besides, we confirmed the association of thrombocytopenia and high leukocyte count with severe malaria phenotypes. creator: Alassane Thiam creator: Sabrina Baaklini creator: Babacar Mbengue creator: Samia Nisar creator: Maryam Diarra creator: Sandrine Marquet creator: Mouhamadou Mansour Fall creator: Michel Sanka creator: Fatou Thiam creator: Rokhaya Ndiaye Diallo creator: Magali Torres creator: Alioune Dieye creator: Pascal Rihet uri: https://doi.org/10.7717/peerj.6048 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Thiam et al. title: Exploring mechanisms that affect coral cooperation: symbiont transmission mode, cell density and community composition link: https://peerj.com/articles/6047 last-modified: 2018-12-03 description: The coral symbiosis is the linchpin of the reef ecosystem, yet the mechanisms that promote and maintain cooperation between hosts and symbionts have not been fully resolved. We used a phylogenetically controlled design to investigate the role of vertical symbiont transmission, an evolutionary mechanism in which symbionts are inherited directly from parents, predicted to enhance cooperation and holobiont fitness. Six species of coral, three vertical transmitters and their closest horizontally transmitting relatives, which exhibit environmental acquisition of symbionts, were fragmented and subjected to a 2-week thermal stress experiment. Symbiont cell density, photosynthetic function and translocation of photosynthetically fixed carbon between symbionts and hosts were quantified to assess changes in physiological performance and cooperation. All species exhibited similar decreases in symbiont cell density and net photosynthesis in response to elevated temperature, consistent with the onset of bleaching. Yet baseline cooperation, or translocation of photosynthate, in ambient conditions and the reduction in cooperation in response to elevated temperature differed among species. Although Porites lobata and Galaxea acrhelia did exhibit the highest levels of baseline cooperation, we did not observe universally higher levels of cooperation in vertically transmitting species. Post hoc sequencing of the Symbiodinium ITS-2 locus was used to investigate the potential role of differences in symbiont community composition. Interestingly, reductions in cooperation at the onset of bleaching tended to be associated with increased symbiont community diversity among coral species. The theoretical benefits of evolving vertical transmission are based on the underlying assumption that the host-symbiont relationship becomes genetically uniform, thereby reducing competition among symbionts. Taken together, our results suggest that it may not be vertical transmission per se that influences host-symbiont cooperation, but genetic uniformity of the symbiont community, although additional work is needed to test this hypothesis. creator: Carly D. Kenkel creator: Line K. Bay uri: https://doi.org/10.7717/peerj.6047 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Kenkel and Bay title: Compatibility between object size and response side in grasping: the left hand prefers smaller objects, the right hand prefers larger objects link: https://peerj.com/articles/6026 last-modified: 2018-12-03 description: It has been proposed that the brain processes quantities such as space, size, number, and other magnitudes using a common neural metric, and that this common representation system reflects a direct link to motor control, because the integration of spatial, temporal, and other quantity-related information is fundamental for sensorimotor transformation processes. In the present study, we examined compatibility effects between physical stimulus size and spatial (response) location during a sensorimotor task. Participants reached and grasped for a small or large object with either their non-dominant left or their dominant right hand. Our results revealed that participants initiated left hand movements faster when grasping the small cube compared to the large cube, whereas they initiated right hand movements faster when grasping the large cube compared to the small cube. Moreover, the compatibility effect influenced the timing of grip aperture kinematics. These findings indicate that the interaction between object size and response hand affects the planning of grasping movements and supports the notion of a strong link between the cognitive representation of (object) size, spatial (response) parameters, and sensorimotor control. creator: Christian Seegelke creator: Peter Wühr uri: https://doi.org/10.7717/peerj.6026 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Seegelke and Wühr title: Flower visitation by hoverflies (Diptera: Syrphidae) in a temperate plant-pollinator network link: https://peerj.com/articles/6025 last-modified: 2018-12-03 description: Hoverflies (Diptera: Syrphidae) are among the most important pollinators, although they attract less attention than bees. They are usually thought to be rather opportunistic flower visitors, although previous studied demonstrated that they show colour preferences and their nectar feeding is affected by morphological constraints related to flower morphology. Despite the growing appreciation of hoverflies and other non-bee insects as pollinators, there is a lack of community-wide studies of flower visitation by syrphids. The aim of this paper is to provide a detailed analysis of flower visitation patterns in a species rich community of syrphids in a Central European grassland and to evaluate how species traits shape the structure of the plant-hoverfly flower visitation network. We found that different species varied in the level of specialisation, and while some species visited a similar spectre of flowers, others partitioned resources