title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=922 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Student health behavior and academic performance link: https://peerj.com/articles/11107 last-modified: 2021-04-16 description: ObjectiveTo explore the association between health behaviors and habits of university students and academic achievement.ParticipantsSix hundred fourteen undergraduate students at a state university in the United States.MethodsStudents were invited over a 2-year period to participate in an anonymous online survey that asked questions concerning a wide range of health behaviors and habits; participants were asked to report their current grade point average (GPA). Standard Least Squares Models were used to examine differences in self-reported GPA across the different health behaviors and habits, with individuals as replicates.ResultsThe study found positive associations between breakfast consumption, physical activity, and strength training and self-reported GPA, and negative associations between the hours of sleep per night, hours worked per week, fast food and energy drinks consumption, and use of marijuana, alcohol and electronic vaping products.ConclusionsWhile there is an association for some of the studied health behaviors and habits with self-reported GPA, the effect sizes for these health behaviors were low. The significant effect of vaping on GPA as well as the increased use reported in this study indicates that the topic should be explored further. Furthermore, students should be educated on the potential positive and negative effects of health behavior choices to help them make better choices. creator: Peter R. Reuter creator: Bridget L. Forster uri: https://doi.org/10.7717/peerj.11107 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Reuter and Forster title: The physiological response of Ectomycorrhizal fungus Lepista sordida to Cd and Cu stress link: https://peerj.com/articles/11115 last-modified: 2021-04-16 description: Ectomycorrhizal fungi (ECMF) can develop the resistance of host plants to heavy metal stress. However, little is known about the response of ECMF to heavy metal exposure. In this study, the growth and physiological indices of Lepista sordida under Cd and Cu stress were studied. The growth of L. sordida on PDA medium under Cd and Cu stress was observed using scanning electron microscopy (SEM). After the addition of Cd and Cu to the medium, the mycelium started twisting, breaking, sticking together, and even dissolving. In the control group, a good and luxuriant mycelium growth of L. sordida along with the numerous clamp connections was observed. The mycelial biomass decreased with increasing concentrations of heavy metals in a liquid medium. The catalase (CAT), peroxidase (POD), superoxide dismutase (SOD), and ascorbate peroxidase (APX) activities were also investigated, and the results showed that the Cd and Cu treatments caused a significant increase in the antioxidant enzyme activities. The contents of soluble protein, soluble sugar, and free proline in L. sordida were investigated, and it was found that the contents initially increased and then decreased with the increasing concentrations of Cd and Cu. However, the content of malondialdehyde (MDA) increased with the increasing concentrations of Cd and Cu. In conclusion, the present study provides a theoretical basis for the better utilization of Ectomycorrhizal fungal resources for the remediation of soil contaminated with heavy metal. creator: Yin Dachuan creator: Qi Jinyu uri: https://doi.org/10.7717/peerj.11115 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Dachuan and Jinyu title: A new fossil mantis shrimp and the convergent evolution of a lobster-like morphotype link: https://peerj.com/articles/11124 last-modified: 2021-04-16 description: Eumalacostracan crustaceans all have a more or less stereotypic body organisation in the sense of tagmosis. Originally, this included a head with six segments (ocular segment plus five appendage-bearing segments), a thorax region with eight segments, and a pleon with six segments. Interestingly, despite these restrictions in variability in terms of tagmosis, the morphological diversity within Eumalacostraca is rather high. A group providing representative examples that are commonly known is Decapoda. Decapodan crustaceans include shrimp-like forms, lobster-like forms and crab-like forms. The stem species of Eucarida, the group including Decapoda and Euphausiacea, presumably possessed a rather shrimp-like morphology, quite similar to the stem species of Eumalacostraca. Also two other lineages within Eumalacostraca, namely Hoplocarida (with the mantis shrimps as modern representatives) and Neocarida (with the sister groups Thermosbaenacea and Peracarida) evolved from the shrimp-like body organisation to include a lobster-like one. In this study, we demonstrate that the stepwise evolution towards a lobster morphotype occurred to a certain extent in similar order in these three lineages, Hoplocarida, Eucarida and Peracarida, leading to similar types of derived body organisation. This evolutionary reconstruction is based not only on observations of modern fauna, but especially on exceptionally preserved Mesozoic fossils, including the description of a new species of mantis shrimps