title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1095 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Description of two new species of the genus Heterochelamon Türkay & Dai, 1997 (Crustacea: Decapoda: Brachyura: Potamidae), from southern China link: https://peerj.com/articles/9565 last-modified: 2020-07-22 description: This study describes two new species of freshwater crab of the genus HeterochelamonTürkay & Dai, 1997 from southern China, H. huidongense from Guangdong Province and H. jinxiuense from Guangxi Zhuang Autonomous Region. The two new species can be differentiated from congeners by characters derived from the shape of the epibranchial tooth, external orbital angle, cheliped proportions and structure of the male first gonopod. The present study brings the number of Heterochelamon species to seven. We used the mitochondrial 16S rRNA gene for a molecular analysis and the results are consistent with the morphological features that support the recognition of two new taxa. creator: Song-Bo Wang creator: Yi-Yang Xu creator: Jie-Xin Zou uri: https://doi.org/10.7717/peerj.9565 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wang et al. title: An overview of biomass conversion: exploring new opportunities link: https://peerj.com/articles/9586 last-modified: 2020-07-22 description: Recycling biomass is indispensable these days not only because fossil energy sources are gradually depleted, but also because pollution of the environment, caused by the increasing use of energy, must be reduced. This article intends to overview the results of plant biomass processing methods that are currently in use. Our aim was also to review published methods that are not currently in use. It is intended to explore the possibilities of new methods and enzymes to be used in biomass recycling. The results of this overview are perplexing in almost every area. Advances have been made in the pre-treatment of biomass and in the diversity and applications of the enzymes utilized. Based on molecular modeling, very little progress has been made in the modification of existing enzymes for altered function and adaptation for the environmental conditions during the processing of biomass. There are hardly any publications in which molecular modeling techniques are used to improve enzyme function and to adapt enzymes to various environmental conditions. Our view is that using modern computational, biochemical, and biotechnological methods would enable the purposeful design of enzymes that are more efficient and suitable for biomass processing. creator: László Fülöp creator: János Ecker uri: https://doi.org/10.7717/peerj.9586 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Fülöp and Ecker title: Role of methyltransferase-like enzyme 3 and methyltransferase-like enzyme 14 in urological cancers link: https://peerj.com/articles/9589 last-modified: 2020-07-22 description: N6-methyladenosine (m6A) modifications can be found in eukaryotic messenger RNA (mRNA), long non-coding RNA (lncRNA), and microRNA (miRNA). Several studies have demonstrated a close relationship between m6A modifications and cancer cells. Methyltransferase-like enzyme 3 (METTL3) and methyltransferase-like enzyme 14 (METTL14) are two major enzymes involved in m6A modifications that play vital roles in various cancers. However, the roles and regulatory mechanisms of METTL3 and METTL14 in urological cancers are largely unknown. In this review, we summarize the current research results for METTL3 and METTL14 and identify potential pathways involving these enzymes in kidney, bladder, prostate, and testicular cancer. We found that METTL3 and METTL14 have different expression patterns in four types of urological cancers. METTL3 is highly expressed in bladder and prostate cancer and plays an oncogenic role on cancer cells; however, its expression and role are opposite in kidney cancer. METTL14 is expressed at low levels in kidney and bladder cancer, where it has a tumor suppressive role. Low METTL3 or METTL14 expression in cancer cells negatively regulates cell growth-related pathways (e.g., mTOR, EMT, and P2XR6) but positively regulates cell death-related pathways (e.g., P53, PTEN, and Notch1). When METTL3 is highly expressed, it positively regulates the NF-kB and SHH-GL1pathways but negatively regulates PTEN. These results suggest that although METTL3 and METTL14 have different expression levels and regulatory mechanisms in urological cancers, they control cancer cell fate via cell growth- and cell death-related pathways. These findings suggest that m6A modification may be a potential new therapeutic target in urological cancer. creator: Zijia Tao creator: Yiqiao Zhao creator: Xiaonan Chen uri: https://doi.org/10.7717/peerj.9589 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Tao et al. title: Doing nothing and what it looks like: inactivity in fattening cattle link: https://peerj.com/articles/9395 last-modified: 2020-07-21 description: