title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2020-04 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Soil water consumption, water use efficiency and winter wheat production in response to nitrogen fertilizer and tillage link: https://peerj.com/articles/8892 last-modified: 2020-04-30 description: Sustainability of winter wheat yield under dryland conditions depends on improving soil water stored during fallow and its efficient use. A 3-year field experiment was conducted in Loess Plateau to access the effect of tillage and N (nitrogen) rates on soil water, N distribution and water- and nitrogen-use efficiency of winter wheat. Deep tillage (DT, 25–30 cm depth) and no-tillage (NT) were operated during fallow season, whereas four N rates (0, 90, 150 and 210 kg ha−1) were applied before sowing. Rates of N and variable rainfall during summer fallow period led to the difference of soil water storage. Soil water storage at anthesis and maturity was decreased with increasing N rate especially in the year with high precipitation (2014–2015). DT has increased the soil water storage at sowing, N content, numbers of spike, grain number, 1,000 grain weight, grain yield, and water and N use efficiency as compared to NT. Grain yield was significantly and positively related to soil water consumption at sowing to anthesis and anthesis to maturity, total plant N, and water-use efficiency. Our study implies that optimum N rate and deep tillage during the fallow season could improve dryland wheat production by balancing the water consumption and biomass production. creator: Shahbaz Khan creator: Sumera Anwar creator: Yu Shaobo creator: Zhiqiang Gao creator: Min Sun creator: M. Yasin Ashraf creator: Aixia Ren creator: Zhenping Yang uri: https://doi.org/10.7717/peerj.8892 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Khan et al. title: Phylogeography of the widespread Caribbean spiny orb weaver Gasteracantha cancriformis link: https://peerj.com/articles/8976 last-modified: 2020-04-30 description: BackgroundModern molecular analyses are often inconsistent with pre-cladistic taxonomic hypotheses, frequently indicating higher richness than morphological taxonomy estimates. Among Caribbean spiders, widespread species are relatively few compared to the prevalence of single island endemics. The taxonomic hypothesis Gasteracantha cancriformis circumscribes a species with profuse variation in size, color and body form. Distributed throughout the Neotropics, G. cancriformis is the only morphological species of Gasteracantha in the New World in this globally distributed genus.MethodsWe inferred phylogenetic relationships across Neotropical populations of Gasteracantha using three target genes. Within the Caribbean, we estimated genetic diversity, population structure, and gene flow among island populations.ResultsOur findings revealed a single widespread species of Gasteracantha throughout the Caribbean, G. cancriformis, while suggesting two recently divergent mainland populations that may represent separate species, diverging linages, or geographically isolated demes. The concatenated and COI (Cytochrome c oxidase subunit 1) phylogeny supported a Caribbean clade nested within the New World. Genetic variability was high between island populations for our COI dataset; however, gene flow was also high, especially between large, adjacent islands. We found structured genetic and morphological variation within G. cancriformis island populations; however, this variation does not reflect genealogical relationships. Rather, isolation by distance and local morphological adaptation may explain the observed variation. creator: Lisa Chamberland creator: Fabian C. Salgado-Roa creator: Alma Basco creator: Amanda Crastz-Flores creator: Greta J. Binford creator: Ingi Agnarsson uri: https://doi.org/10.7717/peerj.8976 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Chamberland et al. title: Migratory behaviour and survival of Great Egrets after range expansion in Central Europe link: https://peerj.com/articles/9002 last-modified: 2020-04-30 description: Great Egret Ardea alba is one of few Western Palearctic species that underwent a rapid range expansion in the recent decades. Originally breeding in central and eastern Europe, the species has spread in northern (up to the Baltic coast) and western (up to the western France) directions and established viable breeding populations throughout almost entire continent. We monitored one of the first Great Egrets colonies established in Poland to infer migratory patterns and survival rates directly after range expansion. For this purpose, we collected resightings from over 200 Great Egret chicks marked between 2002–2017 in central Poland. Direction of migration was non-random, as birds moved almost exclusively into the western direction. Wintering grounds were located mainly in the western Europe (Germany to France) within 800–950 km from the breeding colony. First-year birds migrated farther than adults. We found some, although relatively weak, support for age-dependent survival of Great Egrets and under the best-fitted capture-recapture model, the estimated annual survival rate of adults was nearly twice higher than for first-year birds (φad = 0.85 ± 0.05 vs. φfy = 0.48 ± 0.15). Annual survival rate under the constant model (no age-related variation) was estimated at φ = 0.81 ± 0.05. Our results suggest that Great Egrets rapidly adapted to novel ecological and environmental conditions during range expansion. We suggest that high survival rate of birds from central Poland and their western direction of migration may facilitate further colonization processes in western Europe. creator: Radosław Włodarczyk creator: Daria Szafara creator: Krzysztof Kaczmarek creator: Tomasz Janiszewski creator: Piotr Minias uri: https://doi.org/10.7717/peerj.9002 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Włodarczyk et al. title: Fear and stressing in predator–prey ecology: considering the twin stressors of predators and people on mammals link: https://peerj.com/articles/9104 last-modified: 2020-04-30 description: Predators induce stress in prey and can have beneficial effects in ecosystems, but can also have negative effects on biodiversity if they are overabundant or have been introduced. The growth of human populations is, at the same time, causing degradation of natural habitats and increasing interaction rates of humans with wildlife, such that conservation management routinely considers the effects of human disturbance as tantamount to or surpassing those of predators. The need to simultaneously manage both of these threats is particularly acute in urban areas that are, increasingly, being recognized as global hotspots of wildlife activity. Pressures from altered predator–prey interactions and human activity may each initiate fear responses in prey species above those that are triggered by natural stressors in ecosystems. If fear responses are experienced by prey at elevated levels, on top of responses to multiple environmental stressors, chronic stress impacts may occur. Despite common knowledge of the negative effects of stress, however, it is rare that stress management is considered in conservation, except in intensive ex situ situations such as in captive breeding facilities or zoos. We propose that mitigation of stress impacts on wildlife is crucial for preserving biodiversity, especially as the value of habitats within urban areas increases. As such, we highlight the need for future studies to consider fear and stress in predator–prey ecology to preserve both biodiversity and ecosystem functioning, especially in areas where human disturbance occurs. We suggest, in particular, that non-invasive in situ investigations of endocrinology and ethology be partnered in conservation planning with surveys of habitat resources to incorporate and reduce the effects of fear and stress on wildlife. creator: Loren L. Fardell creator: Chris R. Pavey creator: Christopher R. Dickman uri: https://doi.org/10.7717/peerj.9104 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Fardell et al. title: Activity-specific mobility of adults in a rural region of western Kenya link: https://peerj.com/articles/8798 last-modified: 2020-04-29 description: Improving rural household access to resources such as markets, schools and healthcare can help alleviate poverty in low-income settings. Current models of geographic accessibility to various resources rarely take individual variation into account due to a lack of appropriate data, yet understanding mobility at an individual level is key to knowing how people access their local resources. Our study used both an activity-specific survey and GPS trackers to evaluate how adults in a rural area of western Kenya accessed local resources. We calculated the travel time and time spent at six different types of resource and compared the GPS and survey data to see how well they matched. We found links between several demographic characteristics and the time spent at different resources, and that the GPS data reflected the survey data well for time spent at some types of resource, but poorly for others. We conclude that demography and activity are important drivers of mobility, and a better understanding of individual variation in mobility could be obtained through the use of GPS trackers on a wider scale. creator: Jessica R. Floyd creator: Joseph Ogola creator: Eric M. Fèvre creator: Nicola Wardrop creator: Andrew J. Tatem creator: Nick W. Ruktanonchai uri: https://doi.org/10.7717/peerj.8798 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Floyd et al. title: Molecular clocks, biogeography and species diversity in Herichthys with evaluation of the role of Punta del Morro as a vicariant brake along the Mexican Transition Zone in the context of local and global time frame of cichlid diversification link: https://peerj.com/articles/8818 last-modified: 2020-04-29 description: Using molecular dated phylogenies and biogeographic reconstructions, the species diversity, biogeography and time frame of evolution of the genus Herichthys were evaluated. In particular, we test the role of Punta del Morro (PdM) as a vicariant brake along the Mexican Transition Zone in the context of local and global time frame of cichlid diversification using several sets of calibrations. Species diversity in Herichthys is complex and the here employed dating methods suggest young age and rapid divergence for many species while species delimitation methods did not resolve these young species including both sympatric species pairs. Based on our molecular clock dating analyses, Herichthys has colonized its present distribution area significantly prior to the suggested vicariance by PdM (10–17.1 Ma vs. 5 to 7.5 Ma). The PdM constraint is in conflict with all other paleogeographic and fossil constraints including novel ones introduced in this study that are, however, congruent among each other. Our study demonstrates that any cichlid datings significantly older or younger than the bounds presented by our analyses and discussion have to be taken as highly questionable from the point of view of Middle American paleogeography and cichlid biogeography unless we allow the option that cichlid biogeography is completely independent from ecological and geological constraints. creator: Fabian Pérez-Miranda creator: Omar Mejia creator: Benjamín López creator: Oldřich Říčan uri: https://doi.org/10.7717/peerj.8818 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Pérez-Miranda et al. title: The predictive value of PRDM2 in solid tumor: a systematic review and meta-analysis link: https://peerj.com/articles/8826 last-modified: 2020-04-29 description: BackgroundMany studies have reported the presence of Positive Regulatory/Su(var)3-9, Enhancer-of-zeste and Trithorax Domain 2 (PRDM2) downregulation in cancer. However, its potential as a diagnostic biomarker is still unclear. Hence, a systematic review and meta-analysis were conducted to address this issue.IntroductionAs of 2018, cancer has become the second leading cause of death worldwide. Thus, cancer control is exceptionally vital in reducing mortality. One such example is through early diagnosis of cancer using tumor biomarkers. Having a function as a tumor suppressor gene (TSG), PRDM2 has been linked with carcinogenesis in several solid tumor. This study aims to assess the relationship between PRDM2 downregulation and solid tumor, its relationship with clinicopathological data, and its potential as a diagnostic biomarker. This study also aims to evaluate the quality of the studies, data reliability and confidence in cumulative evidence.Materials & MethodsA protocol of this study is registered at the International Prospective Register of Systematic Reviews (PROSPERO) with the following registration number: CRD42019132156. PRISMA was used as a guideline to conduct this review. A comprehensive electronic search was performed from inception to June 2019 in Pubmed, Cochrane Library, ProQuest, EBSCO and ScienceDirect. Studies were screened and included studies were identified based on the criteria made. Finally, data synthesis and quality assessment were conducted.ResultsThere is a significant relationship between PRDM2 downregulation with solid tumor (RR 4.29, 95% CI [2.58–7.13], P < 0.00001). The overall sensitivity and specificity of PRDM2 downregulation in solid tumors is 84% (95% CI [39–98%]) and 86% (95% CI [71–94%]), respectively. There is a low risk of bias for the studies used. TSA results suggested the presence of marked imprecision. The overall quality of evidence for this study is very low.DiscussionWe present the first meta-analysis that investigated the potential of PRDM2 downregulation as a diagnostic biomarker in solid tumor. In line with previous studies, our results demonstrated that PRDM2 downregulation occurs in solid tumor. A major source of limitation in this study is the small number of studies.ConclusionsOur review suggested that PRDM2 is downregulated in solid tumor. The relationship between PRDM2 downregulation and clinicopathological data is still inconclusive. Although the sensitivity and specificity of PRDM2 downregulation are imprecise, its high values, in addition to the evidence that suggested PRDM2 downregulation in solid tumor, hinted that it might still have a potential to be used as a diagnostic biomarker. In order to further strengthen these findings, more research regarding PRDM2 in solid tumors are encouraged. creator: Caroline Tanadi creator: Alfredo Bambang creator: Indra Putra Wendi creator: Veronika M. Sidharta creator: Linawati Hananta creator: Anton Sumarpo uri: https://doi.org/10.7717/peerj.8826 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Tanadi et al. title: Performance in a novel environment subject to ghost competition link: https://peerj.com/articles/8931 last-modified: 2020-04-29 description: BackgroundA central tenet of the evolutionary theory of communities is that competition impacts evolutionary processes such as local adaptation. Species in a community exert a selection pressure on other species and may drive them to extinction. We know, however, very little about the influence of unsuccessful or ghost species on the evolutionary dynamics within the community.MethodsHere we report the long-term influence of a ghost competitor on the performance of a more successful species using experimental evolution. We transferred the spider mite Tetranychus urticae onto a novel host plant under initial presence or absence of a competing species, the congeneric mite T. ludeni.ResultsThe competitor species, T. ludeni, unintentionally went extinct soon after the start of the experiment, but we nevertheless completed the experiment and found that the early competitive pressure of this ghost competitor positively affected the performance (i.e., fecundity) of the surviving species, T. urticae. This effect on T. urticae lasted for at least 25 generations.DiscussionOur study suggests that early experienced selection pressures can exert a persistent evolutionary signal on species’ performance in novel environments. creator: Karen Bisschop creator: Frederik Mortier creator: Dries Bonte creator: Rampal S. Etienne uri: https://doi.org/10.7717/peerj.8931 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Bisschop et al. title: Post-transcriptional regulation of several biological processes involved in latex production in Hevea brasiliensis link: https://peerj.com/articles/8932 last-modified: 2020-04-29 description: BackgroundSmall RNAs modulate plant gene expression at both the transcriptional and post-transcriptional level, mostly through the induction of either targeted DNA methylation or transcript cleavage, respectively. Small RNA networks are involved in specific plant developmental processes, in signaling pathways triggered by various abiotic stresses and in interactions between the plant and viral and non-viral pathogens. They are also involved in silencing maintenance of transposable elements and endogenous viral elements. Alteration in small RNA production in response to various environmental stresses can affect all the above-mentioned processes. In rubber trees, changes observed in small RNA populations in response to trees affected by tapping panel dryness, in comparison to healthy ones, suggest a shift from a transcriptional to a post-transcriptional regulatory pathway. This is the first attempt to characterise small RNAs involved in post-transcriptional silencing and their target transcripts in Hevea.MethodsGenes producing microRNAs (MIR genes) and loci producing trans-activated small interfering RNA (ta-siRNA) were identified in the clone PB 260 re-sequenced genome. Degradome libraries were constructed with a pool of total RNA from six different Hevea tissues in stressed and non-stressed plants. The analysis of cleaved RNA data, associated with genomics and transcriptomics data, led to the identification of transcripts that are affected by 20–22 nt small RNA-mediated post-transcriptional regulation. A detailed analysis was carried out on gene families related to latex production and in response to growth regulators.ResultsCompared to other tissues, latex cells had a higher proportion of transcript cleavage activity mediated by miRNAs and ta-siRNAs. Post-transcriptional regulation was also observed at each step of the natural rubber biosynthesis pathway. Among the genes involved in the miRNA biogenesis pathway, our analyses showed that all of them are expressed in latex. Using phylogenetic analyses, we show that both the Argonaute and Dicer-like gene families recently underwent expansion. Overall, our study underlines the fact that important biological pathways, including hormonal signalling and rubber biosynthesis, are subject to post-transcriptional silencing in laticifers. creator: Julie Leclercq creator: Shuangyang Wu creator: Benoît Farinas creator: Stéphanie Pointet creator: Bénédicte Favreau creator: Hélène Vignes creator: Kuswanhadi Kuswanhadi creator: Enrique Ortega-Abboud creator: Jean-François Dufayard creator: Shenghan Gao creator: Gaëtan Droc creator: Songnian Hu creator: Chaorong Tang creator: Pascal Montoro uri: https://doi.org/10.7717/peerj.8932 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Leclercq et al. title: School self-efficacy is affected by gender and motor skills: findings from an Italian study link: https://peerj.com/articles/8949 last-modified: 2020-04-29 description: BackgroundPerceived school self-efficacy (SE) is an important variable in students’ activities as it affects their motivation and learning. Further, self-efficacy might represent a good predictor of performance, persistence and perseverance. Motor skills and other physical health determinants are extensively debated and linked to cognitive function in children of developmental age. However, inconclusive evidence supports a definitive relationship between perceived school SE and motor skills among schoolchildren. We conducted a cross-sectional study on 6–11-year-old schoolchildren to evaluate the extent by which perceived school SE and physical health determinants were related.MethodsA SE questionnaire and motor performance battery tests were administered to primary school pupils recruited from 154 sampled schools of northwest Italy. Perceived SE at school was assessed via 12 items from the Caprara’s questionnaire. Motor performance scores were obtained from motor skill tests: 4 × 10 m shuttle run test, SRT; standing broad jump, SBJ; six-minute walking test, 6MWT.ResultsA total of 3,962 children (M = 2,019; F = 1943) were studied and 68% were normal weight. Overall, a 58% of the sample perceived a high SE, while, as to gender differences, a greater percentage of females perceived high levels of school SE with respect to any other level (χ2 = 38.93, p < 0.0001). Results from multinomial logistic regression analysis revealed that: (i) females perceived higher SE compared to males; (ii) children who performed better in SRT and 6MWT showed higher levels of perceived school SE; (iii) no significant effect was registered for the body weight. Alternative strategies are encouraged to enhance SE through physical education: structured interventions might enhance both complex motor skills and high-order cognitive skills, like SE, in young children. creator: Roberto Codella creator: Mariangela Valentina Puci creator: Matteo Vandoni creator: Luca Correale creator: Christel Galvani creator: Fabio Togni creator: Francesco Casolo creator: Alberto Passi creator: Claudio Orizio creator: Giampietro Alberti creator: Fabio Esposito creator: Cristina Montomoli creator: Antonio La Torre uri: https://doi.org/10.7717/peerj.8949 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Codella et al. title: Diversity and paleoenvironmental implications of an elasmobranch assemblage from the Oligocene–Miocene boundary of Ecuador link: https://peerj.com/articles/9051 last-modified: 2020-04-29 description: The occurrence and diversity of elasmobranchs from the Oligocene–Miocene boundary from Tropical America is poorly known in comparison with the paleodiversity from younger Neogene intervals of the region. Here we describe a new elasmobranch assemblage from the rich fossil site of Montañita-Olón (Dos Bocas Formation, Santa Elena, Ecuador), where other vertebrates have already been described: for example, sea turtles and cetaceans. We report a total of 27 elasmobranch taxa, 19 of which are new fossil records for Ecuador, 10 new records for the Central Eastern Pacific and four new records for South America. Additionally, in order to reconstruct the environment where these marine remains were deposited, we performed abundance, paleobathymetric and habitat preference analyses, concluding that they were likely deposited in an outer neritic (open shelf) environment. The study of Oligocene and early Miocene marine elasmobranchs faunas in Tropical America is key to addressing the issues in the evolutionary history of this group. creator: Jorge D. Carrillo-Briceño creator: Jaime A. Villafaña creator: Carlos De Gracia creator: F. Fernando Flores-Alcívar creator: René Kindlimann creator: Juan Abella uri: https://doi.org/10.7717/peerj.9051 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Carrillo-Briceño et al. title: A non-linear reverse-engineering method for inferring genetic regulatory networks link: https://peerj.com/articles/9065 last-modified: 2020-04-29 description: Hematopoiesis is a highly complex developmental process that produces various types of blood cells. This process is regulated by different genetic networks that control the proliferation, differentiation, and maturation of hematopoietic stem cells (HSCs). Although substantial progress has been made for understanding hematopoiesis, the detailed regulatory mechanisms for the fate determination of HSCs are still unraveled. In this study, we propose a novel approach to infer the detailed regulatory mechanisms. This work is designed to develop a mathematical framework that is able to realize nonlinear gene expression dynamics accurately. In particular, we intended to investigate the effect of possible protein heterodimers and/or synergistic effect in genetic regulation. This approach includes the Extended Forward Search Algorithm to infer network structure (top-down approach) and a non-linear mathematical model to infer dynamical property (bottom-up approach). Based on the published experimental data, we study two regulatory networks of 11 genes for regulating the erythrocyte differentiation pathway and the neutrophil differentiation pathway. The proposed algorithm is first applied to predict the network topologies among 11 genes and 55 non-linear terms which may be for heterodimers and/or synergistic effect. Then, the unknown model parameters are estimated by fitting simulations to the expression data of two different differentiation pathways. In addition, the edge deletion test is conducted to remove possible insignificant regulations from the inferred networks. Furthermore, the robustness property of the mathematical model is employed as an additional criterion to choose better network reconstruction results. Our simulation results successfully realized experimental data for two different differentiation pathways, which suggests that the proposed approach is an effective method to infer the topological structure and dynamic property of genetic regulations. creator: Siyuan Wu creator: Tiangang Cui creator: Xinan Zhang creator: Tianhai Tian uri: https://doi.org/10.7717/peerj.9065 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Wu et al. title: ECMPride: prediction of human extracellular matrix proteins based on the ideal dataset using hybrid features with domain evidence link: https://peerj.com/articles/9066 last-modified: 2020-04-29 description: Extracellular matrix (ECM) proteins play an essential role in various biological processes in multicellular organisms, and their abnormal regulation can lead to many diseases. For large-scale ECM protein identification, especially through proteomic-based techniques, a theoretical reference database of ECM proteins is required. In this study, based on the experimentally verified ECM datasets and by the integration of protein domain features and a machine learning model, we developed ECMPride, a flexible and scalable tool for predicting ECM proteins. ECMPride achieved excellent performance in predicting ECM proteins, with appropriate balanced accuracy and sensitivity, and the performance of ECMPride was shown to be superior to the previously developed tool. A new theoretical dataset of human ECM components was also established by applying ECMPride to all human entries in the SwissProt database, containing a significant number of putative ECM proteins as well as the abundant biological annotations. This dataset might serve as a valuable reference resource for ECM protein identification. creator: Binghui Liu creator: Ling Leng creator: Xuer Sun creator: Yunfang Wang creator: Jie Ma creator: Yunping Zhu uri: https://doi.org/10.7717/peerj.9066 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Liu et al. title: Reassessing the observational evidence for nitrogen deposition impacts in acid grassland: spatial Bayesian linear models indicate small and ambiguous effects on species richness link: https://peerj.com/articles/9070 last-modified: 2020-04-29 description: Nitrogen deposition (Ndep) is considered a significant threat to plant diversity in grassland ecosystems around the world. The evidence supporting this conclusion comes from both observational and experimental research, with “space-for-time” substitution surveys of pollutant gradients a significant portion of the former. However, estimates of regression coefficients for Ndep impacts on species richness, derived with a focus on causal inference, are hard to locate in the observational literature. Some influential observational studies have presented estimates from univariate models, overlooking the effects of omitted variable bias, and/or have used P-value-based stepwise variable selection (PSVS) to infer impacts, a strategy known to be poorly suited to the accurate estimation of regression coefficients. Broad-scale spatial autocorrelation has also generally been unaccounted for. We re-examine two UK observational datasets that have previously been used to investigate the relationship between Ndep and plant species richness in acid grasslands, a much-researched habitat in this context. One of these studies (Stevens et al., 2004, Science, 303: 1876–1879) estimated a large negative impact of Ndep on richness through the use of PSVS; the other reported smaller impacts (Maskell et al., 2010, Global Change Biology, 16: 671–679), but did not explicitly report regression coefficients or partial effects, making the actual size of the estimated Ndep impact difficult to assess. We reanalyse both datasets using a spatial Bayesian linear model estimated using integrated nested Laplace approximation (INLA). Contrary to previous results, we found similar-sized estimates of the Ndep impact on plant richness between studies, both with and without bryophytes, albeit with some disagreement over the most likely direction of this effect. Our analyses suggest that some previous estimates of Ndep impacts on richness from space-for-time substitution studies are likely to have been over-estimated, and that the evidence from observational studies could be fragile when confronted with alternative model specifications, although further work is required to investigate potentially nonlinear responses. Given the growing literature on the use of observational data to estimate the impacts of pollutants on biodiversity, we suggest that a greater focus on clearly reporting important outcomes with associated uncertainty, the use of techniques to account for spatial autocorrelation, and a clearer focus on the aims of a study, whether explanatory or predictive, are all required. creator: Oliver L. Pescott creator: Mark Jitlal uri: https://doi.org/10.7717/peerj.9070 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Pescott and Jitlal title: Bi-Level ventilation decreases pulmonary shunt and modulates neuroinflammation in a cardiopulmonary resuscitation model link: https://peerj.com/articles/9072 last-modified: 2020-04-29 description: BackgroundOptimal ventilation strategies during cardiopulmonary resuscitation are still heavily debated and poorly understood. So far, no convincing evidence could be presented in favour of outcome relevance and necessity of specific ventilation patterns. In recent years, alternative models to the guideline-based intermittent positive pressure ventilation (IPPV) have been proposed. In this randomized controlled trial, we evaluated a bi-level ventilation approach in a porcine model to assess possible physiological advantages for the pulmonary system as well as resulting changes in neuroinflammation compared to standard measures.MethodsSixteen male German landrace pigs were anesthetized and instrumented with arterial and venous catheters. Ventricular fibrillation was induced and the animals were left untreated and without ventilation for 4 minutes. After randomization, the animals were assigned to either the guideline-based group (IPPV, tidal volume 8–10 ml/kg, respiratory rate 10/min, FiO21.0) or the bi-level group (inspiratory pressure levels 15–17 cmH2O/5cmH2O, respiratory rate 10/min, FiO21.0). Mechanical chest compressions and interventional ventilation were initiated and after 5 minutes, blood samples, including ventilation/perfusion measurements via multiple inert gas elimination technique, were taken. After 8 minutes, advanced life support including adrenaline administration and defibrillations were started for up to 4 cycles. Animals achieving ROSC were monitored for 6 hours and lungs and brain tissue were harvested for further analyses.ResultsFive of the IPPV and four of the bi-level animals achieved ROSC. While there were no significant differences in gas exchange or hemodynamic values, bi-level treated animals showed less pulmonary shunt directly after ROSC and a tendency to lower inspiratory pressures during CPR. Additionally, cytokine expression of tumour necrosis factor alpha was significantly reduced in hippocampal tissue compared to IPPV animals.ConclusionBi-level ventilation with a constant positive end expiratory pressure and pressure-controlled ventilation is not inferior in terms of oxygenation and decarboxylation when compared to guideline-based IPPV ventilation. Additionally, bi-level ventilation showed signs for a potentially ameliorated neurological outcome as well as less pulmonary shunt following experimental resuscitation. Given the restrictions of the animal model, these advantages should be further examined. creator: Robert Ruemmler creator: Alexander Ziebart creator: Frances Kuropka creator: Bastian Duenges creator: Jens Kamuf creator: Andreas Garcia-Bardon creator: Erik K. Hartmann uri: https://doi.org/10.7717/peerj.9072 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Ruemmler et al. title: Purification, characterization and antioxidant activities in vitro of polysaccharides from Amaranthus hybridus L. link: https://peerj.com/articles/9077 last-modified: 2020-04-29 description: BackgroundAmaranthus hybridus L. is an annual, erect or less commonly ascending herb that is a member of the Amaranthaceae family. Polysaccharides extracted from traditional Chinese medicines may be effective substances with antioxidant activity.MethodsIn this study, we isolated crude polysaccharides from A. hybridus (AHP-M) using microwave-assisted extraction. Then, the AHP-M was purified by chromatography with DEAE-32 cellulose, and two fractions, AHP-M-1 and AHP-M-2, were obtained. The structural characteristics of AHP-M-1 and AHP-M-2 were investigated, and their antioxidant activities were analyzed in vitro.ResultsWe found that the monosaccharide composition of AHP-M-1 was different from that of AHP-M-2. The molecular weights of AHP-M-1 and AHP-M-2 were 77.625 kDa and 93.325 kDa, respectively. The results showed that the antioxidant activity of AHP-M-2 was better than that of AHP-M-1. For AHP-M-2, the DPPH radical scavenging rate at a concentration of 2 mg/mL was 78.87%, the hydroxyl radical scavenging rate was 39.34%, the superoxide anion radical scavenging rate was 80.2%, and the reduction ability of Fe3+ was approximately 0.90. The total antioxidant capacity per milligram of AHP-M-2 was 6.42, which was higher than that of Vitamin C (Vc).ConclusionThe in vitro test indicated that AHP-M-1 and AHP-M-2 have good antioxidant activity, demonstrating that A. hybridus L. polysaccharide has immense potential as a natural antioxidants. creator: Zizhong Tang creator: Caixia Zhou creator: Yi Cai creator: Yujia Tang creator: Wenjun Sun creator: Huipeng Yao creator: Tianrun Zheng creator: Hui Chen creator: Yirong Xiao creator: Zhi Shan creator: Tongliang Bu creator: Xiaoli Wang creator: Lin Huang creator: Lin Gou uri: https://doi.org/10.7717/peerj.9077 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Tang et al. title: Effect of stocking density and effective fiber on the ruminal bacterial communities in lactating Holstein cows link: https://peerj.com/articles/9079 last-modified: 2020-04-29 description: Overstocking can be a major issue in the dairy cattle industry, leading to negative changes in feeding and resting behavior. Additional stress imposed and alterations in feeding behavior may significantly impact the rumen microbiome. The rumen microbiome is responsible for the successful conversion of feed to usable energy for its host. Thus, understanding the effects of stocking density on the rumen microbiome is imperative for further elucidation of potentially negative consequences of overstocking in dairy cattle. This study implemented a Latin Square design accounting for four pens of cattle and four treatment periods so that all treatment combinations were assigned to every pen during one period of the study. Two treatment factors, including two levels of physically effective neutral detergent fiber, achieved with addition of chopped straw, and stocking density (100% vs. 142%) of freestalls and headlocks, were combined and tested within a factorial treatment design. Within each pen, three or four cannulated cows (n = 15 total) were sampled for rumen content on the final day of each treatment period. Each treatment was randomly assigned to a single pen for a 14-day period. The V1–V3 hypervariable regions of the 16S rRNA gene were targeted for bacterial analyses. Variables with approximately normally-distributed residuals and a Shapiro–Wilk statistic of ≥0.85 were analyzed using a mixed model analysis of variance with the GLIMMIX procedure with fixed effects of feed (straw vs. no straw), stocking density (100% vs. 142%), and the interaction of feed × stocking density, and random effects of pen, period, feed × stocking × pen × period. Pen was included as the experimental unit in a given period and the sampling unit as cow. Variables included Shannon’s Diversity Index, Faith’s phylogenetic diversity index, chao1, observed OTU, and Simpson’s evenness E as well as most individual taxa. Data were analyzed in SAS 9.4 utilizing the GLIMMIX procedure to perform mixed model analysis of variance. If data were not normally distributed, a ranked analysis was performed. No differences were observed in α-diversity metrics by fiber or stocking density (P > 0.05). Beta diversity was assessed using weighted and unweighted Unifrac distances in QIIME 1.9.1 and analyzed using ANOSIM. No differences were observed in weighted (P = 0.6660; R = −0.0121) nor unweighted (P = 0.9190; R = −0.0261) metrics and R values suggested similar bacterial communities among treatments. At the phylum level, Tenericutes differed among treatments with an interaction of stocking density by feed (P = 0.0066). At the genus level, several differences were observed by treatment, including Atopobium (P = 0.0129), unidentified members of order RF39 (P = 0.0139), and unidentified members of family Succinivibrionaceae (P = 0.0480). Although no diversity differences were observed, taxa differences may indicate that specific taxa are affected by the treatments, which may, in turn, affect animal production. creator: Brooke A. Clemmons creator: Mackenzie A. Campbell creator: Liesel G. Schneider creator: Richard J. Grant creator: Heather M. Dann creator: Peter D. Krawczel creator: Phillip R. Myer uri: https://doi.org/10.7717/peerj.9079 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Clemmons et al. title: Aberrant expression of two miRNAs promotes proliferation, hepatitis B virus amplification, migration and invasion of hepatocellular carcinoma cells: evidence from bioinformatic analysis and experimental validation link: https://peerj.com/articles/9100 last-modified: 2020-04-29 description: BackgroundAs key negative regulators of gene expression, microRNAs (miRNAs) play an important role in the onset and progression of hepatocellular carcinoma (HCC). This study aimed to identify the miRNAs involved in HCC carcinogenesis and their regulated genes.MethodsThe Gene Expression Omnibus (GEO) dataset (GSE108724) was chosen and explored to identify differentially expressed miRNAs using GEO2R. For the prediction of potential miRNA target genes, the miRTarBase was explored. Enrichment analysis of Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) was performed by the DAVID online tool. The hub genes were screened out using the CytoHubba plug-in ranked by degrees. The networks between miRNAs and hub genes were constructed by Cytoscape software. MiRNA mimics and negative control were transfected into HCC cell lines and their effects on proliferation, hepatitis B virus DNA (HBV-DNA) replication, TP53 expression, migration, and invasion were investigated. The following methods were employed: MTT assay, quantitative PCR (qPCR) assay, western blotting, wound healing assay, and transwell assay.ResultsA total of 50 differentially expressed miRNAs were identified, including 20 upregulated and 30 downregulated miRNAs, in HCC tumor tissues compared to matched adjacent tumor-free tissues. The top three upregulated (miR-221-3p, miR-222-3p, and miR-18-5p) and downregulated (miR-375, miR-214-3p and miR-378d) miRNAs, ranked by |log2 fold change (log2FC)|, were chosen and their potential target genes were predicted. Two gene sets, targeted by the upregulated and the downregulated miRNAs, were identified respectively. GO and KEGG pathway analysis showed that the predicted target genes of upregulated and downregulated miRNAs were mainly enriched in the cell cycle and cancer-related pathways. The top ten hub nodes of gene sets ranked by degrees were identified as hub genes. Analysis of miRNA-hub gene network showed that miR-221-3p and miR-375 modulated most of the hub genes, especially involving regulation of TP53. The q-PCR results showed that miR-221-3p and miR-375 were markedly upregulated and downregulated, respectively, in HCC cells and HCC clinical tissue samples compared to non-tumoral tissues. Furthermore, miR-221-3p overexpression significantly enhanced proliferation, HBV-DNA replication, as well as the migration and invasion of HCC cells, whereas miR-375 overexpression resulted in opposite effects. Western blotting analysis showed that the overexpression of miR-221-3p and miR-375 reduced and increased TP53 expression, respectively.ConclusionThe present study revealed that miR-211-3p and miR-375 may exert vital effects on cell proliferation, HBV-DNA replication, cell migration, and invasion through the regulation of TP53 expression in HCC. creator: Yanming Liu creator: Yue Cao creator: Wencan Cai creator: Liangyin Wu creator: Pingsen Zhao creator: Xin-guang Liu uri: https://doi.org/10.7717/peerj.9100 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Liu et al. title: intansv: an R package for integrative analysis of structural variations link: https://peerj.com/articles/8867 last-modified: 2020-04-28 description: Identification of structural variations between individuals is very important for the understanding of phenotype variations and diseases. Despite the existence of dozens of programs for prediction of structural variations, none of them is the golden standard in this field and the results of multiple programs were usually integrated to get more reliable predictions. Annotation and visualization of structural variations are important for the understanding of their functions. However, no program provides these functions currently as far as we are concerned. We report an R package, intansv, which can integrate the predictions of multiple programs as well as annotate and visualize structural variations. The source code and the help manual of intansv is freely available at https://github.com/venyao/intansv and http://www.bioconductor.org/packages/devel/bioc/html/intansv.html. creator: Lihua Jia creator: Na Liu creator: Fangfang Huang creator: Zhengfu Zhou creator: Xin He creator: Haoran Li creator: Zhizhan Wang creator: Wen Yao uri: https://doi.org/10.7717/peerj.8867 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Jia et al. title: Transient expression and purification of β-caryophyllene synthase in Nicotiana benthamiana to produce β-caryophyllene in vitro link: https://peerj.com/articles/8904 last-modified: 2020-04-28 description: The sesquiterpene β-caryophyllene is an ubiquitous component in many plants that has commercially been used as an aroma in cosmetics and perfumes. Recent studies have shown its potential use as a therapeutic agent and biofuel. Currently, β-caryophyllene is isolated from large amounts of plant material. Molecular farming based on the Nicotiana benthamiana transient expression system may be used for a more sustainable production of β-caryophyllene. In this study, a full-length cDNA of a new duplicated β-caryophyllene synthase from Artemisia annua (AaCPS1) was isolated and functionally characterized. In order to produce β-caryophyllene in vitro, the AaCPS1 was cloned into a plant viral-based vector pEAQ-HT. Subsequently, the plasmid was transferred into the Agrobacterium and agroinfiltrated into N. benthamiana leaves. The AaCPS1 expression was analyzed by quantitative PCR at different time points after agroinfiltration. The highest level of transcripts was observed at 9 days post infiltration (dpi). The AaCPS1 protein was extracted from the leaves at 9 dpi and purified by cobalt–nitrilotriacetate (Co-NTA) affinity chromatography using histidine tag with a yield of 89 mg kg−1 fresh weight of leaves. The protein expression of AaCPS1 was also confirmed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and western blot analyses. AaCPS1 protein uses farnesyl diphosphate (FPP) as a substrate to produce β-caryophyllene. Product identification and determination of the activity of purified AaCPS1 were done by gas chromatography–mass spectrometry (GC–MS). GC–MS results revealed that the AaCPS1 produced maximum 26.5 ± 1 mg of β-caryophyllene per kilogram fresh weight of leaves after assaying with FPP for 6 h. Using AaCPS1 as a proof of concept, we demonstrate that N. benthamiana can be considered as an expression system for production of plant proteins that catalyze the formation of valuable chemicals for industrial applications. creator: Saraladevi Muthusamy creator: Ramesh R. Vetukuri creator: Anneli Lundgren creator: Suresh Ganji creator: Li-Hua Zhu creator: Peter E. Brodelius creator: Selvaraju Kanagarajan uri: https://doi.org/10.7717/peerj.8904 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Muthusamy et al. title: Stomatal conductance bears no correlation with transpiration rate in wheat during their diurnal variation under high air humidity link: https://peerj.com/articles/8927 last-modified: 2020-04-28 description: A good understanding of the response of photosynthesis rate (PN) and transpiration rate (Tr) to stomatal alteration during the diurnal variations is important to cumulative photosynthetic production and water loss of crops. Six wheat genotypes were studied for 2 years with pot cultivation in rain-shelter. Among different genotypes, stomatal conductance (gs) was significantly correlated with both PN and Tr. But for each genotype, though gs was significantly correlated with PN regardless of relative air humidity (RH) status and it was also significantly correlated with Tr under lower RH (LRH, 15.4%) and moderate RH (MRH, 28.3%), it was not correlated with Tr under higher RH (HRH, 36.7%) during the diurnal changes. The conditional correlation between gs and Tr of wheat evoked new thinking on the relationships among gs, PN and Tr. Path analysis was further carried out to clarify the correlations of gs with the four atmospheric factors, that of Tr with gs and the four factors and the direct and indirect effects of the factors, during their diurnal dynamic variation. The effects of these factors on gs or Tr were related to RH. All the four factors had a much higher correlation with gs under HRH than that under LRH and MRH. Air temperature (T) had a rather higher direct effect than RH and photosynthetically active radiation (PAR). Also, the other factors had a much higher indirect effect on gs through vapor pressure deficit (VPD) and T. Transpiration rate was highly correlated with gs under LRH and MRH, with gs having a higher direct effect on it. In comparison, Tr was not correlated with gs under HRH but highly correlated with the atmospheric factors, with T, RH, and PAR having a higher indirect effect through VPD. creator: Xinying Zhang creator: Xurong Mei creator: Yajing Wang creator: Guirong Huang creator: Fu Feng creator: Xiaoying Liu creator: Rui Guo creator: Fengxue Gu creator: Xin Hu creator: Ziguang Yang creator: Xiuli Zhong creator: Yuzhong Li uri: https://doi.org/10.7717/peerj.8927 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Zhang et al. title: The mitochondrial phylogeny of land plants shows support for Setaphyta under composition-heterogeneous substitution models link: https://peerj.com/articles/8995 last-modified: 2020-04-28 description: Congruence among analyses of plant genomic data partitions (nuclear, chloroplast and mitochondrial) is a strong indicator of accuracy in plant molecular phylogenetics. Recent analyses of both nuclear and chloroplast genome data of land plants (embryophytes) have, controversially, been shown to support monophyly of both bryophytes (mosses, liverworts, and hornworts) and tracheophytes (lycopods, ferns, and seed plants), with mosses and liverworts forming the clade Setaphyta. However, relationships inferred from mitochondria are incongruent with these results, and typically indicate paraphyly of bryophytes with liverworts alone resolved as the earliest-branching land plant group. Here, we reconstruct the mitochondrial land plant phylogeny from a newly compiled data set. When among-lineage composition heterogeneity is accounted for in analyses of codon-degenerate nucleotide and amino acid data, the clade Setaphyta is recovered with high support, and hornworts are supported as the earliest-branching lineage of land plants. These new mitochondrial analyses demonstrate partial congruence with current hypotheses based on nuclear and chloroplast genome data, and provide further incentive for revision of how plants arose on land. creator: Filipe Sousa creator: Peter Civáň creator: João Brazão creator: Peter G. Foster creator: Cymon J. Cox uri: https://doi.org/10.7717/peerj.8995 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Sousa et al. title: Identification and expression analysis of the DREB transcription factor family in pineapple (Ananas comosus (L.) Merr.) link: https://peerj.com/articles/9006 last-modified: 2020-04-28 description: BackgroundDehydration responsive element-binding (DREB) transcription factors play a crucial role in plant growth, development and stress responses. Although DREB genes have been characterized in many plant species, genome-wide identification of the DREB gene family has not yet been reported in pineapple (Ananas comosus (L.) Merr.).ResultsUsing comprehensive genome-wide screening, we identified 20 AcoDREB genes on 14 chromosomes. These were categorized into five subgroups. AcoDREBs within a group had similar gene structures and domain compositions. Using gene structure analysis, we showed that most AcoDREB genes (75%) lacked introns, and that the promoter regions of all 20 AcoDREB genes had at least one stress response-related cis-element. We identified four genes with high expression levels and six genes with low expression levels in all analyzed tissues. We detected expression changes under abiotic stress for eight selected AcoDREB genes.ConclusionsThis report presents the first genome-wide analysis of the DREB transcription factor family in pineapple. Our results provide preliminary data for future functional analysis of AcoDREB genes in pineapple, and useful information for developing