bridging the morphological gap between the more ancestral-appearing Carboniferous forms and the more modern-appearing Jurassic forms. With this, Mesozoic eumalacostracans represent an important (if not unique) ‘experimental set-up’ for research on factors leading to convergent evolution, the understanding of which is still one of the puzzling challenges of modern evolutionary theory. creator: Carolin Haug creator: Joachim T. Haug uri: https://doi.org/10.7717/peerj.11124 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Haug and Haug title: TP53 mutation and MET amplification in circulating tumor DNA analysis predict disease progression in patients with advanced gastric cancer link: https://peerj.com/articles/11146 last-modified: 2021-04-16 description: BackgroundGastric cancer (GC) is a heterogeneous disease that encompasses various molecular subtypes. The molecular mutation characteristics of circulating tumor DNA (ctDNA) in advanced gastric cancer (AGC), especially the clinical utility of TP53 mutation and MET amplification in ctDNA need to be further explored.ObjectivesThe aim of this study was mainly to assess the clinical utility of TP53 mutation and MET amplification in ctDNA as biomarkers for monitoring disease progression of AGC.Patients and MethodsWe used multigene NGS-panel technology to study the characteristics of ctDNA gene mutations and screen the key mutant genes in AGC patients. The Kaplan-Meier method was used to calculate the survival probability and log-rank test was used to compare the survival curves of TP53 mutation and MET amplification in ctDNA of AGC patients. The survival time was set from the blood test time to the follow-up time to observe the relationship between the monitoring index and tumor prognosis.ResultsWe performed mutation detection on ctDNA in 23 patients with AGC and identified the top 20 mutant genes. The five most frequently mutated genes were TP53 (55%), EGFR (20%), ERBB2 (20%), MET (15%) and APC (10%). TP53 was the most common mutated gene (55%) and MET had a higher frequency of mutations (15%) in our study. Kaplan-Meier analysis showed that patients with TP53 mutant in ctDNA had shorter overall survival (OS) than these with TP53 wild (P < 0.001). The Allele frequency (AF) of TP53 mutations in patient number 1 was higher in the second time (0.94%) than in the first time (0.36%); the AF of TP53 mutations in patient number 16 was from scratch (0∼0.26%). In addition, the AF of TP53 mutations in patients who survive was relatively low (P = 0.047). Simultaneously, Kaplan-Meier analysis showed that patients with MET amplification also had shorter OS than these with MET without amplification (P < 0.001).ConclusionTP53 and MET are the two common frequently mutant genes in ctDNA of AGC patients.TP53 mutation and MET amplification in ctDNA could predict disease progression of AGC patients. creator: Jia Li creator: Zhaoyan Li creator: Yajie Ding creator: Yan Xu creator: Xiaohong Zhu creator: Nida Cao creator: Chen Huang creator: Mengmeng Qin creator: Feng Liu creator: Aiguang Zhao uri: https://doi.org/10.7717/peerj.11146 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Li et al. title: Predicting migration routes for three species of migratory bats using species distribution models link: https://peerj.com/articles/11177 last-modified: 2021-04-16 description: Understanding seasonal variation in the distribution and movement patterns of migratory species is essential to monitoring and conservation efforts. While there are many species of migratory bats in North America, little is known about their seasonal movements. In terms of conservation, this is important because the bat fatalities from wind energy turbines are significant and may fluctuate seasonally. Here we describe seasonally resolved distributions for the three species that are most impacted by wind farms (Lasiurus borealis (eastern red bat), L. cinereus (hoary bat) and Lasionycteris noctivagans (silver-haired bat)) and use these distributions to infer their most likely migratory pathways. To accomplish this, we collected 2,880 occurrence points from the Global Biodiversity Information Facility over five decades in North America to model species distributions on a seasonal basis and used an ensemble approach for modeling distributions. This dataset included 1,129 data points for L. borealis, 917 for L. cinereus and 834 for L. noctivagans. The results suggest that all three species exhibit variation in distributions from north to south depending on season, with each species showing potential migratory pathways during the fall migration that follow linear features. Finally, we describe proposed migratory pathways for these three species that can be used to identify stop-over sites, assess small-scale migration and highlight areas that should be prioritized for actions to reduce the effects of wind farm mortality. creator: Jamin G. Wieringa creator: Bryan C. Carstens creator: H Lisle Gibbs uri: https://doi.org/10.7717/peerj.11177 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Wieringa et al. title: Evaluation potential of PGPR to protect tomato against Fusarium wilt and promote plant growth link: https://peerj.com/articles/11194 last-modified: 2021-04-16 description: Soilborne fungal diseases are most common among vegetable crops and have major