BackgroundAnimals kept in barren environments often show increased levels of inactivity and first studies indicate that inactive behaviour may reflect boredom or depression-like states. However, to date, knowledge of what inactivity looks like in different species is scarce and methods to precisely describe and analyse inactive behaviour are thus warranted.MethodsWe developed an Inactivity Ethogram including detailed information on the postures of different body parts (Standing/Lying, Head, Ears, Eyes, Tail) for fattening cattle, a farm animal category often kept in barren environments. The Inactivity Ethogram was applied to Austrian Fleckvieh heifers kept in intensive, semi-intensive and pasture-based husbandry systems to record inactive behaviour in a range of different contexts. Three farms per husbandry system were visited twice; once in the morning and once in the afternoon to cover most of the daylight hours. During each visit, 16 focal animals were continuously observed for 15 minutes each (96 heifers per husbandry system, 288 in total). Moreover, the focal animals’ groups were video recorded to later determine inactivity on the group level. Since our study was explorative in nature, we refrained from statistical hypothesis testing, but analysed both the individual- and group-level data descriptively. Moreover, simultaneous occurrences of postures of different body parts (Standing/Lying, Head, Ears and Eyes) were analysed using the machine learning algorithm cspade to provide insight into co-occurring postures of inactivity.ResultsInspection of graphs indicated that with increasing intensity of the husbandry system, more animals were inactive (group-level data) and the time the focal animals were inactive increased (individual-level data). Frequently co-occurring postures were generally similar between husbandry systems, but with subtle differences. The most frequently observed combination on farms with intensive and semi-intensive systems was lying with head up, ears backwards and eyes open whereas on pasture it was standing with head up, ears forwards and eyes open.ConclusionOur study is the first to explore inactive behaviour in cattle by applying a detailed description of postures from an Inactivity Ethogram and by using the machine learning algorithm cspade to identify frequently co-occurring posture combinations. Both the ethogram created in this study and the cspade algorithm may be valuable tools in future studies aiming to better understand different forms of inactivity and how they are associated with different affective states. creator: Sara Hintze creator: Freija Maulbetsch creator: Lucy Asher creator: Christoph Winckler uri: https://doi.org/10.7717/peerj.9395 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Hintze et al. title: An RNA-sequencing-based transcriptome for a significantly prognostic novel driver signature identification in bladder urothelial carcinoma link: https://peerj.com/articles/9422 last-modified: 2020-07-21 description: Bladder cancer (BC) is the ninth most common malignancy worldwide. Bladder urothelial carcinoma (BLCA) constitutes more than 90% of bladder cancer (BC). The five-year survival rate is 5–70%, and patients with BLCA have a poor clinical outcome. The identification of novel clinical molecular markers in BLCA is still urgent to allow for predicting clinical outcomes. This study aimed to identify a novel signature integrating the three-dimension transcriptome of protein coding genes, long non-coding RNAs, microRNAs that is related to the overall survival of patients with BLCA, contributing to earlier prediction and effective treatment selection, as well as to the verification of the established model in the subtypes identified. Gene expression profiling and the clinical information of 400 patients diagnosed with BLCA were retrieved from The Cancer Genome Atlas (TCGA) database. A univariate Cox regression analysis, robust likelihood-based survival modelling analysis and random forests for survival regression and classification algorithms were used to identify the critical biomarkers. A multivariate Cox regression analysis was utilized to construct a risk score formula with a maximum area under the curve (AUC = 0.7669 in the training set). The significant signature could classify patients into high-risk and low-risk groups with significant differences in overall survival time. Similar results were confirmed in the test set (AUC = 0.645) and in the entire set (AUC = 0.710). The multivariate Cox regression analysis indicated that the five-RNA signature was an independent predictive factor for patients with BLCA. Non-negative matrix factorization and a similarity network fusion algorithm were applied for identifying three molecular subtypes. The signature could separate patients in every subtype into high- and low- groups with a distinct difference. Gene set variation analysis of protein-coding genes associated with the five prognostic RNAs