new pineapple varieties with key agronomic traits such as stress tolerance. creator: Mengnan Chai creator: Han Cheng creator: Maokai Yan creator: SVGN Priyadarshani creator: Man Zhang creator: Qing He creator: Youmei Huang creator: Fangqian Chen creator: Liping Liu creator: Xiaoyi Huang creator: Linyi Lai creator: Huihuang Chen creator: Hanyang Cai creator: Yuan Qin uri: https://doi.org/10.7717/peerj.9006 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Chai et al. title: Long-term continuously monocropped peanut significantly changed the abundance and composition of soil bacterial communities link: https://peerj.com/articles/9024 last-modified: 2020-04-28 description: Soil sickness is the progressive loss of soil quality due to continuous monocropping. The bacterial populations are critical to sustaining agroecosystems, but their responses to long-term peanut monocropping have not been determined. In this study, based on a previously constructed gradient of continuous monocropped plots, we tracked the detailed feedback responses of soil bacteria to short- and long-term continuous monocropping of four different peanut varieties using high-throughput sequencing techniques. The analyses showed that soil samples from 1- and 2-year monocropped plots were grouped into one class, and samples from the 11- and 12-year plots were grouped into another. Long-term consecutive monocropping could lead to a general loss in bacterial diversity and remarkable changes in bacterial abundance and composition. At the genera level, the dominant genus Bacillus changed in average abundance from 1.49% in short-term monocropping libraries to 2.96% in the long-term libraries. The dominant species Bacillus aryabhattai and Bacillus funiculus and the relatively abundant species Bacillus luciferensis and Bacillus decolorationis all showed increased abundance with long-term monocropping. Additionally, several other taxa at the genus and species level also presented increased abundance with long-term peanut monocropping; however, several taxa showed decreased abundance. Comparing analyses of predicted bacterial community functions showed significant changes at different KEGG pathway levels with long-term peanut monocropping. Combined with our previous study, this study indicated that bacterial communities were obviously influenced by the monocropping period, but less influenced by peanut variety and growth stage. Some bacterial taxa with increased abundance have functions of promoting plant growth or degrading potential soil allelochemicals, and should be closely related with soil remediation and may have potential application to relieve peanut soil sickness. A decrease in diversity and abundance of bacterial communities, especially beneficial communities, and simplification of bacterial community function with long-term peanut monocropping could be the main cause of peanut soil sickness. creator: Mingna Chen creator: Hu Liu creator: Shanlin Yu creator: Mian Wang creator: Lijuan Pan creator: Na Chen creator: Tong Wang creator: Xiaoyuan Chi creator: Binghai Du uri: https://doi.org/10.7717/peerj.9024 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Chen et al. title: First transcriptome analysis of bryozoan Fredericella sultana, the primary host of myxozoan parasite Tetracapsuloides bryosalmonae link: https://peerj.com/articles/9027 last-modified: 2020-04-28 description: Bryozoans are aquatic invertebrate moss animals that are found worldwide. Fredericella sultana is a freshwater bryozoan and is the most common primary host of myxozoan parasite, Tetracapsuloides bryosalmonae. However, limited genomic resources are available for this bryozoan, which hampers investigations into the molecular mechanisms of host-parasite interactions. To better understand these interactions, there is a need to build a transcriptome dataset of F. sultana, for functional genomics analysis by large-scale RNA sequencing. Total RNA was extracted from zooids of F. sultana cultivated under controlled laboratory conditions. cDNA libraries were prepared and were analyzed by the Illumina paired-ends sequencing. The sequencing data were used for de novo transcriptome assembly and functional annotation. Approximately 118 million clean reads were obtained, and assembled into 85,544 contigs with an average length of 852 bp, an N50 of 1,085 bp, and an average GC content 51.4%. A total of 23,978 (28%) contigs were annotated using BLASTX analysis. Of these transcripts, 4,400 contigs had highest similarity to brachiopod species Lingula anatina. Based on Gene ontology (GO) annotation, the most highly scored categories of biological process were categorized into cellular process (27%), metabolic process (24%), and biological regulation (8%) in the transcriptome of F. sultana. This study gives first insights into the transcriptome of F. sultana and provides comprehensive genetic resources for the species. We believe that the transcriptome of F. sultana will serve as a useful genomic dataset to accelerate research of functional genomics and will help facilitate whole genome sequencing and annotation. Candidate genes potentially involved in growth, proteolysis, and stress/immunity-response were identified, and are worthy of further investigation. creator: Gokhlesh Kumar creator: Reinhard Ertl creator: Jerri L. Bartholomew creator: Mansour El-Matbouli uri: https://doi.org/10.7717/peerj.9027 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Kumar et al. title: The GAR domain integrates functions that are necessary for the proper localization of fibrillarin (FBL) inside eukaryotic cells link: https://peerj.com/articles/9029 last-modified: 2020-04-28 description: Fibrillarin (FBL) is an essential nucleolar protein that participates in pre-rRNA methylation and processing. The methyltransferase domain of FBL is an example of an extremely well-conserved protein domain in which the amino acid sequence was not substantially modified during the evolution from Archaea to Eukaryota. An additional N-terminal glycine–arginine-rich (GAR) domain is present in the FBL of eukaryotes. Here, we demonstrate that the GAR domain is involved in FBL functioning and integrates the functions of the nuclear localization signal and the nucleolar localization signal (NoLS). The methylation of the arginine residues in the GAR domain is necessary for nuclear import but decreases the efficiency of nucleolar retention via the NoLS. The presented data indicate that the GAR domain can be considered an evolutionary innovation that integrates several functional activities and thereby adapts FBL to the highly compartmentalized content of the eukaryotic cell. creator: Maria Y. Shubina creator: Eugene A. Arifulin creator: Dmitry V. Sorokin creator: Mariya A. Sosina creator: Maria A. Tikhomirova creator: Marina V. Serebryakova creator: Tatiana Smirnova creator: Svyatoslav S. Sokolov creator: Yana R. Musinova creator: Eugene V. Sheval uri: https://doi.org/10.7717/peerj.9029 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Shubina et al. title: Two species of Thoracostomopsidae (Nematoda: Enoplida) from Jeju Island, South Korea link: https://peerj.com/articles/9037 last-modified: 2020-04-28 description: During a survey of intertidal zones at beaches on Jeju Island, two species belonging to the family Thoracostomopsidae were discovered. One new species, Enoploides koreanus sp. nov. and one known species, Epacanthion hirsutumShi & Xu, 2016 are reported. Along with morphological analysis, mitochondrial cytochrome oxidase c subunit 1 (mtCOI) sequences and 18S rRNA sequences of the species were also obtained and used to check relative p-distance and phylogenetic positions. While most species of Enoploides have long spicules, the new species belongs to a group of Enoploides with short spicules < 150 µm). Of the seven species with short spicules, the new species is most closely related to E. disparilisSergeeva, 1974. They both have similar body length, fairly similar sized and shaped spicules with small gubernaculum running parallel to distal end of spicule, and an index value of b. The new species can be distinguished from E. disparilis by having pre-anal supplementary organ with short conical tail, while E. disparilis lacks pre-anal supplementary organ and has a long conico-cylindrical tail. Along with the description of the new species, the genus EnoploidesSsaweljev, 1912 is bibliographically reviewed and revised. Of 45 species described to date, 27 are now considered valid, 16 species inquirendae due to inadequate descriptions and ambiguity of the material examined, along with two cases of nomen nudum. With this review, we provide an updated diagnosis and list of valid species, a tabular key comparing diagnostic characters of all valid species, and a new complete key to species. One known species, Epacanthion hirsutumShi & Xu, 2016, is reported in Korea for the first time. The morphology agrees well with the original description provided by Shi & Xu, 2016. As they had already reviewed the genus at the time of reporting four Epacanthion species, we provide only a description, depiction, and measurements for comparison purposes. creator: Raehyuk Jeong creator: Alexei V. Tchesunov creator: Wonchoel Lee uri: https://doi.org/10.7717/peerj.9037 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Jeong et al. title: Impact of Phellinus gilvus mycelia on growth, immunity and fecal microbiota in weaned piglets link: https://peerj.com/articles/9067 last-modified: 2020-04-28 description: BackgroundAntibiotics are the most commonly used growth-promoting additives in pig feed especially for weaned piglets. But in recent years their use has been restricted because of bacterial resistance. Phellinus, a genus of medicinal fungi, is widely used in Asia to treat gastroenteric dysfunction, hemrrhage, and tumors. Phellinus is reported to improve body weight on mice with colitis. Therefore, we hypothesize that it could benefit the health and growth of piglets, and could be used as an alternative to antibiotic. Here, the effect of Phellinus gilvus mycelia (SH) and antibiotic growth promoter (ATB) were investigated on weaned piglets.MethodsA total of 72 crossbred piglets were randomly assigned to three dietary treatment groups (n = 4 pens per treatment group with six piglets per pen). The control group was fed basal diet; the SH treatment group was fed basal diet containing 5 g/kg SH; the ATB treatment group was feed basal diet containing 75 mg/kg aureomycin and 20 mg/kg kitasamycin. The experiment period was 28 days. Average daily gain (ADG), average daily feed intake (ADFI), and feed intake to gain ratio were calculated. The concentrations of immunoglobulin G (IgG), interleukin-1β (IL-1β), tumor necrosis factor (TNF)-α and myeloperoxidase (MPO) in serum were assessed. Viable plate counts of Escherichia coli in feces were measured. Fecal microbiota was analyzed via the 16S rRNA gene sequencing method.ResultsThe ADG (1–28 day) of piglets was significantly higher in SH and ATB treatment groups (P < 0.05) compared to the control, and the ADG did not show significant difference between SH and ATB treatment groups (P > 0.05). Both SH and ATB treatments increased the MPO, IL-1β, and TNF-α levels in serum compared to the control (P < 0.05), but the levels in SH group were all significantly higher than in the ATB group (P < 0.05). Fecal microbiological analysis showed that viable E. coli counts were dramatically decreased by SH and ATB. The 16S rRNA gene sequencing analysis showed that ATB shifted the microbiota structure drastically, and significantly increased the relative abundance of Prevotella, Megasphaera, and Faecalibacterium genera. But SH slightly influenced the microbiota structure, and only increased the relative abundance of Alloprevotella genus.ConclusionOur work demonstrated that though SH slightly influenced the microbiota structure, it markedly reduced the fecal E. coli population, and improved growth and innate immunity in piglets. Our finding suggested that SH could be an alternative to ATB in piglet feed. creator: Yuqing Sun creator: Shi Zhong creator: Bo Deng creator: Qinsheng Jin creator: Jie Wu creator: Jinxi Huo creator: Jianxun Zhu creator: Cheng Zhang creator: Yougui Li uri: https://doi.org/10.7717/peerj.9067 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Sun et al. title: Size matters: micro-evolution in Polynesian rats highlights body size changes as initial stage in evolution link: https://peerj.com/articles/9076 last-modified: 2020-04-28 description: Microevolutionary patterns in populations of introduced rodent species have often been the focus of analytic studies for their potential relevance to understanding vertebrate evolution. The Polynesian rat (Rattus exulans) is an excellent proxy species because of its wide geographic and temporal distribution: its native and introduced combined range spans half the globe and it has been living for at least seven centuries wherever it was introduced. The objective of this study was to assess the effects of long-term isolation (insularity; up to 4,000 years) and geographic variables on skull shape variation using geometric morphometrics. A sample of 513 specimens from 103 islands and four mainland areas was analysed. This study, to my knowledge the first to extensively sample introduced rats, analysed 59 two-dimensional landmarks on the skull. Landmarks were obtained in three separate aspects (dorsal, lateral, ventral skull view). The coordinate data were then subjected to a multivariate ordination analysis (principal components analysis, or PCA), multivariate regressions, and a canonical variates analysis (CVA). Three measures of disparity were evaluated for each view. The results show that introduced Polynesian rats evolve skull shapes that conform to the general mammalian interspecific pattern of cranial evolutionary allometry (CREA), with proportionally longer snouts in larger specimens. In addition, larger skulls are more tubular in shape than the smaller skulls, which are more balloon-shaped with a rounder and wider braincase relative to those of large skulls. This difference is also observed between the sexes (sexual dimorphism), due to the slightly larger average male size. Large, tubular skulls with long snouts are typical for Polynesia and Remote Oceania, where no native mammals occur. The greater disparity of Polynesian rats on mammal species-poor islands (’exulans-only’ region) provides further insight into how diversity may affect diversification through ecological release from predators and competitors. creator: Alexandra A.E. van der Geer uri: https://doi.org/10.7717/peerj.9076 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 van der Geer title: Knockdown of CDCA8 inhibits the proliferation and enhances the apoptosis of bladder cancer cells link: https://peerj.com/articles/9078 last-modified: 2020-04-28 description: Bladder cancer is a tumour of the urinary system with high mortality, and there is also a great lack of therapeutic targets in the clinic. Cell division cycle associated 8 (CDCA8), an important component of the vertebrate chromosomal passenger complex, is highly expressed in various tumours and promotes tumour development. However, the role of CDCA8 in bladder cancer is not fully understood. This study aimed to reveal the function of CDCA8 in bladder cancer by determining the relationship between CDCA8 expression and proliferation, metastasis and apoptosis of bladder cancer cells. Firstly, we studied the mRNA expression of CDCA8 through the Gene Expression Omnibus (GEO) and the Cancer Genome Atlas (TCGA) databases and analysed the correlation between CDCA8 expression and prognosis of patients with bladder cancer. We also verified CDCA8 expression in bladder cancer tissues by immunohistochemistry. In addition, CDCA8 expression was inhibited in bladder cancer T24 and 5637 cells, and the effects of CDCA8 on the proliferation, migration and invasion of bladder cancer cell lines were investigated using cell counting kit-8, colony formation, cell cycle, apoptosis, wound healing and Transwell invasion assays. Results showed that CDCA8 was highly expressed in bladder cancer compared with normal tissues, and the high CDCA8 expression was significantly correlated with the poor prognosis of patients. Inhibiting CDCA8 expression inhibited the proliferation, migration and invasion of T24 and 5637 cells and induced the apoptosis of bladder cancer cells. CDCA8 was involved in the regulation of the growth cycle of bladder cancer cells. Bioinformatics-based mechanism analysis revealed that high CDCA8 expression may affect the cell cycle and P53 signalling pathways. In conclusion, our results suggest that CDCA8 is highly expressed in bladder cancer and can promote tumour development. Hence, CDCA8 may serve as an effective therapeutic target for treatment of bladder cancer. creator: Xin Gao creator: Xiaohong Wen creator: Haowei He creator: Linlin Zheng creator: Yibo Yang creator: Jinlian Yang creator: Haifang Liu creator: Xiguo Zhou creator: Changshun Yang creator: Yinyi Chen creator: Mei Chen creator: Shufang Zhang uri: https://doi.org/10.7717/peerj.9078 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Gao et al. title: Estimation of soil salt content by combining UAV-borne multispectral sensor and machine learning algorithms link: https://peerj.com/articles/9087 last-modified: 2020-04-28 description: Soil salinization is a global problem closely related to the sustainable development of social economy. Compared with frequently-used satellite-borne sensors, unmanned aerial vehicles (UAVs) equipped with multispectral sensors provide an opportunity to monitor soil salinization with on-demand high spatial and temporal resolution. This study aims to quantitatively estimate soil salt content (SSC) using UAV-borne multispectral imagery, and explore the deep mining of multispectral data. For this purpose, a total of 60 soil samples (0–20 cm) were collected from Shahaoqu Irrigation Area in Inner Mongolia, China. Meanwhile, from the UAV sensor we obtained the multispectral data, based on which 22 spectral covariates (6 spectral bands and 16 spectral indices) were constructed. The sensitive spectral covariates were selected by means of gray relational analysis (GRA), successive projections algorithm (SPA) and variable importance in projection (VIP), and from these selected covariates estimation models were built using back propagation neural network (BPNN) regression, support vector regression (SVR) and random forest (RF) regression, respectively. The performance of the models was assessed by coefficient of determination (R2), root mean squared error (RMSE) and ratio of performance to deviation (RPD). The results showed that the estimation accuracy of the models had been improved markedly using three variable selection methods, and VIP outperformed GRA and GRA outperformed SPA. However, the model accuracy with the three machine learning algorithms turned out to be significantly different: RF > SVR > BPNN. All the 12 SSC estimation models could be used to quantitatively estimate SSC (RPD > 1.4) while the VIP-RF model achieved the highest accuracy (Rc2 = 0.835, RP2 = 0.812, RPD = 2.299). The result of this study proved that UAV-borne multispectral sensor is a feasible instrument for SSC estimation, and provided a reference for further similar research. creator: Guangfei Wei creator: Yu Li creator: Zhitao Zhang creator: Yinwen Chen creator: Junying Chen creator: Zhihua Yao creator: Congcong Lao creator: Huifang Chen uri: https://doi.org/10.7717/peerj.9087 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Wei et al. title: Measuring recognition memory in zebrafish larvae: issues and limitations link: https://peerj.com/articles/8890 last-modified: 2020-04-27 description: Recognition memory is the capacity to recognize previously encountered objects, events or places. This ability is crucial for many fitness-related activities, and it appears very early in the development of several species. In the laboratory, recognition memory is most often investigated using the novel object recognition test (NORt), which exploits the tendency of most vertebrates to explore novel objects over familiar ones. Despite that the use of larval zebrafish is rapidly increasing in research on brain, cognition and neuropathologies, it is unknown whether larvae possess recognition memory and whether the NORt can be used to assess it. Here, we tested a NOR procedure in zebrafish larvae of 7-, 14- and 21-days post-fertilization (dpf) to investigate when recognition memory first appears during ontogeny. Overall, we found that larvae explored a novel stimulus longer than a familiar one. This response was fully significant only for 14-dpf larvae. A control experiment evidenced that larvae become neophobic at 21-dpf, which may explain the poor performance at this age. The preference for the novel stimulus was also affected by the type of stimulus, being significant with tri-dimensional objects varying in shape and bi-dimensional geometrical figures but not with objects differing in colour. Further analyses suggest that lack of effect for objects with different colours was due to spontaneous preference for one colour. This study highlights the presence of recognition memory in zebrafish larvae but also revealed non-cognitive factors that may hinder the application of NORt paradigms in the early developmental stages of zebrafish. creator: Matteo Bruzzone creator: Elia Gatto creator: Tyrone Lucon Xiccato creator: Luisa Dalla Valle creator: Camilla Maria Fontana creator: Giacomo Meneghetti creator: Angelo Bisazza uri: https://doi.org/10.7717/peerj.8890 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Bruzzone et al. title: Direct measurement forest carbon protocol: a commercial system-of-systems to incentivize forest restoration and management link: https://peerj.com/articles/8891 last-modified: 2020-04-27 description: Forest carbon sequestration offsets are methodologically uncertain, comprise a minor component of carbon markets and do not effectively slow deforestation. The objective of this study is to describe a commercial scale in situ measurement approach for determination of net forest carbon sequestration projects, the Direct Measurement Forest Carbon Protocol™, to address forest carbon market uncertainties. In contrast to protocols that rely on limited forest mensuration, growth simulation and exclusion of CO2 data, the Direct Measurement Forest Carbon Protocol™ is based on standardized methods for direct determination of net ecosystem exchange (NEE) of CO2 employing eddy covariance, a meteorological approach integrating forest carbon fluxes. NEE is used here as the basis for quantifying the first of its kind carbon financial products. The DMFCP differentiates physical, project and financial carbon within a System-of-Systems™ (SoS) network architecture. SoS sensor nodes, the Global Monitoring Platform™ (GMP), housing analyzers for CO2 isotopologues (e.g., 12CO2,13CO2, 14CO2) and greenhouse gases are deployed across the project landscape. The SoS standardizes and automates GMP measurement, uncertainty and reporting functions creating diverse forest carbon portfolios while reducing cost and investment risk in alignment with modern portfolio theory. To illustrate SoS field deployment and operation, published annual NEE data for a tropical (Ankasa Park, Ghana, Africa) and a deciduous forest (Harvard Forest, Petersham, MA, USA) are used to forecast carbon revenue. Carbon pricing scenarios are combined with historical in situ NEE annual time-series to extrapolate pre-tax revenue for each project applied to 100,000 acres (40,469 hectares) of surrounding land. Based on carbon pricing of $5 to $36 per ton CO2 equivalent (tCO2eq) and observed NEE sequestration rates of 0.48 to 15.60 tCO2eq acre−1 yr−1, pre-tax cash flows ranging from $230,000 to $16,380,000 across project time-series are calculated, up to 5×  revenue for contemporary voluntary offsets, demonstrating new economic incentives to reverse deforestation. The SoS concept of operation and architecture, with engineering development, can be extended to diverse gas species across terrestrial, aquatic and oceanic ecosystems, harmonizing voluntary and compliance market products worldwide to assist in the management of global warming. The Direct Measurement Forest Carbon Protocol reduces risk of invalidation intrinsic to estimation-based protocols such as the Climate Action Reserve and the Clean Development Mechanism that do not observe molecular CO2 to calibrate financial products. Multinational policy applications such as the Paris Agreement and the United Nations Reducing Emissions from Deforestation and Degradation, constrained by Kyoto Protocol era processes, will benefit from NEE measurement avoiding unsupported claims of emission reduction, fraud, and forest conservation policy failure. creator: Bruno D.V. Marino creator: Vinh Truong creator: J. William Munger creator: Richard Gyimah uri: https://doi.org/10.7717/peerj.8891 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Marino et al. title: Uricase-deficient rat is generated with CRISPR/Cas9 technique link: https://peerj.com/articles/8971 last-modified: 2020-04-27 description: Urate oxidase (uricase, Uox) is a big obstacle for scientists to establish stable animal models for studying hyperuricemia and associated disorders. Due to the low survival rate of uricase-deficient mice, we generated a Uox-knockout model animal from Sprague Dawley (SD) rats using the CRISPR/Cas9 technique by deleting exons 2 to 4 of the Uox gene. The uricase-deficient rats were named “Kunming-DY rats”, and were apparently healthy with more than a 95% survival up to one year. The male rats’ serum uric acid (SUA) increased to 48.3  ± 19.1 µg/ml, significantly higher than those of wild-type rats. Some indexes of the blood fat like total triglyceride, low density lipoprotein, and renal function indexes including blood urea nitrogen and serum creatinine were significantly different from those of wild-type rats, however, all the indexes were close to or in normal ranges. Histological renal changes including mild glomerular/tubular lesions were observed in these uricase-deficient rats. Thus, “Kunming-DY rats” with stable uricase-deficiency were successfully established and are an alternative model animal to study hyperuricemia and associated diseases mimicking human conditions. creator: Yun Yu creator: Nan Zhang creator: Xianxiang Dong creator: Nan Fan creator: Lei Wang creator: Yuhui Xu creator: Huan Chen creator: Weigang Duan uri: https://doi.org/10.7717/peerj.8971 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Yu et al. title: Carbon dioxide fluxes in a farmland ecosystem of the southern Chinese Loess Plateau measured using a chamber-based method link: https://peerj.com/articles/8994 last-modified: 2020-04-27 description: BackgroundFarmland accounts for a relatively large fraction of the world’s vegetation cover, and the quantification of carbon fluxes over farmland is critical for understanding regional carbon budgets. The carbon cycle of farmland ecosystems has become a focus of global research in the field of carbon dynamics and cycling. The objectives of this study are to monitor the temporal variation in the net ecosystem exchange (NEE) and soil respiration in a spring maize (Zea mays L.) farmland ecosystem of the southern Loess Plateau of China.MethodsA fully automated temperature-controlled flux chamber system was adopted in this study. The system contained nine chambers for CO2 flux measurements, and three treatments were conducted: with and without maize plants in the chamber, as well as a bare field. Observations were conducted from June to September 2011. This time period covers the seedling, jointing, heading, grain filling, and ripening stages of spring maize. Other factors, such as air temperature (Ta), soil temperature (Ts), soil water content (SWC), photosynthetically active radiation (PAR), and precipitation (P), were simultaneously monitored.ResultsThere was observed diurnal variation in the NEE of the maize ecosystem (NEE-maize). A short “noon break” occurred when the PAR intensity was at its maximum, while soil respiration rates had curves with a single peak. During the overall maize growth season, the total NEE-maize was –68.61 g C m−2, and the soil respiration from the maize field (SR-maize) and bare field (SR-bare field) were 245.69 g C m−2 and 114.08 g C m−2, respectively. The temperature sensitivity of soil respiration in the maize field exceeded that in the bare field. Significant negative correlations were found between the NEE, PAR, and temperature (all p-values < 0.01), with both Ta and PAR being the primary factors that affected the CO2 fluxes, collectively contributing 61.7%, 37.2%, and 56.8% to the NEE-maize, SR-maize, and SR-bare field, respectively. It was therefore concluded that both meteorological factors and farming practices have an important impact on the carbon balance process in corn farmland ecosystems. However, it is necessary to conduct long-term observational studies, in order to get a better understanding of the driving mechanism. creator: Fengru Fang creator: Xiaoyang Han creator: Wenzhao Liu creator: Ming Tang uri: https://doi.org/10.7717/peerj.8994 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Fang et al. title: A new species of Cenopalpus Pritchard & Baker (Acari: Tenuipalpidae) from Japan, with ontogeny of chaetotaxy and a key to the world species link: https://peerj.com/articles/9081 last-modified: 2020-04-27 description: A new species of flat mite, Cenopalpus umbellatus sp. nov. (Acari: Trombidiformes: Tenuipalpidae) is described and illustrated based on females, males, deutonymphs, protonymphs and larvae. The morphological ontogeny in idiosomal and leg chaetotaxy is briefly described for all stages. Mite specimens were collected from the leaves of Rhaphiolepis indica var. umbellata Makino (Rosaceae), an evergreen shrub native to Japan. An identification key to the world species of Cenopalpus is also provided. creator: Mohamed W. Negm creator: Edward A. Ueckermann creator: Tetsuo Gotoh uri: https://doi.org/10.7717/peerj.9081 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Negm et al. title: Patterns of association of native and exotic boring polychaetes on the southeastern Pacific coast of Chile: the combined importance of negative, positive and random interactions link: https://peerj.com/articles/8560 last-modified: 2020-04-24 description: BackgroundStudies of biological invasions focus on negative interactions between exotic and native biotas, emphasizing niche overlap between species and competitive exclusion. However, the effects of positive interactions and coexistence are poorly known. In this study we evaluate the importance of positive, negative, or random species associations in explaining the coexistence of native and exotic boring polychaetes inhabiting invertebrate hosts, on the southeastern Pacific coast of Chile. We assess three hypotheses to explain the observed patterns: positive species interactions, weak competitive interactions, and competitive intransitivity.MethodologyTo assess the potential effect of competition between native and exotic polychaetes we analyzed patterns of co-occurrence of species pairs in northern and southern regions, using the metric of the probabilistic model. Since biotic interactions can affect not only native species, we also evaluated correlations between native and exotic polychaete abundance, using reduced major axis regression linear models. To assess the transitivity of competitive hierarchies we used metrics and analytical methods based on abundance matrices to estimate species competition and patch transition matrices.ResultsOn average 50% of the species pairs presented significant weak negative associations, all associated with the exotic species Polydora rickettsi; the remaining 50% had random associations, and none showed positive associations. However, the relationship of abundance between native and exotic boring polychates supports a tendency towards coexistence. At local and regional scales, we observed the presence of a transitive network competition structure, where the exotic boring polychaete, P. rickettsi was generally the dominant species.ConclusionsOur results support that native and exotic boring polychaete species coexist through weak competitive interactions. Nevertheless, the large number of random interactions observed indicates that species coexistence can be accounted for by stochastic processes, as proposed by neutral theory. Coexistence may be a frequent result of interactions between native and exotic species, although less apparent than competitive exclusion. Thus, the probabilistic point-of-view used here provides a statistical tool for evaluating coexistence as a result of exotic and native species’ interactions, an idea which has been proposed in invasion ecology, but largely lacks empirical support and methodologies for detecting underlying mechanisms. Finally, we found evidence that P. rickettsi is a successful invader by being competitively dominant, but not excluding other species. creator: Paula E. Neill creator: Nicolás Rozbaczylo creator: Cristóbal Villaseñor-Parada creator: Garen Guzmán-Rendón creator: Sandra Sampértegui creator: Cristián E. Hernández uri: https://doi.org/10.7717/peerj.8560 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Neill et al. title: Yearling proportion correlates with habitat structure in a boreal forest landbird community link: https://peerj.com/articles/8898 last-modified: 2020-04-24 description: Landbird vital rates, such as productivity and adult survivorship, can be estimated by modeling mist-netting capture data. The proportion in which an adult breeding bird is 1 year of age (a “yearling”), however, has been studied only minimally in a few landbird species. Here we relate yearling proportion to habitat-structure covariates, including reclamation age, in a boreal forest landbird community. Data were collected at 35 constant-effort mist-netting stations over a 6-year period, and consisted of 12,714 captures of adults, of 29 landbird species, including 4,943 captures of yearlings. Accuracy of age determination (yearling or older) was assessed based on recapture data and error rates were estimated at a mean of 8.1% (range 0.0–19.4%) among the 29 species, with 20 species showing age-error rates <10%. The estimated mean yearling proportion was 0.407, ranging from 0.178 to 0.613 among species. Remote-sensed Enhanced Vegetation Index (EVI), a measure of habitat greenness, was positively correlated with age since reclamation up to 20 years, at which time it became comparable to that of natural stations. The probability of capturing a yearling for species associated with mature forest was lower at stations with higher EVI and the opposite was the case for species favoring successional habitats. These results suggest that yearling birds are being excluded from preferred breeding habitats by older birds through despotism and/or that yearlings are simply selecting poorer habitat due to lack of breeding experience or other factors. This dynamic appears to be operating in multiple species within this forest landbird community. Captured yearlings may also be “floaters”, or non-breeding individuals not holding territories. However, presuming that yearlings show lower reproductive success whether floating or not, our results suggest that stations with high yearling proportions could be located within sink as opposed to source habitats. Overall, we infer that yearling proportion may become an important vital-rate measure of habitat quality and reclamation efforts, when combined with indices of population size, productivity, reproductive condition and survivorship. creator: Peter Pyle creator: Kenneth R. Foster creator: Christine M. Godwin creator: Danielle R. Kaschube creator: James F. Saracco uri: https://doi.org/10.7717/peerj.8898 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Pyle et al. title: The association between a free medicine program and functioning in people with schizophrenia: a cross-sectional study in Liuyang, China link: https://peerj.com/articles/8929 last-modified: 2020-04-24 description: BackgroundPersons with schizophrenia frequently discontinue or avoid medications. Under a national community-based mental health program many places in China have started to provide free medications to people with severe mental health disorders in their communities. In the free medication program (FMP) in Liuyang, China, peripatetic psychiatrists prescribed and dispensed antipsychotic medications free of charge at regular intervals and places convenient for all patients through the primary health care system since 2006. Our study aims to test whether adherence to this FMP improves the functioning of people with schizophrenia.MethodsThe research was conducted in Liuyang, a rural county in central China. Data were obtained from three sources: an ad-hoc survey and the program’s management system in 2013 and in-home interviews in 2014 in Liuyang. We conducted a cross-sectional propensity-score based analysis of the “dose” effect of FMP participation on their level of functioning, using medication refill adherence as a proxy for the participatory intensity in the program.ResultsOnly 50.9% of 2,332 participants came for all refills in 2012. Higher refill adherence was associated with slightly worse functional outcomes. The main reasons for refill non-adherence were “unwilling to take medication or only took medication when unwell” (23.6%), “forgot or missed the appointment” (20.6%) and “hospitalized” (20.1%).ConclusionsThe FMP program in Liuyang seemed to have successfully removed barriers in cost and access. However, better refill adherence was not associated with better functional outcomes in this study, which might have been the result of reverse causation. To improve the effectiveness of the FMP, patient-centered measures should be considered. creator: Wenjie Gong creator: Chao Zhang creator: Dong (Roman) Xu creator: Shuiyuan Xiao creator: Yu Yu creator: Eric D. Caine uri: https://doi.org/10.7717/peerj.8929 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Gong et al. title: Exosomes derived from M0, M1 and M2 macrophages exert distinct influences on the proliferation and differentiation of mesenchymal stem cells link: https://peerj.com/articles/8970 last-modified: 2020-04-24 description: BackgroundDifferent phenotypes of macrophages (M0, M1 and M2 Mφs) have been demonstrated to play distinct roles in regulating mesenchymal stem cells in various in vitro and in vivo systems. Our previous study also found that cell-conditioned medium (CM) derived from M1 Mφs supported the proliferation and adipogenic differentiation of bone marrow mesenchymal stem cells (BMMSCs), whereas CM derived from either M0 or M2 Mφs showed an enhanced effect on cell osteogenic differentiation. However, the underlying mechanism remains incompletely elucidated. Exosomes, as key components of Mφ-derived CM, have received increasing attention. Therefore, it is possible that exosomes may modulate the effect of Mφ-derived CM on the property of BMMSCs. This hypothesis was tested in the present study.MethodsIn this study, RAW264.7 cells were induced toward M1 or M2 polarization with different cytokines, and exosomes were isolated from the unpolarized (M0) and polarized (M1 and M2) Mφs. Mouse BMMSCs were then cultured with normal complete medium or inductive medium supplemented with M0-Exos, M1-Exos or M2-Exos. Finally, the proliferation ability and the osteogenic, adipogenic and chondrogenic differentiation capacity of the BMMSCs were measured and analyzed.ResultsWe found that only the medium containing M1-Exos, rather than M0-Exos or M2-Exos, supported cell proliferation and osteogenic and adipogenic differentiation. This was inconsistent with CM-based incubation. In addition, all three types of exosomes had a suppressive effect on chondrogenic differentiation.ConclusionAlthough our data demonstrated that exosomes and CM derived from the same phenotype of Mφs didn’t exert exactly the same cellular influences on the cocultured stem cells, it still confirmed the hypothesis that exosomes are key regulators during the modulation effect of Mφ-derived CM on BMMSC property. creator: Yu Xia creator: Xiao-Tao He creator: Xin-Yue Xu creator: Bei-Min Tian creator: Ying An creator: Fa-Ming Chen uri: https://doi.org/10.7717/peerj.8970 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Xia et al. title: Identification of exosomal miRNAs associated with the anthracycline-induced liver injury in postoperative breast cancer patients by small RNA sequencing link: https://peerj.com/articles/9021 last-modified: 2020-04-24 description: BackgroundAnthracycline-induced liver injury (AILI) is one of the serious complications of anthracycline-based adjuvant chemotherapy for postoperative breast cancer patients. Exosomal miRNAs, as signaling molecules in intercellular communication, play the essential roles in drug-induced liver injury (DILI). However, the expression profiles of them in patients with AILI remains unknown.MethodsSeven post-chemotherapy patients were recruited in this study. After isolated plasma-derived exosomes, small RNA sequencing revealed exosomal miRNA profiles and differentially expressed miRNAs (DE-miRNAs) were identified between the liver injury group and non-liver injury group. miRTarBase and miRDB were used to predict the potential target genes of DE-miRNAs. DILI-related genes were downloaded from the CTD Database. The intersection of predicted genes and DILI-related genes were identified as the AILI-related target genes of the DE-miRNAs. GO annotation and KEGG pathway enrichment analysis were performed by the DAVID database. Furthermore, the protein-protein interaction (PPI) network was established by the STRING database and essential exosomal miRNAs were identified via Cytoscape software.ResultsA total of 30 DE-miRNAs and 79 AILI-related target genes were identified. AILI-related target genes of the DE-miRNAs are significantly enriched in NOD-like receptor signaling pathway, the HIF-1 signaling pathway, and the FoxO signaling pathway. Then, the hub genes were screened and we discovered that IL-6 and SOD2 are the most critical genes that may be involved in the development of AILI through the activation of immune response and the occurrence of oxidative stress, respectively. In addition, we found that miR-1-3p could potentially regulate most of the hub genes in the miRNA-hub gene network.ConclusionWe explored the potential functions of DE-miRNAs and suggested exosomal miR-1-3p might be the essential exosomal miRNA in the pathogenesis of AILI. Moreover, our study provided an experimental basis for experimental verification to reveal the actual function and mechanism of miRNAs in AILI. creator: Yue Zhang creator: Di Wang creator: Di Shen creator: Yang Luo creator: Yi-Qun Che uri: https://doi.org/10.7717/peerj.9021 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhang et al. title: A scoping review of determinants of performance in dressage link: https://peerj.com/articles/9022 last-modified: 2020-04-24 description: As a first step in achieving an evidence-based classification system for the sport of Para Dressage, there is a clear need to define elite dressage performance. Previous studies have attempted to quantify performance with able-bodied riders using scientific methods; however, definitive measures have yet to be established for the horse and/or the rider. This may be, in part, due to the variety of movements and gaits that are found within a dressage test and also due to the complexity of the horse-rider partnership. The aim of this review is therefore to identify objective measurements of horse performance in dressage and the functional abilities of the rider that may influence them to achieve higher scores. Five databases (SportDiscuss, CINAHL, MEDLINE, EMBASE, VetMed) were systematically searched from 1980 to May 2018. Studies were included if they fulfilled the following criteria: (1) English language; (2) employ objective, quantitative outcome measures for describing equine and human performance in dressage; (3) describe objective measures of superior horse performance using between-subject comparisons and/or relating outcome measures to competitive scoring methods; (4) describe demands of dressage using objective physiological and/or biomechanical measures from human athletes and/or how these demands are translated into superior performance. In total, 773 articles were identified. Title and abstract screening resulted in 155 articles that met the eligibility criteria, 97 were excluded during the full screening of articles, leaving 58 included articles (14 horse, 44 rider) involving 311 equine and 584 able-bodied human participants. Mean ± sd (%) quality scores were 63.5 ± 15.3 and 72.7 ± 14.7 for the equine and human articles respectively. Significant objective measures of horse performance (n = 12 articles) were grouped into themes and separated by gait/movement. A range of temporal variables that indicated superior performance were found in all gaits/movements. For the rider, n = 5 articles reported variables that identified significant differences in skill level, which included the postural position and ROM of the rider’s pelvis, trunk, knee and head. The timing of rider pelvic and trunk motion in relation to the movement of the horse emerged as an important indicator of rider influence. As temporal variables in the horse are consistently linked to superior performance it could be surmised that better overall dressage performance requires minimal disruption from the rider whilst the horse maintains a specific gait/movement. Achieving the gait/movement in the first place depends upon the intrinsic characteristics of the horse, the level of training achieved and the ability of the rider to apply the correct aid. The information from this model will be used to develop an empirical study to test the relative strength of association between impairment and performance in able-bodied and Para Dressage riders. creator: Sarah Jane Hobbs creator: Lindsay St George creator: Janet Reed creator: Rachel Stockley creator: Clare Thetford creator: Jonathan Sinclair creator: Jane Williams creator: Kathryn Nankervis creator: Hilary M. Clayton uri: https://doi.org/10.7717/peerj.9022 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Hobbs et al. title: Dietary squid paste supplementation promotes feed intake via brain-gut dynamic response in Chinese soft-shelled turtle Pelodiscus sinensis link: https://peerj.com/articles/9031 last-modified: 2020-04-24 description: BackgroundAs the primary source of protein for aquaculture, fishmeal has reached the extremity of sustainable development, our previous studies have proven that rice protein concentrate and squid paste are outstanding protein source and stimulant for Pelodiscus sinensis. However, little attention has been given to the molecular mechanism of the appetite modulated by the dietary nutrient factor, especially for a reptile. Thus, the present study aimed to evaluate feed intake and brain-gut dynamic responses to dietary rice protein concentrate and squid paste in Chinese soft-shelled turtle Pelodiscus sinensis.MethodsThree isonitrogenous and isoenergetic practical diets were formulated including 60% fishmeal (CT), 42% fishmeal + 18% rice protein concentrate (RP) and 42% fishmeal + 18% rice protein concentrate + 1% squid paste (RPS), respectively. Microcapsule lysine was supplemented in RP and RPS diets to balance the amino acid profile. Turtles (initial weight 30.65 ± 0.97 g) were fed three times daily to apparent satiation. After the 8-week feeding trial, the turtles were exposed to 48h food deprivation, then the dynamic expression of the orexigenic and anorexigenic peptides were measured.ResultsThe results showed that no significant effect was observed on feed intake when fishmeal was replaced by rice protein concentrate (P = 0.421), while significantly improved feed intake was found by squid paste supplemented (P = 0.02). The mRNA expression of anorexigenic peptides, such as leptin receptor, insulin receptor, pro-opiomelanocortin, cocaine and amphetamine-regulated transcript, cholecystokinin (and its receptor) and glucagon-like peptide-1 receptor in the brain increased significantly at 3 h past feeding (P < 0.05), and then decreased. Nevertheless, neuropeptide Y and peptide YY mRNA expression showed the valley at 3h and peak at 12h past feeding. Intestinal cholecystokinin receptor and glucagon-like peptide-1 receptor mRNA expression showed no difference during the postprandial time (P > 0.05). The results suggested that squid paste is an outstanding stimulant for Pelodiscus sinensis. Furthermore, the orexigenic and anorexigenic peptides evaluated here might play an essential role in short-term fasting to this species, of which the dynamic expression levels were regulated by squid paste. creator: Cunxin Sun creator: Yu Qian creator: Wenbin Liu creator: Weina Xu creator: Kaizhou Wang creator: Bo Liu uri: https://doi.org/10.7717/peerj.9031 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Sun et al. title: Ursolic acid improves the bacterial community mapping of the intestinal tract in liver fibrosis mice link: https://peerj.com/articles/9050 last-modified: 2020-04-24 description: Liver fibrosis often appears in chronic liver disease, with extracellular matrix (ECM) deposition as the main feature. Due to the presence of the liver-gut axis, the destruction of intestinal homeostasis is often accompanied by the development of liver fibrosis. The inconsistent ecological environment of different intestinal sites may lead to differences in the microbiota. The traditional Chinese medicine ursolic acid (UA) has been proven to protect the liver from fibrosis. We investigated the changes in the microbiota of different parts of the intestine during liver fibrosis and the effect of UA on these changes based on high-throughput sequencing technology. Sequencing results suggest that the diversity and abundance of intestinal microbiota decline and the composition of the microbiota is disordered, the potentially beneficial Firmicutes bacteria are reduced, and the pathways for functional prediction are changed in the ilea and anal faeces of liver fibrosis mice compared with normal mice. However, in UA-treated liver fibrosis mice, these disorders improved. It is worth noting that the bacterial changes in the ilea and anal faeces are not consistent. In conclusion, in liver fibrosis, the microbiota of different parts of the intestines have different degrees of disorder, and UA can improve this disorder. This may be a potential mechanism for UA to achieve anti-fibrosis. This study provides theoretical guidance for the UA targeting of intestinal microbiota for the treatment