implications for crop yield and productivity. Eco-friendly sustainable agriculture practices that can overcome biotic and abiotic stresses are of prime importance. In this study, we evaluated the ability of plant growth-promoting rhizobacterium (PGPR) Bacillus aryabhattai strain SRB02 to control the effects of tomato wilt disease caused by Fusarium oxysporum f. sp. lycopersici (strain KACC40032) and promote plant growth. In vitro bioassays showed significant inhibition of fungal growth by SRB02. Inoculation of susceptible and tolerant tomato cultivars in the presence of SRB02 showed significant protection of the cultivar that was susceptible to infection and promotion of plant growth and biomass production in both of the cultivars. Further analysis of SRB02-treated plants revealed a significantly higher production of amino acids following infection by F. oxysporum. Analysis of plant defense hormones after inoculation by the pathogen revealed a significantly higher accumulation of salicylic acid (SA), with a concomitant reduction in jasmonic acid (JA). These results indicate that B. aryabhattai strain SRB02 reduces the effects of Fusarium wilt disease in tomato by modulating endogenous phytohormones and amino acid levels. creator: Rizwana begum Syed Nabi creator: Raheem Shahzad creator: Rupesh Tayade creator: Muhammad Shahid creator: Adil Hussain creator: Muhammad Waqas Ali creator: Byung-Wook Yun uri: https://doi.org/10.7717/peerj.11194 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Syed Nabi et al. title: NGScloud2: optimized bioinformatic analysis using Amazon Web Services link: https://peerj.com/articles/11237 last-modified: 2021-04-16 description: BackgroundNGScloud was a bioinformatic system developed to perform de novo RNAseq analysis of non-model species by exploiting the cloud computing capabilities of Amazon Web Services. The rapid changes undergone in the way this cloud computing service operates, along with the continuous release of novel bioinformatic applications to analyze next generation sequencing data, have made the software obsolete. NGScloud2 is an enhanced and expanded version of NGScloud that permits the access to ad hoc cloud computing infrastructure, scaled according to the complexity of each experiment.MethodsNGScloud2 presents major technical improvements, such as the possibility of running spot instances and the most updated AWS instances types, that can lead to significant cost savings. As compared to its initial implementation, this improved version updates and includes common applications for de novo RNAseq analysis, and incorporates tools to operate workflows of bioinformatic analysis of reference-based RNAseq, RADseq and functional annotation. NGScloud2 optimizes the access to Amazon’s large computing infrastructures to easily run popular bioinformatic software applications, otherwise inaccessible to non-specialized users lacking suitable hardware infrastructures.ResultsThe correct performance of the pipelines for de novo RNAseq, reference-based RNAseq, RADseq and functional annotation was tested with real experimental data, providing workflow performance estimates and tips to make optimal use of NGScloud2. Further, we provide a qualitative comparison of NGScloud2 vs. the Galaxy framework. NGScloud2 code, instructions for software installation and use are available at https://github.com/GGFHF/NGScloud2. NGScloud2 includes a companion package, NGShelper that contains Python utilities to post-process the output of the pipelines for downstream analysis at https://github.com/GGFHF/NGShelper. creator: Fernando Mora-Márquez creator: José Luis Vázquez-Poletti creator: Unai López de Heredia uri: https://doi.org/10.7717/peerj.11237 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Mora-Márquez et al. title: Antifungal properties of volatile organic compounds produced by Daldinia eschscholtzii MFLUCC 19-0493 isolated from Barleria prionitis leaves against Colletotrichum acutatum and its post-harvest infections on strawberry fruits link: https://peerj.com/articles/11242 last-modified: 2021-04-16 description: Fungal endophytes are microorganisms living symbiotically with a host plant. They can produce volatile organic compounds (VOCs) that have antimicrobial activity. This study aimed to isolate endophytic fungi from Barleria prionitis plants grown in Thailand and to investigate the antifungal properties of their VOCs against Colletotrichum acutatum, a causal agent of anthracnose disease on post-harvest strawberry fruits. A total of 34 endophytic fungi were isolated from leaves of B. prionitis. The VOCs produced from each individual isolate were screened for their antifungal activity against C. acutatum using a dual-culture plate method. From this in vitro screening experiment, the VOCs produced by the endophytic isolate BP11 were found to have the highest inhibition percentage (80.3%) against the mycelial growth of C. acutatum. The endophytic isolate BP11 was molecularly identified as Daldinia eschscholtzii MFLUCC 19-0493. This strain was then selected for an in vivo experiment. Results from the in vivo experiment indicated that the VOCs produced by D. eschscholtzii MFLUCC 19-0493 were able to inhibit infections by C. acutatum on organic fresh strawberry fruits with an average inhibition percentage of 72.4%. The quality