more strongly. There was a consistent difference in both specialisation and flower preferences between three syrphid subfamilies. Eristalinae and Pipizinae were more specialised than Syrphinae. Trait-based analyses showed that relative flower visitation (i) increased with plant height, but most strongly in Eristalinae; (ii) increased with inflorescence size in small species from all three subfamilies, but was independent of inflorescence size in large species of Eristalinae and Syrphinae; and (iii) depended on flower colour, but in a subfamily-specific way. Eristalinae showed the strongest flower colour preferences for white flowers, Pipizinae visited mostly white and yellow flowers, while Syrphinae were less affected by flower colour. Exploration of the structure of the plant-hoverfly flower visitation network showed that the network was both modular and nested. We also found that there were almost no differences in specialisation and relative visitation frequency between males and females. Overall, we showed that flower visitation in syrphids was affected by phylogenetic relatedness, body size of syrphids and several plant traits. creator: Jan Klecka creator: Jiří Hadrava creator: Paolo Biella creator: Asma Akter uri: https://doi.org/10.7717/peerj.6025 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Klecka et al. title: Shielding effects of myelin sheath on axolemma depolarization under transverse electric field stimulation link: https://peerj.com/articles/6020 last-modified: 2018-12-03 description: Axonal stimulation with electric currents is an effective method for controlling neural activity. An electric field parallel to the axon is widely accepted as the predominant component in the activation of an axon. However, recent studies indicate that the transverse component to the axolemma is also effective in depolarizing the axon. To quantitatively investigate the amount of axolemma polarization induced by a transverse electric field, we computed the transmembrane potential (Vm) for a conductive body that represents an unmyelinated axon (or the bare axon between the myelin sheath in a myelinated axon). We also computed the transmembrane potential of the sheath-covered axonal segment in a myelinated axon. We then systematically analyzed the biophysical factors that affect axonal polarization under transverse electric stimulation for both the bare and sheath-covered axons. Geometrical patterns of polarization of both axon types were dependent on field properties (magnitude and field orientation to the axon). Polarization of both axons was also dependent on their axolemma radii and electrical conductivities. The myelin provided a significant “shielding effect” against the transverse electric fields, preventing excessive axolemma depolarization. Demyelination could allow for prominent axolemma depolarization in the transverse electric field, via a significant increase in myelin conductivity. This shifts the voltage drop of the myelin sheath to the axolemma. Pathological changes at a cellular level should be considered when electric fields are used for the treatment of demyelination diseases. The calculated term for membrane polarization (Vm) could be used to modify the current cable equation that describes axon excitation by an external electric field to account for the activating effects of both parallel and transverse fields surrounding the target axon. creator: Hui Ye creator: Jeffrey Ng uri: https://doi.org/10.7717/peerj.6020 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Ye and Ng title: When and where to hatch? Red-eyed treefrog embryos use light cues in two contexts link: https://peerj.com/articles/6018 last-modified: 2018-12-03 description: Hatching timing is under strong selection and environmentally cued in many species. Embryos use multiple sensory modalities to inform hatching timing and many have spontaneous hatching patterns adaptively synchronized to natural cycles. Embryos can also adaptively shift their hatching timing in response to environmental cues indicating immediate threats or opportunities. Such cued shifts in hatching are widespread among amphibians; however, we know little about what, if anything, regulates their spontaneous hatching. Moreover, in addition to selection on hatching timing, embryos may experience benefits or suffer costs due to the spatial orientation of hatching. Amphibian eggs generally lack internal constraints on hatching direction but embryos might, nonetheless, use external cues to inform hatching orientation. The terrestrial embryos of red-eyed treefrogs, Agalychnis callidryas, hatch rapidly and prematurely in response to vibrational cues in egg-predator attacks and hypoxia if flooded. Here we examined A. callidryas’ use of light cues in hatching timing and orientation. To assess patterns of spontaneous hatching and the role of light cues in their diel timing, we recorded hatching times for siblings distributed across three light environments: continuous light, continuous dark, and a 12L:12D photoperiod. Under a natural photoperiod, embryos showed a clear diel pattern of synchronous hatching shortly after nightfall. Hatching was desynchronized in both continuous light and continuous darkness. It was also delayed by continuous light, but not accelerated by continuous dark, suggesting the onset of dark serves as a hatching cue. We examined hatching orientation and light as a potential directional cue for flooded embryos. Embryos flooded in their clutches almost always hatched toward open water, whereas individual eggs flooded in glass cups often failed to do so, suggesting the natural context provides a directional cue. To test if flooded embryos orient hatching toward light, we placed individual eggs in tubes with one end