of liver fibrosis. creator: Sizhe Wan creator: Chenkai Huang creator: Anjiang Wang creator: Xuan Zhu uri: https://doi.org/10.7717/peerj.9050 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wan et al. title: Predictive value of three Inflammation-based Glasgow Prognostic Scores for major cardiovascular adverse events in patients with acute myocardial infarction during hospitalization: a retrospective study link: https://peerj.com/articles/9068 last-modified: 2020-04-24 description: AimInflammation-based Glasgow Prognostic Scores (GPS) have been reported to predict the prognosis of patients with acute ST-elevation myocardial infarction (STEMI) undergoing primary percutaneous coronary intervention (PPCI). The goal of this study was to investigate whether three kinds of GPSs can effectively predict major cardiovascular adverse events (MACEs) in STEMI or non-ST-segment elevation myocardial infarction (NSTEMI) patients undergoing PPCI, elective PCI (EPCI) or conservative drug therapy during hospitalization.MethodsIn this retrospective cohort study, patients with acute myocardial infarction (AMI) were divided into 0, 1 or 2 score according to the GPSs. Logistic regression and receiver operating characteristic (ROC) curve analysis were performed to assess the predictive value of GPSs for MACE and all-cause mortality during hospitalization. Three kinds of GPSs, Inflammation-based Glasgow Prognostic Score (GPS), modified GPS (MGPS) and high-sensitivity CRP-modified GPS (HS-MGPS) and Global Registry of Acute Coronary Events (GRACE) score were applied in this study.ResultsA total of 188 patients were enrolled. The ROC curve with MACE showed that the AUC of GPS (0.820 (95% confidence interval (CI) [0.754–0.885]), P < 0.001) was larger than that of MGPS (0.789 (95% CI [0.715–0.863]), P < 0.001), HS-MGPS (0.787 (95% CI [0.717–0.856]), P < 0.001) and GRACE score (0.743 (95% CI [0.672–0.814]), P < 0.001). The ROC curve with all-cause mortality showed that the AUC of GPS (0.696 (95% CI [0.561–0.831]), P = 0.005) was similar to the HS-MGPS (0.698 (95% CI [0.569–0.826]), P = 0.005) and higher than the MGPS (0.668 (95% CI [0.525–0.812]), P = 0.016), but lower than the GRACE score (0.812 (95% CI [0.734–0.889]), P < 0.001). Multivariate logistic regression analysis showed that the GPS was an independent risk factor for the incidence of MACE during hospitalization. Compared with the odds ratio (OR) value for a GPS of 0, the OR for a GPS of 1 was 7.173 (95% CI [2.425–21.216]), P < 0.001), and that for a GPS of 2 was 18.636 (95% CI [5.813–59.746]), P < 0.001), but not an independent risk factor for all-cause mortality (P = 0.302). GRACE score was an independent risk factor for MACE (1.019 (95% CI [1.004–1.035]), P = 0.015) and all-cause mortality (1.040 (95% CI [1.017–1.064]), P = 0.001). In the subgroups classified according to the type of AMI, the presence of disease interference GPSs and the type of PCI, the ability of GPS to predict the occurrence of MACE seemed to be greater than that of MGPS and HS-MGPS.ConclusionThe GPS has a good predictive value for the occurrence of MACE during hospitalization in patients with AMI, regardless of STEMI or NSTEMI, the choice of PCI mode and the presence or absence of diseases that interfere with GPS. However, GPS is less predictive of all-cause mortality during hospitalization than GRACE score, which may be due to the interference of patients with other diseases. creator: Houyong Zhu creator: Zhaodong Li creator: Xiaoqun Xu creator: Xiaojiang Fang creator: Tielong Chen creator: Jinyu Huang uri: https://doi.org/10.7717/peerj.9068 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Zhu et al. title: Multi-walled carbon nanotubes produced after forest fires improve germination and development of Eysenhardtia polystachya link: https://peerj.com/articles/8634 last-modified: 2020-04-23 description: BackgroundMulti-walled carbon nanotubes (MWCNTs) are nanoparticles with countless applications. MWCNTs are typically of synthetic origin. However, recently, the formation of MWCNTs in nature after forest fires has been documented. Previous reports have demonstrated the positive effects of synthetic MWCNTs on the germination and development of species of agronomic interest; nevertheless, there is practically no information on how synthetic or natural MWCNTs affect forest plant development. In this report, based on insights from dose-response assays, we elucidate the comparative effects of synthetic MWCNTs, amorphous carbon, and natural MWCNTs obtained after a forest fire on Eysenhardtia polystachya plant.MethodsE. polystachya seeds were sown in peat moss-agrolite substrate and conserved in a shade house. Germination was recorded daily up to 17 days after sowing, and plant development (manifested in shoot and root length, stem diameter, foliar area, and root architecture parameters) was recorded 60 days after sowing.ResultsThe treatments with natural MWCNTs accelerated the emergence and improved the germination of this plant, thus while untreated seeds achieve 100% of germination within 16th day, seeds supplemented with natural MWCNTs at doses of 20 µg/mL achieve the above percentage within the 4th day. Natural MWCNTs also promoted fresh and dry biomass in all applied treatments, specially at doses of 40 µg/mL where natural MWCNTs significantly promoted leaf number, root growth, and the dry and fresh weights of shoots and roots of seedlings. Seeds supplemented with doses between 20 and 40 µg/mL of amorphous carbon achieving 100% of germination within the 6th day; however, seeds supplemented either with doses of 60 µg/mL of the above carbon or with synthetic MWCNTs at all the tested concentrations could achieve at most 80 % and 70% of germination respectively within the 17 days. Finally, neither treatments added with amorphous carbon nor those added with synthetic MWCNTs, showed significant increases in the fresh and dry biomass of the tested plant. Likewise, the survival of seedlings was reduced between 10 and 20 % with 40 and 60 µg/mL of amorphous carbon, and with synthetic MWCNTs in all the doses applied was reduced at 30% of survival plants.ConclusionsThese findings indicate that MWCNTs produced by wildfire act as plant growth promoters, contributing to the germination and development of adapted to fire-prone conditions species such as E. polystachya. creator: Gladys Juárez-Cisneros creator: Mariela Gómez-Romero creator: Homero Reyes de la Cruz creator: Jesús Campos-García creator: Javier Villegas uri: https://doi.org/10.7717/peerj.8634 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Juárez-Cisneros et al. title: Comparative proteogenomics profiling of non-small and small lung carcinoma cell lines using mass spectrometry link: https://peerj.com/articles/8779 last-modified: 2020-04-23 description: BackgroundEvidences indicated that non-small-cell lung cancer (NSCLC) and small-cell lung cancer (SCLC) might originate from the same cell type, which however ended up to be two different subtypes of lung carcinoma, requiring different therapeutic regimens. We aimed to identify the differences between these two subtypes of lung cancer by using integrated proteome and genome approaches.Methods and MaterialsTwo representative cell lines for each lung cancer subtype were comparatively analysed by quantitative proteomics, and their corresponding transcriptomics data were obtained from the Gene Expression Omnibus database. The integrated analyses of proteogenomic data were performed to determine key differentially expressed proteins that were positively correlated between proteomic and transcriptomic data.ResultThe proteomics analysis revealed 147 differentially expressed proteins between SCLC and NSCLC from a total of 3,970 identified proteins. Combined with available transcriptomics data, we further confirmed 14 differentially expressed proteins including six known and eight new lung cancer related proteins that were positively correlated with their transcriptomics data. These proteins are mainly involved in cell migration, proliferation, and invasion.ConclusionThe proteogenomic data on both NSCLC and SCLC cell lines presented in this manuscript is complementary to existing genomic and proteomic data related to lung cancers and will be crucial for a systems biology-level understanding of the molecular mechanism of lung cancers. The raw mass spectrometry data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD015270. creator: Jingyu Wu creator: Zhifang Hao creator: Chen Ma creator: Pengfei Li creator: Liuyi Dang creator: Shisheng Sun uri: https://doi.org/10.7717/peerj.8779 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wu et al. title: Lightness induction enhancements and limitations at low frequency modulations across a variety of stimulus contexts link: https://peerj.com/articles/8918 last-modified: 2020-04-23 description: Lightness illusions are often studied under static viewing conditions with figures varying in geometric design, containing different types of perceptual grouping and figure-ground cues. A few studies have explored the perception of lightness induction while modulating lightness illusions continuously in time, where changes in perceived lightness are often linked to the temporal modulation frequency, up to around 2–4 Hz. These findings support the concept of a cut-off frequency for lightness induction. However, another critical change (enhancement) in the magnitude of perceived lightness during slower temporal modulation conditions has not been addressed in previous temporal modulation studies. Moreover, it remains unclear whether this critical change applies to a variety of lightness illusion stimuli, and the degree to which different stimulus configurations can demonstrate enhanced lightness induction in low modulation frequencies. Therefore, we measured lightness induction strength by having participants cancel out any perceived modulation in lightness detected over time within a central target region, while the surrounding context, which ultimately drives the lightness illusion, was viewed in a static state or modulated continuously in time over a low frequency range (0.25–2 Hz). In general, lightness induction decreased as temporal modulation frequency was increased, with the strongest perceived lightness induction occurring at lower modulation frequencies for visual illusions with strong grouping and figure-ground cues. When compared to static viewing conditions, we found that slow continuous surround modulation induces a strong and significant increase in perceived lightness for multiple types of lightness induction stimuli. Stimuli with perceptually ambiguous grouping and figure-ground cues showed weaker effects of slow modulation lightness enhancement. Our results demonstrate that, in addition to the existence of a cut-off frequency, an additional critical temporal modulation frequency of lightness induction exists (0.25–0.5 Hz), which instead maximally enhances lightness induction and seems to be contingent upon the prevalence of figure-ground and grouping organization. creator: Louis Nicholas Vinke creator: Arash Yazdanbakhsh uri: https://doi.org/10.7717/peerj.8918 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Vinke and Yazdanbakhsh title: “Candidatus Trichorickettsia mobilis”, a Rickettsiales bacterium, can be transiently transferred from the unicellular eukaryote Paramecium to the planarian Dugesia japonica link: https://peerj.com/articles/8977 last-modified: 2020-04-23 description: Most of the microorganisms responsible for vector-borne diseases (VBD) have hematophagous arthropods as vector/reservoir. Recently, many new species of microorganisms phylogenetically related to agents of VBD were found in a variety of aquatic eukaryotic hosts; in particular, numerous new bacterial species related to the genus Rickettsia (Alphaproteobacteria, Rickettsiales) were discovered in protist ciliates and other unicellular eukaryotes. Although their pathogenicity for humans and terrestrial animals is not known, several indirect indications exist that these bacteria might act as etiological agents of possible VBD of aquatic organisms, with protists as vectors. In the present study, a novel strain of the Rickettsia-Like Organism (RLO) endosymbiont “Candidatus (Ca.) Trichorickettsia mobilis” was identified in the macronucleus of the ciliate Paramecium multimicronucleatum. We performed transfection experiments of this RLO to planarians (Dugesia japonica) per os. Indeed, the latter is a widely used model system for studying bacteria pathogenic to humans and other Metazoa. In transfection experiments, homogenized paramecia were added to food of antibiotic-treated planarians. Treated and non-treated (i.e. control) planarians were investigated at day 1, 3, and 7 after feeding for endosymbiont presence by means of PCR and ultrastructural analyses. Obtained results were fully concordant and suggest that this RLO endosymbiont can be transiently transferred from ciliates to metazoans, being detected up to day 7 in treated planarians’ enterocytes. Our findings might offer insights into the potential role of ciliates or other protists as putative vectors for diseases caused by Rickettsiales or other RLOs and occurring in fish farms or in the wild. creator: Letizia Modeo creator: Alessandra Salvetti creator: Leonardo Rossi creator: Michele Castelli creator: Franziska Szokoli creator: Sascha Krenek creator: Valentina Serra creator: Elena Sabaneyeva creator: Graziano Di Giuseppe creator: Sergei I. Fokin creator: Franco Verni creator: Giulio Petroni uri: https://doi.org/10.7717/peerj.8977 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Modeo et al. title: Site selection for subtropical thicket restoration: mapping cold-air pooling in the South African sub-escarpment lowlands link: https://peerj.com/articles/8980 last-modified: 2020-04-23 description: Restoration of subtropical thicket in South Africa using the plant Portulacaria afra (an ecosystem engineer) has been hampered, in part, by selecting sites that are frost prone—this species is intolerant of frost. Identifying parts of the landscape that are exposed to frost is often challenging. Our aim is to calibrate an existing cold-air pooling (CAP) model to predict where frost is likely to occur in the valleys along the sub-escarpment lowlands (of South Africa) where thicket is dominant. We calibrated this model using two valleys that have been monitored during frost events. To test the calibrated CAP model, model predictions of frost-occurrence for six additional valleys were assessed using a qualitative visual comparison of existing treelines in six valleys—we observe a strong visual match between the predicted frost and frost-free zones with the subtropical thicket (frost-intolerant) and Nama-Karoo shrubland (frost-tolerant) treelines. In addition, we tested the model output using previously established transplant experiments; ∼300 plots planted with P. afra (known as the Thicket-Wide Plots) were established across the landscape—without consideration of frost—to assess the potential factors influencing the survival and growth of P. afra. Here we use a filtered subset of these plots (n = 70), and find that net primary production of P. afra was significantly lower in plots that the model predicted to be within the frost zone. We suggest using this calibrated CAP model as part of the site selection process when restoring subtropical thicket in sites that lie within valleys—avoiding frost zones will greatly increase the likelihood of restoration success. creator: Robbert Duker creator: Richard M. Cowling creator: Marius L. van der Vyver creator: Alastair J. Potts uri: https://doi.org/10.7717/peerj.8980 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Duker et al. title: Proteomic analysis and interactions network in leaves of mycorrhizal and nonmycorrhizal sorghum plants under water deficit link: https://peerj.com/articles/8991 last-modified: 2020-04-23 description: For understanding the water deficit stress mechanism in sorghum, we conducted a physiological and proteomic analysis in the leaves of Sorghum bicolor L. Moench (a drought tolerant crop model) of non-colonized and colonized plants with a consortium of arbuscular mycorrhizal fungi. Physiological results indicate that mycorrhizal fungi association enhances growth and photosynthesis in plants, under normal and water deficit conditions. 2D-electrophoresis profiles revealed 51 differentially accumulated proteins in response to water deficit, of which HPLC/MS successfully identified 49. Bioinformatics analysis of protein–protein interactions revealed the participation of different metabolic pathways in nonmycorrhizal compared to mycorrhizal sorghum plants under water deficit. In noninoculated plants, the altered proteins are related to protein synthesis and folding (50S ribosomal protein L1, 30S ribosomal protein S10, Nascent polypeptide-associated complex subunit alpha), coupled with multiple signal transduction pathways, guanine nucleotide-binding beta subunit (Rack1) and peptidyl-prolyl-cis-trans isomerase (ROC4). In contrast, in mycorrhizal plants, proteins related to energy metabolism (ATP synthase-24kDa, ATP synthase β), carbon metabolism (malate dehydrogenase, triosephosphate isomerase, sucrose-phosphatase), oxidative phosphorylation (mitochondrial-processing peptidase) and sulfur metabolism (thiosulfate/3-mercaptopyruvate sulfurtransferase) were found. Our results provide a set of proteins of different metabolic pathways involved in water deficit produced by sorghum plants alone or associated with a consortium of arbuscular mycorrhizal fungi isolated from the tropical rain forest Los Tuxtlas Veracruz, México. creator: Víctor Olalde-Portugal creator: José Luis Cabrera-Ponce creator: Argel Gastelum-Arellanez creator: Armando Guerrero-Rangel creator: Robert Winkler creator: Silvia Valdés-Rodríguez uri: https://doi.org/10.7717/peerj.8991 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Olalde-Portugal et al. title: Identification and in silico structural and functional analysis of a trypsin-like protease from shrimp Macrobrachium carcinus link: https://peerj.com/articles/9030 last-modified: 2020-04-23 description: Macrobrachium carcinus (Linnaeus, 1758) is a species of freshwater shrimp widely distributed from Florida southwards to southern Brazil, including southeast of Mexico. In the present work, we identified a putative trypsin-like protease cDNA fragment of 736 nucleotides from M. carcinus hepatopancreas tissue by the 3′RACE technique and compared the deduced amino acid sequence to other trypsin-related proteases to describe its structure and function relationship. The bioinformatics analyses showed that the deduced amino acid sequence likely corresponds to a trypsin-like protease closely related to brachyurins, which comprise a subset of serine proteases with collagenolytic activity found in crabs and other crustacea. The M. carcinus trypsin-like protease sequence showed a global sequence identity of 94% with an unpublished trypsin from Macrobrachium rosenbergii (GenBank accession no. AMQ98968), and only 57% with Penaeus vannamei trypsin (GenBank accession no. CAA60129). A detailed analysis of the amino acid sequence revealed specific differences with crustacean trypsins, such as the sequence motif at the beginning of the mature protein, activation mechanism of the corresponding zymogen, amino acid residues of the catalytic triad and residues responsible for substrate specificity. creator: José M. Viader-Salvadó creator: José Alberto Aguilar Briseño creator: Juan A. Gallegos-López creator: José A. Fuentes-Garibay creator: Carlos Alfonso Alvarez-González creator: Martha Guerrero-Olazarán uri: https://doi.org/10.7717/peerj.9030 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Viader-Salvadó et al. title: Monitoring body condition score of reintroduced banteng (Bos javanicus D’Alton, 1923) into Salakphra Wildlife Sanctuary, Thailand link: https://peerj.com/articles/9041 last-modified: 2020-04-23 description: BackgroundBanteng (Bos javanicus d’Alton 1823) are an endangered species, highly sensitive to habitat structure and quality. In many areas, banteng were extinct and needed to be reintroduced to restore their population. Thus, understanding the responses of body condition of reintroduced banteng to their habitat was important for ensuring the sustainability of a reintroduction program. The aim of the present study was to evaluate the body condition of banteng after reintroduction into the Salakphra Wildlife Sanctuary in Thailand based on photographs from camera-traps carried out between July 2016 and November 2018.MethodsSeven banteng were bred at the Khao Nampu Nature and Wildlife Education Center and systematically reintroduced into the Salakphra Wildlife Sanctuary in December 2015 (four) and July 2016 (three). The seven reintroduced adults and two newborns (from the 2015 group) were captured via camera traps in 2018. The body condition scoring (BCS) obtained from these photographs was used to identify the individual performance of all seven adults after their reintroduction.ResultsThe BCS scores in reintroduced adult banteng, both males and females, (between 5 and 7 years old) increased significantly over time after reintroduction into a natural habitat (p < 0.05), although the BCS scores in females were not significantly different between the second and third years (p > 0.05).ConclusionsThe results from the present study suggest that camera traps are a practical tool to assess the BCS of reintroduced banteng, and can be used to monitor their condition post-release. These techniques may be appropriate for translocation programs elsewhere. creator: Praeploy Kongsurakan creator: Rattanawat Chaiyarat creator: Seree Nakbun creator: Nikorn Thongthip creator: Panat Anuracpreeda uri: https://doi.org/10.7717/peerj.9041 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Kongsurakan et al. title: Neither heat pulse, nor multigenerational exposure to a modest increase in water temperature, alters the susceptibility of Guadeloupean Biomphalaria glabrata to Schistosoma mansoni infection link: https://peerj.com/articles/9059 last-modified: 2020-04-23 description: There are increasing concerns regarding the role global climate change will have on many vector-borne diseases. Both mathematical models and laboratory experiments suggest that schistosomiasis risk may change as a result of the effects of increasing temperatures on the planorbid snails that host schistosomes. Heat pulse/heat shock of the BS90 strain of Biomphalaria glabrata was shown to increase the rate of infection by Schistosoma mansoni, but the result was not replicable in a follow up experiment by a different lab. We characterised the susceptibility and cercarial shedding of Guadeloupean B. glabrata after infection with S. mansoni under two temperature regimes: multigenerational exposure to small increases in temperature, and extreme heat pulse events. Neither long-term, multigenerational rearing at elevated temperatures, nor transient heat pulse modified the susceptibility of Guadeloupean B. glabrata to infection (prevalence) or shedding of schistosome cercaria (intensity of infection). These findings suggest that heat pulse-induced susceptibility in snail hosts may be dependent on the strain of the snail and/or schistosome, or on some as-yet unidentified environmental co-factor. creator: Euan R.O. Allan creator: Stephanie Bollmann creator: Ekaterina Peremyslova creator: Michael Blouin uri: https://doi.org/10.7717/peerj.9059 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Allan et al. title: Insight into the kinematics of blue whale surface foraging through drone observations and prey data link: https://peerj.com/articles/8906 last-modified: 2020-04-22 description: To understand how predators optimize foraging strategies, extensive knowledge of predator behavior and prey distribution is needed. Blue whales employ an energetically demanding lunge feeding method that requires the whales to selectively feed where energetic gain exceeds energetic loss, while also balancing oxygen consumption, breath holding capacity, and surface recuperation time. Hence, blue whale foraging behavior is primarily driven by krill patch density and depth, but many studies have not fully considered surface feeding as a significant foraging strategy in energetic models. We collected predator and prey data on a blue whale (Balaenoptera musculus brevicauda) foraging ground in New Zealand in February 2017 to assess the distributional and behavioral response of blue whales to the distribution and density of krill prey aggregations. Krill density across the study region was greater toward the surface (upper 20 m), and blue whales were encountered where prey was relatively shallow and more dense. This relationship was particularly evident where foraging and surface lunge feeding were observed. Furthermore, New Zealand blue whales also had relatively short dive times (2.83 ± 0.27 SE min) as compared to other blue whale populations, which became even shorter at foraging sightings and where surface lunge feeding was observed. Using an unmanned aerial system (UAS; drone) we also captured unique video of a New Zealand blue whale’s surface feeding behavior on well-illuminated krill patches. Video analysis illustrates the whale’s potential use of vision to target prey, make foraging decisions, and orient body mechanics relative to prey patch characteristics. Kinematic analysis of a surface lunge feeding event revealed biomechanical coordination through speed, acceleration, head inclination, roll, and distance from krill patch to maximize prey engulfment. We compared these lunge kinematics to data previously reported from tagged blue whale lunges at depth to demonstrate strong similarities, and provide rare measurements of gape size, and krill response distance and time. These findings elucidate the predator-prey relationship between blue whales and krill, and provide support for the hypothesis that surface feeding by New Zealand blue whales is an important component to their foraging ecology used to optimize their energetic efficiency. Understanding how blue whales make foraging decisions presents logistical challenges, which may cause incomplete sampling and biased ecological knowledge if portions of their foraging behavior are undocumented. We conclude that surface foraging could be an important strategy for blue whales, and integration of UAS with tag-based studies may expand our understanding of their foraging ecology by examining surface feeding events in conjunction with behaviors at depth. creator: Leigh G. Torres creator: Dawn R. Barlow creator: Todd E. Chandler creator: Jonathan D. Burnett uri: https://doi.org/10.7717/peerj.8906 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Torres et al. title: The use of pseudo-multivariate standard error to improve the sampling design of coral monitoring programs link: https://peerj.com/articles/8429 last-modified: 2020-04-22 description: The characteristics of coral reef sampling and monitoring are highly variable, with numbers of units and sampling effort varying from one study to another. Numerous works have been carried out to determine an appropriate effect size through statistical power; however, these were always from a univariate perspective. In this work, we used the pseudo multivariate dissimilarity-based standard error (MultSE) approach to assess the precision of sampling scleractinian coral assemblages in reefs of Venezuela between 2017 and 2018 when using different combinations of number of transects, quadrats and points. For this, the MultSE of 36 sites previously sampled was estimated, using four 30m-transects with 15 photo-quadrats each and 25 random points per quadrat. We obtained that the MultSE was highly variable between sites and is not correlated with the univariate standard error nor with the richness of species. Then, a subset of sites was re-annotated using 100 uniformly distributed points, which allowed the simulation of different numbers of transects per site, quadrats per transect and points per quadrat using resampling techniques. The magnitude of the MultSE stabilized by adding more transects, however, adding more quadrats or points does not improve the estimate. For this case study, the error was reduced by half when using 10 transects, 10 quadrats per transect and 25 points per quadrat. We recommend the use of MultSE in reef monitoring programs, in particular when conducting pilot surveys to optimize the estimation of the community structure. creator: Luis M. Montilla creator: Emy Miyazawa creator: Alfredo Ascanio creator: María López-Hernández creator: Gloria Mariño-Briceño creator: Zlatka Rebolledo-Sánchez creator: Andreína Rivera creator: Daniela S. Mancilla creator: Alejandra Verde creator: Aldo Cróquer uri: https://doi.org/10.7717/peerj.8429 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Montilla et al. title: The corepressor NCOR1 and OCT4 facilitate early reprogramming by suppressing fibroblast gene expression link: https://peerj.com/articles/8952 last-modified: 2020-04-22 description: Reprogramming somatic cells to induced pluripotent stem cells (iPSC) succeeds only in a small fraction of cells within the population. Reprogramming occurs in distinctive stages, each facing its own bottlenecks. It initiates with overexpression of transcription factors OCT4, SOX2, KLF4 and c-MYC (OSKM) in somatic cells such as mouse embryonic fibroblasts (MEFs). OSKM bind chromatin, silencing the somatic identity and starting the stepwise reactivation of the pluripotency programme. However, inefficient suppression of the somatic lineage leads to unwanted epigenetic memory from the tissue of origin, even in successfully generated iPSCs. Thus, it is essential to shed more light on chromatin regulators and processes involved in dissolving the somatic identity. Recent work characterised the role of transcriptional corepressors NCOR1 and NCOR2 (also known as NCoR and SMRT), showing that they cooperate with c-MYC to silence pluripotency genes during late reprogramming stages. NCOR1/NCOR2 were also proposed to be involved in silencing fibroblast identity, however it is unclear how this happens. Here, we shed light on the role of NCOR1 in early reprogramming. We show that siRNA-mediated ablation of NCOR1 and OCT4 results in very similar phenotypes, including transcriptomic changes and highly correlated high-content colony phenotypes. Both NCOR1 and OCT4 bind to promoters co-occupied by c-MYC in MEFs. During early reprogramming, downregulation of one group of somatic MEF-expressed genes requires both NCOR1 and OCT4, whereas another group of MEF-expressed genes is downregulated by NCOR1 but not OCT4. Our data suggest that NCOR1, assisted by OCT4 and c-MYC, facilitates transcriptional repression of genes with high expression in MEFs, which is necessary to bypass an early reprogramming block; this way, NCOR1 facilitates early reprogramming progression. creator: Georgina Peñalosa-Ruiz creator: Klaas W. Mulder creator: Gert Jan C. Veenstra uri: https://doi.org/10.7717/peerj.8952 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Peñalosa-Ruiz et al. title: Intra-articular injection of decellularized extracellular matrices in the treatment of osteoarthritis in rabbits link: https://peerj.com/articles/8972 last-modified: 2020-04-22 description: BackgroundWe investigated the role of decellularized cartilage matrix in osteoarthritis to seek a new treatment for this disease.MethodsKnee cartilage from rabbits was decellularized and the degree of decellularization was assessed. A grinder was used to turn acellular cartilage into particles, which were then used in a suspension. Thirty New Zealand white rabbits were subjected to an operation on their anterior cruciate ligament for the osteoarthritis model. The success of the animal model of osteoarthritis was evaluated using results from six rabbits. The remaining 24 rabbits were randomly divided into four groups (groups A, B, C, and D). Rabbits in groups A, B, C, and D were injected with 200 µl of normal saline, 200 µl of 10% (w/v) cartilage decellularized suspension, 200 µl of 20% (w/v) cartilage decellularized suspension, and 200 µl of 40% (w/v) cartilage decellularized suspension into the knee joints, respectively. Macroscopic and microscopic assessments were performed three months after surgery to assess the degree of osteoarthritic changes.ResultsHistological and biochemical analysis revealed that the cartilage decellularized matrix removed cells after decellularization but retained components of collagen and glycosaminoglycan. Group A exhibited the most significant changes from osteophyte and cartilage erosion, which was macroscopically observable on the surface of the femoral cartilage. HE staining in group A revealed damage to the cartilage surface, disorganized chondrocytes, and spontaneous fibrocartilage formation. Safranin O-fast green staining revealed a cavity formed at the osteochondral junction in group A that did not appear in other groups.ConclusionOur study shows that decellularized cartilage matrix has a certain therapeutic effect on osteoarthritis and provides new insights in the treatment of osteoarthritis. creator: Yaxin Zhang creator: Jihang Dai creator: Lianqi Yan creator: Yu Sun uri: https://doi.org/10.7717/peerj.8972 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhang et al. title: Population structure and microbial community diversity of two common tetillid sponges in a tropical reef lagoon link: https://peerj.com/articles/9017 last-modified: 2020-04-22 description: Sponges are predicted to dominate future reef ecosystems influenced by anthropogenic stressors and global climate change. The ecological success of sponges is attributed to their complex physiology, which is in part due to the diversity of their associated prokaryotic microbiome. However, the lack of information on the microbial community of many sponge species makes it difficult to gauge their interactions and functional contributions to the ecosystem. Here, we investigated the population dynamics and microbial community composition of two tetillid sponges identified as Cinachyrella sp. and Paratetilla sp., which are common on coral bommies in a reef lagoon in Bolinao, northwestern Philippines. The sponges ranged in size from 2.75 ± 2.11 to 6.33 ± 3.98 cm (mean ± standard deviation) and were found at an average density of 1.57 ± 0.79 to 4.46 ± 3.60 individuals per sq. m. on the bommies. The tetillid sponge population structure remained stable over the course of four years of monitoring. Prokaryotic communities associated with the sponges were distinct but had overlapping functions based on PICRUSt2 predictions. This convergence of functions may reflect enrichment of metabolic processes that are crucial for the survival of the tetillid sponges under prevailing conditions in the reef lagoon. Differentially enriched functions related to carbon, sulfur, fatty acid, and amino acid metabolism, cellular defense, and stress response, may influence the interactions of tetillid sponges with other biota on the bommies. creator: Jake Ivan P. Baquiran creator: Michael Angelou L. Nada creator: Niño Posadas creator: Dana P. Manogan creator: Patrick C. Cabaitan creator: Cecilia Conaco uri: https://doi.org/10.7717/peerj.9017 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Baquiran et al. title: Long-reads reveal that Rhododendron delavayi plastid genome contains extensive repeat sequences, and recombination exists among plastid genomes of photosynthetic Ericaceae link: https://peerj.com/articles/9048 last-modified: 2020-04-22 description: BackgroundRhododendron delavayi Franch. var. delavayi is a wild ornamental plant species in Guizhou Province, China. The lack of its plastid genome information seriously hinders the further application and conservation of the valuable resource.MethodsThe complete plastid genome of R. delavayi was assembled from long sequence reads. The genome was then characterized, and compared with those of other photosynthetic Ericaceae species.ResultsThe plastid genome of R. delavayi has a typical quadripartite structure, and a length of 202,169 bp. It contains a large number of repeat sequences and shows preference for codon usage. The comparative analysis revealed the irregular recombination of gene sets, including rearrangement and inversion, in the large single copy region. The extreme expansion of the inverted repeat region shortened the small single copy, and expanded the full length of the genome. In addition, consistent with traditional taxonomy, R. delavayi with nine other species of the same family were clustered into Ericaceae based on the homologous protein-coding sequences of the plastid genomes. Thus, the long-read assembly of the plastid genome of R. delavayi would provide basic information for the further study of the evolution, genetic diversity, and conservation of R. delavayi and its relatives. creator: Huie Li creator: Qiqiang Guo creator: Qian Li creator: Lan Yang uri: https://doi.org/10.7717/peerj.9048 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Li et al. title: Production of cupcake-like dessert containing microbial biosurfactant as an emulsifier link: https://peerj.com/articles/9064 last-modified: 2020-04-22 description: This work describes the application of the biosurfactant from Candida bombicola URM 3718 as a meal additive like cupcake. The biosurfactant was produced in a culture medium containing 5% sugar cane molasses, 5% residual soybean oil and 3% corn steep liquor. The surface and interfacial tension of the biosurfactant were 30.790 ± 0.04 mN/m and 0.730 ± 0.05 mN/m, respectively. The yield in isolated biosurfactant was 25 ± 1.02 g/L and the CMC was 0.5 g/L. The emulsions of the isolated biosurfactant with vegetable oils showed satisfactory results. The microphotographs of the emulsions showed that increasing the concentration of biosurfactant decreased the oil droplets, increasing the stability of the emulsions. The biosurfactant was incorporated into the cupcake dessert formulation, replacing 50%, 75% and 100% of the vegetable fat in the standard formulation. Thermal analysis showed that the biosurfactant is stable for cooking cupcakes (180 °C). The biosurfactant proved to be promising for application in foods low in antioxidants and did not show cytotoxic potential in the tested cell lines. Cupcakes with biosurfactant incorporated in their dough did not show significant differences in physical and physical–chemical properties after baking when compared to the standard formulation. In this way, the biosurfactant has potential for application in the food industry as an emulsifier for flour dessert. creator: Ivison A. Silva creator: Bruno O. Veras creator: Beatriz G. Ribeiro creator: Jaciana S. Aguiar creator: Jenyffer M. Campos Guerra creator: Juliana M. Luna creator: Leonie A. Sarubbo uri: https://doi.org/10.7717/peerj.9064 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Silva et al. title: Home range size and habitat use of the blue-crowned laughingthrush during the breeding season link: https://peerj.com/articles/8785 last-modified: 2020-04-21 description: The home range size and habitat use of the blue-crowned laughingthrush (Garrulax courtoisi, hereafter BCLT), a critically endangered, subtropical, cooperative-breeding bird species in southeast China, were studied during its breeding period using radio telemetry at different sites during 3 consecutive years (2016–18, from May to June of each year). A total of 17 birds (12 males, four females, and one of unknown sex) were tagged, and a total 1515 locations (mean ± se = 89.12 ± 11.42) were obtained over 54 days of tracking. The average 100% minimum convex polygon (MCP) home range size was 10.05 ± 1.17 ha, and the estimated KDE core area (fiexed kernel density estimator, KDE) size was 7.84 ± 1.18 ha. According to the Wilcoxon rank sum tests, both the 100% MCP and KDE core area size of males did not significantly differ from those of females. There were no significant differences in the 100% MCP or KDE core area sizes of the three breeding sites. The available habitats in the breeding sites included water areas, shrubs, grass plots, woodland, residential areas, vegetable field, farmland, and sandy beaches; among them, only woodland was significantly preferred by BCLTs. Woodland (average use ratio was 45.86 ± 1.74%) was strongly preferred by BCLTs for nesting, foraging and roosting. Shrubs/grass plots (24.72 ± 3.39%) and vegetable plots (11.80 ± 1.83%) were used relatively more often than the other habitats, except woodland, since shrubs were always used as perches, and vegetable plots were rich in food resources. Vertically, the canopy layer was used most often from April to June, but it was used most in May when the birds were hatching and brooding. This result indicates that BCLT is predominantly active in the upper strata during the breeding season. In addition, broadleaved trees within or adjacent to villages were important activity areas for the breeding birds; protection and management measures should be increased in these areas. creator: Tao Liu creator: Yongtao Xu creator: Bai Mo creator: Jinze Shi creator: Yachang Cheng creator: Weiwei Zhang creator: Fumin Lei uri: https://doi.org/10.7717/peerj.8785 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Liu et al. title: Within-host competition drives energy allocation trade-offs in an insect parasitoid link: https://peerj.com/articles/8810 last-modified: 2020-04-21 description: Organismal body size is an important biological trait that has broad impacts across scales of biological organization, from cells to ecosystems. Size is also deeply embedded in life history theory, as the size of an individual is one factor that governs the amount of available resources an individual is able to allocate to different structures and systems. A large body of work examining resource allocation across body sizes (allometry) has demonstrated patterns of allocation to different organismal systems and morphologies, and extrapolated rules governing biological structure and organization. However, the full scope of evolutionary and ecological ramifications of these patterns have yet to be realized. Here, we show that density-dependent larval competition in a natural population of insect parasitoids (Drino rhoeo: Tachinidae) results in a wide range of body sizes (largest flies are more than six times larger (by mass) than the smallest flies). We describe strong patterns of trade-offs between different body structures linked to dispersal and reproduction that point to life history strategies that differ between both males and females and individuals of different sizes. By better understanding the mechanisms that generate natural variation in body size and subsequent effects on the evolution of life history strategies, we gain better insight into the evolutionary and ecological impacts of insect parasitoids in tri-trophic systems. creator: J. Keaton Wilson creator: Laura Ruiz creator: Goggy Davidowitz uri: https://doi.org/10.7717/peerj.8810 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Wilson et al. title: Dynamics of ammonia oxidizers and denitrifiers in response to compost addition in black soil, Northeast China link: https://peerj.com/articles/8844 last-modified: 2020-04-21 description: Organic fertilizer application could have an impact on the nitrogen cycle mediated by microorganisms in arable soils. However, the dynamics of soil ammonia oxidizers and denitrifiers in response to compost addition are less understood. In this study, we examined the effect of four compost application rates (0, 11.25, 22.5 and 45 t/ha) on soil ammonia oxidizers and denitrifiers at soybean seedling, flowering and mature stage in a field experiment in Northeast China. As revealed by quantitative PCR, compost addition significantly enhanced the abundance of ammonia oxidizing bacteria (AOB) at seedling stage, while the abundance of ammonia oxidizing archaea was unaffected across the growing season. The abundance of genes involved in denitrification (nirS, nirK and nosZ) were generally increased along with compost rate at seedling and flowering stages, but not in mature stage. The non-metric multidimensional scaling analysis revealed that moderate and high level of compost addition consistently induced shift in AOB and nirS containing denitrifers community composition across the growing season. Among AOB lineages, Nitrosospira cluster 3a gradually decreased along with the compost rate across the growing season, while Nitrosomonas exhibited an opposite trend. Network analysis indicated that the complexity of AOB and nirS containing denitrifiers network gradually increased along with the compost rate. Our findings highlighted the positive effect of compost addition on the abundance of ammonia oxidizers and denitrifiers and emphasized that compost addition play crucial roles in shaping their community compositions and co-occurrence networks in black soil of Northeast China. creator: Zhongzan Yang creator: Yupeng Guan creator: Ayodeji Bello creator: Yanxiang Wu creator: Jiayi Ding creator: Leiqi Wang creator: Yuqing Ren creator: Guangxin Chen creator: Wei Yang uri: https://doi.org/10.7717/peerj.8844 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Yang et al. title: Data-driven classification of the certainty of scholarly assertions link: https://peerj.com/articles/8871 last-modified: 2020-04-21 description: The grammatical structures scholars use to express their assertions are intended to convey various degrees of certainty or speculation. Prior studies have suggested a variety of categorization systems for scholarly certainty; however, these have not been objectively tested for their validity, particularly with respect to representing the interpretation by the reader, rather than the intention of the author. In this study, we use a series of questionnaires to determine how researchers classify various scholarly assertions, using three distinct certainty classification systems. We find that there are three distinct categories of certainty along a spectrum from high to low. We show that these categories can be detected in an automated manner, using a machine learning model, with a cross-validation accuracy of 89.2% relative to an author-annotated corpus, and 82.2% accuracy against a publicly-annotated corpus. This finding provides an opportunity for contextual metadata related to certainty to be captured as a part of text-mining pipelines, which currently miss these subtle linguistic cues. We provide an exemplar machine-accessible representation—a Nanopublication—where certainty category is embedded as metadata in a formal, ontology-based manner within text-mined scholarly assertions. creator: Mario Prieto creator: Helena Deus creator: Anita de Waard creator: Erik Schultes creator: Beatriz García-Jiménez creator: Mark D. Wilkinson uri: https://doi.org/10.7717/peerj.8871 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Prieto et al. title: RNA sequencing of CD4 T-cells reveals the relationships between lncRNA-mRNA co-expression in elite controller vs. HIV-positive infected patients link: https://peerj.com/articles/8911 last-modified: 2020-04-21 description: BackgroundElite controller refers to a patient with human immunodeficiency virus infection with an undetected viral load in the absence of highly active antiretroviral therapy. Studies on gene expression and regulation in these individuals are limited but significant, and have helped researchers and clinicians to understand the interrelationships between HIV and its host.MethodsWe collected CD4 T-cell samples from two elite controllers (ECs), two HIV-positive infected patients (HPs), and two healthy controls (HCs) to perform second-generation transcriptome sequencing. Using the Cufflinks software, we calculated the Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) and identified differentially expressed (DE) mRNAs and long non-coding RNAs (lncRNAs), with corrected P value < 0.05 (based on a false discovery rate (FDR) < 0.05). We then constructed a protein-protein interaction network using cytoHubba and a long non-coding RNA-mRNA co-expression network based on the Pearson correlation coefficient.ResultsIn total, 1109 linear correlations of DE lncRNAs targeting DE mRNAs were found and several interesting interactions were identified as being associated with viral infections and immune responses within the networks based on these correlations. Among these lncRNA-mRNA relationships, hub mRNAs including HDAC6, MAPK8, MAPK9, ATM and their corresponding annotated co-expressed lncRNAs presented strong correlations with the MAPK-NF-kappa B pathway, which plays a role in the reactivation and replication of the virus.ConclusionsUsing RNA-sequencing, we systematically analyzed the expression profiles of lncRNAs and mRNAs from CD4+ T cells from ECs, HPs, and HCs, and constructed a co-expression network based on the relationships among DE transcripts and database annotations. This was the first study to examine gene transcription in elite controllers and to study their functional relationships. Our results provide a reference for subsequent functional verification at the molecular or cellular level. creator: Chaoyu Chen creator: Xiangyun Lu creator: Nanping Wu uri: https://doi.org/10.7717/peerj.8911 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Chen et al. title: Expression of 1B capsid protein of Foot-and-mouth disease virus (FMDV) using baculovirus expression system and its validation in detecting SAT 2- specific antisera link: https://peerj.com/articles/8946 last-modified: 2020-04-21 description: Foot-and-mouth disease virus (FMDV) is one of the most devastating animal viruses that affect livestock worldwide. The 1B capsid of FMDV has been widely used to detect and confirm the infection. In the present study, the sequence coding for 1B subunit of FMDV capsid was expressed in insect cells using the baculovirus expression system under the polyhedrin (polh) promoter. The expression of 1B capsid protein was validated in the culture filtrate of insect cells using SDS-PAGE and western blotting. The culture filtrate containing recombinant 1B capsid (r1B) was used as a coated antigen in an indirect enzyme-linked immunosorbent assay (ELISA). The antigenicity and specificity of r1B against SAT 2 serotype-specific antibodies were assessed. Our results revealed that a protein concentration as low as 25 ng could detect SAT 2-specific antibodies in ELISA. The results highlight the application of insect cells developed r1B protein in the detection of FMDV. Further studies are required to determine the ability of r1B to detect other FMDV serotypes. creator: Wael Elmenofy creator: Ismail Mohamed creator: Lamiaa El-Gaied creator: Reda Salem creator: Gamal Osman creator: Mohamed Ibrahim uri: https://doi.org/10.7717/peerj.8946 