of the pathogen-inoculated strawberry fruits treated with VOCs produced by D. eschscholtzii MFLUCC 19-0493 was evaluated. Their fruit firmness, total soluble solids, and pH were found to be similar to the untreated strawberry fruits. Solid phase microextraction-gas chromatographic-mass spectrometric analysis of the VOCs produced by D. eschscholtzii MFLUCC 19-0493 led to the detection and identification of 60 compounds. The major compounds were elemicin (23.8%), benzaldehyde dimethyl acetal (8.5%), ethyl sorbate (6.8%), methyl geranate (6.5%), trans-sabinene hydrate (5.4%), and 3,5-dimethyl-4-heptanone (5.1%). Each major compound was tested for its antifungal activity against C. acutatum using the in vitro assay. While all these selected VOCs showed varying degrees of antifungal activity, elemicin was found to possess the strongest antifungal activity. This work suggests that D. eschscholtzii MFLUCC 19-0493 could be a promising natural preservative for controlling C. acutatum associated anthracnose disease in strawberry fruits during the post-harvest period. creator: Sarunpron Khruengsai creator: Patcharee Pripdeevech creator: Chutima Tanapichatsakul creator: Chanin Srisuwannapa creator: Priya Esilda D’Souza creator: Parinya Panuwet uri: https://doi.org/10.7717/peerj.11242 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Khruengsai et al. title: Recombinant fusion protein by lysozyme and antibacterial peptide enhances ischemic wound healing via angiogenesis and reduction of inflammation in diabetic db/db mice link: https://peerj.com/articles/11256 last-modified: 2021-04-16 description: Background & aimsLysozyme and antibacterial peptides have been reported to broad-spectrum antibacterial activity and can further improve wound healing. The aim of this study was to assess the effectiveness of a recombinant fusion protein created by combining lysozyme and an antibacterial peptide in forming new vessels and wound healing in an ischemic hind limb.MethodsAn ischemic hind limb model was established by isolation and ligation of the femoral artery in diabetic db/db mice. Cutaneous wounds were created with or without ischemia. Adductor muscles and wounds were treated with or without the fusion protein.ResultsThe fusion protein accelerated ischemic diabetic wound healing and attenuated impairment of ischemic adductor muscle . Further, the fusion protein elevated expression of platelet derived growth factor (PDGF) and vascular endothelial growth factor (VEGF) protein and mRNA in ischemic adductor muscle, reduced levels of tumor necrosis factor-alpha (TNF-α) and interleukin-6 (IL-6) in serum and expression of phosphorylated nuclear factor κB (p-NF-κB) and p-IKB α in ischemic adductor. The fusion protein also enhanced levels of phosphorylated VEGF and PDGF receptors in the ischemic adductor muscles from diabetic db/db mice.ConclusionThe data showed that the beneficial effects of the fusion protein on ischemic wound healing may be associated with angiogenesis and reduction of inflammatory response in the ischemic adductor muscles of diabetic db/db mice. creator: Wei Li creator: Yu-Xin Jiang creator: Qing-Ying Chen creator: Guo-Guang Wang uri: https://doi.org/10.7717/peerj.11256 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Li et al. title: Optimizing speleological monitoring efforts: insights from long-term data for tropical iron caves link: https://peerj.com/articles/11271 last-modified: 2021-04-16 description: Understanding the factors underpinning species abundance patterns in space and time is essential to implement effective cave conservation actions. Yet, the methods employed to monitor cave biodiversity still lack standardization, and no quantitative assessment has yet tried to optimize the amount and type of information required to efficiently identify disturbances in cave ecosystems. Using a comprehensive monitoring dataset for tropical iron caves, comprising abundance measurements for 33 target taxa surveyed across 95 caves along four years, here we provide the first evidence-based recommendations to optimize monitoring programs seeking to follow target species abundance through time. We found that seasonality did not influence the ability to detect temporal abundance trends. However, in most species, abundance estimates assessed during the dry season resulted in a more accurate detection of temporal abundance trends, and at least three surveys were required to identify global temporal abundance trends. Finally, we identified a subset of species that could potentially serve as short-term disturbance indicators. Results suggest that iron cave monitoring programs implemented in our study region could focus sampling efforts in the dry season, where detectability of target species is higher, while assuring data collection for at least three years. More generally, our study reveals the importance of long-term cave monitoring programs for detecting possible disturbances in subterranean ecosystems, and for using the generated information to optimize future monitoring efforts. creator: Leonardo Carreira Trevelin creator: Matheus Henrique Simões creator: Xavier Prous creator: Thadeu Pietrobon creator: Iuri Viana Brandi creator: Rodolfo Jaffé uri: https://doi.org/10.7717/peerj.11271 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Trevelin et al.