illuminated and the other dark, then flooded them and recorded hatching direction. Most embryos hatched toward the light, suggesting they use light as a directional cue. Our results support that A. callidryas embryos use light cues to inform both when and where to hatch. Both the spatial orientation of hatching and the timing of spontaneous hatching may affect fitness and be informed by cues in a broader range of species than is currently appreciated. creator: Brandon A. Güell creator: Karen M. Warkentin uri: https://doi.org/10.7717/peerj.6018 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Güell and Warkentin title: Coral disease prevalence estimation and sampling design link: https://peerj.com/articles/6006 last-modified: 2018-12-03 description: In the last decades diseases have changed coral communities’ structure and function in reefs worldwide. Studies conducted to evaluate the effect of diseases on corals frequently use modified adaptations of sampling designs that were developed to study ecological aspects of coral reefs. Here we evaluate how efficient these sampling protocols are by generating virtual data for a coral population parameterized with mean coral density and disease prevalence estimates from the Caribbean scleractinian Orbicella faveolata at the Mexican Caribbean. Six scenarios were tested consisting of three patterns of coral colony distribution (random, randomly clustered and randomly over-dispersed) and two disease transmission modes (random and contagious). The virtual populations were sampled with the commonly used method of belt-transects with variable sample-unit sizes (10 × 1, 10 × 2, 25 × 2, 50 × 2 m). Results showed that the probability of obtaining a mean coral disease prevalence estimate of ±5% of the true prevalence value was low (range: 11–48%) and that two-sample comparisons achieved rather low power, unless very large effect sizes existed. Such results imply low statistical confidence to assess differences or changes in coral disease prevalence. The main problem identified was insufficient sample size because local mean colony size, density and spatial distribution of targeted coral species was not taken into consideration to properly adjust the sampling protocols. creator: Eric Jordán-Dahlgren creator: Adán G. Jordán-Garza creator: Rosa E. Rodríguez-Martínez uri: https://doi.org/10.7717/peerj.6006 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Jordán-Dahlgren et al. title: Intestinal microbiome and its potential functions in bighead carp (Aristichthys nobilis) under different feeding strategies link: https://peerj.com/articles/6000 last-modified: 2018-12-03 description: Bighead carps (Aristichthys nobilis) were divided into four groups with different feeding strategies: group A, nature live food only (fertiliser only, 200 g urea + 160 g ethylamine phosphate + 250 g Huangjintai bio-fertiliser); group B, nature live food + 1/2 formulated feed; group C, nature live food + formulated feed; and group D, formulated feed only. The intestinal microbiomes of the different groups were compared through the Illumina MiSeq sequencing of the bacterial 16S rRNA gene. The specific growth rate (SGR), survival and blood biochemical factors of the fish were also investigated. Results showed that feeding treatment influenced the intestinal communities in the fish. In specific, more bacterial phyla dominated in groups A and B (phyla Bacteroidetes, Fusobacteria, Firmicutes and Proteobacteria in group A, phyla Proteobacteria and Fusobacteria in group B) than in groups C and D (phylum Proteobacteria). The diversity was also lower in groups C and D than in groups A and B. Unweighted pair-group method analysis revealed a clear difference in intestinal microbiota among the different feeding treatments. No difference in survival rate was found among the treatment groups, but the SGR was significantly higher (P < 0.01) in groups B, C and D than in group A. Functional analysis showed that the intestinal bacteria correlated with fish glucose metabolism in group A but with lipid metabolic activity in groups B, C and D. In summary, the intestinal microbiomes and their potential functions vary in bighead carp under different feeding treatments. This study provides new insights into the gut microbiomes of filter-feeding and formulated diet-fed fish. creator: Xuemei Li creator: Yongjiu Zhu creator: Einar Ringø creator: Xuge Wang creator: Jinling Gong creator: Deguo Yang uri: https://doi.org/10.7717/peerj.6000 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Li et al. title: In-situ incubation of a coral patch for community-scale assessment of metabolic and chemical processes on a reef slope link: https://peerj.com/articles/5966 last-modified: 2018-12-03 description: Anthropogenic pressures threaten the health of coral reefs globally. Some of these pressures directly affect coral functioning, while others are indirect, for example by promoting the capacity of bioeroders to dissolve coral aragonite. To assess the coral reef status, it is necessary to validate community-scale measurements of metabolic and geochemical processes in the field, by determining fluxes from enclosed coral reef patches. Here, we investigate diurnal trends of carbonate chemistry, dissolved organic carbon, oxygen, and nutrients on a 20 m deep coral reef patch offshore from the island of Saba, Dutch Caribbean by means of tent incubations. The obtained trends are related to benthic carbon fluxes by quantifying net community calcification (NCC) and net community production (NCP). The relatively strong currents and swell-induced near-bottom surge at this location caused minor seawater exchange between the incubated reef and ambient water. Employing a compensating interpretive model, the exchange