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2020 Elmenofy et al. title: Awareness and experiences of cosmetic treatment providers with body dysmorphic disorder in Saudi Arabia link: https://peerj.com/articles/8959 last-modified: 2020-04-21 description: Body Dysmorphic Disorder (BDD) is defined as a constant obsession with one’s external appearance and flaws, and it falls under the criteria of neuropsychiatric disorders. Individuals suffering from this disorder may seek unnecessary cosmetic procedures from cosmetic treatment providers such as dermatologists or plastic surgeons. Cosmetic treatments have become readily available, which has led to an influx of undiagnosed BDD patients electing to undergo such treatments. Therefore, physicians should have the clinical knowledge about BDD to diagnose and manage these cases to avoid psychological and physical harm to these patients. However, there were no studies conducted in our region to assess the awareness of BDD among physicians who provide cosmetic treatments with regards to their attitude toward such cases and how they would manage it. This study aims to assess the awareness of Body Dysmorphic Disorder among Saudi physicians who provide cosmetic treatments. We conducted an observational cross-sectional study among physicians practicing in hospitals and cosmetic clinics in Riyadh and Jeddah city (Saudi Arabia), who perform cosmetic procedures, namely dermatologists, plastic surgeons, and otorhinolaryngologists. A paper-based questionnaire consisting of multiple-choice questions was distributed among them. The total number of participants was 155 physicians: 113 (72.9%) males and 42 (27.1%) females. Eighty-two (52.9%) participants reported that they have been familiar with the diagnostic criteria of BDD for a long time and ninety-nine (63.8%) reported being familiar with the clinical picture of BDD. Sixty-three (40.6%) participants estimated the prevalence of BDD cases seen in cosmetic practice to range from 1%-5%, and most agreed on an equal prevalence of BDD among female and male patients. Half of the participants (n = 76) (49%) reported that they sometimes share knowledge about BDD with patients whom they suspect to suffer from this condition. In conclusion, cosmetic treatment providers in Saudi Arabia are aware of BDD, but we have identified a discrepancy between the self-reported participant knowledge of diagnostic criteria and their ability to accurately estimate the prevalence of BDD cases seen in clinical practice. creator: Abdullah E. Kattan creator: Nujaim H. Alnujaim creator: Omar Barasain creator: Theo K. Bouman creator: Reema AlHammad creator: Berend Van der Lei uri: https://doi.org/10.7717/peerj.8959 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Kattan et al. title: Effect of additional body weight on arch index and dynamic plantar pressure distribution during walking and gait termination link: https://peerj.com/articles/8998 last-modified: 2020-04-21 description: The medial longitudinal arch is considered as an essential feature which distinguishes humans from other primates. The longitudinal arch plays a supporting and buffering role in human daily physical activities. However, bad movement patterns could lead to deformation of arch morphology, resulting in foot injuries. The authors aimed to investigate any alterations in static and dynamic arch index following different weight bearings. A further aim was to analyze any changes in plantar pressure distribution characteristics on gait during walking and stopping, Twelve males were required to complete foot morphology scans and three types of gait tests with 0%, 10%, 20% and 30% of additional body weight. The dynamic gait tests included walking, planned and unplanned gait termination. Foot morphology details and plantar pressure data were collected from subjects using the Easy-Foot-Scan and Footscan pressure platform. No significant differences were observed in static arch index when adding low levels of additional body weight (10%). There were no significant changes observed in dynamic arch index when loads were added in the range of 20% to 30%, except in unplanned gait termination. Significant maximal pressure increases were observed in the rearfoot during walking and in both the forefoot and rearfoot during planned gait termination. In addition, significant maximum pressure increases were shown in the lateral forefoot and midfoot during unplanned gait termination when weight was increased. Findings from the study indicated that excessive weight bearing could lead to a collapse of the arch structure and, therefore, increases in plantar loading. This may result in foot injuries, especially during unplanned gait termination. creator: Xuanzhen Cen creator: Datao Xu creator: Julien S. Baker creator: Yaodong Gu uri: https://doi.org/10.7717/peerj.8998 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Cen et al. title: On the potential for saturated buffers in northwest Ohio to remediate nutrients from agricultural runoff link: https://peerj.com/articles/9007 last-modified: 2020-04-21 description: Nutrient loading from nonpoint source runoff in the Midwest has emerged as one of the largest threats to water quality as the frequency of harmful algal blooms, hypoxic zones, and issues associated with human-resource interactions have risen abruptly over the past several decades. In this study, a saturated buffer ~500 m in length located in the western basin of the Lake Erie watershed was evaluated for its potential to reduce edge of field runoff and nutrient loading. Saturated buffers reduce runoff by routing subsurface tile drainage water into the riparian zone, providing an opportunity for drainage volume as well as nutrient reduction of runoff waters. Over a 12-month study period, controlled drainage was used to redirect nearly 25% of the total tile flow into the riparian zone from a subwatershed in corn/soybean rotation with near complete reductions of dissolved nitrogen and phosphorus from tile inflows averaging 4.7 and 0.08 mg/L, respectively, as well as total reduction of suspended sediments (average 10.4 mg/L). This study provides additional evidence that riparian areas are an important part of nutrient reduction strategies as they can act as both controlled drainage points by raising water tables in fields as well as nutrient sinks which couple to help mitigate nutrient runoff in the region. creator: Stephen J. Jacquemin creator: Greg McGlinch creator: Theresa Dirksen creator: Angela Clayton uri: https://doi.org/10.7717/peerj.9007 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Jacquemin et al. title: Additions to the phylogeny of colubrine snakes in Southwestern Asia, with description of a new genus and species (Serpentes: Colubridae: Colubrinae) link: https://peerj.com/articles/9016 last-modified: 2020-04-21 description: Reptiles are still being described worldwide at a pace of hundreds of species a year. While many discoveries are from remote tropical areas, biodiverse arid regions still harbor many novel taxa. Here, we present an updated phylogeny of colubrid snakes from the Western Palearctic by analyzing a supermatrix of all available global snake species with molecular data and report on the discovery of a new genus and species of colubrine snake from southeastern Iran. The new taxon, named Persiophis fahimiiGen. et sp. nov., is nested within a clade containing Middle Eastern and South Asian ground racers (Lytorhynchus, Rhynchocalamus, Wallaceophis, and Wallophis). This species has a derived morphology including an edentulous pterygoid and occurrence of short and blunt teeth on the palatine, maxillae and dentary bones, an elongated snout and a relatively trihedral first supralabial scale that is slightly bigger than the second, and elongated toward the tip of rostral. We also report on the osteology and phylogenetic placement of several poorly studied colubrines: Hierophis andreanus (reassigned to Dolichophis) and Muhtarophis barani. creator: Mahdi Rajabizadeh creator: R. Alexander Pyron creator: Roman Nazarov creator: Nikolay A. Poyarkov creator: Dominique Adriaens creator: Anthony Herrel uri: https://doi.org/10.7717/peerj.9016 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Rajabizadeh et al. title: Genetic variability and structure of an important wild steppe grass Psathyrostachys juncea (Triticeae: Poaceae) germplasm collection from north and central Asia link: https://peerj.com/articles/9033 last-modified: 2020-04-21 description: Russian wildrye, Psathyrostachys junceus (Fisch.) Nevski, is an important wild steppe perennial grass, which is characterized by longevity and short robust rhizomes. It also has highly resistance in grazing and abiotic stress. In this study, the genetic diversity of eleven P. juncea wild germplasms from north and central Asia was investigated using AFLP markers. The P. juncea populations were divided into three clades in both UPGMA dendrogram and PCoA clustering corresponding to the three genetic memberships in STRUCTURE analysis. The genetic specificity of Xinjiang (XJ) populations was revealed by the highest Ne (1.5411) and Hj (0.3553) and their dispersion shown in UPGMA. High inbreeding coefficient (Wright’s F statistics, f = 0.496, Fst = 0.128) was observed although a moderate degree of gene flow (Nm = 1.4736) existed, that may ascribe to habitat fragmentation or the low seedling recruitment, which ultimately resulted in decrease of population size and their genetic diversity. The key factors inducing moderate genetic differentiation detected in this study were isolation by distance (IBD), climatic variabilities and geographical barriers. All these results provide insights into the study of genetic status and germplasm collecting of Russian wildrye. creator: Yi Xiong creator: Yanli Xiong creator: Qingqing Yu creator: Junming Zhao creator: Xiong Lei creator: Zhixiao Dong creator: Jian Yang creator: Sijia Song creator: Yan Peng creator: Wenhui Liu creator: Shiqie Bai creator: Xiao Ma uri: https://doi.org/10.7717/peerj.9033 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2020 Xiong et al. title: Fitness benefits and costs of shelters to the sea urchin Glyptocidaris crenularis link: https://peerj.com/articles/8886 last-modified: 2020-04-20 description: Understanding the ecological role of shelters is greatly hampered by the scarcity of long-term laboratory experiments on the trade-off between fitness benefits and costs. This lack probably leads to an underestimation of the negative and/or positive effects on behaviors and growth of marine invertebrates in benthic ecosystems. Although our previous study revealed a significant effect on fitness-related traits of Glyptocidaris crenularis after 31 months, the present study extended it and investigated fitness benefits and/or costs of long-term sheltering on sea urchins to over 7 years. The present long-term study suggests that the previously reported reduction in feeding rate probably resulted from a reduction in reflexive feeding motions (Aristotle’s lantern reflex) rather than changes in foraging behavior. Actively seeking sheltering behavior was negatively impacted in individuals with continuous access to shelters. However, covering and righting behaviors did not differ in sheltered sea urchins, indicating that these behaviors are maintained to escape from adverse environments regardless of shelter. Body size of sea urchins in the group with shelters was significantly lower than those without shelters after 7 years. Weights of gonads and gut were not significantly different after 7 years despite previous observations of differences after ~2.5 years. The present study provides valuable information on the trade-off between fitness benefits and costs to sea urchins residing in shelters. However, the present study is only a laboratory investigation for one urchin species (G. crenularis) which does not consider the complexity of natural environments. Field studies should be carried out with G. crenularis and other sea urchin species, before a more universal conclusion can be drawn. creator: Xiaomei Chi creator: Jiangnan Sun creator: Yushi Yu creator: Jia Luo creator: Bao Zhao creator: Feng Han creator: Yaqing Chang creator: Chong Zhao uri: https://doi.org/10.7717/peerj.8886 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Chi et al. title: Comparative transcriptomics characterized the distinct biosynthetic abilities of terpenoid and paeoniflorin biosynthesis in herbaceous peony strains link: https://peerj.com/articles/8895 last-modified: 2020-04-20 description: The herbaceous peony (Paeonia lactiflora Pall.) is a perennial flowering plant of the Paeoniaceae species that is widely cultivated for medical and ornamental uses. The monoterpene glucoside paeoniflorin and its derivatives are the active compounds of the P. lactiflora roots. However, the gene regulation pathways associated with monoterpene and paeoniflorin biosynthesis in P. lactiflora are still unclear. Here, we selected three genotypes of P. lactiflora with distinct morphologic features and chemical compositions that were a result of long-term reproductive isolation. We performed an RNA-sequencing experiment to profile the transcriptome changes of the shoots and roots. Using de novo assembly analysis, we identified 36,264 unigenes, including 521 genes responsible for encoding transcription factors. We also identified 28,925 unigenes that were differentially expressed in different organs and/or genotypes. Pathway enrichment analysis showed that the P. lactiflora unigenes were significantly overrepresented in several secondary metabolite biosynthesis pathways. We identified and profiled 33 genes responsible for encoding the enzymescontrolling the major catalytic reactions in the terpenoid backbone and in monoterpenoid biosynthesis. Our study identified the candidate genes in the terpenoid biosynthesis pathways, providing useful information for metabolic engineering of P. lactiflora intended for pharmaceutical uses and facilitating the development of strategies to improve marker-assist P. lactiflora in the future. creator: Baowei Lu creator: Fengxia An creator: Liangjing Cao creator: Qian Gao creator: Xuan Wang creator: Yongjian Yang creator: Pengming Liu creator: Baoliang Yang creator: Tong Chen creator: Xin-Chang Li creator: Qinghua Chen creator: Jun Liu uri: https://doi.org/10.7717/peerj.8895 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Lu et al. title: Comparison of early-stage changes of osteoarthritis in cartilage and subchondral bone between two different rat models link: https://peerj.com/articles/8934 last-modified: 2020-04-20 description: Osteoarthritis (OA) is a chronic degenerative joint disease and the major cause of joint pain and disability in the elderly. It is mainly characterized by articular cartilage degradation and subchondral bone remodeling. There are two main types of OA: natural occurring OA and secondary OA, mainly associated with aging and trauma, respectively. In this study, we established two OA models in rat knee joints to simulate the two types of OA, using the type II collagenase injection (CI) and anterior cruciate ligament transection (ACLT), respectively. After intervention for 2–6 weeks, cartilage and subchondral bone changes were detected in histological staining, immunochemistry, and micro-CT. Results showed that both models with typical pathology changes of OA were successfully induced, while the development and severity of OA process in the models were different. In ACLT rats, the cartilage damage was milder, lasted for a shorter time, and subchondral bone reconstruction occurred earlier, compared with the changes in CI rats. The cartilage damage was secondary to subchondral bone change in ACLT rats, while subchondral bone change was secondary to cartilage degeneration in CI rats. In conclusion, the interaction between cartilage and subchondral bone is different between the natural-occurring and secondary OA models. These two models not only suggest potential different mechanisms of the two types of OA, but also provide new directions for OA treatment and prevention. creator: Yutao Yang creator: Peiran Li creator: Songsong Zhu creator: Ruiye Bi uri: https://doi.org/10.7717/peerj.8934 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Yang et al. title: Icariin protects against sodium azide—induced neurotoxicity by activating the PI3K/Akt/GSK-3β signaling pathway link: https://peerj.com/articles/8955 last-modified: 2020-04-20 description: BackgroundIcariin (ICA) is one of the major active flavonoids extracted from the traditional Chinese herb Epimedium brevicornum Maxim and has been shown to have neuroprotective effects. This study was designed to investigate the effect of ICA on sodium azide (NaN3)-induced rat adrenal pheochromocytoma (PC12) cell damage and to further examine the underlying mechanisms.MethodsTo explore its possible mechanism, we used NaN3 (50 mM)-induced neuronal PC12 cell damage. Cell viability was evaluated by CCK-8 and lactate dehydrogenase (LDH) assays. Mitochondrial membrane potential (MMP) was detected by JC-1. Glucose concentration was assessed by the glucose oxidase method. The role of ICA in the PI3K/Akt/GSK-3β signaling pathway was explored by Western blotting.ResultsThe results indicate that pretreatment with ICA reduced NaN3-induced cell damage and significantly reduced the leakage rate of LDH in PC12 cells. ICA pretreatment increased the MMP and a decrease in glucose concentration indicate increased glucose consumption. Furthermore, the protein levels of p-PI3K (p85), PI3K-110α, p-Ser473-Akt and p-Ser9-GSK-3β were markedly decreased in PC12 cells after NaN3 treatment for 24 h, whereas these effects were reverted after pretreatment with ICA. Tau phosphorylation at the Ser396/404 and Thr217 sites was significantly decreased by pretreatment with ICA.ConclusionsThese results suggest that ICA protects against NaN3-induced neurotoxicity in PC12 cells by activating the PI3K/Akt/GSK-3β signaling pathway. creator: Ying Zhang creator: Nanqu Huang creator: Hao Lu creator: Juan Huang creator: Hai Jin creator: Jingshan Shi creator: Feng Jin uri: https://doi.org/10.7717/peerj.8955 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Zhang et al. title: Immune response of human cultured cells towards macrocyclic Fe2PO and Fe2PC bioactive cyclophane complexes link: https://peerj.com/articles/8956 last-modified: 2020-04-20 description: Synthetic molecules that mimic the function of natural enzymes or molecules have untapped potential for use in the next generation of drugs. Cyclic compounds that contain aromatic rings are macrocyclic cyclophanes, and when they coordinate iron ions are of particular interest due to their antioxidant and biomimetic properties. However, little is known about the molecular responses at the cellular level. This study aims to evaluate the changes in immune gene expression in human cells exposed to the cyclophanes Fe2PO and Fe2PC. Confluent human embryonic kidney cells were exposed to either the cyclophane Fe2PO or Fe2PC before extraction of RNA. The expression of a panel of innate and adaptive immune genes was analyzed by quantitative real-time PCR. Evidence was found for an inflammatory response elicited by the cyclophane exposures. After 8 h of exposure, the cells increased the relative expression of inflammatory mediators such as interleukin 1; IRAK, which transduces signals between interleukin 1 receptors and the NFκB pathway; and the LPS pattern recognition receptor CD14. After 24 h of exposure, regulatory genes begin to counter the inflammation, as some genes involved in oxidative stress, apoptosis and non-inflammatory immune responses come into play. Both Fe2PO and Fe2PC induced similar immunogenetic changes in transcription profiles, but equal molar doses of Fe2PC resulted in more robust responses. These data suggest that further work in whole animal models may provide more insights into the extent of systemic physiological changes induced by these cyclophanes. creator: Alex J. Salazar-Medina creator: Enrique F. Velazquez-Contreras creator: Rocio Sugich-Miranda creator: Hisila Santacruz creator: Rosa E. Navarro creator: Fernando Rocha-Alonzo creator: Maria A. Islas-Osuna creator: Patricia L. Chen creator: Sarah G.B. Christian creator: Amelia A. Romoser creator: Scott V. Dindot creator: Christie M. Sayes creator: Rogerio R. Sotelo-Mundo creator: Michael F. Criscitiello uri: https://doi.org/10.7717/peerj.8956 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Salazar-Medina et al. title: CFSP: a collaborative frequent sequence pattern discovery algorithm for nucleic acid sequence classification link: https://peerj.com/articles/8965 last-modified: 2020-04-20 description: BackgroundConserved nucleic acid sequences play an essential role in transcriptional regulation. The motifs/templates derived from nucleic acid sequence datasets are usually used as biomarkers to predict biochemical properties such as protein binding sites or to identify specific non-coding RNAs. In many cases, template-based nucleic acid sequence classification performs better than some feature extraction methods, such as N-gram and k-spaced pairs classification. The availability of large-scale experimental data provides an unprecedented opportunity to improve motif extraction methods. The process for pattern extraction from large-scale data is crucial for the creation of predictive models.MethodsIn this article, a Teiresias-like feature extraction algorithm to discover frequent sub-sequences (CFSP) is proposed. Although gaps are allowed in some motif discovery algorithms, the distance and number of gaps are limited. The proposed algorithm can find frequent sequence pairs with a larger gap. The combinations of frequent sub-sequences in given protracted sequences capture the long-distance correlation, which implies a specific molecular biological property. Hence, the proposed algorithm intends to discover the combinations. A set of frequent sub-sequences derived from nucleic acid sequences with order is used as a base frequent sub-sequence array. The mutation information is attached to each sub-sequence array to implement fuzzy matching. Thus, a mutate records a single nucleotide variant or nucleotides insertion/deletion (indel) to encode a slight difference between frequent sequences and a matched subsequence of a sequence under investigation.ConclusionsThe proposed algorithm has been validated with several nucleic acid sequence prediction case studies. These data demonstrate better results than the recently available feature descriptors based methods based on experimental data sets such as miRNA, piRNA, and Sigma 54 promoters. CFSP is implemented in C++ and shell script; the source code and related data are available at https://github.com/HePeng2016/CFSP. creator: He Peng uri: https://doi.org/10.7717/peerj.8965 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Peng title: Effects of biodegradable plastic film mulching on soil microbial communities in two agroecosystems link: https://peerj.com/articles/9015 last-modified: 2020-04-20 description: Plastic mulch films are used globally in crop production but incur considerable disposal and environmental pollution issues. Biodegradable plastic mulch films (BDMs), an alternative to polyethylene (PE)-based films, are designed to be tilled into the soil where they are expected to be mineralized to carbon dioxide, water and microbial biomass. However, insufficient research regarding the impacts of repeated soil incorporation of BDMs on soil microbial communities has partly contributed to limited adoption of BDMs. In this study, we evaluated the effects of BDM incorporation on soil microbial community structure and function over two years in two geographical locations: Knoxville, TN, and in Mount Vernon, WA, USA. Treatments included four plastic BDMs (three commercially available and one experimental film), a biodegradable cellulose paper mulch, a non-biodegradable PE mulch and a no mulch plot. Bacterial community structure determined using 16S rRNA gene amplicon sequencing revealed significant differences by location and season. Differences in bacterial communities by mulch treatment were not significant for any season in either location, except for Fall 2015 in WA where differences were observed between BDMs and no-mulch plots. Extracellular enzyme assays were used to characterize communities functionally, revealing significant differences by location and sampling season in both TN and WA but minimal differences between BDMs and PE treatments. Overall, BDMs had comparable influences on soil microbial communities to PE mulch films. creator: Sreejata Bandopadhyay creator: Henry Y. Sintim creator: Jennifer M. DeBruyn uri: https://doi.org/10.7717/peerj.9015 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Bandopadhyay et al. title: Comparative transcriptomic analyses of powdery mildew resistant and susceptible cultivated cucumber (Cucumis sativus L.) varieties to identify the genes involved in the resistance to Sphaerotheca fuliginea infection link: https://peerj.com/articles/8250 last-modified: 2020-04-17 description: BackgroundCucumber (Cucumis sativus L.) is a widely cultivated vegetable crop, and its yield and quality are greatly affected by various pathogen infections. Sphaerotheca fuliginea is a pathogen that causes powdery mildew (PM) disease in cucumber. However, the genes involved in the resistance to PM in cucumber are largely unknown.MethodsIn our study, a cucumber PM resistant cultivated variety “BK2” and a susceptible cultivated variety “H136” were used to screen and identify differential expressed genes (DEGs) under the S. fuliginea infection.ResultsThere were only 97 DEGs between BK2 and H136 under the control condition, suggesting a similarity in the basal gene expression between the resistant and susceptible cultivated varieties. A large number of hormone signaling-related DEGs (9.2% of all DEGs) between resistant and susceptible varieties were identified, suggesting an involvement of hormone signaling pathways in the resistance to PM. In our study, the defense-related DEGs belonging to Class I were only induced in susceptible cultivated variety and the defense-related DEGs belonging to Class II were only induced in resistant cultivated variety. The peroxidase, NBS, glucanase and chitinase genes that were grouped into Class I and II might contribute to production of the resistance to PM in resistant cultivated variety. Furthermore, several members of Pathogen Response-2 family, such as glucanases and chitinases, were identified as DEGs, suggesting that cucumber might enhance the resistance to PM by accelerating the degradation of the pathogen cell walls. Our data allowed us to identify and analyze more potential genes related to PM resistance. creator: Peng Zhang creator: Yuqiang Zhu creator: Shengjun Zhou uri: https://doi.org/10.7717/peerj.8250 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2020 Zhang et al. title: The impact of diel vertical migration on fatty acid patterns and allocation in Daphnia magna link: https://peerj.com/articles/8809 last-modified: 2020-04-17 description: In freshwater zooplankton diel vertical migration (DVM) is a widespread predator-avoidance behavior that is induced by kairomones released from fish. Thereby zooplankton reduces predation by fish by staying in deep and dark colder strata during daytime and migrating into warmer layers during night, and thus experiences diel alterations in temperature. Constantly lower temperatures have been shown to increase the relative abundance of polyunsaturated fatty acids (PUFAs) in Daphnia sp. Furthermore, a low dietary supply of the ω3-PUFA eicosapentaenoic acid (EPA) has been shown to limit the induction of DVM in Daphnia magna and the performance of D. magna under fluctuating temperatures, as experienced during DVM. In nature DVM of D. magna in response to fish is accompanied by the presence of fish-borne kairomone and diel fluctuations of depth dependent-parameters like temperature, food, and oxygen supply. Here we investigated the effect of factors, which are differing between Daphnia that perform DVM and those which do not. We selected to examine the effect of changing temperature and light conditions and of the presence/absence of fish kairomones on D. magna. For this purpose, we conducted a full factorial experimental design in which we grew D. magna under constantly warm temperatures in a diel light-dark regime or under alternating temperatures in darkness crossed with the presence or absence of fish kairomones. We analyzed the fatty acid composition of mature animals and of their offspring in each treatment. Simulation of the light and temperature regime of migrating animals in presence of the fish kairomone resulted in an increased relative allocation of the ω3-PUFA EPA, from adult animals to their offspring, manifesting as decreased EPA concentrations in mothers and increased EPA concentrations in their offspring in response to simulated DVM (mothers). Additionally, EPA concentrations in the offspring were affected by the interaction of simulated DVM and the fish cue. The presence of the fish kairomone alone increased the EPA concentration in the offspring, that was not experiencing simulated DVM. These findings lead to the conclusion that the temperature and light regime associated with DVM alone, as well as in combination with the DVM-inducing fish kairomones, alter the allocation of fatty acids to the offspring in a manner, which is beneficial for the offspring under the decreased average temperatures, which migrating animals are exposed to. A low dietary supply of ω3-PUFAs may constrain D. magna’s amplitude of DVM, but our results suggest that the next generation of animals may be capable of regaining the full DVM amplitude due to the effect of the fish kairomone and the experienced temperature fluctuations (and darkness) on tissue fatty acid composition. These findings suggest that fatty acid limitation in DVM performing Daphnia may be more severe for the maternal than for the offspring generation. creator: Meike Anika Hahn creator: Eric Von Elert uri: https://doi.org/10.7717/peerj.8809 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Hahn and Von Elert title: New fossil lizard specimens from a poorly-known squamate assemblage in the Upper Cretaceous (Campanian) San Juan Basin, New Mexico, USA link: https://peerj.com/articles/8846 last-modified: 2020-04-17 description: Recent collection efforts in the upper Campanian (∼76-73.5 Ma) Fruitland and Kirtland formations of northwestern New Mexico have significantly increased the taxonomic diversity of lizards in this historically poorly understood squamate assemblage. New lizard specimens from the “Hunter Wash Local Fauna” of the upper Fruitland and lower Kirtland formations include: (1) new specimens referable to Chamopsiidae; (2) new material belonging to Scincomorpha, (3) new material belonging to Anguidae; and (4) the first reported predatory lizard (Platynota) material from the Campanian of New Mexico. The increase in lizard diversity in the “Hunter Wash Local Fauna” expands our understanding of Late Cretaceous squamate taxonomy, distribution, and diversity in the Western Interior of North America (Laramidia). Collectively, the described specimens represent family-level diversity similar to that seen in other Campanian foreland basin deposits of the Western Interior, such as the mid-paleolatitude Kaiparowits Formation of southern Utah, the higher paleolatitude Dinosaur Park Formation of southern Alberta, and the lower paleolatitude Aguja Formation of southwestern Texas. The lizards of the “Hunter Wash Local Fauna” represent crucial mid-paleolatitude data from a coastal plain depositional setting in Laramidia—allowing for comparisons to more well-studied assemblages at different latitudes and in different depositional settings. creator: C. Henrik Woolley creator: Nathan D. Smith creator: Joseph J.W. Sertich uri: https://doi.org/10.7717/peerj.8846 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Woolley et al. title: Assessing and genotyping threatened staghorn coral Acropora cervicornis nurseries during restoration in southeast Dominican Republic link: https://peerj.com/articles/8863 last-modified: 2020-04-17 description: Acropora cervicornis is a structurally and functionally important Caribbean coral species. Since the 1980s, it has suffered drastic population losses with no signs of recovery and has been classified as a critically endangered species. Its rapid growth rate makes it an excellent candidate for coral restoration programs. In 2011, the Fundación Dominicana de Estudios Marinos (Dominican Marine Studies Foundation, FUNDEMAR) began an A. cervicornis restoration program in Bayahibe, southeast Dominican Republic. In this study, we present the methodology and results of this program from its conception through 2017, a preliminary analysis of the strong 2016 and 2017 cyclonic seasons in the greater Caribbean, and a genetic characterization of the “main nursery”. The mean survival of the fragments over 12 months was 87.45 ± 4.85% and the mean productivity was 4.01 ± 1.88 cm year−1 for the eight nurseries. The mean survival of six outplanted sites over 12 months was 71.55 ± 10.4%, and the mean productivity was 3.03 ± 1.30 cm year−1. The most common cause of mortality during the first 12 months, in both nurseries and outplanted sites, was predation by the fireworm, Hermodice carunculata. We identified 32 multilocus genotypes from 145 total analyzed individuals. The results and techniques described here will aid in the development of current and future nursery and outplanted site restoration programs. creator: Johanna Calle-Triviño creator: Renata Rivera-Madrid creator: María Geovana León-Pech creator: Camilo Cortés-Useche creator: Rita Inés Sellares-Blasco creator: Margarita Aguilar-Espinosa creator: Jesús Ernesto Arias-González uri: https://doi.org/10.7717/peerj.8863 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Calle-Triviño et al. title: Reproductive behavior drives female space use in a sedentary Neotropical frog link: https://peerj.com/articles/8920 last-modified: 2020-04-17 description: Longer-range movements of anuran amphibians such as mass migrations and habitat invasion have received a lot of attention, but fine-scale spatial behavior remains largely understudied. This gap is especially striking for species that show long-term site fidelity and display their whole behavioral repertoire in a small area. Studying fine-scale movement with conventional capture-mark-recapture techniques is difficult in inconspicuous amphibians: individuals are hard to find, repeated captures might affect their behavior and the number of data points is too low to allow a detailed interpretation of individual space use and time budgeting. In this study, we overcame these limitations by equipping females of the Brilliant-Thighed Poison Frog (Allobates femoralis) with a tag allowing frequent monitoring of their location and behavior. Neotropical poison frogs are well known for their complex behavior and diverse reproductive and parental care strategies. Although the ecology and behavior of the polygamous leaf-litter frog Allobates femoralis is well studied, little is known about the fine-scale space use of the non-territorial females who do not engage in acoustic and visual displays. We tracked 17 females for 6 to 17 days using a harmonic direction finder to provide the first precise analysis of female space use in this species. Females moved on average 1 m per hour and the fastest movement, over 20 m per hour, was related to a subsequent mating event. Traveled distances and activity patterns on days of courtship and mating differed considerably from days without reproduction. Frogs moved more on days with lower temperature and more precipitation, but mating seemed to be the main trigger for female movement. We observed 21 courtships of 12 tagged females. For seven females, we observed two consecutive mating events. Estimated home ranges after 14 days varied considerably between individuals and courtship and mating associated space use made up for ∼30% of the home range. Allobates femoralis females spent large parts of their time in one to three small centers of use. Females did not adjust their time or space use to the density of males in their surroundings and did not show wide-ranging exploratory behavior. Our study demonstrates how tracking combined with detailed behavioral observations can reveal the patterns and drivers of fine-scale spatial behavior in sedentary species. creator: Marie-Therese Fischer creator: Max Ringler creator: Eva Ringler creator: Andrius Pašukonis uri: https://doi.org/10.7717/peerj.8920 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Fischer et al. title: Size-frequency distribution of coral assemblages in insular shallow reefs of the Mexican Caribbean using underwater photogrammetry link: https://peerj.com/articles/8957 last-modified: 2020-04-17 description: The characterisation of changes in coral communities depends heavily on systematic monitoring programs and the collection of necessary metrics to assess reef health. Coral cover is the most used metric to determine reef health. The current organizational shift in coral requires the evaluation of complementary metrics, such as colony size and frequency distributions, which help to infer the responses of the coral populations to local stress or larger scale environmental changes. In this study, underwater digital photogrammetry techniques were used to assess the live cover of all coral colonies ≥3 cm2 and determine the size-frequency distribution of the dominant species in the shallow reefs of the Cozumel Reefs National Park (CRNP). In addition, the minimum sampling area (m2) needed to obtain a representative sample of the local species pool was estimated. Areas between 550 and 825 m2 per reef were photographed to generate high-resolution digital ortho-mosaics. The live area of the colonies was digitised to generate community matrices of species and abundance. EstimateS software was used to generate accumulation curves and diversity (Shannon H′) at increasing area intervals. Chi-Square tests (χ2, p = 0.05) were used to compare the observed vs estimated species richness. Spearman’s coefficients (rs), were calculated to correlate the increase in sampling area (m2) vs H′, and the Clench’s function was used to validate the observed richness (R2 = 1 and R > 90%). SIMPER analysis was performed to identify dominant species. Comparisons in terms of abundance, coral cover and size-frequencies were performed with Kruskal-Wallis (H test, p = 0.05), and paired Mann-Whitney (U test, p = 0.05). In order to obtain 90% of the species richness, a minimum sampling area of 374 m2is needed. This sampling area could be used in shallow Caribbean reefs with similar characteristics. Twelve (mainly non-massive) species: Agaricia agaricites, A humilis, A. tenuifolia, Eusmilia fastigiata, Meandrina meandrites, Montastrea cavernosa, Orbicella annularis, Porites astreoides, P. porites, Pseudodiploria strigosa, Siderastrea radians andS. siderea, were dominant in terms of abundance and coral cover. A significant increase (p < 0.05) in the number of colonies and live coral (m2) was observed from north to south of the study area. Furthermore, a wide intraspecific variation of size-frequency, even between adjacent reefs, was also observed. The size-frequency distributions presented positive skewness and negative kurtosis, which are related to stable populations, with a greater number of young colonies and a constant input of recruits. Considering the increase in disturbances in the Caribbean and the appearance of a new coral disease, digital photogrammetry techniques allow coral community characteristics to be assessed at high spatial resolutions and over large scales, which would be complementary to conventional monitoring programs. creator: Roberto C. Hernández-Landa creator: Erick Barrera-Falcon creator: Rodolfo Rioja-Nieto uri: https://doi.org/10.7717/peerj.8957 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Hernández-Landa et al. title: CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content link: https://peerj.com/articles/9001 last-modified: 2020-04-17 description: Shotgun metagenomics applied to archaeological feces (paleofeces) can bring new insights into the composition and functions of human and animal gut microbiota from the past. However, paleofeces often undergo physical distortions in archaeological sediments, making their source species difficult to identify on the basis of fecal morphology or microscopic features alone. Here we present a reproducible and scalable pipeline using both host and microbial DNA to infer the host source of fecal material. We apply this pipeline to newly sequenced archaeological specimens and show that we are able to distinguish morphologically similar human and canine paleofeces, as well as non-fecal sediments, from a range of archaeological contexts. creator: Maxime Borry creator: Bryan Cordova creator: Angela Perri creator: Marsha Wibowo creator: Tanvi Prasad Honap creator: Jada Ko creator: Jie Yu creator: Kate Britton creator: Linus Girdland-Flink creator: Robert C. Power creator: Ingelise Stuijts creator: Domingo C. Salazar-García creator: Courtney Hofman creator: Richard Hagan creator: Thérèse Samdapawindé Kagoné creator: Nicolas Meda creator: Helene Carabin creator: David Jacobson creator: Karl Reinhard creator: Cecil Lewis creator: Aleksandar Kostic creator: Choongwon Jeong creator: Alexander Herbig creator: Alexander Hübner creator: Christina Warinner uri: https://doi.org/10.7717/peerj.9001 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Borry et al. title: Deep conservation of prion-like composition in the eukaryotic prion-former Pub1/Tia1 family and its relatives link: https://peerj.com/articles/9023 last-modified: 2020-04-17 description: Pub1 protein is an important RNA-binding protein functional in stress granule assembly in budding yeast Saccharomyces cerevisiae and, as its co-ortholog Tia1, in humans. It is unique among proteins in evidencing prion-like aggregation in both its yeast and human forms. Previously, we noted that Pub1/Tia1 was the only protein linked to human disease that has prion-like character and and has demonstrated such aggregation in both species. Thus, we were motivated to probe further into the evolution of the Pub1/Tia1 family (and its close relative Nam8 and its orthologs) to gain a picture of how such a protein has evolved over deep evolutionary time since the last common ancestor of eukaryotes. Here, we discover that the prion-like composition of this protein family is deeply conserved across eukaryotes, as is the prion-like composition of its close relative Nam8/Ngr1. A sizeable minority of protein orthologs have multiple prion-like domains within their sequences (6–20% depending on criteria). The number of RNA-binding RRM domains is conserved at three copies over >86% of the Pub1 family (>71% of the Nam8 family), but proteins with just one or two RRM domains occur frequently in some clades, indicating that these are not due to annotation errors. Overall, our results indicate that a basic scaffold comprising three RNA-binding domains and at least one prion-like region has been largely conserved since the last common ancestor of eukaryotes, providing further evidence that prion-like aggregation may be a very ancient and conserved phenomenon for certain specific proteins. creator: Wan-Chun Su creator: Paul M. Harrison uri: https://doi.org/10.7717/peerj.9023 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Su and Harrison title: Distinct gene expression and secondary metabolite profiles in suppressor of prosystemin-mediated responses2 (spr2) tomato mutants having impaired mycorrhizal colonization link: https://peerj.com/articles/8888 last-modified: 2020-04-16 description: Arbuscular mycorrhizal fungi (AMF) colonization, sampled at 32–50 days post-inoculation (dpi), was significantly reduced in suppressor of prosystemin-mediated responses2 (spr2) mutant tomato plants impaired in the ω−3 FATTY ACID DESATURASE7 (FAD7) gene that limits the generation of linolenic acid and, consequently, the wound-responsive jasmonic acid (JA) burst. Contrary to wild-type (WT) plants, JA levels in root and leaves of spr2 mutants remained unchanged in response to AMF colonization, further supporting its regulatory role in the AM symbiosis. Decreased AMF colonization in spr2 plants was also linked to alterations associated with a disrupted FAD7 function, such as enhanced salicylic acid (SA) levels and SA-related defense gene expression and a reduction in fatty acid content in both mycorrhizal spr2 roots and leaves. Transcriptomic data revealed that lower mycorrhizal colonization efficiency in spr2 mutants coincided with the modified expression of key genes controlling gibberellin and ethylene signaling, brassinosteroid, ethylene, apocarotenoid and phenylpropanoid synthesis, and the wound response. Targeted metabolomic analysis, performed at 45 dpi, revealed augmented contents of L-threonic acid and DL-malic acid in colonized spr2 roots which suggested unfavorable conditions for AMF colonization. Additionally, time- and genotype-dependent changes in root steroid glycoalkaloid levels, including tomatine, suggested that these metabolites might positively regulate the AM symbiosis in tomato. Untargeted metabolomic analysis demonstrated that the tomato root metabolomes were distinctly affected by genotype, mycorrhizal colonization and colonization time. In conclusion, reduced AMF colonization efficiency in spr2 mutants is probably caused by multiple and interconnected JA-dependent and independent gene expression and metabolomic alterations. creator: Kena Casarrubias-Castillo creator: Josaphat M. Montero-Vargas creator: Nicole Dabdoub-González creator: Robert Winkler creator: Norma A. Martinez-Gallardo creator: Julia Zañudo-Hernández creator: Hamlet Avilés-Arnaut creator: John P. Délano-Frier uri: https://doi.org/10.7717/peerj.8888 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Casarrubias-Castillo et al. title: Identification of genes involved in the evolution of human intelligence through combination of inter-species and intra-species genetic variations link: https://peerj.com/articles/8912 last-modified: 2020-04-16 description: Understanding the evolution of human intelligence is an important undertaking in the science of human genetics. A great deal of biological research has been conducted to search for genes which are related to the significant increase in human brain volume and cerebral cortex complexity during hominid evolution. However, genetic changes affecting intelligence in hominid evolution have remained elusive. We supposed that a subset of intelligence-related genes, which harbored intra-species variations in human populations, may also be evolution-related genes which harbored inter-species variations between humans (Homo sapiens) and great apes (including Pan troglodytes and Pongo abelii). Here we combined inter-species and intra-species genetic variations to discover genes involved in the evolution of human intelligence. Information was collected from published GWAS works on intelligence and a total of 549 genes located within the intelligence-associated loci were identified. The intelligence-related genes containing human-specific variations were detected based on the latest high-quality genome assemblies of three human’s closest species. Finally, we identified 40 strong candidates involved in human intelligence evolution. Expression analysis using RNA-Seq data revealed that most of the genes displayed a relatively high expression in the cerebral cortex. For these genes, there is a distinct expression pattern between humans and other species, especially in neocortex tissues. Our work provided a list of strong candidates for the evolution of human intelligence, and also implied that some intelligence-related genes may undergo inter-species evolution and contain intra-species variation. creator: Mengjie Li creator: Wenting Zhang creator: Xiaoyi Zhou uri: https://doi.org/10.7717/peerj.8912 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Li et al. title: The preclinical pharmacological study on HX0969W, a novel water-soluble pro-drug of propofol, in rats link: https://peerj.com/articles/8922 last-modified: 2020-04-16 description: BackgroundPropofol is the most widely used intravenous sedative-hypnotic anesthetic in clinical practice. However, many serious side effects have been related to its lipid emulsion formulation. The pro-drug design approach was used to develop the water-soluble propofol, which could effectively resolve the limitations associated with the lipid emulsion formulation. Thus, the new water-soluble pro-drug of propofol, HX0969W, was designed and synthesized. The objective of this study was to conduct preclinical pharmacological studies on this novel water-soluble pro-drug of propofol.MethodsThe assessment of the loss of the righting reflex (LoRR) was used for the pharmacodynamic study, and liquid chromatography-tandem mass spectrometry and high-performance liquid chromatography- fluorescence were used for the pharmacokinetic study.ResultsThe potency of HX0969W (ED50 [95% CI], 46.49 [43.89–49.29] mg/kg) was similar to that of fospropofol disodium (43.66 [43.57–43.75] mg/kg), but was lower than that of propofol (4.82 [4.8–14.82] mg/kg). Administered with a dose of 2-fold ED50, propofol required a shorter time to cause LoRR than that of HX0969W and fospropofol. However, the LoRR duration was significantly longer in response to the administration of HX0969W and fospropofol disodium than that caused by propofol. In the pharmacokinetic study, the Cmax of fospropofol was higher than that of HX0969W. HX0969W had a shorter mean residual time and a rapid clearance rate than that of fospropofol disodium. There was no significant difference between the Tmax of the propofol whether it was released by HX0969W or fospropofol disodium; the Cmax of propofol released by HX0969W was similar to that of propofol, which was higher than the propofol released by fospropofol disodium. creator: YuJun Zhang creator: YingYing Jiang creator: HaiYan Wang creator: Bin Wang creator: Jun Yang creator: Yi Kang creator: Jun Chen creator: Jin Liu creator: Wen-sheng Zhang uri: https://doi.org/10.7717/peerj.8922 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhang et al. title: Impact of grazing intensities on reproduction patterns of elm trees (Ulmus pumila) in degraded sandy lands in China link: https://peerj.com/articles/9013 last-modified: 2020-04-16 description: The effect of grazing on patterns of reproduction in trees has been little reported. We explored the effects of grazing intensities on reproductive growth, allocation patterns, and duration in elm trees (Ulmus pumila L.) at the Horqin Sandy Land, a degraded area in northern China. Current-year shoots were selected from branches and harvested from individual elm trees subjected to one of four grazing intensities (heavy, moderate, light, and no grazing). Shoots, flower buds, flowers, seeds, leaf buds, and leaves were collected, dried, and weighed. Results showed that the biomass in heavy, moderate and light grazing treatments is significantly higher than in no grazing treatment (P < 0.05). The reproductive allocation of U. pumila in heavy grazing treatment was significantly higher from that in the no grazing treatment (P < 0.05). Additionally, we found that reproduction of U. pumila ended later in grazed plots, suggesting the duration of reproduction is extended with grazing disturbance. Our findings suggest that U. pumila may prolong it s duration of reproduction and alter its reproductive biomass in response to grazing. It is not clear whether these effects are related to damage to U. pumila trees by grazers or whether they are due to grazers affecting soil properties or plant competitors around U. pumila trees. creator: Yi Tang uri: https://doi.org/10.7717/peerj.9013 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Tang title: Predicting the risk of sarcopenia in elderly patients with patellar fracture: development and assessment of a new predictive nomogram link: https://peerj.com/articles/8793 last-modified: 2020-04-15 description: PurposeTo develop a risk prediction model for postoperative sarcopenia in elderly patients with patellar fractures in China.Patients and methodsWe conducted a community survey of patients aged ≥55 years who underwent surgery for patellar fractures between January 2013 and October 2018, through telephone interviews, community visits, and outpatient follow-up. We established a predictive model for assessing the risk of sarcopenia after patellar fractures. We developed the prediction model by combining multivariate logistic regression analysis with the least absolute shrinkage model and selection operator regression (lasso analysis) as well as the Support Vector Machine (SVM) algorithm. The predictive quality and clinical utility of the predictive model were determined using C-index, calibration plots, and decision curve analysis. We also conducted internal sampling methods for qualitative assessment.ResultWe recruited 137 participants (53 male; mean age, 65.7 years). Various risk factors were assessed, and low body mass index and advanced age were identified as the most important risk factor (P < 0.05). The prediction rate of the model was good (C-index: 0.88; 95% CI [0.80552–0.95448]), with a satisfactory correction effect. The C index is 0.97 in the validation queue and 0.894 in the entire cohort. Decision curve analysis suggested good clinical practicability.ConclusionOur prediction model shows promise as a cost-effective tool for predicting the risk of postoperative sarcopenia in elderly patients based on the following: advanced age, low body mass index, diabetes, less outdoor exercise, no postoperative rehabilitation, different surgical methods, diabetes, open fracture, and removal of internal fixation. creator: Yi-sheng Chen creator: Yan-xian Cai creator: Xue-ran Kang creator: Zi-hui Zhou creator: Xin Qi creator: Chen-ting Ying creator: Yun-peng Zhang creator: Jie Tao uri: https://doi.org/10.7717/peerj.8793 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Chen et al. title: LncRNA LOC100506178 promotes osteogenic differentiation via regulating miR-214-5p-BMP2 axis in human bone marrow mesenchymal stem cells link: https://peerj.com/articles/8909 last-modified: 2020-04-15 description: Osteogenic differentiation is an important role in dental implantation. Long no coding RNAs (lncRNAs) are a novel class of noncoding RNAs that have significant effects in a variety of diseases. However, the function and mechanisms of LOC100506178 in osteogenic differentiation and migration of bone morphogenetic protein 2 (BMP2)-induced osteogenic differentiation of human bone marrow mesenchymalstem cells (hBMSCs) remain largely unclear. BMP2 was used to induce osteogenic differentiation of hBMSCs. Quantitative real time PCR (qRT-PCR) was used to examine the expression of LOC100506178, miR-214-5p, Runt-related transcription factor 2 (RUNX2), Osterix (Osx), and Alkaline Phosphatase (ALP) in BMP2-induced osteogenic differentiation of hBMSCs. The function of LOC100506178 and miR-214-5p was explored in vitro using Alizarin Red S Staining, ALP activity, as well as in vivo ectopic bone formation. Luciferase reporter assay was performed to assess the association between LOC100506178 and miR-214-5p, as well as miR-214-5p and BMP2. The miR-214-5p sponging potential of LOC100506178 was evaluated by RNA immunoprecipitation. In the present study, the expression of LOC100506178 was found to be increased in BMP2-induced osteogenic differentiation of hBMSCs, accompanied with decreased miR-214-5p expression and increased RUNX2, Osx and ALP expression. LOC100506178 significantly induced, while miR-214-5p suppressed the BMP2-induced osteogenic differentiation of hBMSCs. Mechanistically, LOC100506178 was directly bound to miR-214-5p and miR-214-5p targeted the 3′-untranslated region of BMP2 to negatively regulate its expression. In conclusion, our data indicate a novel molecular pathway LOC100506178/miR-214-5p/BMP2 in relation to hBMSCs differentiation into osteoblasts, which may facilitate bone anabolism. creator: Lina Li creator: Jie Fang creator: Yi Liu creator: Li Xiao uri: https://doi.org/10.7717/peerj.8909 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Li et al. title: Transcriptome for the breast muscle of Jinghai yellow chicken at early growth stages link: https://peerj.com/articles/8950 last-modified: 2020-04-15 description: BackgroundThe meat quality of yellow feathered broilers is better than the quality of its production. Growth traits are important in the broiler industry. The exploration of regulation mechanisms for the skeletal muscle would help to increase the growth performance of chickens. At present, some progress has been made by researchers, but the molecular mechanisms of the skeletal muscle still remain unclear and need to be improved.MethodsIn this study, the breast muscles of fast- and slow-growing female Jinghai yellow chickens (F4F, F8F, F4S, F8S) and slow-growing male Jinghai yellow chickens (M4S, M8S) aged four and eight weeks were selected for transcriptome sequencing (RNA-seq). All analyses of differentially expressed genes (DEGs) and functional enrichment were performed. Finally, we selected nine DEGs to verify the accuracy of the sequencing by qPCR.ResultsThe differential gene expression analysis resulted in 364, 219 and 111 DEGs (adjusted P-value ≤ 0.05) for the three comparison groups, F8FvsF4F, F8SvsF4S, and M8SvsM4S, respectively. Three common DEGs (ADAMTS20, ARHGAP19, and Novel00254) were found, and they were all highly expressed at four weeks of age. In addition, some other genes related to growth and development, such as ANXA1, COL1A1, MYH15, TGFB3 and ACTC1, were obtained. The most common DEGs (n = 58) were found between the two comparison groups F8FvsF4F and F8SvsF4S, and they might play important roles in the growth of female chickens. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway also showed some significant enrichment pathways, for instance, extracellular matrix (ECM)-receptor interaction, focal adhesion, cell cycle, and DNA replication. The two pathways that were significantly enriched in the F8FvsF4F group were all contained in that of F8SvsF4S. The same two pathways were ECM–receptor interaction and focal adhesion, and they had great influence on the growth of chickens. However, many differences existed between male and female chickens in regards to common DEGs and KEGG pathways. The results would help to reveal the regulation mechanism of the growth and development of chickens and serve as a guideline to propose an experimental design on gene function with the DEGs and pathways. creator: Pengfei Wu creator: Xinchao Zhang creator: Genxi Zhang creator: Fuxiang Chen creator: Mingliang He creator: Tao Zhang creator: Jinyu Wang creator: Kaizhou Xie creator: Guojun Dai uri: https://doi.org/10.7717/peerj.8950 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wu et al. title: REG γ knockdown suppresses proliferation by inducing apoptosis and cell cycle arrest in osteosarcoma link: https://peerj.com/articles/8954 last-modified: 2020-04-15 description: BackgroundOsteosarcoma (OS) is the most common malignant bone tumor with high mortality in children and adolescents. REG γ is overexpressed and plays oncogenic roles in various types of human cancers. However, the expression and potential roles of REG γ in osteosarcoma are elusive. This study aims at exploring possible biological functions of REG γ in the pathogenesis of osteosarcoma and its underlying mechanism.MethodsQuantitativereverse transcription-polymerase chain reaction (qRT-PCR), western blotting andimmunohistochemistry (IHC)were performed to detect the expression levels of REG γ in OS tissues and cell lines. Then, the effects of REG γ expression on OS cell proliferation in vitro were analyzed by Cell Counting Kit-8 (CCK-8), ethylene deoxyuridine (EdU), colony formation, flow cytometry. The protein levels of apoptosis and cell-cycle related proteins were evaluated using western blotting.ResultsIn present study, we found for the first time that REG γ is overexpressed in osteosarcoma tissues and cell lines and knockdown of REG γ significantly inhibits cell proliferation and induces apoptosis and cell cycle arrest in osteosarcoma cells. Furthermore, we observed that p21, caspase-3 and cleaved caspase-3 are increased while the expression of cycinD1 and bcl-2 are decreased after REG γ depletion in osteosarcoma cells. In conclusion, REG γ may be involved in the proliferation of osteosarcoma and serve as a novel therapeutic target in patients with osteosarcoma. creator: Zhiqiang Yin creator: Hao Jin creator: Shibo Huang creator: Guofan Qu creator: Qinggang Meng uri: https://doi.org/10.7717/peerj.8954 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Yin et al. title: Isolation and identification of flavonoid-producing endophytic fungi from medicinal plant Conyza blinii H.Lév that exhibit higher antioxidant and antibacterial activities link: https://peerj.com/articles/8978 last-modified: 2020-04-15 description: BackgroundConyza blinii H. Lév is a medicinal plant that has a variety of pharmacological activities, but its study is at a standstill due to the shortage of resources.MethodThis study utilized the surface sterilization method to isolate endophytic fungi, and they were preliminarily identified by morphology. Flavonoid-producing strains were screened by NaNO2-Al(NO)3 colorimetry and further identified by the ITS sequence. Additionally, we used five antioxidant assays (DPPH, Hydroxyl radical, ABTS, FRAP and T-AOC assays) to systematically evaluate the antioxidant capacity of total flavonoids , and we also determined their antibacterial activity.ResultsIn this study, 21 endophytic fungi were isolated from wild Conyza blinii H. Lév for the first time. There were six flavonoid-producing strains, especially CBL11, whose total flavonoid content reached 50.78 ± 2.4 mg/L. CBL12, CBL12-2 and CBL1-1 all exhibited excellent antioxidant activity. The effect of CBL12 was similar to that of ascorbic acid at low concentrations, and its radical scavenging rates for DPPH and ABTS were 94.56 ± 0.29 % and 99.88 ± 0.27%, respectively, while its IC50 values were only 0.11 ± 0.01 mg/mL and 0.2 ± 0.01 mg/mL. Through LC-MS, we found that CBL12 could produce many high-value flavonoids, such as 3-methoxyflavone, nobiletin, formononetin, scopoletin, and daidzein. Additionally, CBL9 had good antibacterial activity against both gram-positive and gram-negative bacteria. Notably, we obtained the high-yield strains CBL12 and CBL9, which not only had high yields (10.64 ± 1.01 mg/L and 10.17 ± 0.11 mg/L, respectively) but also had excellent biological activity. Hence, the results of this study provide new ideas for endophytic fungi that can be exploited as a source of flavonoids and other medicinal components from Conyza blinii H. Lév. Moreover, this study can serve as a reference for the development of rare medicinal materials. creator: Zizhong Tang creator: Yinsheng Wang creator: Jingyu Yang creator: Yirong Xiao creator: Yi Cai creator: Yujun Wan creator: Hui Chen creator: Huipeng Yao creator: Zhi Shan creator: Chenglei Li creator: Gang Wang uri: https://doi.org/10.7717/peerj.8978 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Tang et al. title: Invasive crayfish does not influence spawning microhabitat selection of brown frogs link: https://peerj.com/articles/8985 last-modified: 2020-04-15 description: Microhabitat selection is a key component of amphibian breeding biology and can be modulated in response to the features of breeding sites and the presence of predators. Despite invasive alien species being among the major threats to amphibians, there is limited information on the role of invasive species in shaping amphibians’ breeding microhabitat choice. The invasive red swamp crayfish (Procambarus clarkii) is a major predator of amphibians’ larvae, including those of the brown frogs Rana dalmatina and Rana latastei. Although qualitative information about the spawning site preferences and breeding microhabitat choice of brown frogs is available in the literature, only a few studies performed quantitative analyses, and the relationship between microhabitat choice and the presence of alien predators has not been investigated yet. The aims of this study were: (1) to characterize the microhabitats selected for clutch deposition by R. dalmatina and R. latastei and (2) to test if the position and the aggregation of egg clutches differ in sites invaded or not invaded by P. clarkii. During spring 2017, we surveyed multiple times 15 breeding sites of both brown frogs in Northern Italy; in each site we assessed the features of the microhabitat where each egg clutch was laid, considering its position (distance from the shore, depth of the water column) and the degree of aggregation of clutches. In each site we also assessed the presence/absence of the invasive crayfish and the relative abundance in the breeding period. We detected egg clutches in all sites; the crayfish occurred in eight ponds. Our results showed substantial differences between the spawning microhabitat features of the two brown frogs: Rana latastei clutches showed a higher degree of aggregation and were associated with deeper areas of the ponds , while Rana dalmatina deposited more spaced out clutches in areas of the ponds that were less deep. For both species, spawning microhabitat features were not significantly different between sites with and without P. clarkii. Although we did not detect behavioural responses to P. clarkii in the choice of spawning microhabitat , additional studies are required to assess whether these frogs modulate other behavioural traits (e.g. during larval development) in response to the invasive predator. creator: Samuele Romagnoli creator: Gentile Francesco Ficetola creator: Raoul Manenti uri: https://doi.org/10.7717/peerj.8985 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Romagnoli et al. title: Disturbed neurovascular coupling in hemodialysis patients link: https://peerj.com/articles/8989 last-modified: 2020-04-15 description: BackgroundAltered cerebral blood flow (CBF) and amplitude of low-frequency fluctuation (ALFF) have been reported in hemodialysis patients. However, neurovascular coupling impairments, which provide a novel insight into the human brain, have not been reported in hemodialysis patients.MethodsWe combined arterial spin labeling (ASL) and blood oxygen level dependent (BOLD) techniques to investigate neurovascular coupling alterations and its relationships with demographic and clinical data in 46 hemodialysis patients and 47 healthy controls. To explore regional neuronal activity, ALFF was obtained from resting-state functional MRI. To measure cerebral vascular response, CBF was calculated from ASL. The across-voxel CBF–ALFF correlations for global neurovascular coupling and CBF/ALFF ratio for regional neurovascular coupling were compared between hemodialysis patients and healthy controls. Two-sample t-tests were used to compare the intergroup differences in CBF and ALFF. Multiple comparisons were corrected using a voxel-wise false discovery rate (FDR) method (P < 0.05).ResultsAll hemodialysis patients and healthy controls showed significant across-voxel correlations between CBF and ALFF. Hemodialysis patients showed a significantly reduced global CBF–ALFF coupling (P = 0.0011) compared to healthy controls at the voxel-level. Of note, decreased CBF/ALFF ratio was exclusively located in the bilateral amygdala involved in emotional regulation and cognitive processing in hemodialysis patients. In hemodialysis patients, the decreased CBF (right olfactory cortex, anterior cingulate gyrus and bilateral insula) and ALFF (bilateral precuneus and superior frontal gyrus) were mainly located in the default mode network and salience network-related regions as well as increased CBF in the bilateral thalamus.ConclusionsThese novel findings reveal that disrupted neurovascular coupling may be a potential neural mechanism in hemodialysis patients. creator: Mei Jin creator: Liyan Wang creator: Hao Wang creator: Xue Han creator: Zongli Diao creator: Wang Guo creator: Zhenghan Yang creator: Heyu Ding creator: Zheng Wang creator: Peng Zhang creator: Pengfei Zhao creator: Han Lv creator: Wenhu Liu creator: Zhenchang Wang uri: https://doi.org/10.7717/peerj.8989 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Jin et al. title: Identification of hub genes and small-molecule compounds in medulloblastoma by integrated bioinformatic analyses link: https://peerj.com/articles/8670 last-modified: 2020-04-14 description: BackgroundMedulloblastoma (MB) is the most common intracranial malignant tumor in children. The genes and pathways involved in the pathogenesis of MB are relatively unknown. We aimed to identify potential biomarkers and small-molecule drugs for MB.MethodsGene expression profile data sets were obtained from the Gene Expression Omnibus (GEO) database and the differentially expressed genes (DEGs) were identified using the Limma package in R. Functional annotation, and cell signaling pathway analysis of DEGs was carried out using DAVID and Kobas. A protein-protein interaction network was generated using STRING. Potential small-molecule drugs were identified using CMap.ResultWe identified 104 DEGs (29 upregulated; 75 downregulated). Gene ontology analysis showed enrichment in the mitotic cell cycle, cell cycle, spindle, and DNA binding. Cell signaling pathway analysis identified cell cycle, HIF-1 signaling pathway, and phospholipase D signaling pathway as key pathways. SYN1, CNTN2, FAIM2, MT3, and SH3GL2 were the prominent hub genes and their expression level were verified by RT-qPCR. Vorinostat, resveratrol, trichostatin A, pyrvinium, and prochlorperazine were identified as potential drugs for MB. The five hub genes may be targets for diagnosis and treatment of MB, and the small-molecule compounds are promising drugs for effective treatment of MB.ConclusionIn this study we obtained five hub genes of MB, SYN1, CNTN2, FAIM2, MT3, and SH3GL2 were confirmed as hub genes. Meanwhile, Vorinostat, resveratrol, trichostatin A, pyrvinium, and prochlorperazine were identified as potential drugs for MB. creator: Zhendong Liu creator: Ruotian Zhang creator: Zhenying Sun creator: Jiawei Yao creator: Penglei Yao creator: Xin Chen creator: Xinzhuang Wang creator: Ming Gao creator: Jinzhao Wan creator: Yiming Du creator: Shiguang Zhao uri: https://doi.org/10.7717/peerj.8670 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Liu et al. title: Rare ground data confirm significant warming and drying in western equatorial Africa link: https://peerj.com/articles/8732 last-modified: 2020-04-14 description: BackgroundThe humid tropical forests of Central Africa influence weather worldwide and play a major role in the global carbon cycle. However, they are also an ecological anomaly, with evergreen forests dominating the western equatorial region despite less than 2,000 mm total annual rainfall. Meteorological data for Central Africa are notoriously sparse and incomplete and there are substantial issues with satellite-derived data because of persistent cloudiness and inability to ground-truth estimates. Long-term climate observations are urgently needed to verify regional climate and vegetation models, shed light on the mechanisms that drive climatic variability and assess the viability of evergreen forests under future climate scenarios.MethodsWe have the rare opportunity to analyse a 34 year dataset of rainfall and temperature (and shorter periods of absolute humidity, wind speed, solar radiation and aerosol optical depth) from Lopé National Park, a long-term ecological research site in Gabon, western equatorial Africa. We used (generalized) linear mixed models and spectral analyses to assess seasonal and inter-annual variation, long-term trends and oceanic influences on local weather patterns.ResultsLopé’s weather is characterised by a cool, light-deficient, long dry season. Long-term climatic means have changed significantly over the last 34 years, with warming occurring at a rate of +0.25 °C per decade (minimum daily temperature) and drying at a rate of −75 mm per decade (total annual rainfall). Inter-annual climatic variability at Lopé is highly influenced by global weather patterns. Sea surface temperatures of the Pacific and Atlantic oceans have strong coherence with Lopé temperature and rainfall on multi-annual scales.ConclusionsThe Lopé long-term weather record has not previously been made public and is of high value in such a data poor region. Our results support regional analyses of climatic seasonality, long-term warming and the influences of the oceans on temperature and rainfall variability. However, warming has occurred more rapidly than the regional products suggest and while there remains much uncertainty in the wider region, rainfall has declined over the last three decades at Lopé. The association between rainfall and the Atlantic cold tongue at Lopé lends some support for the ‘dry’ models of climate change for the region. In the context of a rapidly warming and drying climate, urgent research is needed into the sensitivity of dry season clouds to ocean temperatures and the viability of humid evergreen forests in this dry region should the clouds disappear. creator: Emma R. Bush creator: Kathryn Jeffery creator: Nils Bunnefeld creator: Caroline Tutin creator: Ruth Musgrave creator: Ghislain Moussavou creator: Vianet Mihindou creator: Yadvinder Malhi creator: David Lehmann creator: Josué Edzang Ndong creator: Loïc Makaga creator: Katharine Abernethy uri: https://doi.org/10.7717/peerj.8732 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Bush et al. title: Agility-based exercise training compared to traditional strength and balance training in older adults: a pilot randomized trial link: https://peerj.com/articles/8781 last-modified: 2020-04-14 description: BackgroundIn addition to generally high levels of physical activity, multi-component exercise training is recommended for the maintenance of health and fitness in older adults, including the prevention of falls and frailty. This training often encompasses serial sequencing of balance, strength, endurance and other types of exercise. Exercise training featuring integrative training of these components (i.e. agility training) has been proposed, as it more likely reflects real life challenges like stop-and-go patterns, cutting manoeuvers, turns and decision-making. In this study, we compared the efficacy of an agility-based training to the traditional strength and balance training approach with regard to selected risk factors for falls and frailty.MethodsWe trained twenty-seven community-dwelling healthy seniors (16♂; 11♀; age: 69.5 ± 5.3 y; BMI: 26.4 ± 3.7 kg/m2) for 8 weeks in a group setting with 3 sessions per week, each lasting 50 minutes. Participants were randomized into either the agility group (AGI; n = 12), that used the integrative multi-component training, or the traditional strength and balance group (TSB; n = 15). TSB performed balance and strength exercises separately, albeit within the same session. The training of both groups progressively increased in difficulty. Outcomes were static and dynamic balance (single leg eyes open stand, Y-balance test, reactive balance), lower limb (plantar flexion and dorsal extension) and trunk flexion and extension maximum strength and rate of torque development (RTD). In addition, we tested endurance by the six-minute walk test (6MWT). We calculated linear mixed effects models for between-groups comparisons as well as effect sizes (ES) with 95 % confidence intervals.ResultsSmall ES in favor of AGI were found for plantar flexion strength (ES > 0.18[−0.27;0.89]) and RTD (ES > 0.43[−0.19;1.36]) as well as trunk extension RTD (ES = 0.35[−0.05;0.75]). No other parameters showed notable between group differences. Compliance was high in both groups (AGI: 90 ± 8% of sessions; TSB: 91 ± 7% of sessions).DiscussionAgility-based exercise training seems at least as efficacious as traditional strength and balance training in affecting selected physical performance indicators among community-dwelling healthy seniors. In particular, lower limb and trunk extension explosive strength seem to benefit from the agility training. creator: Eric Lichtenstein creator: Mareike Morat creator: Ralf Roth creator: Lars Donath creator: Oliver Faude uri: https://doi.org/10.7717/peerj.8781 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Lichtenstein et al. title: Characterization of the mitochondrial genomes of two toads, Anaxyrus americanus (Anura: Bufonidae) and Bufotes pewzowi (Anura: Bufonidae), with phylogenetic and selection pressure analyses link: https://peerj.com/articles/8901 last-modified: 2020-04-14 description: Mitogenomes are useful in analyzing phylogenetic relationships and also appear to influence energy metabolism, thermoregulation and osmoregulation. Much evidence has accumulated for positive selection acting on mitochondrial genes associated with environmental adaptation. Hence, the mitogenome is a likely target for environmental selection. The family Bufonidae (true toads) has only nine complete and four partial mitogenomes published compared to the 610 known species of this family. More mitogenomes are needed in order to obtain a clearer understanding of the phylogenetic relationships within Bufonidae that are currently controversial. To date, no mitogenomes have been reported from the genera Anaxyrus and Bufotes. Anaxyrus americanus can live in low temperature environments and Bufotes pewzowi can live in high salinity environments. We sequenced the mitogenomes of these two species to discuss the phylogenetic relationships within Bufonidae and the selection pressures experienced by specimens living in low temperature or saline environments. Like other toads, the circular mitogenomes of both species contained the typical 37 genes. Anaxyrus americanus had the highest A+T content of the complete mitogenome among the Bufonidae. In addition, A. americanus showed a negative AT-skew in the control region, whereas Bufotes pewzowi showed a positive AT-skew. Additionally, both toad species had unique molecular features in common: an ND1 gene that uses TTG as the start codon, an extra unpaired adenine (A) in the anticodon arm of trnS (AGY), and the loss of the DHU loop in trnC. The monophyly of Bufonidae was corroborated by both BI and ML trees. An analysis of selective pressure based on the 13 protein coding genes was conducted using the EasyCodeML program. In the branch model analysis, we found two branches of A. americanus and Bufotes pewzowi that were under negative selection. Additionally, we found two positively selected sites (at positions 115 and 119, BEB value > 0.90) in the ND6 protein in the site model analysis. The residue D (119) was located only in A. americanus and may be related to adaptive evolution in low temperature environments. However, there was no evidence of a positively selected site in Bufotes pewzowi in this study. creator: Yu-Ting Cai creator: Qin Li creator: Jia-Yong Zhang creator: Kenneth B. Storey creator: Dan-Na Yu uri: https://doi.org/10.7717/peerj.8901 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Cai et al. title: Catalyzing rapid discovery of gold-precipitating bacterial lineages with university students link: https://peerj.com/articles/8925 last-modified: 2020-04-14 description: Intriguing and potentially commercially useful microorganisms are found in our surroundings and new tools allow us to learn about their genetic potential and evolutionary history. Engaging students from different disciplines and courses in the search for microbes requires an exciting project with innovative but straightforward procedures and goals. Here we describe an interdisciplinary program to engage students from different courses in the sampling, identification and analysis of the DNA sequences of a unique yet common microbe, Delftia spp. A campus-wide challenge was created to identify the prevalence of this genus, able to precipitate gold, involving introductory level environmental and life science courses, upper-level advanced laboratory modules taken by undergraduate students (juniors and seniors), graduate students and staff from the campus. The number of participants involved allowed for extensive sampling while undergraduate researchers and students in lab-based courses participated in the sample processing and analyses, helping contextualize and solidify their learning of the molecular biology techniques. The results were shared at each step through publicly accessible websites and workshops. This model allows for the rapid discovery of Delftia presence and prevalence and is adaptable to different campuses and experimental questions. creator: Noah G. Riley creator: Carlos C. Goller creator: Zakiya H. Leggett creator: Danica M. Lewis creator: Karen Ciccone creator: Robert R. Dunn uri: https://doi.org/10.7717/peerj.8925 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Riley et al. title: The prognostic value of preoperative serum CA724 for CEA-normal colorectal cancer patients link: https://peerj.com/articles/8936 last-modified: 2020-04-14 description: Background and PurposeThere had been no recognized serum tumor marker to predict the prognosis of colorectal cancer (CRC) patients with normal preoperative serum carcinoembryonic antigen (CEA) levels. The purpose of this study was to determine whether preoperative serum carbohydrate antigen 724 (CA724) was of predictive function for the prognosis of CRC patients with normal CEA levels.MethodsThe medical records of 295 CRC patients with normal CEA levels who underwent surgery at the Department of Colorectal Anal Surgery of the First Affiliated Hospital of Guangxi Medical University (Guangxi, China) between September 2012 and September 2014 were retrospectively reviewed. The Chi-square test was used to test the correlation between preoperative serum CA724 levels and clinical features. Kaplan–Meier curves were conducted to calculate the overall survival (OS) rate and disease-free survival (DFS) of patients. Cox regression analysis was applied to conduct univariate and multivariate analysis of the following four preoperative serum tumor makers namely CA724, carbohydrate antigen 199 (CA199), carcinoembryonic antigen 125 (CA125), carcinoembryonic antigen 242 (CA242) and clinical features. Nomograms for prognostic parameter of OS and DFS were developed using R v3.2.5.ResultsIn the Chi-square test, only pathological node stage (pN stage) (X2 = 14.514, P = 0.001) and differentiation (X2 = 10.712, P = 0.001) were associated with serum CA724 levels. In the Kaplan–Meier analysis, the results revealed that the OS and DFS in patients with high CA724 was poorer than those with normal. In the multivariate Cox regression analysis of OS and DFS, only pT stage, pN stage, metastasis and serum CA724 were independent prognostic risk factors for CRC patients with normal CEA levels.ConclusionPreoperative serum CA724 might serve as a potential prognostic factor for CRC patients with normal serum CEA levels. creator: Jiaan Kuang creator: Yizhen Gong creator: Hailun Xie creator: Ling Yan creator: Shizhen Huang creator: Feng Gao creator: Shuangyi Tang creator: Jialiang Gan uri: https://doi.org/10.7717/peerj.8936 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Kuang et al. title: Serum microRNAs as potential new biomarkers for cisplatin resistance in gastric cancer patients link: https://peerj.com/articles/8943 last-modified: 2020-04-14 description: BackgroundmicroRNAs (miRNAs) have been studied for their role in the early detection of several diseases. However, there is no current information on the systematic screening of serum-derived cisplatin resistance biomarkers in gastric cancer (GC).MethodsCisplatin-resistant GC cell lines were screened for dysregulated miRNAs using small RNA sequencing (sRNA-seq) and miRNAs were functionally annotated using bioinformatics analyses. Real-time quantitative polymerase chain reaction (RT-qPCR) was used to validate the miRNA-relative transcription levels in GC cells and in 74 GC patients. We analyzed the associations between the clinical characteristics of the patients and their miRNA expression. Receiver operating characteristic (ROC) analysis was used to evaluate the diagnostic value for serum-derived cisplatin resistance.ResultsSeven miRNAs were identified from 35 differentially expressed miRNAs between the MGC803/DDP and MGC803 cells in a public database. We found four miRNA candidates (miR-9-3p, miR-9-5p, miR-146a-5p, and miR-433-3p) that were significantly associated with chemotherapy responses in GC cells and patients. miR-9-5p (AUC = 0.856, 95% CI [0.773–0.939], p < 0.0001) and a combined group (miR-9-5p + miR-9-3p + miR-433-3p) (AUC = 0.915, 95% CI [0.856–0.975], P < 0.0001) distinguished chemoresistant GC patients from chemosensitive GC patients.ConclusionsOur study reveals the potential therapeutic use of two serum-based biomarkers, miR-9-5p and a combined group (miR-9-5p + miR-9-3p + miR-433-3p), as indicators for the successful use of cisplatin in GC patients. creator: Lei Jin creator: Nan Zhang creator: Qian Zhang creator: Guoqian Ding creator: Zhenghan Yang creator: Zhongtao Zhang uri: https://doi.org/10.7717/peerj.8943 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Jin et al. title: Nomograms for predicting overall survival and cancer-specific survival in young patients with pancreatic cancer in the US based on the SEER database link: https://peerj.com/articles/8958 last-modified: 2020-04-14 description: BackgroundThe incidence of young patients with pancreatic cancer (PC) is on the rise, and there is a lack of models that could effectively predict their prognosis. The purpose of this study was to construct nomograms for predicting the overall survival (OS) and cancer-specific survival (CSS) of young patients with PC.MethodsPC patients younger than 50 years old from 2004 to 2015 in the Surveillance, Epidemiology, and End Results (SEER) database were selected and randomly divided into training set and validation set. Univariable and forward stepwise multivariable Cox analysis was used to determine the independent factors affecting OS. The Fine and Gray competing risk regression model was used to determine the independent factors affecting CSS. We used significant variables in the training set to construct nomograms predicting prognosis. The discrimination and calibration power of models were evaluated by concordance index (C-index), calibration curve and 10-flod cross-validation.ResultsA total of 4,146 patients were selected. Multivariable Cox analysis showed that gender, race, grade, pathological types, AJCC stage and surgery were independent factors affecting OS. The C-index of the nomogram predicting OS in training and validation was 0.733 (average = 0.731, 95% CI [0.724–0.738]) and 0.742 (95% CI [0.725–0.759]), respectively. Competing risk analysis showed that primary site, pathological types, AJCC stage and surgery were independent factors affecting CSS. The C-index of the nomogram predicting CSS in training and validation set was 0.792 (average = 0.765, 95% CI [0.742–0.788]) and 0.776 (95% CI [0.773–0.779]), respectively. C-index based on nomogram was better in training and validation set than that based on AJCC stage. Calibration curves showed that these nomograms could accurately predict the 1-, 3- and 5-year OS and CSS both in training set and validation set.ConclusionsThe nomograms could effectively predict OS and CSS in young patients with PC, which help clinicians more accurately and quantitatively judge the prognosis of individual patients. creator: Min Shi creator: Biao Zhou creator: Shu-Ping Yang uri: https://doi.org/10.7717/peerj.8958 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2020 Shi et al. title: Clinical applicability of the Feline Grimace Scale: real-time versus image scoring and the influence of sedation and surgery link: https://peerj.com/articles/8967 last-modified: 2020-04-14 description: BackgroundThe Feline Grimace Scale (FGS) is a facial expression-based scoring system for acute pain assessment in cats with reported validity using image assessment. The aims of this study were to investigate the clinical applicability of the FGS in real-time when compared with image assessment, and to evaluate the influence of sedation and surgery on FGS scores in cats.MethodsSixty-five female cats (age: 1.37 ± 0.9 years and body weight: 2.85 ± 0.76 kg) were included in a prospective, randomized, clinical trial. Cats were sedated with intramuscular acepromazine and buprenorphine. Following induction with propofol, anesthesia was maintained with isoflurane and cats underwent ovariohysterectomy (OVH). Pain was evaluated at baseline, 15 min after sedation, and at 0.5, 1, 2, 3, 4, 6, 8, 12 and 24 h after extubation using the FGS in real-time (FGS-RT). Cats were video-recorded simultaneously at baseline, 15 min after sedation, and at 2, 6, 12, and 24 h after extubation for subsequent image assessment (FGS-IMG), which was performed six months later by the same observer. The agreement between FGS-RT and FGS-IMG scores was calculated using the Bland & Altman method for repeated measures. The effects of sedation (baseline versus 15 min) and OVH (baseline versus 24 h) were assessed using linear mixed models. Responsiveness to the administration of rescue analgesia (FGS scores before versus one hour after) was assessed using paired t-tests.ResultsMinimal bias (−0.057) and narrow limits of agreement (−0.351 to 0.237) were observed between the FGS-IMG and FGS-RT. Scores at baseline (FGS-RT: 0.16 ± 0.13 and FGS-IMG: 0.14 ± 0.13) were not different after sedation (FGS-RT: 0.2 ± 0.15, p = 0.39 and FGS-IMG: 0.16 ± 0.15, p = 0.99) nor at 24 h after extubation (FGS-RT: 0.16 ± 0.12, p = 0.99 and FGS-IMG: 0.12 ± 0.12, p = 0.96). Thirteen cats required rescue analgesia; their FGS scores were lower one hour after analgesic administration (FGS-RT: 0.21 ± 0.18 and FGS-IMG: 0.18 ± 0.17) than before (FGS-RT: 0.47 ± 0.24, p = 0.0005 and FGS-IMG: 0.45 ± 0.19, p = 0.015).ConclusionsReal-time assessment slightly overestimates image scoring; however, with minimal clinical impact. Sedation with acepromazine-buprenorphine and ovariohysterectomy using a balanced anesthetic protocol did not influence the FGS scores. Responsiveness to analgesic administration was observed with both the FGS-RT and FGS-IMG. creator: Marina C. Evangelista creator: Javier Benito creator: Beatriz P. Monteiro creator: Ryota Watanabe creator: Graeme M. Doodnaught creator: Daniel S.J. Pang creator: Paulo V. Steagall uri: https://doi.org/10.7717/peerj.8967 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2020 Evangelista et al. title: Accumulation of sequence variants in genes of Wnt signaling and focal adhesion pathways in human corneas further explains their involvement in keratoconus link: https://peerj.com/articles/8982 last-modified: 2020-04-14 description: BackgroundKeratoconus (KTCN) is a protrusion and thinning of the cornea, resulting in loss of visual acuity. The etiology of KTCN remains unclear. The purpose of this study was to assess the potential involvement of new genetic variants in KTCN etiology based on both the genomic and transcriptomic findings recognized in the same corneal tissues.MethodsCorneal tissues derived from five unrelated Polish individuals with KTCN were examined using exome sequencing (ES), followed by enrichment analyses. For comparison purposes, the datasets comprising ES data of five randomly selected Polish individuals without ocular abnormalities and five Polish patients with high myopia were used. Expression levels of selected genes from the overrepresented pathways were obtained from the previous RNA-Seq study.ResultsExome capture discovered 117 potentially relevant variants that were further narrowed by gene overrepresentation analyses. In each of five patients, the assessment of functional interactions revealed rare (MAF ≤ 0.01) DNA variants in at least one gene from Wnt signaling (VANGL1, WNT1, PPP3CC, LRP6, FZD2) and focal adhesion (BIRC2, PAK6, COL4A4, PPP1R12A, PTK6) pathways. No genes involved in pathways enriched in KTCN corneas were overrepresented in our control sample sets.ConclusionsThe results of this first pilot ES profiling of human KTCN corneas emphasized that accumulation of sequence variants in several genes from Wnt signaling and/or focal adhesion pathways might cause the phenotypic effect and further points to a complex etiology of KTCN. creator: Justyna A. Karolak creator: Tomasz Gambin creator: Malgorzata Rydzanicz creator: Piotr Polakowski creator: Rafal Ploski creator: Jacek P. Szaflik creator: Marzena Gajecka uri: https://doi.org/10.7717/peerj.8982 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Karolak et al. title: Heavy metal accumulation potential in pomegranate fruits and leaves grown in roadside orchards link: https://peerj.com/articles/8990 last-modified: 2020-04-14 description: This study was carried out to determine the possible heavy metal accumulation in fruits and leaves of Zivzik pomegranate (Punica granatum L.) grown in two different roadside orchards located in Pirinçli and Kapılı villages of Siirt province, Turkey. Leaf and fruit samples were collected from trees located at 0, 50, 100 m distances from the main roads. Plant samples were analyzed for cobalt (Co), nickel (Ni), cadmium (Cd), lead (Pb) and chromium (Cr) concentrations. The Co, Ni, Cd, Pb and Cr concentrations of fruit samples collected from Pirinçli village were ranged from 0.082 to 0.238 mg kg−1, from 1.160 to 1.559 mg kg−1, from 0.087 to 0.179 mg kg−1, 0.326 to 0.449 mg kg−1 and 0.606 to 1.054 mg kg−1, respectively. The Co, Ni, Cd, Pb and Cr concentrations of fruit samples from Kapılı village were between 0.085 and 0.137 mg kg−1, 1.042 and 1.123 mg kg−1, 0.037 and 0.076 mg kg−1, 0.277 and 0.520 mg kg−1 and 0.762 and 0.932 mg kg−1, respectively. Heavy metal concentrations of leaf samples from Pirinçli village varied from 0.191 to 0.227 mg Co kg−1, 2.201 to 3.547 mg Ni kg−1, 0.051 to 0.098 mg Cd kg−1, 0.535 to 0.749 mg Pb kg−1 and from 1.444 to 2.017 mg Cr kg−1. Similarly, the heavy metal concentration of leaf samples from Kapılı villages were between 0.213 and 0.217 mg Co kg−1, 2.160 and 2.511 mg Ni kg−1, 0.058 and 0.114 mg Cd kg−1, 0.579 and 0.676 mg Pb kg−1 and 1.688 and 1.518 mg Cr kg−1. The Co, Ni and Cr concentrations in fruit samples collected from 0, 50 and 100 meters to the main road in Pirinçli village were at statistically significant level, while only Ni concentration in leaf samples collected from 0, 50 and 100 meters to the main road was at significant level. In contrast, heavy metal concentrations in fruit and leaf samples collected from 0, 50 and 100 m to the main road in Kapılı village were not statistically significant level. creator: Şeyma Demirhan Aydın creator: Mine Pakyürek uri: https://doi.org/10.7717/peerj.8990 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Demirhan Aydın and Pakyürek title: Proteomic profiling analysis of postmenopausal osteoporosis and osteopenia identifies potential proteins associated with low bone mineral density link: https://peerj.com/articles/9009 last-modified: 2020-04-14 description: Postmenopausal osteoporosis (PMOP) is a major global public health concern and older women are more susceptible to experiencing fragility fractures. Our study investigated the associations between circulating proteins with bone mineral density (BMD) in postmenopausal women with or without low BMD (osteoporosis and osteopenia) using a tandem mass tag (TMT) labeling proteomic experiment and parallel reaction monitoring testing. Across all plasma samples, we quantitatively measured 1,092 proteins, and the OP and normal control (NC) samples were differentiated by principal component analysis and a partial least squares-discrimination analysis model based on the protein profiling data. The differentially abundant proteins between the low BMD and NC samples mostly exhibited binding, molecular function regulator, transporter and molecular transducer activity, and were involved in metabolic and cellular processes, stimulus response, biological regulation, immune system processes and so forth. TMT analysis and RRM validation indicated that the expression of protein Lysozyme C (P61626) was negatively related to BMD, while the expression of proteins Glucosidase (A0A024R592) and Protein disulfideisomerase A5 (Q14554) was positively related to BMD values. Collectively, our results suggest that postmenopausal women with low BMD have a different proteomic profile or signature. Protein alterations may play an important role in the pathogenesis of PMOP, and they may act as novel biomarkers and targets of therapeutic agents for this disease. creator: Dageng Huang creator: Yangyang Wang creator: Jing Lv creator: Yuzhu Yan creator: Ya Hu creator: Cuicui Liu creator: Feng Zhang creator: Jihan Wang creator: Dingjun Hao uri: https://doi.org/10.7717/peerj.9009 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Huang et al. title: Assessment of locomotive syndrome among older individuals: a confirmatory factor analysis of the 25-question Geriatric Locomotive Function Scale link: https://peerj.com/articles/9026 last-modified: 2020-04-14 description: BackgroundThe 25-question Geriatric Locomotive Function Scale (GLFS-25) is widely used in daily clinical practice in evaluating locomotive syndrome (LS). The questionnaire contains 25 questions aiming to describe 6 aspects, including body pain, movement-related difficulty, usual care, social activities, cognitive status, and daily activities. However, its potential underlying latent factor structure of the questionnaire has not been fully examined so far.MethodsFive hundred participants who were 60 years or older and were able to walk independently with or without a cane but had complaints of musculoskeletal disorders were recruited face to face at the out-patient ward of Aichi Medical University Hospital between April 2018 and June 2019. All participants completed the GLFS-25. Confirmatory factor analysis (CFA) models (single-factor model, 6-factor model as designed by the developers of the GLFS-25) were fitted and compared using Mplus 8.3 with a maximum likelihood minimization function. Modification indices, standardized expected parameter change were used, a standard strategy for scale development was followed in the search for an alternative and simpler model that could well fit the collected data. Cronbach’s α and its 95% confidence interval (CI) were also calculated.ResultsMean (standard deviation) participants age was 72.6 (7.4) years old; 63.6% of them were women. Under the current criteria, 132 (26.4%) and 262 (52.4%) of the study subjects would be classified as LS stage 1 and stage 2, respectively. Overall, the Cronbach’s α (95% CI) for GLFS-25 evaluated using these data was 0.959 (0.953, 0.964). The single- and 6-factor models were rejected due to poor fit. The alternative models with either full 25 questions or a shortened GLFS-16 were found to fit the data better. These alternative models included three latent factors (body pain, movement-related difficulty, and psycho-social complication) and allowed for cross-loading and residual correlations.DiscussionThe findings of the CFA models provided evidence that the factor structure of the GLFS-25 might be simpler than the 6-factor model as suggested by the designers. The complex relationships between the latent factors and the observed items may also indicate that individual sub-scale use or simply combining the raw scores for evaluation is likely to be inadequate or unsatisfactory. Thus, future revisions of the scoring algorithm or questions of the GLFS-25 may be required. creator: Chaochen Wang creator: Tatsunori Ikemoto creator: Atsuhiko Hirasawa creator: Young-Chang Arai creator: Shogo Kikuchi creator: Masataka Deie uri: https://doi.org/10.7717/peerj.9026 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Wang et al. title: Epiphytic fungi induced pathogen resistance of invasive plant Ipomoea cairica against Colletotrichum gloeosporioides link: https://peerj.com/articles/8889 last-modified: 2020-04-13 description: BackgroundIpomoea cairica (L.) Sweet is a destructive invasive weed in South China but rarely infected with pathogens in nature. Its pathogen resistance mechanism is largely unknown at present. Some non-pathogenic isolates of Fusarium oxysporum and Fusarium fujikuroi are prevalent on many plant species and function as pathogen resistance inducers of host plants. The objective of the present research is to investigate whether the symbiosis between the both fungi and I. cairica is present, and thereby induces pathogen resistance of I. cairica.MethodsThrough field investigation, we explored the occurrence rates of F. oxysporum and F. fujikuroi on leaf surfaces of I. cairica plants in natural habitats and compared their abundance between healthy leaves and leaves infected with Colletotrichum gloeosporioides, a natural pathogen. With artificial inoculation, we assessed their pathogenicity to I. cairica and studied their contribution of pathogen resistance to I. cairica against C. gloeosporioides.ResultsWe found that F. oxysporum and F. fujikuroi were widely epiphytic on healthy leaf surfaces of I. cairica in sunny non-saline, shady non-saline and sunny saline habitats. Their occurrence rates reached up to 100%. Moreover, we found