demonstrated that the co-expressed protein-coding genes were involved in the pathways and biological process of tumourigenesis. The five-RNA signature could serve as to some degree a reliable independent signature for predicting outcome in patients with BLCA. creator: Danqi Liu creator: Boting Zhou creator: Rangru Liu uri: https://doi.org/10.7717/peerj.9422 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Liu et al. title: School health assessment tools: a systematic review of measurement in primary schools link: https://peerj.com/articles/9459 last-modified: 2020-07-21 description: Background This systematic review aimed to investigate the psychometric properties of the school health’s assessment tools in primary schools through COSMIN Risk of Bias checklist. We examined the studies that have addressed the measurement properties of school-health instruments to give a clear overview of the quality of all available tools measuring school health in primary schools. This systematic review was registered in PROPERO with the Registration ID: CRD42020158158.MethodDatabases of EBSCOhost, PubMed, ProQuest, Wily, PROSPERO, and OpenGrey were systematically searched without any time limitation to find all full-text English journal articles studied at least one of the COSMIN checklist measurement properties of a school-health assessment tool in primary schools. The instruments should be constructed based on a school health model. The eligible studies were assessed by COSMIN Risk of Bias checklist to report their quality of methodology for each measurement property and for the whole study by rating high, moderate or low quality.ResultsAt the final screening just seven studies remained for review. Four studies were tool development, three of them were rated as “adequate” and the other study as “very good”; five studies examined the content validity, three of them were appraised as “very good”, and the two remaining as “inadequate”. All seven studies measured structural validity, three of them were evaluated as “very good”, three other were scored as “adequate”, and the last study as “inadequate”. All the seven studies investigated the internal consistency, five of them were assessed as “very good”, one was rated as “doubtful”, and the last one as “inadequate”. Just one study examined the cross-cultural validity and was rated as “adequate”. Finally, all seven studies measured reliability, two of them were rated as “very good” and the rest five studies were appraised as “doubtful”. All rating was based on COSMIN checklist criteria for quality of measurement properties assessment.ConclusionThe number of studies addressing school health assessment tools was very low and therefore not sufficient. Hence, there is a serious need to investigate the psychometric properties of the available instruments measuring school health at primary schools. Moreover, the studies included in the present systematic review did not fulfill all the criteria of the COSMIN checklist for assessing measurement properties. We suggest that future studies consider these criteria for measuring psychometric properties and developing school health assessment tools. creator: Maryam Kazemitabar creator: Ali Moghadamzadeh creator: Mojtaba Habibi creator: Rezvan Hakimzadeh creator: Danilo Garcia uri: https://doi.org/10.7717/peerj.9459 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Kazemitabar et al. title: Identification of key genes of human bone marrow stromal cells adipogenesis at an early stage link: https://peerj.com/articles/9484 last-modified: 2020-07-21 description: BackgroundBone marrow adipocyte (BMA), closely associated with bone degeneration, shares common progenitors with osteoblastic lineage. However, the intrinsic mechanism of cells fate commitment between BMA and osteogenic lineage remains unclear.MethodsGene Expression Omnibus (GEO) dataset GSE107789 publicly available was downloaded and analyzed. Differentially expressed genes (DEGs) were analyzed using GEO2R. Functional and pathway enrichment analyses of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes were conducted by The Database for Annotation, Visualization and Integrated Discovery and Gene set enrichment analysis software. Protein–protein interactions (PPI) network was obtained using STRING database, visualized and clustered by Cytoscape software. Transcriptional levels of key genes were verified by real-time quantitative PCR in vitro in Bone marrow stromal cells (BMSCs) undergoing adipogenic differentiation at day 7 and in vivo in ovariectomized mice model.ResultsA total of 2,869 DEGs, including 1,357 up-regulated and 1,512 down-regulated ones, were screened out from transcriptional profile of human BMSCs undergoing adipogenic induction at day 7 vs. day 0. Functional and pathway enrichment analysis, combined with modules analysis of PPI network, highlighted ACSL1, sphingosine 1-phosphate receptors 3 (S1PR3), ZBTB16 and glypican 3 as key genes up-regulated at the