is used to our advantage as it maintains reasonably ventilated conditions, which conceivably prevents metabolic arrest during incubation periods of multiple hours. No diurnal trends in carbonate chemistry were detected and all net diurnal rates of production were strongly skewed towards respiration suggesting net heterotrophy in all incubations. The NCC inferred from our incubations ranges from −0.2 to 1.4 mmol CaCO3 m−2 h−1 (−0.2 to 1.2 kg CaCO3 m−2 year−1) and NCP varies from −9 to −21.7 mmol m−2 h−1 (net respiration). When comparing to the consensus-based ReefBudget approach, the estimated NCC rate for the incubated full planar area (0.36 kg CaCO3 m−2 year−1) was lower, but still within range of the different NCC inferred from our incubations. Field trials indicate that the tent-based incubation as presented here, coupled with an appropriate interpretive model, is an effective tool to investigate, in situ, the state of coral reef patches even when located in a relatively hydrodynamic environment. creator: Steven M.A.C. van Heuven creator: Alice E. Webb creator: Didier M. de Bakker creator: Erik Meesters creator: Fleur C. van Duyl creator: Gert-Jan Reichart creator: Lennart J. de Nooijer uri: https://doi.org/10.7717/peerj.5966 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 van Heuven et al. title: Urbanisation and wing asymmetry in the western honey bee (Apis mellifera, Linnaeus 1758) at multiple scales link: https://peerj.com/articles/5940 last-modified: 2018-12-03 description: Changes in the mean and variance of phenotypic traits like wing and head morphology are frequently used as indicators of environmental stress experienced during development and may serve as a convenient index of urbanization exposure. To test this claim, we collected adult western honey bee (Apis mellifera Linnaeus 1758, Hymenoptera, Apidae) workers from colonies located across an urbanization gradient, and quantified associations between the symmetries of both wing size and wing shape, and several landscape traits associated with urbanization. Landscape traits were assessed at two spatial scales (three km and 500 m) and included vegetation and anthropogenic land cover, total road length, road proximity and, population and dwelling density. We then used geometric morphometric techniques to determine two wing asymmetry scores—centroid size, a measure of wing size asymmetry and Procrustes distance, a measure of wing shape asymmetry. We found colony dependent differences in both wing size and shape asymmetry. Additionally, we found a negative association between wing shape asymmetry and road proximity at the three km buffer, and associations between wing shape asymmetry and road proximity, anthropogenic land cover and vegetation cover at the 500 m buffer. Whilst we were unable to account for additional variables that may influence asymmetry including temperature, pesticide presence, and parasitism our results demonstrate the potential usefulness of wing shape asymmetry for assessing the impact of certain landscape traits associated with urbanization. Furthermore, they highlight important spatial scale considerations that warrant investigation in future phenotypic studies assessing urbanization impact. creator: Ryan J. Leonard creator: Katie K.Y. Wat creator: Clare McArthur creator: Dieter F. Hochuli uri: https://doi.org/10.7717/peerj.5940 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Leonard et al. title: Characterization of bacterioplankton communities and quantification of organic carbon pools off the Galapagos Archipelago under contrasting environmental conditions link: https://peerj.com/articles/5984 last-modified: 2018-12-03 description: Bacteria play a crucial role in the marine carbon cycle, contributing to the production and degradation of organic carbon. Here, we investigated organic carbon pools, aggregate formation, and bacterioplankton communities in three contrasting oceanographic settings in the Galapagos Archipelago. We studied a submarine CO2 vent at Roca Redonda (RoR), an upwelling site at Bolivar Channel (BoC) subjected to a weak El Niño event at the time of sampling in October 2014, as well as a site without volcanic or upwelling influence at Cowley Islet (CoI). We recorded physico-chemical parameters, and quantified particulate and dissolved organic carbon, transparent exopolymeric particles, and the potential of the water to form larger marine aggregates. Free-living and particle-attached bacterial communities were assessed via 16S rRNA gene sequencing. Both RoR and BoC exhibited temperatures elevated by 1–1.5 °C compared to CoI. RoR further experienced reduced pH between 6.8 and 7.4. We observed pronounced differences in organic carbon pools at each of the three sites, with highest dissolved organic carbon concentrations at BoC and RoR, and highest particulate organic carbon concentrations and aggregate formation at BoC. Bacterioplankton communities at BoC were dominated by opportunistic copiotrophic taxa, such as Alteromonas and Roseobacter, known to thrive in phytoplankton blooms, as opposed to oligotrophic taxa dominating at CoI, such as members of the SAR11 clade. Therefore, we propose that bacterial communities were mainly influenced by the availability of organic carbon at the investigated sites. Our study provides a comprehensive characterization of organic carbon pools and bacterioplankton communities, highlighting the high heterogeneity of various components of the marine carbon cycle around the Galapagos Archipelago. creator: Nataly Carolina Guevara Campoverde creator: Christiane Hassenrück creator: Pier Luigi Buttigieg creator: Astrid Gärdes uri: https://doi.org/10.7717/peerj.5984 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Guevara Campoverde et al.