that the abundance of F. oxysporum and F. fujikuroi on leaves infected with C. gloeosporioides were significantly lower than that of healthy leaves. With artificial inoculation, we empirically confirmed that F. oxysporum and F. fujikuroi were non-pathogenic to I. cairica. It was interesting that colonization by F. fujikuroi, F. oxysporum alone and a mixture of both fungi resulted in a reduction of C. gloeosporioides infection to I. cairica accompanied by lower lesion area to leaf surface area ratio, increased hydrogen peroxide (H2O2) concentration and salicylic acid (SA) level relative to the control. However, NPR1 expression, chitinase and β-1,3-glucanase activities as well as stem length and biomass of I. cairica plant only could be significantly improved by F. oxysporum and a mixture of both fungi but not by F. fujikuroi. In addition, as compared to colonization by F. oxysporum and a mixture of both fungi, F. fujikuroi induced significantly higher jasmonic acid (JA) level but significantly lower β-1,3-glucanase activity in leaves of I. cairica plants. Thus, our findings indicated the symbiosis of epiphytic fungiF. fujikuroi and F. oxysporum induced systemic resistance of I. cairica against C. gloeosporioides. F. oxysporum played a dominant role in inducing pathogen resistance of I. cairica. Its presence alleviated the antagonism of the JA signaling on SA-dependent β-1,3-glucanase activity and enabled I. cairica plants to maintain relatively higher level of resistance against C. gloeosporioides. creator: Hua Xu creator: Minjie Zhu creator: Shaoshan Li creator: Weibin Ruan creator: Can Xie uri: https://doi.org/10.7717/peerj.8889 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Xu et al. title: Intraspecific variation in the cochleae of harbour porpoises (Phocoena phocoena) and its implications for comparative studies across odontocetes link: https://peerj.com/articles/8916 last-modified: 2020-04-13 description: In morphological traits, variation within species is generally considered to be lower than variation among species, although this assumption is rarely tested. This is particularly important in fields like palaeontology, where it is common to use a single individual as representative of a species due to the rarity of fossils. Here, we investigated intraspecific variation in the cochleae of harbour porpoises (Phocoena phocoena). Interspecific variation of cochlear morphology is well characterised among odontocetes (toothed whales) because of the importance of the structure in echolocation, but generally these studies use only a single cochlea to represent each species. In this study we compare variation within the cochleae of 18 specimens of P. phocoena with variations in cochlear morphology across 51 other odontocete species. Using both 3D landmark and linear measurement data, we performed Generalised Procrustes and principal component analyses to quantify shape variation. We then quantified intraspecific variation in our sample of P. phocoena by estimating disparity and the coefficient of variation for our 3D and linear data respectively. Finally, to determine whether intraspecific variation may confound the results of studies of interspecific variation, we used multivariate and univariate analyses of variance to test whether variation within the specimens of P. phocoena was significantly lower than that across odontocetes. We found low levels of intraspecific variation in the cochleae of P. phocoena, and that cochlear shape within P. phocoena was significantly less variable than across odontocetes. Although future studies should attempt to use multiple cochleae for every species, our results suggest that using just one cochlea for each species should not strongly influence the conclusions of comparative studies if our results are consistent across Cetacea. creator: Maria Clara Iruzun Martins creator: Travis Park creator: Rachel Racicot creator: Natalie Cooper uri: https://doi.org/10.7717/peerj.8916 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Martins et al. title: Dynamic changes in intestinal microbiota in young forest musk deer during weaning link: https://peerj.com/articles/8923 last-modified: 2020-04-13 description: Weaning is an important event for all mammals, including young forest musk deer. However, weaning stress may cause intestinal microbiota-related disorders. Therefore, high-throughput 16S rRNA gene sequencing was applied to study the dynamic changes in intestinal microbiota during pre-weaning (10 days before weaning) and post-weaning (10 days after weaning) in 15 young forest musk deer. We saw that intestinal microbiota diversity in the post-weaning period was significantly higher than that in the pre-weaning period. The most dominant bacterial phyla were similar in the two groups (Firmicutes, Bacteroidetes and Verrucomicrobia). Meanwhile, we applied Linear discriminant analysis effect size (LefSe) to identify the most differentially microbial taxa in the pre-weaning and post-weaning groups. In the post-weaning forest musk deer, the relative abundance of Actinobacteria, Spirochaetes, Ruminococcaceae_UCG-005, Treponema and Prevotella was higher than in the pre-weaning group. However, higher relative abundance of the phyla Bacteroidetes was found in the pre-weaning group compared with that in the post-weaning group. In summary, this research provides a theoretical foundation for the dynamics of young forest musk deer intestinal microbiota during the weaning transition, which may benefit in understanding the growth and health of forest musk deer. creator: Yimeng Li creator: Minghui Shi creator: Tianxiang Zhang creator: Xin Hu creator: Baofeng Zhang creator: Shanghua Xu creator: Jianhong Ding creator: Defu Hu creator: Shuqiang Liu uri: https://doi.org/10.7717/peerj.8923 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Li et al. title: Estimating the evolutionary rates in mosasauroids and plesiosaurs: discussion of niche occupation in Late Cretaceous seas link: https://peerj.com/articles/8941 last-modified: 2020-04-13 description: Observations of temporal overlap of niche occupation among Late Cretaceous marine amniotes suggest that the rise and diversification of mosasauroid squamates might have been influenced by competition with or disappearance of some plesiosaur taxa. We discuss that hypothesis through comparisons of the rates of morphological evolution of mosasauroids throughout their evolutionary history with those inferred for contemporary plesiosaur clades. We used expanded versions of two species-level phylogenetic datasets of both these groups, updated them with stratigraphic information, and analyzed using the Bayesian inference to estimate the rates of divergence for each clade. The oscillations in evolutionary rates of the mosasauroid and plesiosaur lineages that overlapped in time and space were then used as a baseline for discussion and comparisons of traits that can affect the shape of the niche structures of aquatic amniotes, such as tooth morphologies, body size, swimming abilities, metabolism, and reproduction. Only two groups of plesiosaurs are considered to be possible niche competitors of mosasauroids: the brachauchenine pliosaurids and the polycotylid leptocleidians. However, direct evidence for interactions between mosasauroids and plesiosaurs is scarce and limited only to large mosasauroids as the predators/scavengers and polycotylids as their prey. The first mosasauroids differed from contemporary plesiosaurs in certain aspects of all discussed traits and no evidence suggests that early representatives of Mosasauroidea diversified after competitions with plesiosaurs. Nevertheless, some mosasauroids, such as tylosaurines, might have seized the opportunity and occupied the niche previously inhabited by brachauchenines, around or immediately after they became extinct, and by polycotylids that decreased their phylogenetic diversity and disparity around the time the large-sized tylosaurines started to flourish. creator: Daniel Madzia creator: Andrea Cau uri: https://doi.org/10.7717/peerj.8941 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Madzia and Cau title: Response of organic carbon mineralization and bacterial communities to soft rock additions in sandy soils link: https://peerj.com/articles/8948 last-modified: 2020-04-13 description: Bacteria play a vital role in biotransformation of soil organic carbon (SOC). However, mechanisms of bacterium and organic carbon mineralization remain unclear during improvement of sandy soil using soft rock additions. In this study, four treatments with differing ratios of soft rock to sand of 0:1 (CK), 1:5 (C1), 1:2 (C2) and 1:1 (C3) were selected for mineralization incubation and high-throughput sequencing. The results showed that SOC, total nitrogen (TN), available phosphorus (AP), nitrate nitrogen (NO${}_{3}^{-}$3−-N), and mass water content (WC) of sandy soil increased significantly after addition of soft rock (P < 0.05). Compared with the CK treatment, cumulative mineralization and potential mineralized organic carbon content of C1, C2 and C3 increased by 71.79%–183.86% and 71.08%–173.33%. The cumulative mineralization rates of organic carbon treated with C1 and C2 were lower, 16.96% and 17.78%, respectively (P > 0.05). The three dominant bacteria were Actinobacteria, Proteobacteria and Chloroflexi, among which Proteobacteria was negatively correlated with mineralization of organic carbon (P < 0.01). The mineralization rate constant (k) was positively correlated and negatively correlated with Cyanobacteria and Nitrospirae, respectively. Under C2 treatment, Proteobacteria and Nitrospirae had the largest increase, and Cyanobacteria had the largest decrease. Compared with other treatments, C2 treatment significantly increased bacterial diversity index, richness index and evenness index, and the richness index had a negative correlation with k value. In conclusion, when the ratio of soft rock to sand was 1:2, the k of SOC could be reduced. In addition, the retention time of SOC can be increased, and resulting carbon fixation was improved. creator: Zhen Guo creator: Jichang Han creator: Juan Li uri: https://doi.org/10.7717/peerj.8948 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Guo et al. title: Association of weaning preparedness with extubation outcome of mechanically ventilated patients in medical intensive care units: a retrospective analysis link: https://peerj.com/articles/8973 last-modified: 2020-04-13 description: BackgroundAssessment of preparedness of weaning has been recommended before extubation for mechanically ventilated patients. We aimed to understand the association of a structured assessment of weaning preparedness with successful liberation.MethodsWe retrospectively investigated patients with acute respiratory failure who experienced an extubation trial at the medical intensive care units of a medical center and compared the demographic and clinical characteristics between those patients with successful and failed extubation. A composite score to assess the preparedness of weaning, the WEANSNOW score, was generated consisting of eight components, including Weaning parameters, Endotracheal tube, Arterial blood gas analysis, Nutrition, Secretions, Neuromuscular-affecting agents, Obstructive airway problems and Wakefulness. The prognostic ability of the WEANSNOW score for extubation was then analyzed.ResultsOf the 205 patients included, 138 (67.3%) patients had successful extubation. Compared with the failure group, the success group had a significantly shorter duration of MV before the weaning attempt (11.2 ± 11.6 vs. 31.7 ± 26.2 days, p < 0.001), more with congestive heart failure (42.0% vs. 25.4%, p = 0.020), and had different distribution of the types of acute respiratory failure (p = 0.037). The failure group also had a higher WEANSNOW score (1.22 ± 0.85 vs. 0.51 ± 0.71, p < 0.001) and worse Rapid Shallow Breathing Index (93.9 ± 63.8 vs. 56.3 ± 35.1, p < 0.001). Multivariate logistic regression analysis showed that a WEANSNOW Score = 1 or higher (OR = 2.880 (95% CI [1.291–6.426]), p = 0.010) and intubation duration >21 days (OR = 7.752 (95% CI [3.560–16.879]), p < 0.001) were independently associated with an increased probability of extubation failure.ConclusionAssessing the pre-extubation status of intubated patients in a checklist-based approach using the WEANSNOW score might provide valuable insights into extubation failure in patients in a medical ICU for acute respiratory failure. Further prospective studies are warranted to elucidate the practice of assessing weaning preparedness. creator: Feng-Ching Lin creator: Yao-Wen Kuo creator: Jih-Shuin Jerng creator: Huey-Dong Wu uri: https://doi.org/10.7717/peerj.8973 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Lin et al. title: Interthalamic adhesion size in aging dogs with presumptive spontaneous brain microhemorrhages: a comparative retrospective MRI study of dogs with and without evidence of canine cognitive dysfunction link: https://peerj.com/articles/9012 last-modified: 2020-04-13 description: ObjectiveSpontaneous brain microhemorrhages in elderly people are present to some degree in Alzheimer’s disease patients but have been linked to brain atrophy in the absence of obvious cognitive decline. Brain microhemorrhages have recently been described in older dogs, but it is unclear whether these are associated with brain atrophy. Diminution of interthalamic adhesion size-as measured on MRI or CT-has been shown to be a reliable indicator of brain atrophy in dogs with canine cognitive dysfunction (CCD) in comparison with successfully aging dogs. We hypothesized that aging dogs with brain microhemorrhages presenting for neurologic dysfunction but without obvious features of cognitive decline would have small interthalamic adhesion measurements, like dogs with CCD, compared with control dogs. The objective of this study was to compare interthalamic adhesion size between three groups of aging (>9 years) dogs: (1) neurologically impaired dogs with presumptive spontaneous brain microhemorrhages and no clinical evidence of cognitive dysfunction (2) dogs with CCD (3) dogs without clinical evidence of encephalopathy on neurologic examination (control dogs). MR images from 52 aging dogs were reviewed and measurements were obtained of interthalamic adhesion height (thickness) and mid-sagittal interthalamic adhesion area for all dogs, in addition to total brain volume. Interthalamic adhesion measurements, either absolute or normalized to total brain volume were compared between groups. Signalment (age, breed, sex), body weight, presence and number of SBMs, as well as other abnormal MRI findings were recorded for all dogs.ResultsAll interthalamic adhesion measurement parameters were significantly (P < 0.05) different between control dogs and affected dogs. Both dogs with cognitive dysfunction (12/15; 80%) and dogs with isolated brain microhemorrhages had more microhemorrhages than control dogs (3/25; 12%). Affected dogs without cognitive dysfunction had significantly more microhemorrhages than dogs with cognitive dysfunction. In addition to signs of cognitive impairment for the CCD group, main clinical complaints for SBM and CCD dogs were referable to central vestibular dysfunction, recent-onset seizure activity, or both. Geriatric dogs with spontaneous brain microhemorrhages without cognitive dysfunction have similar MRI abnormalities as dogs with cognitive dysfunction but may represent a distinct disease category. creator: Curtis W. Dewey creator: Mark Rishniw creator: Philippa J. Johnson creator: Emma S. Davies creator: Joseph J. Sackman creator: Marissa O’Donnell creator: Simon Platt creator: Kelsey Robinson uri: https://doi.org/10.7717/peerj.9012 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Dewey et al. title: Association between self-rated health and physical performance in middle-aged and older women from Northeast Brazil link: https://peerj.com/articles/8876 last-modified: 2020-04-10 description: BackgroundSelf-rated Health (SRH) is regarded as a simple and valid measure of a person’s health status, given its association to adverse health outcomes, including low physical performance in older populations. However, studies investigating these associations in low- and middle-income settings are scarce, especially for middle-aged populations. Understanding the validity of SRH in relation to objective health measures in low-income populations could assist in decision making about health policy and strategies, especially in under-resourced settings.ObjectiveAssess the relationship between SRH and physical performance measures in middle-aged and older women in a low-income setting of Brazil.MethodsThis is a cross-sectional study of 571 middle-aged (40–59 years old) and older (60–80 years old) women living in Parnamirim and Santa Cruz in the Northeast region of Brazil. Participants reported their health status and were allocated to the “SRH good” or “SRH poor” groups. The physical performance evaluation included: handgrip strength, one-legged balance with eyes open and closed and chair stand test. The relationship between SRH and physical performance for middle-aged and older women was assessed by quantile regression (modeling medians) adjusted for potential confounders (age, socioeconomic variables, body mass index, menopause status, age at first birth, parity, chronic conditions and physical activity).ResultsMiddle-aged women from the “SRH good” group presented better physical performance with 1.75 kgf stronger handgrip strength (95% CI [0.47–3.02]; p = 0.004), 1.31 s longer balance with eyes closed ([0.00–2.61]; p = 0.030), and they were 0.56 s faster in the chair stand test ([0.18–0.94]; p = 0.009) than those who reported “SRH poor”. No association was found for balance with eyes open. For older women, there was no evidence of associations between physical performance and SRH.ConclusionThis study showed that SRH is significantly associated with objective measures of physical performance in a sample of low-income middle-aged women. SRH can be an important tool to indicate the need for further evaluation of physical performance among middle-aged women and can be particularly useful for low-income communities. creator: Sabrina Gabrielle Gomes Fernandes creator: Catherine M. Pirkle creator: Tetine Sentell creator: José Vilton Costa creator: Alvaro Campos Cavalcanti Maciel creator: Saionara Maria Aires da Câmara uri: https://doi.org/10.7717/peerj.8876 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Fernandes et al. title: A 7-lncRNA signature associated with the prognosis of colon adenocarcinoma link: https://peerj.com/articles/8877 last-modified: 2020-04-10 description: BackgroundColon adenocarcinoma (COAD) is the most common colon cancer exhibiting high mortality. Due to their association with cancer progression, long noncoding RNAs (lncRNAs) are now being used as prognostic biomarkers. In the present study, we used relevant clinical information and expression profiles of lncRNAs originating from The Cancer Genome Atlas database, aiming to construct a prognostic lncRNA signature to estimate the prognosis of patients.MethodsThe samples were randomly spilt into training and validation cohorts. In the training cohort, prognosis-related lncRNAs were selected from differentially expressed lncRNAs using the univariate Cox analysis. Furthermore, the least absolute shrinkage and selection operator (LASSO) regression and multivariate Cox analysis were employed for identifying prognostic lncRNAs. The prognostic signature was constructed by these lncRNAs.ResultsThe prognostic model was able to calculate each COAD patient’s risk score and split the patients into groups of low and high risks. Compared to the low-risk group, the high-risk group had significant poor prognosis. Next, the prognostic signature was validated in the validation, as well as all cohorts. The receiver operating characteristic (ROC) curve and c-index were determined in all cohorts. Moreover, these prognostic lncRNA signatures were combined with clinicopathological risk factors to construct a nomogram for predicting the prognosis of COAD in the clinic. Finally, seven lncRNAs (CTC-273B12.10, AC009404.2, AC073283.7, RP11-167H9.4, AC007879.7, RP4-816N1.7, and RP11-400N13.2) were identified and validated by different cohorts. The Kyoto Encyclopedia of Genes and Genomes analysis of the mRNAs co-expressed with the seven prognostic lncRNAs suggested four significantly upregulated pathways, which were AGE-RAGE, focal adhesion, ECM-receptor interaction, and PI3K/Akt signaling pathways.ConclusionThus, our study verified that the seven lncRNAs mentioned can be used as biomarkers to predict the prognosis of COAD patients and design personalized treatments. creator: Xiaorui Fu creator: Jinzhong Duanmu creator: Taiyuan Li creator: Qunguang Jiang uri: https://doi.org/10.7717/peerj.8877 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Fu et al. title: The whole body transcriptome of Coleophora obducta reveals important olfactory proteins link: https://peerj.com/articles/8902 last-modified: 2020-04-10 description: BackgroundThe tiny casebearer moth Coleophora obducta, an important defoliator of Larix spp., is a major threat to ecological security in north China. Studies have shown that C. obducta is strongly specific to host plants; it is unable complete its life cycle without Larix spp. The sex pheromones of C. obducta Z5-10:OH have been elucidated; and eight types of antennae sensilla, have been detected, indicating that an exploration of its olfactory proteins is necessary, due to the general lack of information on this topic.MethodsWe investigated the whole body transcriptome of C. obducta, performed a phylogenetic analysis of its olfactory proteins and produced expression profiles of three pheromone-binding proteins (CobdPBPs) by qRT–PCR.ResultsWe identified 16 odorant binding proteins, 14 chemosensory proteins, three sensory neuron membrane proteins, six odorant degrading enzymes, five antennal esterases, 13 odorant receptors, seven ionotropic receptors and 10 gustatory receptors, including three PBPs and one odorant co-receptor. Additionally, three putative pheromone receptors, two bitter gustatory receptors and five functional ionotropic receptors were found by phylogenetic analysis. The expression profiles of three PBPs in males and females showed that all of them exhibited male-specific expression and two were expressed at significantly higher levels in males. These data provide a molecular foundation from which to explore the olfactory recognition process and may be useful in the development of a new integrated pest management strategy targeting olfactory recognition of C. obducta. creator: Dongbai Wang creator: Jing Tao creator: Pengfei Lu creator: Youqing Luo creator: Ping Hu uri: https://doi.org/10.7717/peerj.8902 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Wang et al. title: Evolution of switchable aposematism: insights from individual-based simulations link: https://peerj.com/articles/8915 last-modified: 2020-04-10 description: Some defended prey animals can switch on their normally hidden aposematic signals. This switching may occur in reaction to predators’ approach (pre-attack signals) or attack (post-attack signals). Switchable aposematism has been relatively poorly studied, but we can expect that it might bring a variety of benefits to an aposmetic organism. First, the switching could startle the predators (deimatism). Second, it could facilitate aversive learning. Third, it could minimize exposure or energetic expense, as the signal can be switched off. These potential benefits might offset costs of developing, maintaining and utilizing the switchable traits. Here we focused on the third benefit of switchability, the cost-saving aspect, and developed an individual-based computer simulation of predators and prey. In 88,128 model runs, we observed evolution of permanent, pre-attack, or post-attack aposematic signals of varying strength. We found that, in general, the pre-attack switchable aposematism may require moderate predator learning speed, high basal detectability, and moderate to high signal cost. On the other hand, the post-attack signals may arise under slow predator learning, low basal detectability and high signal cost. When predator population turnover is fast, it may lead to evolution of post-attack aposematic signals that are not conforming to the above tendency. We also suggest that a high switching cost may exert different selection pressure on the pre-attack than the post-attack switchable strategies. To our knowledge, these are the first theoretical attempts to systematically explore the evolution of switchable aposematism relative to permanent aposematism in defended prey. Our simulation model is capable of addressing additional questions beyond the scope of this article, and we open the simulation software, program manual and source code for free public use. creator: Woncheol Song creator: Sang-im Lee creator: Piotr G. Jablonski uri: https://doi.org/10.7717/peerj.8915 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Song et al. title: Functional characterization of maize heat shock transcription factor gene ZmHsf01 in thermotolerance link: https://peerj.com/articles/8926 last-modified: 2020-04-10 description: BackgroundHeat waves can critically influence maize crop yields. Plant heat shock transcription factors (HSFs) play a key regulating role in the heat shock (HS) signal transduction pathway.MethodIn this study, a homologous cloning method was used to clone HSF gene ZmHsf01 (accession number: MK888854) from young maize leaves. The transcript levels of ZmHsf01 were detected using qRT-PCR in different tissues and treated by HS, abscisic acid (ABA), hydrogen peroxide (H2O2), respectively, and the functions of gene ZmHsf01 were studied in transgenic yeast and Arabidopsis.ResultZmHsf01 had a coding sequence (CDS) of 1176 bp and encoded a protein consisting of 391 amino acids. The homologous analysis results showed that ZmHsf01 and SbHsfA2d had the highest protein sequence identities. Subcellular localization experiments confirmed that ZmHsf01 was localized in the nucleus. ZmHsf01 was expressed in many maize tissues. It was up-regulated by HS, and up-regulated in roots and down-regulated in leaves under ABA and H2O2treatments. ZmHsf01-overexpressing yeast cells showed increased thermotolerance. In Arabidopsis seedlings, ZmHsf01 compensated for the thermotolerance defects of mutant athsfa2, and ZmHsf01-overexpressing lines showed enhanced basal and acquired thermotolerance. When compared to wild type (WT) seedlings, ZmHsf01-overexpressing lines showed higher chlorophyll content and survival rates after HS. Heat shock protein (HSP) gene expression levels were more up-regulated in ZmHsf01-overexpressing Arabidopsis seedlings than WT seedlings. These results suggest that ZmHsf01 plays a vital role in response to HS in plant. creator: Huaning Zhang creator: Guoliang Li creator: Dong Hu creator: Yuanyuan Zhang creator: Yujie Zhang creator: Hongbo Shao creator: Lina Zhao creator: Ruiping Yang creator: Xiulin Guo uri: https://doi.org/10.7717/peerj.8926 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhang et al. title: Validation of a handheld β-hydroxybutyrate acid meter to identify hyperketonaemia in ewes link: https://peerj.com/articles/8933 last-modified: 2020-04-10 description: BackgroundThe end of pregnancy is the period with the highest risk of occurrences of ketosis and pregnancy toxemia due to fat mobilization and increasing non-esterified fatty acids in the liver which are converted in ketone bodies, mainly β-hydroxybutyrate acid (BHB). This ketone body may also become elevated in the bloodstream. The present study validates the use of a handheld meter for determining the blood concentration of BHB and ascertaining the predictive value and accuracy of BHB measurements in diagnosing hyperketonaemia in ewes.MethodsA total of 19, non-pregnant, crossbred ewes were subjected to 2 h of intravenous infusion of a saturated BHB solution. Over 6 h of evaluation, 247 blood samples were obtained in 13 sampling moments. The BHB concentration was measured by an enzymatic colorimetric method in an automated biochemical analyzer (gold-standard) and by a handheld meter using an electrochemical enzyme technique.ResultsThere was a high correlation between both methods (r = 0.98; P < 0.001). Considering the blood BHB concentrations range 0.8–1.6 mmol/L for moderate ketosis the handheld meter presented sensitivity and specificity of 0.98 and 0.81, respectively. For severe ketosis (BHB ≥ 1.6 mmol/L) sensitivity and specificity were 0.99 and 0.75, respectively. Thus, the handheld device can be useful for diagnoses of cases of mild or severe pregnancy toxemia at field conditions. creator: Carolina Akiko Sato Cabral Araújo creator: Antonio Humberto Hamad Minervino creator: Rejane Santos Sousa creator: Francisco Leonardo Costa Oliveira creator: Frederico Augusto Mazzocca Lopes Rodrigues creator: Clara Satsuki Mori creator: Enrico Lippi Ortolani uri: https://doi.org/10.7717/peerj.8933 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Araújo et al. title: Effects of preservation duration at 4 °C on the quality of RNA in rabbit blood specimens link: https://peerj.com/articles/8940 last-modified: 2020-04-10 description: A prolonged preservation duration of blood specimens at 4 °C may occur due to the distance from collection points to storage facilities in many biobanks, especially for multicenter studies. This could lead to RNA degradation, affecting downstream analyses. However, effects of preservation durations at 4 °C on RNA quality in blood specimens need to be studied. We collected rabbit blood using EDTA tubes and stored them at 4 °C for different preservation durations. Then, we examined the quality of RNA from whole blood and leukocytes isolated from rabbit blood. Our results show that the purity of whole blood RNA and leukocyte RNA does not indicate significant change after rabbit blood is stored at 4 °C for different preservation durations (from 1 h to 7 days). The integrity of leukocyte RNA indicates the same result as above, but the integrity of whole blood RNA is significantly decreased after rabbit blood is stored at 4 °C for over 3 days. Moreover, expression of SMAD7, MKI67, FOS, TGFβ1 and HIF1α of whole blood RNA and leukocyte RNA remains basically stable, but PCNA expression of whole blood RNA or leukocyte RNA is significantly decreased after rabbit blood is stored at 4 °C for over 24 h or 7 days. Therefore, these results suggest that high-quality RNA is obtained from the fresher blood specimens and if blood specimens are stored for over 3 days at 4 °C, the quality of leukocyte RNA is more stable and of better quality than that of whole blood RNA. creator: Jiaojiao Song creator: Junmei Zhou uri: https://doi.org/10.7717/peerj.8940 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Song and Zhou title: A rapid and accurate method for the detection of four aminoglycoside modifying enzyme drug resistance gene in clinical strains of Escherichia coli by a multiplex polymerase chain reaction link: https://peerj.com/articles/8944 last-modified: 2020-04-10 description: BackgroundAntibiotics are highly effective drugs used in the treatment of infectious diseases. Aminoglycoside antibiotics are one of the most common antibiotics in the treatment of bacterial infections. However, the development of drug resistance against those medicines is becoming a serious concern.AimThis study aimed to develop an efficient, rapid, accurate, and sensitive detection method that is applicable for routine clinical use.MethodsEscherichia coli was used as a model organism to develop a rapid, accurate, and reliable multiplex polymerase chain reaction (M-PCR) for the detection of four aminoglycoside modifying enzyme (AME) resistance genes Aac(6′)-Ib, Aac(3)-II, Ant(3″)-Ia, and Aph(3′)-Ia. M-PCR was used to detect the distribution of AME resistance genes in 237 clinical strains of E. coli. The results were verified by simplex polymerase chain reaction (S-PCR).ResultsResults of M-PCR and S-PCR showed that the detection rates of Aac(6′)-Ib, Aac(3)-II, Ant(3″)-Ia, and Aph(3′)-Ia were 32.7%, 59.2%, 23.5%, and 16.8%, respectively, in 237 clinical strains of E. coli. Compared with the traditional methods for detection and identification, the rapid and accurate M-PCR detection method was established to detect AME drug resistance genes. This technique can be used for the clinical detection as well as the surveillance and monitoring of the spread of those specific antibiotic resistance genes. creator: Yaoqiang Shi creator: Chao Li creator: Guangying Yang creator: Xueshan Xia creator: Xiaoqin Mao creator: Yue Fang creator: A-Mei Zhang creator: Yuzhu Song uri: https://doi.org/10.7717/peerj.8944 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Shi et al. title: Inhibition of excessive mitophagy by N-acetyl-L-tryptophan confers hepatoprotection against Ischemia-Reperfusion injury in rats link: https://peerj.com/articles/8665 last-modified: 2020-04-09 description: In order to investigate the mechnism of hepatoprotective of N-acetyl-L-tryptophan (L-NAT) against ischemia-reperfusion (I/R) injury, the effects of L-NAT were investigated in hepatic ischemia-reperfusion injury (HIRI) models both in vitro and in vivo, which were made by BRL cells and Sprague-Dawley (SD) rats, respectively. The cell viability of hepatocyte was assessed by cell counting kit-8 (CCK-8) staining. The activation of autophagy was detected by electron microscopy (EM), quantitative real-time PCR (qRT-PCR), Western blotting and immunofluorescence. The activation of mitophagy was determined by the change of autophagy related protein, change of mitochondrial structure and function, co-location of autophagy protein and MitoTracker. Results showed that the morphological structures of hepatocytes were changed significantly after HIRI, and the cell viability of hydrogen peroxide (H2O2)-induced BRL cells was decreased. Autophagy markers Beclin1, microtubule associated protein 1 light chain 3-II (LC3-II) and autophagy related protein-7 (ATG-7) were highly expressed and the expression of SQSTM1 (P62) was decreased after HIRI, which suggested that autophagy of hepatocytes was activated after I/R. The reduction of ATP, mitochondrial DNA (mtDNA) and the mitochondrial transmembrane potential (ΔΨm) after H2O2-induced revealed that function of mitochondrial had also undergone significant changes. The increased expression of autophagy protein, destructure of mitochondria and mitochondrial dysfunction, the increased co-location of Beclin1 and MitoTracker induced by H2O2 implied the excessive mitophagy. The expression of the autophagy protein was increased by 3-Methyladenine (3-MA), providing another piece of evidence. Importantly, all changes were restored by L-NAT pretreament. In conclusion, the present findings demonstrate that excessive mitophagy involved in the process of HIRI and L-NAT may protect hepatocytes against HIRI by inhibiting activation of mitophagy and improving the structure and function of mitochondria. creator: Huiting Li creator: Yitong Pan creator: Hongjuan Wu creator: Shuna Yu creator: Jianxin Wang creator: Jie Zheng creator: Can Wang creator: Jianguo Li creator: Jiying Jiang uri: https://doi.org/10.7717/peerj.8665 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Li et al. title: Similarity of salivary microbiome in parents and adult children link: https://peerj.com/articles/8799 last-modified: 2020-04-09 description: BackgroundHuman saliva contains approximately 700 bacterial species. It has been reported that the salivary microbiome of a large family of closely related individuals consisting of multiple households is similar but the relatedness of salivary bacteria between generations of parents and their children has not yet been investigated. The objectives were to investigate the entirety of salivary bacterial DNA profiles and whether and how families share these profiles and also compare these communities between grandparents and their first daughter generations (F1) using 16S rRNA gene amplicon sequencing.ResultsThe most abundant phyla in two separate families were Firmicutes, Bacteroidetes, Proteobacteria, Fusobacteria and Actinobacteria. Family ties explained 13% of the variance between individuals’ bacterial communities (R2 = 0.13; P = 0.001). Mothers shared more OTUs with adult children compared to fathers, but this linkage seemed to be weaker in the nuclear family with older adult children. We identified 29 differentially abundant genus level OTUs (FDR < 0.05) between families, which accounted for 31% of the total identified genus level OTUs.ConclusionsOur results indicate that adult family members share bacterial communities and adult children were more similar to mothers than fathers. The observed similarity in oral microbiome between parent–child pairs seemed to weaken over time. We suggest that our analysis approach is suitable for relatedness study of multigenerational salivary bacteria microbiome. creator: Kati Sundström creator: Pashupati P. Mishra creator: Mikko J. Pyysalo creator: Terho Lehtimäki creator: Pekka J. Karhunen creator: Tanja Pessi uri: https://doi.org/10.7717/peerj.8799 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2020 Sundström et al. title: Characterization of calcineurin A and B genes in the abalone, Haliotis diversicolor, and their immune response role during bacterial infection link: https://peerj.com/articles/8868 last-modified: 2020-04-09 description: Calcineurin (CN) is known to be involved in many biological processes, particularly, the immune response mechanism in many invertebrates. In this study, we characterized both HcCNA and HcCNB genes in Haliotis diversicolor, documented their expression in many tissues, and discerned their function as immune responsive genes against Vibrio parahaemolyticus infection. Similar to other mollusk CNs, the HcCNA gene lacked a proline-rich domain and comprised only one isoform of its catalytic unit, in contrast to CNs found in mammals. HcCNB was highly conserved in both sequence and domain architecture. Quantitative PCR and in situ hybridization revealed that the genes were broadly expressed and were not restricted to tissues traditionally associated with immune function. Upon infection of H. diversicolor with V. parahaemolyticus (a bacteria that causes serious disease in crustaceans and mollusks), both HcCNA and HcCNB genes were highly up-regulated at the early phase of bacterial infection. HcCNB was expressed significantly higher than HcCNA in response to bacterial challenge, suggesting its independent or more rapid response to bacterial infection. Together, the two CN genes are unique in their gene structure (particular HcCNA) and distribution in mollusk species and likely function as immune responsive genes along with many other genes that are enhanced in the early phase of V. parahaemolyticus infection in abalone. creator: Tiranan Buddawong creator: Somluk Asuvapongpatana creator: Saengchan Senapin creator: Carmel McDougall creator: Wattana Weerachatyanukul uri: https://doi.org/10.7717/peerj.8868 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Buddawong et al. title: Revision of the mollisoniid chelicerate(?) Thelxiope, with a new species from the middle Cambrian Wheeler Formation of Utah link: https://peerj.com/articles/8879 last-modified: 2020-04-09 description: The recent re-interpretation of the Lower Palaeozoic euarthropod group Mollisonia as belonging to Chelicerata has triggered a renewed interest for the poorly known family Mollisoniidae. In this contribution, we revise the anatomy, taxonomic diversity, and systematics of Thelxiope, the sister-taxon of Mollisonia. This mollisoniid genus comprises four species, and is characterized by the presence of one cephalic, seven thoracic (one per tergite), and three pygidial long sagittal spines. The type species, T. palaeothalassia Simonetta & Delle Cave, is a rare taxon in the Wuliuan Burgess Shale Formation of Canada, which can be recognized by the hypertrophy of a single of its sagittal spines, the posteriomost one. T. spinosa (Conway Morris & Robison)–a species originally assigned to a distinct genus ‘Ecnomocaris’ herein synonymised with Thelxiope–is known from a single specimen found in the Drumian Wheeler Formation of the House Range of Utah. It differs from the type-species in the hypertrophy of both the anteriormost (cephalic) and the posteriormost (third pygidial) sagittal spines. The same Wheeler strata have also yielded a single specimen of a new taxon, T. holmani sp. nov., which lacks hypertrophied sagittal spines and features blunt thoracic tergopleural tips. A putative fourth species, referred to Thelxiope sp. nov. A, extends the stratigraphical range of Thelxiope to the Lower Ordovician (Tremadocian), and its palaeographic range to West Gondwana. Currently under study, this relatively common component of the lower Fezouata Shale fauna is only briefly discussed. Features characterizing the genus Thelxiope and its components almost exclusively pertain to the sagittal spines, for the scarcity and inconsistent preservation of the Cambrian materials as-yet available preclude a confident assessment of the variability of other morphological features. The pygidium in Thelxiope and Mollisonia is not composed of four, but three tergites essentially similar to thoracic ones, except for the lack of articulations. creator: Rudy Lerosey-Aubril creator: Jacob Skabelund creator: Javier Ortega-Hernández uri: https://doi.org/10.7717/peerj.8879 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Lerosey-Aubril et al. title: Reduced fish diversity despite increased fish biomass in a Gulf of California Marine Protected Area link: https://peerj.com/articles/8885 last-modified: 2020-04-09 description: Multi-use marine protected areas (MUMPAs) are a commonly applied tool for marine conservation in developing countries, particularly where large no-take reserves are not socially or politically feasible. Although MUMPAs have produced benefits around the world, the persistence of moderate fishing pressure reduces the likelihood of achieving the primary objective of these areas, which is the conservation of ecosystems. In this study we used traditional and functional metrics to evaluate how fish assemblages changed through time in a MUMPA, including shifts in species responses and in ecological processes. We conducted visual censuses of fishes at Espíritu Santo Island, México (MUMPA; N = 320; 24°N, 110°W) from 2005 to 2017 to assess fish richness, size-distribution and density. Three functional indices were calculated using six traits (size, mobility, period of activity, aggregation, position in water column and diet): functional richness (volume occupied by species), dispersion (complementarity between species) and originality (inverse of functional redundancy). We compared fish diversity among three management zone types (sustainable fishing, traditional fishing and no-take zones), through a 13-year period, assessing which species increased or decreased in occurrence, density, and biomass, and how indices respond over time. Despite a general increase in biomass and stability in density and originality, we detected a reduction in fish biodiversity in the form of declines in species and functional richness, which could imply the risk of local extinction and decrease in certain ecosystem processes. In addition, changes in functional dispersion showed that some functions are losing representation through time. Although no single cause is apparent, such factors as competitive interactions, habitat loss and persistence of fishing pressure potentially explain these decreases. The rise in biomass was associated with a general increase in the average size, rather than increased biomass of commercial species, as the latter remained stable during the study period. Expansion of no-take areas, enforcement of fishing regulations, and surveillance in core zones, should be implemented to reverse the decline in particular species and to promote conservation of fish functional diversity in this MUMPA. creator: Georgina Ramírez-Ortiz creator: Héctor Reyes-Bonilla creator: Eduardo F. Balart creator: Damien Olivier creator: Leonardo Huato-Soberanis creator: Fiorenza Micheli creator: Graham J. Edgar uri: https://doi.org/10.7717/peerj.8885 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Ramírez-Ortiz et al. title: Temporal features of individual and collective self-referential processing: an event-related potential study link: https://peerj.com/articles/8917 last-modified: 2020-04-09 description: BackgroundIndividual and collective self are two fundamental self-representations and are important to human experience. The present study aimed to investigate whether individual and collective self have essential difference in neural mechanism.MethodsEvent-related potentials were recorded to explore the electrophysiological correlates of individual and collective self in a self-referential task in which participants were asked to evaluate whether trait adjectives were suitable to describe themselves (individual self-referential processing), a famous person (individual non-self-referential processing), Chinese (collective self-referential processing) or American (collective non-self-referential processing).ResultsAt the early stages, results showed that larger P2 and smaller N2 amplitudes were elicited by individual self-referential than by individual non-self-referential processing whereas no significant differences were observed between collective self-referential and collective non-self-referential processing at these stages. In addition, at the late P3 stage (350–600 ms), larger P3 amplitudes were also elicited by individual self-referential than by individual non-self-referential processing during 350–600 ms interval. However, the collective self-reference effect, indicated by the differences between collective self-referential and collective non-self-referential processing, did not appear until 450 ms and extended to 600 ms. Moreover, individual self-reference effect was more pronounced than collective self-reference effect in the 350–500 ms interval, whereas individual and collective self-reference effect had no significant difference in the 500–600 ms interval. These findings indicated that the time courses of neural activities were different in processing individual and collective self. creator: Cuihong Liu creator: Wenjie Li creator: Rong Wang creator: Yaohan Cai creator: Jie Chen uri: https://doi.org/10.7717/peerj.8917 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Liu et al. title: Androgen up-regulation of Twist1 gene expression is mediated by ETV1 link: https://peerj.com/articles/8921 last-modified: 2020-04-09 description: Twist1, a basic helix-loop-helix transcription factor that regulates a number of genes involved in epithelial-to-mesenchymal transition (EMT), is upregulated in prostate cancer. Androgen regulation of Twist1 has been reported in a previous study. However, the mechanism of androgen regulation of the Twist1 gene is not understood because the Twist1 promoter lacks androgen receptor (AR)-responsive elements. Previous studies have shown that the Twist1 promoter has putative binding sites for PEA3 subfamily of ETS transcription factors. Our lab has previously identified Ets Variant 1 (ETV1), a member of the PEA3 subfamily, as a novel androgen-regulated gene that is involved in prostate cancer cell invasion through unknown mechanism. In view of these data, we hypothesized that androgen-activated AR upregulates Twist1 gene expression via ETV1. Our data confirmed the published work that androgen positively regulates Twist1 gene expression and further showed that this positive effect was directed at the Twist1 promoter. The positive effect of androgen on Twist1 gene expression was abrogated upon disruption of AR expression by siRNA or of AR activity by Casodex. More importantly, our data show that disruption of ETV1 leads to significant decrease in both androgen-mediated upregulation as well as basal level of Twist1, which we are able to rescue upon re-expression of ETV1. Indeed, we are able to show that ETV1 mediates the androgen upregulation of Twist1 by acting on the proximal region of Twist1 promoter. Additionally, our data show that Twist1 regulates prostate cancer cell invasion and EMT, providing a possible mechanism by which ETV1 mediates prostate cancer cell invasion. In conclusion, in this study we report Twist1 as an indirect target of AR and androgen regulation through ETV1. creator: Prabesh Khatiwada creator: Archana Kannan creator: Mamata Malla creator: Megan Dreier creator: Lirim Shemshedini uri: https://doi.org/10.7717/peerj.8921 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Khatiwada et al. title: Genome-wide identification of the PEBP genes in pears and the putative role of PbFT in flower bud differentiation link: https://peerj.com/articles/8928 last-modified: 2020-04-09 description: Although Phosphatidylethanolamine-binding protein (PEBP) genes have been identified in several plants, little is known about PEBP genes in pears. In this study, a total of 24 PEBP genes were identified, in which 10, 5 and 9 were from Pyrus bretschneideri genome, Pyrus communis genome and Pyrus betuleafolia genome, respectively. Subsequently, gene structure, phylogenetic relationship, chromosomal localization, promoter regions, collinearity and expression were determined with these PEBP genes. It was found that only PbFT from PEBP genes of P. bretschneideri was relatively highly expressed in leaves during flower bud differentiation. Whereas, expression patterns of TFL1 homologues, gene23124 and gene16540, were different from PbFT in buds. The expression pattern and the treatment of reduction day-length indicated that the expression of PbFT in leaves were regulated by day-length and circadian clock. Additionally, the phenotype of transgenic Arabidopsis suggested that PbFT played a role in not only promoting flower bud differentiation, but also regulating the balance between vegetative and reproductive growth. These results may provide important information for further understanding of the evolution and function of PEBP genes in pears. creator: Shuliang Zhao creator: Yarui Wei creator: Hongguang Pang creator: Jianfeng Xu creator: Yingli Li creator: Haixia Zhang creator: Jianguang Zhang creator: Yuxing Zhang uri: https://doi.org/10.7717/peerj.8928 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Zhao et al. title: Life-history features and oceanography drive phylogeographic patterns of the chiton Acanthochitona cf. rubrolineata (Lischke, 1873) in the northwestern Pacific link: https://peerj.com/articles/8794 last-modified: 2020-04-08 description: Chitons are a group of marine mollusks (class Polyplacophora) characterized by having eight articulating shell plates on their dorsal body surface. They represent suitable materials for studying the spatiotemporal processes that underlie population differentiation and speciation in ocean environments. Here we performed population genetic analyses on the northwestern Pacific chiton Acanthochitona cf. rubrolineata (Lischke, 1873) using two mitochondrial gene fragments (COI and 16S) from 180 individuals sampled from 11 populations among the coastal waters of Korea, Japan, and China. The phylogenetic network uncovered a reticulated relationship with several sub-haplogroups for all A. cf. rubrolineata haplotypes. SAMOVA analyses suggested the best grouping occurred at three groups (ΦCT = 0.151, P < 0.0001), which geographically corresponds to hydrographic discontinuity among the coastal regions of Korea, Japan, and China. The assumed limited dispersal ability of A. cf. rubrolineata, coupled with northeasterly flowing, trifurcate warm currents, might have contributed to the genetic differentiation among the three groups. Meanwhile, a high level of within-group genetic homogeneity was detected, indicating extensive coastal currents might facilitate gene flow among the populations within each group. Bayesian skyline plots demonstrated significant population expansion after the Last Glacial Period (110-25 thousand years ago) for all studied populations except the Japan group. Together these results suggest that the present-day phylogeographic patterns of A. cf. rubrolineata are strongly affected by the interplay of historical and/or contemporary oceanography and species-specific life-history features. creator: Gang Ni creator: Taeho Kim creator: Youngheon Shin creator: Jina Park creator: Yucheol Lee creator: Hyun-Jong Kil creator: Joong-Ki Park uri: https://doi.org/10.7717/peerj.8794 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Ni et al. title: Feasibility analysis of flexible bronchoscopy in conjunction with noninvasive ventilation for therapy of hypoxemic patients with Central Airway Obstruction: a retrospective study link: https://peerj.com/articles/8687 last-modified: 2020-04-08 description: BackgroundInterventional bronchoscopy for hypoxemic patients with central airway obstruction (CAO) is typically performed under general anesthesia. This approach poses remarkable challenge for both bronchoscopist and anesthesiologist. Noninvasive ventilation (NIV) during flexible bronchoscopy (FB) has been successfully used in hypoxemic patients, but rarely in the treatment of hypoxemic patients with CAO.ObjectiveTo evaluate the feasibility of therapeutic FB assisted with NIV for therapy of hypoxemic patients with CAO.MethodTwenty-nine hypoxemic CAO patients treated with FB from December 2010 to May 2016 in our hospital were retrospectively reviewed, either aided with NIV under sedation (NIV group ) or through artificial airway under general anesthesia (control group). Interventional procedures included balloon dilation, electrocautery and argon plasma coagulationResultFifteen patients were enrolled in the NIV group and 14 in the control group. The success rate (93.3% VS 92.9%, p = 1.0), procedure time (60.5 ± 4.2 min VS 67.8 ± 5.6 min, p = 0.31) and oxygenation improvement between the two groups have no significant difference. Less reduction of systolic blood pressure and heart rate during procedure was observed in the NIV group. The NIV group showed shorter admission time before procedure than the control group (35.1 ± 4.6 h VS 55.6 ± 5.6 h, p < 0.01). In addition, procedure fee in the NIV group was significantly less than that in the control group (540.7 ± 62.8$ VS975.4 ± 69.5$, p < 0.0001).ConclusionFB assisted with NIV is a safe, efficient and economic method for therapy of selected hypoxemic patients with CAO. creator: Xiaoke Chen creator: Yiping Zhou creator: Haiqiong Yu creator: Yue Peng creator: Liping Xia creator: Nian Liu creator: Hairong Lin uri: https://doi.org/10.7717/peerj.8687 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Chen et al. title: A unified simulation model for understanding the diversity of cancer evolution link: https://peerj.com/articles/8842 last-modified: 2020-04-08 description: Because cancer evolution underlies the therapeutic difficulties of cancer, it is clinically important to understand the evolutionary dynamics of cancer. Thus far, a number of evolutionary processes have been proposed to be working in cancer evolution. However, there exists no simulation model that can describe the different evolutionary processes in a unified manner. In this study, we constructed a unified simulation model for describing the different evolutionary processes and performed sensitivity analysis on the model to determine the conditions in which cancer growth is driven by each of the different evolutionary processes. Our sensitivity analysis has successfully provided a series of novel insights into the evolutionary dynamics of cancer. For example, we found that, while a high neutral mutation rate shapes neutral intratumor heterogeneity (ITH) characterized by a fractal-like pattern, a stem cell hierarchy can also contribute to shaping neutral ITH by apparently increasing the mutation rate. Although It has been reported that the evolutionary principle shaping ITH shifts from selection to accumulation of neutral mutations during colorectal tumorigenesis, our simulation revealed the possibility that this evolutionary shift is triggered by drastic evolutionary events that occur in a short time and confer a marked fitness increase on one or a few cells. This result helps us understand that each process works not separately but simultaneously and continuously as a series of phases of cancer evolution. Collectively, this study serves as a basis to understand in greater depth the diversity of cancer evolution. creator: Atsushi Niida creator: Takanori Hasegawa creator: Hideki Innan creator: Tatsuhiro Shibata creator: Koshi Mimori creator: Satoru Miyano uri: https://doi.org/10.7717/peerj.8842 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Niida et al. title: Monitoring the influx of new species through citizen science: the first introduced ant in Denmark link: https://peerj.com/articles/8850 last-modified: 2020-04-08 description: Climate change and invasive species threaten biodiversity, yet rigorous monitoring of their impact can be costly. Citizen science is increasingly used as a tool for monitoring exotic species, because citizens are geographically and temporally dispersed, whereas scientists tend to cluster in museums and at universities. Here we report on the establishment of the first exotic ant taxon (Tetramorium immigrans) in Denmark, which was discovered by children participating in The Ant Hunt. The Ant Hunt is a citizen science project for children that we ran in 2017 and 2018, with a pilot study in 2015. T. immigrans was discovered in the Botanical Garden of the Natural History Museum of Denmark in 2015 and confirmed as established in 2018. This finding extends the northern range boundary of T. immigrans by almost 460 km. Using climatic niche modelling, we compared the climatic niche of T. immigrans in Europe with that of T. caespitum based on confirmed observations from 2006 to 2019. T. immigrans and T. caespitum had a 13% niche overlap, with T. immigrans showing stronger occurrence in warmer and drier areas compared to T. caespitum. Mapping the environmental niches onto geographic space identified several, currently uninhabited, areas as climatically suitable for the establishment of T. immigrans. Tetramorium immigrans was sampled almost three times as often in areas with artificial surfaces compared to T. caespitum, suggesting that T. immigrans may not be native to all of Europe and is being accidentally introduced by humans. Overall, citizen scientists collected data on ants closer to cities and harbours than scientists did and had a stronger bias towards areas of human disturbance. This increased sampling effort in areas of likely introduction of exotic species naturally increases the likelihood of discovering species sooner, making citizen science an excellent tool for exotic species monitoring, as long as trained scientists are involved in the identification process. creator: Julie K. Sheard creator: Nathan J. Sanders creator: Carsten Gundlach creator: Sämi Schär creator: Rasmus Stenbak Larsen uri: https://doi.org/10.7717/peerj.8850 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Sheard et al. title: Temporal and spatial variability in snow cover over the Xinjiang Uygur Autonomous Region, China, from 2001 to 2015 link: https://peerj.com/articles/8861 last-modified: 2020-04-08 description: Xinjiang, China, is a typical arid and semi-arid region of Central Asia that significantly lacks freshwater resources, and the surface runoff in this region is mainly supplied by mountain glacier and snow cover meltwater. Based on the above background and issues of transnational water resources between Xinjiang and Central Asia along the Silk Road Economic Belt, which were highlighted in the major strategy of “The Belt and Road”, this study analysed the spatial and temporal variations in snow cover and snow cover days in the Xinjiang region from 2001 to 2015. The study area includes four subregions: Northern Xinjiang, Southern Xinjiang, Eastern Xinjiang and the Ili River Valley. Moderate-resolution Imaging Spectroradiometer (MODIS) 8-day snow cover data were used after removing clouds by combining MOD10A2 and MYD10A2. The results showed that seasonal snow cover occurred from October to April in most regions of Xinjiang and that this snow cover consisted of two processes: snow accumulation and snow ablation. The maximum snow cover occurred in January, whereas the minimum snow cover occurred from July to August. During the seasonal snow cover period, the snowfall rates in Northern Xinjiang and the Ili River Valley were higher, while the other regions had a low snowfall probability. To study the relationship between altitude and snow cover, the normalized snow elevation correlation index (NSACI) was calculated. The NSACI showed a significant correlation between snow cover and elevation in most regions of Xinjiang and was classified into five grades. Snow cover days did not fluctuate obviously from 2001 to 2015, and a decreasing trend was observed in the four subregions except for the Ili River Valley (nonsignificant decreasing trend). We also observed a correlation between snow cover and temperature and found that the correlations between monthly snow cover and monthly temperature in the four subregions were strongly related to the underlying land type and global warming background, which also suggests that the special topography of Xinjiang greatly influences both snow cover and climate change. creator: Wenqian Chen creator: Jianli Ding creator: Jingzhe Wang creator: Junyong Zhang creator: Zhe Zhang uri: https://doi.org/10.7717/peerj.8861 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Chen et al. title: Urban–rural differences in perception of trees described by parents bringing up children in Warsaw and Jedlińsk, Poland link: https://peerj.com/articles/8875 last-modified: 2020-04-08 description: Parents’ attitudes to trees and nature are reflected not only in their children’s outdoor activity, but also in the way they perceive, learn and value the environment. One hundred and eleven respondents, divided into two groups by place of residence, assessed statements in a survey questionnaire. Two groups of questions aimed at evaluating tree benefits and disservices as perceived by urban and rural parents, and identifying their preferences concerning outdoor activity of their children. Tree benefits and disadvantages were grouped into five categories (social, economic, environmental, health and aesthetic). Both urban and rural parents presented similar attitudes to trees as well as to their children’s play environments. Among 37 statements concerning tree benefits, only five revealed statistically significant differences. The most important difference appeared in the way urban and rural parents perceived the aspects of danger. Trees were not perceived as posing any risk on playgrounds for city residents, who—unlike villagers—opposed to the removal of trees from playgrounds. creator: Magdalena Wojnowska-Heciak creator: Magdalena Błaszczyk creator: Marzena Suchocka creator: Joanna Kosno-Jończy uri: https://doi.org/10.7717/peerj.8875 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Wojnowska-Heciak et al. title: Functional histology of the skin in the subterranean African giant mole-rat: thermal windows are determined solely by pelage characteristics link: https://peerj.com/articles/8883 last-modified: 2020-04-08 description: Excavation of burrows is an extremely physically demanding activity producing a large amount of metabolic heat. Dissipation of its surplus is crucial to avoid the risk of overheating, but in subterranean mammals it is complicated due to the absence of notable body extremities and high humidity in their burrows. IR-thermography in a previous study on two species of African mole-rats revealed that body heat was dissipated mainly through the ventral body part, which is notably less furred. Here, we analyzed the dorsal and ventral skin morphology, to test if dermal characteristics could contribute to higher heat dissipation through the ventral body part. The thickness of the epidermis and dermis and the presence, extent and connectivity of fat tissue in the dermis were examined using routine histological methods, while vascular density was evaluated using fluorescent dye and confocal microscopy in the giant mole-rat Fukomys mechowii. As in other hitherto studied subterranean mammals, no subcutaneous adipose tissue was found. All examined skin characteristics were very similar for both dorsal and ventral regions: relative content of adipose tissue in the dermis (14.4 ± 3.7% dorsally and 11.0 ± 4.0% ventrally), connectivity of dermal fat (98.5 ± 2.8% and 95.5 ± 6.8%), vascular density (26.5 ± 3.3% and 22.7 ± 2.3%). Absence of large differences in measured characteristics between particular body regions indicates that the thermal windows are determined mainly by the pelage characteristics. creator: Lucie Pleštilová creator: Jan Okrouhlík creator: Hynek Burda creator: Hana Sehadová creator: Eva M. Valesky creator: Radim Šumbera uri: https://doi.org/10.7717/peerj.8883 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Pleštilová et al. title: Synthetic dietary inulin, Fuji FF, delays development of diet-induced obesity by improving gut microbiota profiles and increasing short-chain fatty acid production link: https://peerj.com/articles/8893 last-modified: 2020-04-08 description: BackgroundDietary fiber, including inulin, promotes health via fermentation products, such as short-chain fatty acids (SCFAs), produced from the fiber by gut microbiota. SCFAs exert positive physiological effects on energy metabolism, gut immunity, and the nervous system. Most of the commercial inulin is extracted from plant sources such as chicory roots, but it can also be enzymatically synthesized from sucrose using inulin producing enzymes. Studies conducted on rodents fed with a cafeteria diet have suggested that while increasing plasma propionic acid, synthetic inulin modulates glucose and lipid metabolism in the same manner as natural inulin. Therefore, this study aimed to determine the effects of a synthetic inulin, Fuji FF, on energy metabolism, fecal SCFA production, and microbiota profiles in mice fed with a high-fat/high-sucrose diet.MethodsThree-week-old male C57BL/6J mice were fed a high-fat/high-sucrose diet containing cellulose or Fuji FF for 12 weeks, and the effects on energy metabolism, SCFA production, and microbiota profiles were evaluated.ResultsBody weight gain was inhibited by Fuji FF supplementation in high-fat/high-sucrose diet-fed C57BL/6J mice by reducing white adipose tissue weight while increasing energy expenditure, compared with the mice supplemented with cellulose. Fuji FF also elevated levels of acetic, propionic and butyric acids in mouse feces and increased plasma propionic acid levels in mice. Moreover, 16S rRNA gene amplicon sequencing of fecal samples revealed an elevated abundance of Bacteroidetes and a reduced abundance of Firmicutes at the phylum level in mice supplemented with Fuji FF compared to those supplemented with cellulose. Fuji FF also resulted in abundance of the family Bacteroidales S24-7 and reduction of Desulfovibrionaceae in the feces.ConclusionLong term consumption of Fuji FF improved the gut environment in mice by altering the composition of the microbiota and increasing SCFA production, which might be associated with its anti-obesity effects. creator: Miki Igarashi creator: Miku Morimoto creator: Asuka Suto creator: Akiho Nakatani creator: Tetsuhiko Hayakawa creator: Kenjirou Hara creator: Ikuo Kimura uri: https://doi.org/10.7717/peerj.8893 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Igarashi et al. title: Proteomic variations after short-term heat shock treatment reveal differentially expressed proteins involved in early microspore embryogenesis in cabbage (Brassica oleracea) link: https://peerj.com/articles/8897 last-modified: 2020-04-08 description: Microspore embryogenesis (ME), a widely used haploid breeding method that can considerably shorten the breeding cycle, provides an efficient mean of cultivating many important Brassica crops, such as cabbage, Chinese cabbage, and oilseed rape. For cabbage, in many cases, short-term heat shock treatment can strongly increase the embryogenesis rate, however, the underlying mechanism of this effect has not been elucidated. In this study, we compared the proteomics of isolated microspores with samples pretreated at 32 °C for 24 h and 25 °C for 24 h using two cabbage accessions (Zhonggan 628 and 87–534) showing highly different embryogenic rates. The embryo yield was 19.7 embryos/bud in Zhonggan 628 after 32 °C treatment, while no embryoid was observed in Zhonggan 628 after 25 °C treatment as well as in 87–534 at both temperatures. We identified a total of 363 and 282 differentially expressed proteins (DEPs) for Zhonggan 628 and 87–534 via a label-free proteomics technology. There were 97 DEPs specifically identified only in Zhonggan 628 but not in 87–534 after 32 °C heat-shock treatment that may be related to heat shock-induced embryogenesis in vitro culture. These DEPs were primarily enriched in carbon metabolic process, protein synthesis and degradation process, and signal transduction. Based on protein-protein interaction and pathway enrichment analyses, we proposed that SGT1 homolog A and B(SGT1), heat shock 70 kDa protein 5 (HSP70), cell division control protein 48 homolog A (CDC48) and fatty acyl-CoA reductase (FAR) might play important roles in microspore embryogenesis. This proteomic study may contribute to our molecular understanding of cabbage microspore embryogenesis and help to build a high-efficiency haploid breeding system. creator: Henan Su creator: Guo Chen creator: Limei Yang creator: Yangyong Zhang creator: Yong Wang creator: Zhiyuan Fang creator: Honghao Lv uri: https://doi.org/10.7717/peerj.8897 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Su et al. title: Transcriptome analysis revealed key prognostic genes and microRNAs in hepatocellular carcinoma link: https://peerj.com/articles/8930 last-modified: 2020-04-08 description: BackgroundHepatocellular carcinoma (HCC) is one of the most common cancers worldwide. However, the molecular mechanisms involved in HCC remain unclear and are in urgent need of elucidation. Therefore, we sought to identify biomarkers in the prognosis of HCC through an integrated bioinformatics analysis.MethodsMessenger RNA (mRNA) expression profiles were obtained from the Gene Expression Omnibus database and The Cancer Genome Atlas-Liver Hepatocellular Carcinoma (TCGA-LIHC) for the screening of common differentially expressed genes (DEGs). Function and pathway enrichment analysis, protein-protein interaction network construction and key gene identification were performed. The significance of key genes in HCC was validated by overall survival analysis and immunohistochemistry. Meanwhile, based on TCGA data, prognostic microRNAs (miRNAs) were decoded using univariable and multivariable Cox regression analysis, and their target genes were predicted by miRWalk.ResultsEleven hub genes (upregulated ASPM, AURKA, CCNB2, CDC20, PRC1 and TOP2A and downregulated AOX1, CAT, CYP2E1, CYP3A4 and HP) with the most interactions were considered as potential biomarkers in HCC and confirmed by overall survival analysis. Moreover, AURKA, PRC1, TOP2A, AOX1, CYP2E1, and CYP3A4 were considered candidate liver-biopsy markers for high risk of developing HCC and poor prognosis in HCC. Upregulation of hsa-mir-1269b, hsa-mir-518d, hsa-mir-548aq, hsa-mir-548f-1, and hsa-mir-6728, and downregulation of hsa-mir-139 and hsa-mir-4800 were determined to be risk factors of poor prognosis, and most of these miRNAs have strong potential to help regulate the expression of key genes.ConclusionsThis study undertook the first large-scale integrated bioinformatics analysis of the data from Illumina BeadArray platforms and the TCGA database. With a comprehensive analysis of transcriptional alterations, including mRNAs and miRNAs, in HCC, our study presented candidate biomarkers for the surveillance and prognosis of the disease, and also identified novel therapeutic targets at the molecular and pathway levels. creator: Xi Ma creator: Lin Zhou creator: Shusen Zheng uri: https://doi.org/10.7717/peerj.8930 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Ma et al. title: Establishment of brown anoles (Anolis sagrei) across a southern California county and potential interactions with a native lizard species link: https://peerj.com/articles/8937 last-modified: 2020-04-08 description: The brown anole, Anolis sagrei, is a native species to the Caribbean; however, A. sagrei has invaded multiple parts of the USA, including Florida, Louisiana, Hawai’i and more recently California. The biological impacts of A. sagrei invading California are currently unknown. Evidence from the invasion in Taiwan shows that they spread quickly and when immediate action is not taken eradication stops being a viable option. In Orange County, California, five urban sites, each less than 100 ha, were surveyed for an average of 49.2 min. Approximately 200 A. sagrei were seen and verified across all survey sites. The paucity of native lizards encountered during the surveys within these sites suggests little to no overlap between the dominant diurnal western fence lizard, Sceloporus occidentalis, and A. sagrei. This notable lack of overlap could indicate a potentially disturbing reality that A. sagrei are driving local extirpations of S. occidentalis. creator: Samuel R. Fisher creator: Lelani A. Del Pinto creator: Robert N. Fisher uri: https://doi.org/10.7717/peerj.8937 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Fisher et al. title: Choosing what is left: the spatial structure of a wild herbivore population within a livestock-dominated landscape link: https://peerj.com/articles/8945 last-modified: 2020-04-08 description: Shrublands and grasslands comprise over 30% of the land surface and are among the most exploited ecosystems for livestock production. Across natural landscapes, the distribution and abundance of wild herbivores are affected by interspecific competition for foraging resources, hunting and the development of infrastructure among other factors. In Argentine Patagonia, the abundance of domestic sheep grazing on native vegetation outnumbers the widely distributed guanaco (Lama guanicoe) and sheep ranching monopolizes the most productive lands. In this work, we aimed to assess the spatial variation in the abundance of guanacos in Península Valdés, a representative landscape of Patagonia, investigating the incidence of natural and human-related factors. We conducted ground surveys during the austral autumn in 2017 totaling 383.4 km along areas with and without sheep ranching. We built density surface models to account for the variation in guanaco abundance and obtained a map of guanaco density at a resolution of 4 km2. We estimated an overall density of 11.71 guanacos.km−2 for a prediction area of 3,196 km2, although the density of guanacos tripled in areas where sheep ranching was terminated (in around 20% of the surface of Península Valdés) compared to areas with sheep. Guanacos were more abundant at lower values of primary productivity and sheep stocking rates and further from inhabited ranch buildings, suggesting competition with sheep and conflict with humans. Although guanacos selected open, grass-dominated habitats across sheep-free sites, fences dividing properties and paddocks played a significant role in the spatial structure of their population in Península Valdés affecting negatively the abundance of guanacos. Our results indicate that actions to improve habitat connectivity for guanacos, favor the coexistence among guanacos and sheep ranching, and promote responsible human activities and attitudes towards wildlife are needed. creator: Milagros Antún creator: Ricardo Baldi uri: https://doi.org/10.7717/peerj.8945 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Antún and Baldi title: Deconvolute individual genomes from metagenome sequences through short read clustering link: https://peerj.com/articles/8966 last-modified: 2020-04-08 description: Metagenome assembly from short next-generation sequencing data is a challenging process due to its large scale and computational complexity. Clustering short reads by species before assembly offers a unique opportunity for parallel downstream assembly of genomes with individualized optimization. However, current read clustering methods suffer either false negative (under-clustering) or false positive (over-clustering) problems. Here we extended our previous read clustering software, SpaRC, by exploiting statistics derived from multiple samples in a dataset to reduce the under-clustering problem. Using synthetic and real-world datasets we demonstrated that this method has the potential to cluster almost all of the short reads from genomes with sufficient sequencing coverage. The improved read clustering in turn leads to improved downstream genome assembly quality. creator: Kexue Li creator: Yakang Lu creator: Li Deng creator: Lili Wang creator: Lizhen Shi creator: Zhong Wang uri: https://doi.org/10.7717/peerj.8966 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Li et al. title: ECuADOR—Easy Curation of Angiosperm Duplicated Organellar Regions, a tool for cleaning and curating plastomes assembled from next generation sequencing pipelines link: https://peerj.com/articles/8699 last-modified: 2020-04-07 description: BackgroundWith the rapid increase in availability of genomic resources offered by Next-Generation Sequencing (NGS) and the availability of free online genomic databases, efficient and standardized metadata curation approaches have become increasingly critical for the post-processing stages of biological data. Especially in organelle-based studies using circular chloroplast genome datasets, the assembly of the main structural regions in random order and orientation represents a major limitation in our ability to easily generate “ready-to-align” datasets for phylogenetic reconstruction, at both small and large taxonomic scales. In addition, current practices discard the most variable regions of the genomes to facilitate the alignment of the remaining coding regions. Nevertheless, no software is currently available to perform curation to such a degree, through simple detection, organization and positioning of the main plastome regions, making it a time-consuming and error-prone process. Here we introduce a fast and user friendly software ECuADOR, a Perl script specifically designed to automate the detection and reorganization of newly assembled plastomes obtained from any source available (NGS, sanger sequencing or assembler output).MethodsECuADOR uses a sliding-window approach to detect long repeated sequences in draft sequences, which then identifies the inverted repeat regions (IRs), even in case of artifactual breaks or sequencing errors and automates the rearrangement of the sequence to the widely used LSC–Irb–SSC–IRa order. This facilitates rapid post-editing steps such as creation of genome alignments, detection of variable regions, SNP detection and phylogenomic analyses.ResultsECuADOR was successfully tested on plant families throughout the angiosperm phylogeny by curating 161 chloroplast datasets. ECuADOR first identified and reordered the central regions (LSC–Irb–SSC–IRa) for each dataset and then produced a new annotation for the chloroplast sequences. The process took less than 20 min with a maximum memory requirement of 150 MB and an accuracy of over 99%.ConclusionsECuADOR is the sole de novo one-step recognition and re-ordination tool that provides facilitation in the post-processing analysis of the extra nuclear genomes from NGS data. The program is available at https://github.com/BiodivGenomic/ECuADOR/. creator: Angelo D. Armijos Carrion creator: Damien D. Hinsinger creator: Joeri S. Strijk uri: https://doi.org/10.7717/peerj.8699 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Armijos Carrion et al. title: Rock sponges (lithistid Demospongiae) of the Northeast Atlantic seamounts, with description of ten new species link: https://peerj.com/articles/8703 last-modified: 2020-04-07 description: BackgroundLithistid demosponges, also known as rock sponges, are a polyphyletic group of sponges which are widely distributed. In the Northeast Atlantic (NEA), 17 species are known and the current knowledge on their distribution is mainly restricted to the Macaronesian islands. In the Mediterranean Sea, 14 species are recorded and generally found in marine caves.MethodsLithistids were sampled in nine NEA seamounts during the scientific expeditions Seamount 1 (1987) and Seamount 2 (1993) organized by the MNHN of Paris. Collected specimens were identified through the analyses of external and internal morphological characters using light and scanning electron microscopy, and compared with material from various museum collections as well as literature records.ResultsA total of 68 specimens were analysed and attributed to 17 species across two orders, seven families, and seven genera, representing new records of distribution. Ten of these species are new to science, viz. Neoschrammeniella inaequalis sp. nov., N. piserai sp. nov., N. pomponiae sp. nov., Discodermia arbor sp. nov., D. kellyae sp. nov., Macandrewia schusterae sp. nov., M. minima sp. nov., Exsuperantia levii sp. nov., Leiodermatium tuba sp. nov. and Siphonidium elongatus sp. nov., and are here described and illustrated. New bathymetric records were also found for D. ramifera, D. verrucosa and M. robusta. The Meteor seamount group has a higher species richness (15 species) compared to the Lusitanian seamount group (six species). The majority of the species had their distribution restricted to one seamount, and ten are only known from a single locality, but this can be a result of sample bias.DiscussionThe number of species shared between the seamounts and the Macaronesian islands is very reduced. The same pattern repeats between the NEA and Mediterranean Sea. This study demonstrates that NEA seamounts are ecosystems with a higher diversity of lithistids than previously thought, increasing the number of lithistids known to occur in the NEA and Mediterranean Sea from 26 to 36 species. creator: Francisca C. Carvalho creator: Paco Cárdenas creator: Pilar Ríos creator: Javier Cristobo creator: Hans Tore Rapp creator: Joana R. Xavier uri: https://doi.org/10.7717/peerj.8703 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Carvalho et al. title: Modeling the influence of temperature and water potential on seed germination of Allium tenuissimum L. link: https://peerj.com/articles/8866 last-modified: 2020-04-07 description: Allium tenuissimum L. is a widely distributed perennial herbaceous species in temperate and desert steppes. Relative to other wild Allium species, it produces unique sweet flavors, more biomass in arid and cold environments, and has generated greater interest for crop production. Successful crop establishment, however, will depend on rapid and uniform seed germination. Our study aimed to characterize seed germination of A. tenuissimum under various temperature regimes (11, 15, 20, 24 and 28 °C) and water potential levels (0, −0.2, −0.4 and −0.6 MPa), and model germination by hydrotime (HT) and hydrothermal time (HTT) analysis. Final germination percentage (FGP) increased within the range of 11 to 20 °C, yet it declined within the range of 24 to 28 °C and generally decreased as water potential became more negative within each temperature setting. Maximum FGP was observed at 20 °C at all water potential settings and ranged from 55.0 ± 5.3 to 94.8 ± 1.4%. According to HT and HTT models, the base (Tb) and optimum temperatures (To) for seed germination were 7.0 and 20.5 °C, respectively. In addition, base water potential for the fraction of germination within the seed lot (Ψb(g)) shifted to 0 MPa as temperature increased from Tb to ceiling temperature (Tc). For obtaining 50 % seed germination, Ψb(50) and Tc(50) were estimated to be −0.67 MPa and 27.2 °C, respectively. These values for Tb and Ψb(50) suggest seed germination of A. tenuissimum is both cold and drought tolerant and suitable for production in semi-arid regions. Our characterization of the ideal sowing conditions for A. tenuissimum, i.e., 20.5 °C and soil water potential less negative than −0.67 MPa offers information to forecast suitable settings to enhance crop production. creator: Hong Xiao creator: Helong Yang creator: Thomas Monaco creator: Qian Song creator: Yuping Rong uri: https://doi.org/10.7717/peerj.8866 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Xiao et al. title: A halo of reduced dinoflagellate abundances in and around eelgrass beds link: https://peerj.com/articles/8869 last-modified: 2020-04-07 description: Seagrass beds provide a variety of ecosystem services, both within and outside the bounds of the habitat itself. Here we use environmental DNA (eDNA) amplicons to analyze a broad cross-section of taxa from ecological communities in and immediately surrounding eelgrass (Zostera marina). Sampling seawater along transects extending alongshore outward from eelgrass beds, we demonstrate that eDNA provides meter-scale resolution of communities in the field. We evaluate eDNA abundance indices for 13 major phylogenetic groups of marine and estuarine taxa along these transects, finding highly local changes linked with proximity to Z. marina for a diverse group of dinoflagellates, and for no other group of taxa. Eelgrass habitat is consistently associated with dramatic reductions in dinoflagellate abundance both within the contiguous beds and for at least 15 m outside, relative to nearby sites without eelgrass. These results are consistent with the hypothesis that eelgrass-associated communities have allelopathic effects on dinoflagellates, and that these effects can extend in a halo beyond the bounds of the contiguous beds. Because many dinoflagellates are capable of forming harmful algal blooms (HABs) toxic to humans and other animal species, the apparent salutary effect of eelgrass habitat on neighboring waters has important implications for public health as well as shellfish aquaculture and harvesting. creator: Emily Jacobs-Palmer creator: Ramón Gallego creator: Ana Ramón-Laca creator: Emily Kunselman creator: Kelly Cribari creator: Micah Horwith creator: Ryan P. Kelly uri: https://doi.org/10.7717/peerj.8869 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Jacobs-Palmer et al. title: A real-time PCR assay to accurately quantify polar bear DNA in fecal extracts link: https://peerj.com/articles/8884 last-modified: 2020-04-07 description: DNA extracted from fecal samples contains DNA from the focal species, food, bacteria and pathogens. Most DNA quantification methods measure total DNA and cannot differentiate among sources. Despite the desirability of noninvasive fecal sampling for studying wildlife populations, low amounts of focal species DNA make it difficult to use for next-generation sequencing (NGS), where accurate DNA quantification is critical for normalization. Two factors are required prior to using fecal samples in NGS libraries: (1) an accurate quantification method for the amount of target DNA and (2) a determination of the relative amount of target DNA needed for successful single nucleotide polymorphism genotyping assays. Here, we address these needs by developing primers to amplify a 101 bp region of the nuclear F2 gene and a quantitative PCR (qPCR) assay that allows the accurate quantification of the amount of polar bear (Ursus maritimus) DNA in fecal extracts. We test the assay on pure polar bear DNA extracted from muscle tissue and find a high correlation between fluorometric and qPCR quantifications. The qPCR assay was also successfully used to quantify the amount of DNA derived from polar bears in fecal extractions. Orthologs of the F2 gene have been identified across vertebrates; thus, similar qPCR assays could be developed for other species to enable noninvasive studies. creator: Kristen M. Hayward creator: Michelle P. Harwood creator: Stephen C. Lougheed creator: Zhengxin Sun creator: Peter Van Coeverden de Groot creator: Evelyn L. Jensen uri: https://doi.org/10.7717/peerj.8884 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2020 Hayward et al. title: The role and proteomic analysis of ethylene in hydrogen gas-induced adventitious rooting development in cucumber (Cucumis sativus L.) explants link: https://peerj.com/articles/8896 last-modified: 2020-04-07 description: Previous studies have shown that both hydrogen gas (H2) and ethylene (ETH) play positive roles in plant adventitious rooting. However, the relationship between H2and ETH during this process has not been explored and remains insufficiently understood. In this study, cucumber (Cucumis sativus L.) was used to explore the proteomic changes in ETH-H2-induced rooting. Our results show that hydrogen-rich water (HRW) and ethylene-releasing compound (ethephon) at proper concentrations promote adventitious rooting, with maximal biological responses occurring at 50% HRW or 0.5 µM ethephon. ETH inhibitors aminoethoxyvinylglycine (AVG) and AgNO3 cause partial inhibition of adventitious rooting induced by H2, suggesting that ETH might be involved in H2-induced adventitious rooting. According to two-dimensional electrophoresis (2-DE) and mass spectrometric analyses, compared with the control, 9 proteins were up-regulated while 15 proteins were down-regulated in HRW treatment; four proteins were up-regulated while 10 proteins were down-regulated in ethephon treatment; and one protein was up-regulated while nine proteins were down-regulated in HRW+AVG treatment. Six of these differentially accumulated proteins were further analyzed, including photosynthesis -related proteins (ribulose-1,5-bisphosphate carall boxylase smsubunit (Rubisco), sedoheptulose-1,7-bisphosphatase (SBPase), oxygen-evolving enhancer protein (OEE1)), amino and metabolism-related protein (threonine dehydratase (TDH)), stress response-related protein (cytosolic ascorbate peroxidase (CAPX)), and folding, modification and degradation-related protein (protein disulfide-isomerase (PDI)). Moreover, the results of real-time PCR about the mRNA levels of these genes in various treatments were consistent with the 2-DE results. Therefore, ETH may be the downstream signaling molecule during H2- induced adventitious rooting and proteins Rubisco, SBPase, OEE1, TDH, CAPX and PDI may play important roles during the process. creator: Dengjing Huang creator: Biting Bian creator: Meiling Zhang creator: Chunlei Wang creator: Changxia Li creator: Weibiao Liao uri: https://doi.org/10.7717/peerj.8896 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Huang et al. title: Understanding the spread of de novo and transmitted macrolide-resistance in Mycoplasma genitalium link: https://peerj.com/articles/8913 last-modified: 2020-04-07 description: BackgroundThe rapid spread of azithromycin resistance in sexually transmitted Mycoplasma genitalium infections is a growing concern. It is not yet clear to what degree macrolide resistance in M. genitalium results from the emergence of de novo mutations or the transmission of resistant strains.MethodsWe developed a compartmental transmission model to investigate the contribution of de novo macrolide resistance mutations to the spread of antimicrobial-resistant M. genitalium. We fitted the model to resistance data from France, Denmark and Sweden, estimated the time point of azithromycin introduction and the rates at which infected individuals receive treatment, and projected the future spread of resistance.ResultsThe high probability of de novo resistance in M. genitalium accelerates the early spread of antimicrobial resistance. The relative contribution of de novo resistance subsequently decreases, and the spread of resistant infections in France, Denmark and Sweden is now mainly driven by transmitted resistance. If treatment with single-dose azithromycin continues at current rates, macrolide-resistant M. genitalium infections will reach 25% (95% confidence interval, CI [9–30]%) in France, 84% (95% CI [36–98]%) in Denmark and 62% (95% CI [48–76]%) in Sweden by 2025.ConclusionsBlind treatment of urethritis with single-dose azithromycin continues to select for the spread of macrolide resistant M. genitalium. Clinical management strategies for M. genitalium should limit the unnecessary use of macrolides. creator: Dominique Cadosch creator: Victor Garcia creator: Jørgen S. Jensen creator: Nicola Low creator: Christian L. Althaus uri: https://doi.org/10.7717/peerj.8913 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Cadosch et al. title: Diffusion tubes: a method for the mass culture of ctenophores and other pelagic marine invertebrates link: https://peerj.com/articles/8938 last-modified: 2020-04-07 description: The culture of pelagic marine invertebrates, especially the ctenophore Mnemiopsis leidyi, has been demonstrated in past studies dating back to the 1960s; however, the mass culture of delicate pelagic invertebrates has remained elusive. By using a pair of acrylic tubes and enabling water diffusion between them, we have been able to reliably and cost effectively mass culture several genera of ctenophores (Pleurobrachia, Hormiphora, Bolinopsis, Mnemiopsis and Leucothea), one species of siphonophore (Nanomia) and one species of larvacean (Oikopleura). The simple, compact method is effective enough to support two permanent exhibits of ctenophores at the Monterey Bay Aquarium while minimizing live food culture requirements with the potential to support further investigation of pelagic marine invertebrate ontogeny, ecology and genomics. creator: Wyatt L. Patry creator: MacKenzie Bubel creator: Cypress Hansen creator: Thomas Knowles uri: https://doi.org/10.7717/peerj.8938 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Patry et al. title: Blue carbon of Mexico, carbon stocks and fluxes: a systematic review link: https://peerj.com/articles/8790 last-modified: 2020-04-06 description: Mexico has more than 750,000 ha of mangroves and more than 400,000 ha of seagrasses. However, approximately 200,000 ha of mangroves and an unknown area of seagrass have been lost due to coastal development associated with urban, industrial and tourist purposes. In 2018, the approved reforms to the General Law on Climate Change (LGCC) aligned the Mexican law with the international objectives established in the 2nd Article of the Paris Agreement. This action proves Mexico’s commitment to contributing to the global target of stabilizing the greenhouse gas emissions concentration in the planet. Thus, restoring and conserving mangrove and seagrass habitats could contribute to fulfilling this commitment. Therefore, as a first step in establishing a mitigation and adaptation plan against climate change with respect to conservation and restoration actions of these ecosystems, we evaluated Mexican blue carbon ecosystems through a systematic review of the carbon stock using the standardized method of Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). We used the data from 126 eligible studies for both ecosystems (n = 1220). The results indicated that information is missing at the regional level. However, the average above and below ground organic carbon stocks from mangroves in Mexico is 113.6 ± 5.5 (95% CI [99.3–118.4]) Mg Corg ha−1 and 385.1 ± 22 (95% CI [344.5–431.9]) Mg Corg ha−1, respectively. The variability in the Corg stocks for both blue carbon ecosystems in Mexico is related to variations in climate, hydrology and geomorphology observed along the country’s coasts in addition to the size and number of plots evaluated with respect to the spatial cover. The highest values for mangroves were related to humid climate conditions, although in the case of seagrasses, they were related to low levels of hydrodynamic stress. Based on the official extent of mangrove and seagrass area in Mexico, we estimate a total carbon stock of 237.7 Tg Corg from mangroves and 48.1 Tg Corg from seagrasses. However, mangroves and seagrasses are still being lost due to land use change despite Mexican laws meant to incorporate environmental compensation. Such losses are largely due to loopholes in the legal framework that dilute the laws’ effectiveness and thus ability to protect the ecosystem. The estimated emissions from land use change under a conservative approach in mangroves of Mexico were approximately 24 Tg CO2e in the last 20 years. Therefore, the incorporation of blue carbon into the carbon market as a viable source of supplemental finance for mangrove and seagrass protection is an attractive win-win opportunity. creator: Jorge A. Herrera-Silveira creator: Monica A. Pech-Cardenas creator: Sara M. Morales-Ojeda creator: Siuling Cinco-Castro creator: Andrea Camacho-Rico creator: Juan P. Caamal Sosa creator: Juan E. Mendoza-Martinez creator: Eunice Y. Pech-Poot creator: Jorge Montero creator: Claudia Teutli-Hernandez uri: https://doi.org/10.7717/peerj.8790 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Herrera-Silveira et al. title: Draft genome of Rosenbergiella nectarea strain 8N4T provides insights into the potential role of this species in its plant host link: https://peerj.com/articles/8822 last-modified: 2020-04-06 description: BackgroundRosenbergiella nectarea strain 8N4T, the type species of the genus Rosenbergiella, was isolated from Amygdalus communis (almond) floral nectar. Other strains of this species were isolated from the floral nectar of Citrus paradisi (grapefruit), Nicotiana glauca (tobacco tree) and from Asphodelus aestivus. R. nectarea strain 8N4T is a Gram-negative, oxidase-negative, facultatively anaerobic bacterium in the family Enterobacteriaceae.ResultsHere we describe features of this organism, together with its genome sequence and annotation. The DNA GC content is 47.38%, the assembly size is 3,294,717 bp, and the total number of genes are 3,346. The genome discloses the possible role that this species may play in the plant. The genome contains both virulence genes, like pectin lyase and hemolysin, that may harm plant cells and genes that are predicted to produce volatile compounds that may impact the visitation rates by nectar consumers, such as pollinators and nectar thieves.ConclusionsThe genome of R. nectarea strain 8N4T reveals a mutualistic interaction with the plant host and a possible effect on plant pollination and fitness. creator: Sivan Laviad-Shitrit creator: Ido Izhaki creator: William B. Whitman creator: Nicole Shapiro creator: Tanja Woyke creator: Nikos C. Kyrpides creator: Malka Halpern uri: https://doi.org/10.7717/peerj.8822 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Laviad-Shitrit et al. title: Living (stained) foraminifera in the Lesser Syrtis (Tunisia): influence of pollution and substratum link: https://peerj.com/articles/8839 last-modified: 2020-04-06 description: Foraminifera are protozoans with biomineralized tests that can be successfully used as a low cost monitoring tool to assess the health status of marine environments. Living benthic foraminiferal assemblages can provide essential information on natural and/or anthropogenic stresses and provide baseline conditions for studies on fossil material. Several studies have highlighted the negative impact of phosphate treatment industries along the Gulf of Gabes (Lesser Syrtis, Tunisia) on the marine environment. However, only a few studies, based on living (stained) benthic foraminifera, are presently available to assess environmental and/or ecological conditions in this Gulf. Thirty-eight surface sediment samples were quantitatively investigated to identify the dominant living benthic foraminiferal species and potential pollution-sensitive and stress-tolerant species. One-hundred and sixty-one species were identified, and grouped into seven clusters representing different environments within the Gulf. These groups represent polluted settings (Cluster A and B), polluted environments characterized by physicochemical variability (Cluster C), seagrass meadows and “pristine” sites (Cluster D and E) and the region subjected to major industrial impact (Cluster F). The final outlier Cluster, identified the foraminifera barren and all shallow coastal stations. A SIMPER analysis helped identify species with clear and fast responses to environmental perturbations (Ammonia tepida, Amphistegina lessonii, Brizalina striatula, Bulimina marginata, Buliminella elegantissima, Eggereloides scaber, Peneroplis perutusus, Rosalina macropora, Rosalina villardeboana, Trochammina inflata). A comparison with the measured geochemical parameters (TOC, phosphorus in the sediments and heavy metal concentrations in the seawater) has shown that the benthic foraminiferal assemblages are mainly linked to phosphorus, TOC, As and Cd pollution. We also provide here the first compilation of the identified living species in the Lesser Syrtis, their synonyms and digital images of important species. creator: Akram El Kateb creator: Valentina Beccari creator: Stephanie Stainbank creator: Silvia Spezzaferri creator: Giovanni Coletti uri: https://doi.org/10.7717/peerj.8839 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 El Kateb et al. title: DeepBindPoc: a deep learning method to rank ligand binding pockets using molecular vector representation link: https://peerj.com/articles/8864 last-modified: 2020-04-06 description: Accurate identification of ligand-binding pockets in a protein is important for structure-based drug design. In recent years, several deep learning models were developed to learn important physical–chemical and spatial information to predict ligand-binding pockets in a protein. However, ranking the native ligand binding pockets from a pool of predicted pockets is still a hard task for computational molecular biologists using a single web-based tool. Hence, we believe, by using closer to real application data set as training and by providing ligand information, an enhanced model to identify accurate pockets can be obtained. In this article, we propose a new deep learning method called DeepBindPoc for identifying and ranking ligand-binding pockets in proteins. The model is built by using information about the binding pocket and associated ligand. We take advantage of the mol2vec tool to represent both the given ligand and pocket as vectors to construct a densely fully connected layer model. During the training, important features for pocket-ligand binding are automatically extracted and high-level information is preserved appropriately. DeepBindPoc demonstrated a strong complementary advantage for the detection of native-like pockets when combined with traditional popular methods, such as fpocket and P2Rank. The proposed method is extensively tested and validated with standard procedures on multiple datasets, including a dataset with G-protein Coupled receptors. The systematic testing and validation of our method suggest that DeepBindPoc is a valuable tool to rank near-native pockets for theoretically modeled protein with unknown experimental active site but have known ligand. The DeepBindPoc model described in this article is available at GitHub (https://github.com/haiping1010/DeepBindPoc) and the webserver is available at (http://cbblab.siat.ac.cn/DeepBindPoc/index.php). creator: Haiping Zhang creator: Konda Mani Saravanan creator: Jinzhi Lin creator: Linbu Liao creator: Justin Tze-Yang Ng creator: Jiaxiu Zhou creator: Yanjie Wei uri: https://doi.org/10.7717/peerj.8864 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Zhang et al. title: Genetic editing of the virulence gene of Escherichia coli using the CRISPR system link: https://peerj.com/articles/8881 last-modified: 2020-04-06 description: Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 is an emerging gene-editing technology that is widely used in prokaryotes and eukaryotes. It can realize the specific manipulation of the genome efficiently and accurately. CRISPR/Cas9 coupled λ-Red recombination technology was used to perform genome editing in different genes. For finding an efficient method to edit the virulence genes of enterotoxigenic E. coli (ETEC), the two-plasmid system was used. The coding sequence (CDS) region of the estA, eltI, estB, eltIIc1, and faeG locus were deleted. The coding region of estB was substituted with estA. Gene recombination efficiency ranged from 0 to 77.78% when the length of the homology arm was from 50 to 300 bp. Within this range, the longer the homology arm, the higher the efficiency of genetic recombination. The results showed that this system can target virulence genes located in plasmids and on chromosomes of ETEC strains. A single base mutation was performed by two-step gene fragment replacement. This study lays the foundation for research on virulence factors and genetic engineering of vaccines for ETEC. creator: Meijia Hou creator: Simeng Sun creator: Qizheng Feng creator: Xiumei Dong creator: Ping Zhang creator: Bo Shi creator: Jiali Liu creator: Dongfang Shi uri: https://doi.org/10.7717/peerj.8881 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Hou et al. title: Diversity of rhizosphere and endophytic fungi in Atractylodes macrocephala during continuous cropping link: https://peerj.com/articles/8905 last-modified: 2020-04-06 description: Rhizospheric and endophytic fungi are key factors which influence plant fitness and soil fertility. Atractylodes macrocephala is one of the best-known perennial herbs used in traditional Chinese medicine. Continuous cropping has been shown to have a negative effect on its growth and renders it more susceptible to microbial pathogen attacks. In this study, we investigated the effects of continuous cropping on the endophytic and rhizospheric fungi associated with A.  macrocephala using culture-independent Illumina MiSeq. Continuous cropping was found to decrease fungal diversity inside plant roots, stems, leaves and tubers. Additionally, we found that the structure and diversity of rhizospheric and endophytic fungal communities were altered by root-rot disease. Fusarium was overrepresented among root-rot rhizospheric and endophytic fungi, indicating that it has a major negative impact on plant health during A.  macrocephala monocropping. Canonical correspondence analysis of the control and diseased samples revealed that pH, hydrolysis N, electrical conductivity and Hg content were well-correlated with fungal community composition during continuous cropping. Taken together, these results highlight the ecological significance of fungal communities in maintaining plant fitness and will guide the development strategies to attenuate the negative impacts of A.  macrocephala continuous cropping. creator: Bo Zhu creator: Jianjun Wu creator: Qingyong Ji creator: Wei Wu creator: Shihui Dong creator: Jiayan Yu creator: Qiaoyan Zhang creator: Luping Qin uri: https://doi.org/10.7717/peerj.8905 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhu et al. title: Assessing soil degradation under land-use change: insight from soil erosion and soil aggregate stability in a small karst catchment in southwest China link: https://peerj.com/articles/8908 last-modified: 2020-04-06 description: BackgroundSoil erodibility (K factor) and soil aggregate stability are often used to assess soil degradation in an erodible environment. However, their applicability under land-use change is uncertain, especially agricultural abandonment.MethodsDifferent land-use types, including cropland, abandoned cropland, and native vegetation land, were converted into the successive stages following agricultural abandonment by space-for-time substitution approach in a small karst catchment, Southwest China. The indexes of soil aggregate stability and K factor of the Erosion Productivity Impact Calculator (EPIC) model in soil profiles were calculated to identify which method is suitable to indicate soil degradation under land-use change.ResultsThe indexes of soil aggregate stability in the soils at 0∼30 cm depth under native vegetation land were significantly larger than those under cropland and slightly larger than those under abandoned cropland. The K factor was not significantly different among the three land use examples because the EPIC model does not consider soil permeability. In the soil organic carbon (SOC)-rich soils (>2%), the K factor was significantly correlated with silt and clay content ranging within a narrow scope of near 0.010 t hm2 h/hm2/MJ/mm. While in the SOC-poor soils, the K factor was significantly increased with decreasing SOC content and was significantly correlated with soil aggregate stability.ConclusionsSoil aggregate stability is more suitable to indicate soil degradation under land-use change. Sufficient SOC in erodible soils would restrain soil degradation, while SOC loss can significantly increase soil erosion risk. creator: Man Liu creator: Guilin Han uri: https://doi.org/10.7717/peerj.8908 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Liu and Han title: ELMO2 association with Gαi2 regulates pancreatic cancer cell chemotaxis and metastasis link: https://peerj.com/articles/8910 last-modified: 2020-04-06 description: BackgroundPancreatic cancer is a highly lethal disease. Nearly half of the patients have distant metastasis and remain asymptomatic. Emerging evidence suggests that the chemokine, CXCL12, has a role in cancer metastasis. The interaction between CXCL12 and CXCR4 activates heterotrimeric G proteins, which regulates actin polymerization and cancer cell migration. However, the molecular mechanisms underlying pancreatic cancer cell migration are still largely obscure. Here, we addressed the role of ELMO2 in chemotaxis and metastasis of pancreatic cancer cells.MethodsPancreatic cancer cell lines PANC-1 and AsPC-1 and siRNA-mediated knockdown of ELMO2 were used to determine the effects of ELMO2 on cancer cell chemotaxis, invasion, migration. Co-immunoprecipitation assays were carried out to identify interacting partners of ELMO2.ResultsELMO2 knockdown inhibited pancreatic cancer cell chemotaxis, migration, invasion, and F-actin polymerization. Co-immunoprecipitation assays revealed that ELMO2 interacted with Gαi2 and that CXCL12 triggered Gα i2-dependent membrane translocation of ELMO2. Thus, ELMO2 is a potential therapeutic target for pancreatic cancer. creator: Yecheng Wang creator: Hongyan Li creator: Fei Li uri: https://doi.org/10.7717/peerj.8910 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wang et al. title: First de novo whole genome sequencing and assembly of the bar-headed goose link: https://peerj.com/articles/8914 last-modified: 2020-04-06 description: BackgroundThe bar-headed goose (Anser indicus) mainly inhabits the plateau wetlands of Asia. As a specialized high-altitude species, bar-headed geese can migrate between South and Central Asia and annually fly twice over the Himalayan mountains along the central Asian flyway. The physiological, biochemical and behavioral adaptations of bar-headed geese to high-altitude living and flying have raised much interest. However, to date, there is still no genome assembly information publicly available for bar-headed geese.MethodsIn this study, we present the first de novo whole genome sequencing and assembly of the bar-headed goose, along with gene prediction and annotation.Results10X Genomics sequencing produced a total of 124 Gb sequencing data, which can cover the estimated genome size of bar-headed goose for 103 times (average coverage). The genome assembly comprised 10,528 scaffolds, with a total length of 1.143 Gb and a scaffold N50 of 10.09 Mb. Annotation of the bar-headed goose genome assembly identified a total of 102 Mb (8.9%) of repetitive sequences, 16,428 protein-coding genes, and 282 tRNAs. In total, we determined that there were 63 expanded and 20 contracted gene families in the bar-headed goose compared with the other 15 vertebrates. We also performed a positive selection analysis between the bar-headed goose and the closely related low-altitude goose, swan goose (Anser cygnoides), to uncover its genetic adaptations to the Qinghai-Tibetan Plateau.ConclusionWe reported the currently most complete genome sequence of the bar-headed goose. Our assembly will provide a valuable resource to enhance further studies of the gene functions of bar-headed goose. The data will also be valuable for facilitating studies of the evolution, population genetics and high-altitude adaptations of the bar-headed geese at the genomic level. creator: Wen Wang creator: Fang Wang creator: Rongkai Hao creator: Aizhen Wang creator: Kirill Sharshov creator: Alexey Druzyaka creator: Zhuoma Lancuo creator: Yuetong Shi creator: Shuo Feng uri: https://doi.org/10.7717/peerj.8914 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wang et al. title: Prevalence of chronic obstructive pulmonary disease at high altitude: a systematic review and meta-analysis link: https://peerj.com/articles/8586 last-modified: 2020-04-03 description: Background and objectiveRecently, several studies have investigated the prevalence of chronic obstructive pulmonary disease (COPD) at high altitude (>1,500 m). However, much remains to be understood about the correlation between altitude and COPD. We aimed to summarize the prevalence of COPD at high-altitudes and find out if altitude could be a risk factor for COPD.MethodsWe searched PubMed/Medline, Cochrane Library, Web of Science, SCOPUS, OVID, Chinese Biomedical Literature Database (CBM) and Embase databases from inception to April 30th, 2019, with no language restriction. We used STATA 14.0 to analyze the extracted data. A random-effect model was used to calculate the combined OR and 95% CI. Heterogeneity was assessed by the I2 statistic versus P-value. We performed a subgroup analysis to analyze possible sources of heterogeneity. The Egger’s test and the Begg’s test were used to assess any publication bias.ResultsWe retrieved 4,574 studies from seven databases and finally included 10 studies (54,578 participants). Males ranged from 18.8% to 49.3% and the population who smoked ranged from 3.3% to 53.3%. The overall prevalence of COPD at high-altitude was 10.0% (95% CI [0.08–0.12], P < 0.001). In a subgroup analysis, based on different regions, the results showed that the prevalence in Asia was higher than that in Europe and America. Seven studies compared the relationship between the prevalence of COPD at high-altitudes and the lowlands. The results showed that altitude was not an independent risk factor for the prevalence of COPD (ORadj = 1.18, 95% CI [0.85–1.62], P = 0.321). There was no publication bias among the studies.ConclusionsOur study found a higher prevalence of COPD at high-altitudes than those from average data. However, altitude was not found to be an independent risk factor for developing COPD (PROSPERO Identifier: CRD42019135012). creator: Huaiyu Xiong creator: Qiangru Huang creator: Chengying He creator: Tiankui Shuai creator: Peijing Yan creator: Lei Zhu creator: Kehu Yang creator: Jian Liu uri: https://doi.org/10.7717/peerj.8586 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Xiong et al. title: An unusual 100-million-year old holometabolan larva with a piercing mouth cone link: https://peerj.com/articles/8661 last-modified: 2020-04-03 description: Holometabola is a hyperdiverse group characterised by a strong morphological differentiation between early post-embryonic stages (= larvae) and adults. Adult forms of Holometabola, such as wasps, bees, beetles, butterflies, mosquitoes or flies, are strongly differentiated concerning their mouth parts. The larvae most often seem to retain rather plesiomorphic-appearing cutting-grinding mouth parts. Here we report a new unusual larva preserved in Burmese amber. Its mouth parts appear beak-like, forming a distinct piercing mouth cone. Such a morphology is extremely rare among larval forms, restricted to those of some beetles and lacewings. The mouth parts of the new fossil are forward oriented (prognathous). Additionally, the larva has distinct subdivisions of tergites and sternites into several sclerites. Also, the abdomen segments bear prominent protrusions. We discuss this unusual combination of characters in comparison to the many different types of holometabolan larvae. The here reported larva is a new addition to the ‘unusual zoo’ of the Cretaceous fauna including numerous, very unusual appearing forms that have gone extinct at the Cretaceous–Palaeogene boundary. creator: Joachim T. Haug creator: Mario Schädel creator: Viktor A. Baranov creator: Carolin Haug uri: https://doi.org/10.7717/peerj.8661 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Haug et al. title: Look out: an exploratory study assessing how gaze (eye angle and head angle) and gait speed are influenced by surface complexity link: https://peerj.com/articles/8838 last-modified: 2020-04-03 description: BackgroundMost research investigating the connection between walking and visual behaviour has assessed only eye movements (not head orientation) in respect to locomotion over smooth surfaces in a laboratory. This is unlikely to reflect gaze changes found over the complex surfaces experienced in the real world, especially given that eye and head movements have rarely been assessed simultaneously.Research questionHow does gaze (eye and head) angle and gait speed change when walking over surfaces of different complexity?MethodsIn this exploratory study, we used a mobile eye tracker to monitor eye movements and inertia measurement unit sensors (IMUs) to measure head angle whilst subjects (n = 11) walked over surfaces with different complexities both indoors and outdoors. Gait speed was recorded from ankle IMUs.ResultsOverall, mean gaze angle was lowest over the most complex surface and this surface also elicited the slowest mean gait speed. The head contributed increasingly to the lowering of gaze with increased surface complexity. Less complex surfaces showed no significant difference between gaze and gait behaviour.SignificanceThis study supports previous research showing that increased surface complexity is an important factor in determining gaze and gait behaviour. Moreover, it provides the novel finding that head movements provide important contributions to gaze location. Our future research aims are to further assess the role of the head in determining gaze location during locomotion across a greater range of complex surfaces to determine the key surface characteristics that influence gaze during gait. creator: Nicholas D.A. Thomas creator: James D. Gardiner creator: Robin H. Crompton creator: Rebecca Lawson uri: https://doi.org/10.7717/peerj.8838 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Thomas et al. title: Prevalence and risk factors of Helicobacter pylori infection among children in Kuichong Subdistrict of Shenzhen City, China link: https://peerj.com/articles/8878 last-modified: 2020-04-03 description: BackgroundHelicobacter pylori infection is a significant burden to the public health in China as it can lead to various gastric diseases including peptic ulcers and gastric cancer. Since most infections occurred during childhood, it is therefore necessary to understand the prevalence and risk determinants of this bacterial infection in children. Herewith, we conducted a cross-sectional study in the Kuichong Subdistrict of Shenzhen City to assess the prevalence and risk factors of H. pylori infection among children.MethodsFrom September 2018 to October 2018, 1,355 children aged 6–12 years from four primary schools in the Kuichong Subdistrict of Shenzhen City were recruited. These children were screened for H. pylori infection using the 13C-urea breath test. In addition, parents were requested to fill out a standardized questionnaire. The chi-square test and multivariable logistic regression analysis were used to identify risk factors for H. pylori.ResultsAmong 1,355 children recruited in this study, 226 (16.7%; 95% CI [14.7–18.7]) were positive of H. pylori infection. Multivariable logistic regression analysis identified six factors significantly associated with H. pylori infection children including parent(s) with tertiary education level (OR: 0.64; 95% CI [0.46–0.89]), testing bottle feed temperature using the mouth (OR: 1.79; 95% CI [1.19–2.68]), sharing of cutlery between the feeding person and young children during meals (OR: 1.84; 95% CI [1.22–2.78]), eating fruit after peeling (OR: 2.56; 95% CI [1.4–4.71]), frequent dining out (OR: 3.13; 95% CI [1.46–6.68]) and snacking (OR: 1.43; 95% CI [1.01–2.01]).ConclusionsOverall, better educated parent(s) played a protective role against the acquisition of H. pylori infection in children. Testing bottle feed temperature using the mouth, cutlery sharing between the feeding person and young children, and snacking posed a lower but significant risk for H. pylori infection. Only eating peeled fruits and frequent dining out were associated with greater infection risks. creator: Jingjing Hu creator: Xiangyu Wang creator: Eng Guan Chua creator: Yongsheng He creator: Qing Shu creator: Li Zeng creator: Shiyang Luo creator: Barry J. Marshall creator: Aijun Liu creator: Chin Yen Tay uri: https://doi.org/10.7717/peerj.8878 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Hu et al. title: Weighted gene correlation network analysis reveals novel biomarkers associated with mesenchymal stromal cell differentiation in early phase link: https://peerj.com/articles/8907 last-modified: 2020-04-03 description: Osteoporosis is a major public health problem that is associated with high morbidity and mortality, and its prevalence is increasing as the world’s population ages. Therefore, understanding the molecular basis of the disease is becoming a high priority. In this regard, studies have shown that an imbalance in adipogenic and osteogenic differentiation of bone marrow mesenchymal stem cells (MSCs) is associated with osteoporosis. In this study, we conducted a Weighted Gene Co-Expression Network Analysis to identify gene modules associated with the differentiation of bone marrow MSCs. Gene Ontology and Kyoto Encyclopedia of Genes and Genome enrichment analysis showed that the most significant module, the brown module, was enriched with genes involved in cell cycle regulation, which is in line with the initial results published using these data. In addition, the Cytoscape platform was used to identify important hub genes and lncRNAs correlated with the gene modules. Furthermore, differential gene expression analysis identified 157 and 40 genes that were upregulated and downregulated, respectively, after 3 h of MSCs differentiation. Interestingly, regulatory network analysis, and comparison of the differentially expressed genes with those in the brown module identified potential novel biomarker genes, including two transcription factors (ZNF740, FOS) and two hub genes (FOXQ1, SGK1), which were further validated for differential expression in another data set of differentiation of MSCs. Finally, Gene Set Enrichment Analysis suggested that the two most important candidate hub genes are involved in regulatory pathways, such as the JAK-STAT and RAS signaling pathways. In summary, we have revealed new molecular mechanisms of MSCs differentiation and identified novel genes that could be used as potential therapeutic targets for the treatment of osteoporosis. creator: Bin Xiao creator: Guozhu Wang creator: Weiwei Li uri: https://doi.org/10.7717/peerj.8907 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Xiao et al. title: Shared ecological traits influence shape of the skeleton in flatfishes (Pleuronectiformes) link: https://peerj.com/articles/8919 last-modified: 2020-04-03 description: In the age of phylogenetic comparative methods, evolutionary biologists have been able to explore evolutionary trends in form in unique and extraordinarily diverse groups of animals. Pleuronectiformes, commonly known as flatfishes, is a diverse and specialized order of fishes that have remarkable asymmetry induced by ocular migration and a benthic life style. Although flatfishes are unique from other fishes, species within the group are morphologically diverse. The origin of ocular migration has been a primary focus of research; however, little is known about overall shape diversification among the flatfishes. In this study, we use integrative methods to examine how body shape evolved within the flatfishes. Shape was quantified from X-rays using geometric morphometrics for 389 individuals across 145 species. The most recent and robust phylogeny was overlaid onto the morphospace and phylogenetic signal was calculated to ascertain convergence in the morphospace. In addition, phylogenetic linear models were employed to determine if ecological traits were correlated with shape and if size had an effect on overall body shape. Results revealed that the majority of variation evolved recently, within the past 15–10-million-years in the middle Miocene, and is highly variable within the flatfishes. These changes are best summarized by body depth, jaw length and medial fin length. Dorsal and anal fin length are correlated, which may be due to the unique mode of locomotion used by flatfishes. A phylogenetic linear model and phylomorphospace analysis suggested that several ecological traits are correlated with shape, which indicates an ecological role in the diversification of flatfishes. creator: Corinthia R. Black creator: Peter B. Berendzen uri: https://doi.org/10.7717/peerj.8919 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Black and Berendzen title: Nitrogen eutrophication particularly promotes turf algae in coral reefs of the central Red Sea link: https://peerj.com/articles/8737 last-modified: 2020-04-02 description: While various sources increasingly release nutrients to the Red Sea, knowledge about their effects on benthic coral reef communities is scarce. Here, we provide the first comparative assessment of the response of all major benthic groups (hard and soft corals, turf algae and reef sands—together accounting for 80% of the benthic reef community) to in-situ eutrophication in a central Red Sea coral reef. For 8 weeks, dissolved inorganic nitrogen (DIN) concentrations were experimentally increased 3-fold above environmental background concentrations around natural benthic reef communities using a slow release fertilizer with 15% total nitrogen (N) content. We investigated which major functional groups took up the available N, and how this changed organic carbon (Corg) and N contents using elemental and stable isotope measurements. Findings revealed that hard corals (in their tissue), soft corals and turf algae incorporated fertilizer N as indicated by significant increases in δ15N by 8%, 27% and 28%, respectively. Among the investigated groups, Corg content significantly increased in sediments (+24%) and in turf algae (+33%). Altogether, this suggests that among the benthic organisms only turf algae were limited by N availability and thus benefited most from N addition. Thereby, based on higher Corg content, turf algae potentially gained competitive advantage over, for example, hard corals. Local management should, thus, particularly address DIN eutrophication by coastal development and consider the role of turf algae as potential bioindicator for eutrophication. creator: Denis B. Karcher creator: Florian Roth creator: Susana Carvalho creator: Yusuf C. El-Khaled creator: Arjen Tilstra creator: Benjamin Kürten creator: Ulrich Struck creator: Burton H. Jones creator: Christian Wild uri: https://doi.org/10.7717/peerj.8737 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Karcher et al. title: Development of vocal emotion recognition in school-age children: The EmoHI test for hearing-impaired populations link: https://peerj.com/articles/8773 last-modified: 2020-04-02 description: Traditionally, emotion recognition research has primarily used pictures and videos, while audio test materials are not always readily available or are not of good quality, which may be particularly important for studies with hearing-impaired listeners. Here we present a vocal emotion recognition test with pseudospeech productions from multiple speakers expressing three core emotions (happy, angry, and sad): the EmoHI test. The high sound quality recordings make the test suitable for use with populations of children and adults with normal or impaired hearing. Here we present normative data for vocal emotion recognition development in normal-hearing (NH) school-age children using the EmoHI test. Furthermore, we investigated cross-language effects by testing NH Dutch and English children, and the suitability of the EmoHI test for hearing-impaired populations, specifically for prelingually deaf Dutch children with cochlear implants (CIs). Our results show that NH children’s performance improved significantly with age from the youngest age group onwards (4–6 years: 48.9%, on average). However, NH children’s performance did not reach adult-like values (adults: 94.1%) even for the oldest age group tested (10–12 years: 81.1%). Additionally, the effect of age on NH children’s development did not differ across languages. All except one CI child performed at or above chance-level showing the suitability of the EmoHI test. In addition, seven out of 14 CI children performed within the NH age-appropriate range, and nine out of 14 CI children did so when performance was adjusted for hearing age, measured from their age at CI implantation. However, CI children showed great variability in their performance, ranging from ceiling (97.2%) to below chance-level performance (27.8%), which could not be explained by chronological age alone. The strong and consistent development in performance with age, the lack of significant differences across the tested languages for NH children, and the above-chance performance of most CI children affirm the usability and versatility of the EmoHI test. creator: Leanne Nagels creator: Etienne Gaudrain creator: Deborah Vickers creator: Marta Matos Lopes creator: Petra Hendriks creator: Deniz Başkent uri: https://doi.org/10.7717/peerj.8773 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Nagels et al. title: An investigation of perceptual biases in complex regional pain syndrome link: https://peerj.com/articles/8819 last-modified: 2020-04-02 description: Patients with complex regional pain syndrome (CRPS) report cognitive difficulties, affecting the ability to represent, perceive and use their affected limb. Moseley, Gallace & Spence (2009) observed that CRPS patients tend to bias the perception of tactile stimulation away from the pathological limb. Interestingly, this bias was reversed when CRPS patients were asked to cross their arms, implying that this bias is embedded in a complex representation of the body that takes into account the position of body-parts. Other studies have failed to replicate this finding (Filbrich et al., 2017) or have even found a bias in the opposite direction (Sumitani et al., 2007). Moreover, perceptual biases in CRPS patients have not often been compared to these of other chronic pain patients. Chronic pain patients are often characterized by an excessive focus of attention for bodily sensations. We might therefore expect that non-CRPS pain patients would show a bias towards instead of away from their affected limb. The aim of this study was to replicate the study of Moseley, Gallace & Spence (2009) and to extend it by comparing perceptual biases in a CRPS group with two non-CRPS pain control groups (i.e., chronic unilateral wrist and shoulder pain patients). In a temporal order judgment (TOJ) task, participants reported which of two tactile stimuli, one applied to either hand at various intervals, was perceived as occurring first. TOJs were made, either with the arms in a normal (uncrossed) position, or with the arms crossed over the body midline. We found no consistent perceptual biases in either of the patient groups and in either of the conditions (crossed/uncrossed). Individual differences were large and might, at least partly, be explained by other variables, such as pain duration and temperature differences between the pathological and non-pathological hand. Additional studies need to take these variables into account by, for example, comparing biases in CRPS (and non-CRPS) patients in an acute versus a chronic pain state. creator: Annick L. De Paepe creator: Valéry Legrain creator: Lien Van der Biest creator: Nadine Hollevoet creator: Alexander Van Tongel creator: Lieven De Wilde creator: Herlinde Jacobs creator: Geert Crombez uri: https://doi.org/10.7717/peerj.8819 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 De Paepe et al. title: Capturing variation in floral shape: a virtual3D based morphospace for Pelargonium link: https://peerj.com/articles/8823 last-modified: 2020-04-02 description: BackgroundVariation in floral shapes has long fascinated biologists and its modelling enables testing of evolutionary hypotheses. Recent comparative studies that explore floral shape have largely ignored 3D floral shape. We propose quantifying floral shape by using geometric morphometrics on a virtual3D model reconstructed from 2D photographical data and demonstrate its performance in capturing shape variation.MethodsThis approach offers unique benefits to complement established imaging techniques (i) by enabling adequate coverage of the potential morphospace of large and diverse flowering-plant clades; (ii) by circumventing asynchronicity in anthesis of different floral parts; and (iii) by incorporating variation in copy number of floral organs within structures. We demonstrate our approach by analysing 90 florally-diverse species of the Southern African genus Pelargonium (Geraniaceae). We quantify Pelargonium floral shapes using 117 landmarks and show similarities in reconstructed morphospaces for nectar tube, corolla (2D datasets), and a combined virtual3D dataset.ResultsOur results indicate that Pelargonium species differ in floral shape, which can also vary extensively within a species. PCA results of the reconstructed virtual3D floral models are highly congruent with the separate 2D morphospaces, indicating it is an accurate, virtual, representation of floral shape. Through our approach, we find that adding the third dimension to the data is crucial to accurately interpret the manner of, as well as levels of, shape variation in flowers. creator: Sara J. van de Kerke creator: Tiemen van Engelenhoven creator: Anne L. van Es creator: Laura Schat creator: Lisa M. van Son creator: Sverre Vink creator: Lia Hemerik creator: Robin van Velzen creator: M. Eric Schranz creator: Freek T. Bakker uri: https://doi.org/10.7717/peerj.8823 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 van de Kerke et al. title: Farming system shapes traits and composition of spider assemblages in Mediterranean cherry orchards link: https://peerj.com/articles/8856 last-modified: 2020-04-02 description: Habitat properties, including crop type, farming system, management practices, or topographic features such as the hillside aspect, may act as environmental filters that select organisms sharing traits compatible with those conditions. The more environmentally-friendly management practices implemented in organic farming seem to benefit a range of taxa, but the extent of those benefits is not well understood. In cherry orchards of the Jerte Valley (Extremadura, western Spain), we explored the response of spider assemblages to the farming system (organic and conventional) and the hillside aspect (sunny or shady) from a taxonomical, behavioral, and morphological perspective. Spiders from both the canopy and soil surface were collected and identified to family. According to their foraging strategy, spiders were sorted in guilds and, for a selected family in each guild, body size was measured on each captured individual. Spider traits and composition were determined by local factors derived from farming system, and by climate conditions associated to the hillside aspect. In taxonomical terms, spiders benefit from organic farming and by the shady aspect. However, from a behavioral perspective, spiders with different foraging strategies exhibit strong variations in their response to the evaluated factors. From a morphological perspective, body size within guilds is differently conditioned by management practices that constitute conditioning disturbance events for each guild, resulting in selecting small individuals. The observed differences in taxonomical, behavioral, and morphological responses of spider communities to habitat properties highlight the importance of examining their assemblages from different perspectives when assessing how they respond to changes in management practices and topographic features. creator: Natalia Rosas-Ramos creator: Laura Baños-Picón creator: José Tormos creator: Josep D. Asís uri: https://doi.org/10.7717/peerj.8856 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Rosas-Ramos et al. title: Drought-induced reduction in methane fluxes and its hydrothermal sensitivity in alpine peatland link: https://peerj.com/articles/8874 last-modified: 2020-04-02 description: Accurate estimation of CH4 fluxes in alpine peatland of the Qinghai-Tibetan Plateau under extreme drought is vital for understanding the global carbon cycle and predicting future climate change. However, studies on the impacts of extreme drought on peatland CH4 fluxes are limited. To study the effects of extreme drought on CH4 fluxes of the Zoige alpine peatland ecosystem, the CH4 fluxes during both extreme drought treatment (D) and control treatment (CK) were monitored using a static enclosed chamber in a control platform of extreme drought. The results showed that extreme drought significantly decreased CH4 fluxes in the Zoige alpine peatland by 31.54% (P < 0.05). Extreme drought significantly reduced the soil water content (SWC) (P < 0.05), but had no significant effect on soil temperature (Ts). Under extreme drought and control treatments, there was a significant negative correlation between CH4 fluxes and environmental factors (Ts and SWC), except Ts, at a depth of 5cm (P < 0.05). Extreme drought reduced the correlation between CH4 fluxes and environmental factors and significantly weakened the sensitivity of CH4 fluxes to SWC (P < 0.01). Moreover, it was found that the correlation between subsoil (20 cm) environmental factors and CH4 fluxes was higher than with the topsoil (5, 10 cm) environmental factors under the control and extreme drought treatments. These results provide a better understanding of the extreme drought effects on CH4 fluxes of alpine peatland, and their hydrothermal impact factors, which provides a reliable reference for peatland protection and management. creator: Haidong Wu creator: Liang Yan creator: Yong Li creator: Kerou Zhang creator: Yanbin Hao creator: Jinzhi Wang creator: Xiaodong Zhang creator: Zhongqing Yan creator: Yuan Zhang creator: Xiaoming Kang uri: https://doi.org/10.7717/peerj.8874 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wu et al. title: New anatomical information on Dsungaripterus weii Young, 1964 with focus on the palatal region link: https://peerj.com/articles/8741 last-modified: 2020-04-01 description: Pterosaur specimens with complete and well-preserved palatal region are rare. Here we describe new and previously collected specimens of the pterodactyloid pterosaur Dsungaripterus weii that are three-dimensionally preserved and provide new anatomical information for this species. Among the unique features is a lateral process of the pterygoid divided into two parts: an anterior thin, parabolic arc shaped element that separates the secondary subtemporal and the subtemporal fenestrae, followed by a dorsoventrally flattened portion that is directed inside the subtemporal fenestrae. The interpterygoid fenestrae join forming an irregular oval shape with two symmetrical posterior notches and a smooth anterior margin. Among all pterosaurs where the palate is known, the posterior configuration of the palate of D. weii is similar to some azhdarchoids, which is consistent with the suggested phylogenetic position of the Dsungaripteridae as closely related to the Azhdarchoidea. Furthermore, we identify symmetrical grooves on the lateral surface of the upper and lower jaws, that likely represent the impression of the edge of a keratinous sheath that would cover the upturned toothless rostrum during foraging activity, most likely consisting of hard elements, as has been previously assumed. Wear facets on the teeth also support this feeding mode. creator: He Chen creator: Shunxing Jiang creator: Alexander W.A. Kellner creator: Xin Cheng creator: Xinjun Zhang creator: Rui Qiu creator: Yang Li creator: Xiaolin Wang uri: https://doi.org/10.7717/peerj.8741 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Chen et al. title: The efficiency of universal mitochondrial DNA barcodes for species discrimination of Pomacea canaliculata and Pomacea maculata link: https://peerj.com/articles/8755 last-modified: 2020-04-01 description: Invasive apple snails, Pomacea canaliculata and P. maculata, have a widespread distribution globally and are regarded as devastating pests of agricultural wetlands. The two species are morphologically similar, which hinders species identification via morphological approaches and species-specific management efforts. Advances in molecular genetics may contribute effective diagnostic tools to potentially resolve morphological ambiguity. DNA barcoding has revolutionized the field of taxonomy by providing an alternative, simple approach for species discrimination, where short sections of DNA, the cytochrome c oxidase subunit I (COI) gene in particular, are used as ‘barcodes’ to delineate species boundaries. In our study, we aimed to assess the effectiveness of two mitochondrial markers, the COI and 16S ribosomal deoxyribonucleic acid (16S rDNA) markers for DNA barcoding of P. canaliculata and P. maculata. The COI and 16S rDNA sequences of 40 Pomacea specimens collected from six localities in Peninsular Malaysia were analyzed to assess their barcoding performance using phylogenetic methods and distance-based assessments. The results confirmed both markers were suitable for barcoding P. canaliculata and P. maculata. The phylogenies of the COI and 16S rDNA markers demonstrated species-specific monophyly and were largely congruent with the exception of one individual. The COI marker exhibited a larger barcoding gap (6.06–6.58%) than the 16S rDNA marker (1.54%); however, the magnitude of barcoding gap generated within the barcoding region of the 16S rDNA marker (12-fold) was bigger than the COI counterpart (approximately 9-fold). Both markers were generally successful in identifying P. canaliculata and P. maculata in the similarity-based DNA identifications. The COI + 16S rDNA concatenated dataset successfully recovered monophylies of P. canaliculata and P. maculata but concatenation did not improve individual datasets in distance-based analyses. Overall, although both markers were successful for the identification of apple snails, the COI molecular marker is a better barcoding marker and could be utilized in various population genetic studies of P. canaliculata and P. maculata. creator: Adrian Kannan creator: Suganiya Rama Rao creator: Shyamala Ratnayeke creator: Yoon-Yen Yow uri: https://doi.org/10.7717/peerj.8755 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Kannan et al. title: Artificial intelligence system can achieve comparable results to experts for bone age assessment of Chinese children with abnormal growth and development link: https://peerj.com/articles/8854 last-modified: 2020-04-01 description: ObjectiveBone age (BA) is a crucial indicator for revealing the growth and development of children. This study tested the performance of a fully automated artificial intelligence (AI) system for BA assessment of Chinese children with abnormal growth and development.Materials and MethodsA fully automated AI system based on the Greulich and Pyle (GP) method was developed for Chinese children by using 8,000 BA radiographs from five medical centers nationwide in China. Then, a total of 745 cases (360 boys and 385 girls) with abnormal growth and development from another tertiary medical center of north China were consecutively collected between January and October 2018 to test the system. The reference standard was defined as the result interpreted by two experienced reviewers (a radiologist with 10 years and an endocrinologist with 15 years of experience in BA reading) through consensus using the GP atlas. BA accuracy within 1 year, root mean square error (RMSE), mean absolute difference (MAD), and 95% limits of agreement according to the Bland-Altman plot were statistically calculated.ResultsFor Chinese pediatric patients with abnormal growth and development, the accuracy of this new automated AI system within 1 year was 84.60% as compared to the reference standard, with the highest percentage of 89.45% in the 12- to 18-year group. The RMSE, MAD, and 95% limits of agreement of the AI system were 0.76 years, 0.58 years, and −1.547 to 1.428, respectively, according to the Bland-Altman plot. The largest difference between the AI and experts’ BA result was noted for patients of short stature with bone deformities, severe osteomalacia, or different rates of maturation of the carpals and phalanges.ConclusionsThe developed automated AI system could achieve comparable BA results to experienced reviewers for Chinese children with abnormal growth and development. creator: Fengdan Wang creator: Xiao Gu creator: Shi Chen creator: Yongliang Liu creator: Qing Shen creator: Hui Pan creator: Lei Shi creator: Zhengyu Jin uri: https://doi.org/10.7717/peerj.8854 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wang et al. title: Prediction of antiviral drugs against African swine fever viruses based on protein–protein interaction analysis link: https://peerj.com/articles/8855 last-modified: 2020-04-01 description: The African swine fever virus (ASFV) has severely influenced the swine industry of the world. Unfortunately, there is currently no effective antiviral drug or vaccine against the virus. Identification of new anti-ASFV drugs is urgently needed. Here, an up-to-date set of protein–protein interactions between ASFV and swine were curated by integration of protein–protein interactions from multiple sources. Thirty-eight swine proteins were observed to interact with ASFVs and were defined as ASFV-interacting swine proteins. The ASFV-interacting swine proteins were found to play a central role in the swine protein–protein interaction network, with significant larger degree, betweenness and smaller shortest path length than other swine proteins. Some of ASFV-interacting swine proteins also interacted with several other viruses and could be taken as potential targets of drugs for broad-spectrum effect, such as HSP90AB1. Finally, the antiviral drugs which targeted ASFV-interacting swine proteins and ASFV proteins were predicted. Several drugs with either broad-spectrum effect or high specificity on ASFV-interacting swine proteins were identified, such as Polaprezinc and Geldanamycin. Structural modeling and molecular dynamics simulation showed that Geldanamycin could bind with swine HSP90AB1 stably. This work could not only deepen our understanding towards the ASFV-swine interactions, but also help for the development of effective antiviral drugs against the ASFVs. creator: Zhaozhong Zhu creator: Yunshi Fan creator: Yang Liu creator: Taijiao Jiang creator: Yang Cao creator: Yousong Peng uri: https://doi.org/10.7717/peerj.8855 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Zhu et al. title: Interaction effects of aging, word frequency, and predictability on saccade length in Chinese reading link: https://peerj.com/articles/8860 last-modified: 2020-04-01 description: BackgroundIt was well known that age has an impact on word processing (word frequency or predictability) in terms of fixating time during reading. However, little is known about whether or not age modulates these impacts on saccade behaviors in Chinese reading (i.e., length of incoming/outgoing saccades for a target word).MethodsAge groups, predictability, and frequency of target words were manipulated in the present study. A larger frequency effect on lexical accessing (i.e., gaze duration) and on context integration (i.e., go-past time, total reading time), as well as larger predictability effects on data of raw total reading time, were observed in older readers when compared with their young counterparts.ResultsEffect of predictability and frequency on word skipping and re-fixating rate did not differ across the two age groups. Notably, reliable interaction effects of age, along with word predictability and/or frequency, on the length of the first incoming/outgoing saccade for a target word were also observed.DiscussionOur findings suggest that the word processing function of older Chinese readers in terms of saccade targeting declines with age. creator: Zhifang Liu creator: Wen Tong creator: Yongqiang Su uri: https://doi.org/10.7717/peerj.8860 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Liu et al. title: Palustrine forested wetland vegetation communities change across an elevation gradient, Washington State, USA link: https://peerj.com/articles/8903 last-modified: 2020-04-01 description: BackgroundForested wetlands support distinct vegetation and hydrology relative to upland forests and shrub-dominated or open water wetlands. Although forested wetland plant communities comprise unique habitats, these ecosystems’ community structure is not well documented in the U.S. Pacific Northwest. Here I surveyed forested wetland vegetation to identify changes in community composition and structure across an elevation gradient that corresponds to flooding stress, asking: (1) How do forested wetland plant communities change across an elevation gradient that corresponds to flood frequency and duration? (2) At what relative elevations do different plant species occur within a wetland?MethodsI measured overstory tree basal area and structure and understory vascular plant composition in three zones: wetland buffers (WB) adjacent to the wetland, an upper wetland (UW) extent, and a lower wetland (LW) extent, surveying individual trees’ root collar elevation relative to the wetland ordinary high-water mark (OHWM). I estimated understory plant species abundance in sub-plots and surveyed these plots’ height above the OHWM. I used non-metric multidimensional scaling ordination to identify patterns in vegetation communities relative to wetland elevation, and tested for compositional differences between the WB, UW and LW zones using PERMANOVA. I calculated overstory and understory indicator species for each wetland zone using indicator species analysis.ResultsForest overstory composition changed across the elevation gradient, with broad-leaved trees occupying a distinct hydrologic niche in low-lying areas close to the OHWM. Conifer species occurred higher above the OHWM on drier microsites. Pseudotsuga menziesii (mean elevation = 0.881 m) and Tsuga heterophylla (mean elevation = 1.737 m) were overstory indicator species of the WB, while Fraxinus latifolia (mean elevation = 0.005 m) was an overstory indicator for the upper and lower wetland. Understory vegetation differed between zones and lower zones’ indicator species were generally hydrophytic species with adaptations that allow them to tolerate flooding stress at lower elevations. Average elevations above the OHWM are reported for 19 overstory trees and 61 understory plant species. By quantifying forested wetland plant species’ affinities for different habitats across an inundation gradient, this study illustrates how rarely flooded, forested WB vegetation differs from frequently flooded, LW vegetation. Because common management applications, like restoring forested wetlands and managing wetland responses to forest harvest, are both predicated upon understanding how vegetation relates to hydrology, these data on where different species might establish and persist along an inundation gradient may be useful in planning for anticipated forested wetland responses to restoration and disturbance. creator: Nate Hough-Snee uri: https://doi.org/10.7717/peerj.8903 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Hough-Snee