early stage of BMSCs adipogenic differentiation. Furthermore, up-regulated mRNA expression levels of ACSL1, S1PR3 and ZBTB16 were confirmed both in vitro and in vivo.ConclusionACSL1, S1PR3 and ZBTB16 may play crucial roles in early regulation of BMSCs adipogenic differentiation creator: Pengyu Chen creator: Mingrui Song creator: Yutian Wang creator: Songyun Deng creator: Weisheng Hong creator: Xianrong Zhang creator: Bin Yu uri: https://doi.org/10.7717/peerj.9484 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Chen et al. title: Microbial and chemical dynamics of a toxic dinoflagellate bloom link: https://peerj.com/articles/9493 last-modified: 2020-07-21 description: Harmful Algal Blooms (HABs) exert considerable ecological and economic damage and are becoming increasingly frequent worldwide. However, the biological factors underlying HABs remain uncertain. Relationships between algae and bacteria may contribute to bloom formation, strength, and duration. We investigated the microbial communities and metabolomes associated with a HAB of the toxic dinoflagellate Karenia brevis off the west coast of Florida in June 2018. Microbial communities and intracellular metabolite pools differed based on both bacterial lifestyle and bloom level, suggesting a complex role for blooms in reshaping microbial processes. Network analysis identified K. brevis as an ecological hub in the planktonic ecosystem, with significant connections to diverse microbial taxa. These included four flavobacteria and one sequence variant unidentified past the domain level, suggesting uncharacterized diversity in phytoplankton-associated microbial communities. Additionally, intracellular metabolomic analyses associated high K. brevis levels with higher levels of aromatic compounds and lipids. These findings reveal water column microbial and chemical characteristics with potentially important implications for understanding HAB onset and duration. creator: Nastassia V. Patin creator: Emily Brown creator: Gabriella Chebli creator: Claire Garfield creator: Julia Kubanek creator: Frank J. Stewart uri: https://doi.org/10.7717/peerj.9493 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Patin et al. title: Genotypic characterization and genome comparison reveal insights into potential vaccine coverage and genealogy of Neisseria meningitidis in military camps in Vietnam link: https://peerj.com/articles/9502 last-modified: 2020-07-21 description: BackgroundNeisseria meningitidis remains the main cause of sporadic meningitis and sepsis in military camps in Vietnam. Yet, very limited molecular data of their genotypic and epidemiological characteristics are available from Vietnam, and particularly the military environment. Whole genome sequencing (WGS) has proven useful for meningococcal disease surveillance and guiding preventative vaccination programs. Previously, we characterized key genetic and epidemiological features of an invasive N. meningitidis B isolate from a military unit in Vietnam. Here, we extend these findings by sequencing two additional invasive N. meningitidis B isolated from cerebrospinal fluid (CSF) of two meningitis cases at another military unit and compared their genomic sequences and features. We also report the sequence types and antigenic profiles of 25 historical and more recently emerged N. meningitidis isolates from these units and other units in proximity.MethodsStrains were sequenced using the Illumina HiSeq platform, de novo assembled and annotated. Genomes were compared within and between military units, as well as against the global N. meningitidis collection and other isolates from the Southeast Asia region using PubMLST. Variations at the nucleotide level were determined, and phylogenetic relationships were estimated. Antigenic genotypes and vaccine coverage were analyzed using gMATS and PubMLST. Susceptibility of isolates against commonly used antibiotic agents was examined using E-test.ResultsGenome comparison revealed a high level of similarity among isolates both within and between units. All isolates showed resistance to chloramphenicol and carried identical catP gene with other Southeast Asian isolates, suggesting a common lineage. Their antigenic genotypes predicted no coverage by either Bexsero®or Trumenba®, and nucleotide variation analysis revealed diverse new, unassigned alleles at multiple virulence loci of all strains. Groups of singleton and unique novel sequence types extending beyond individual camps were found from epidemiological data of 25 other isolates. Our results add to the sparse published molecular data of N. meningitidis in the military units in Vietnam, highlight their diversity, distinct genetic features and antibiotic resistance pattern, and emphasize the need for further studies on the molecular characteristics of N. meningitidis in Vietnam. creator: Trang Thu Le creator: Thach Xuan Tran creator: Long Phi Trieu creator: Christopher M. Austin creator: Huong Minh Nguyen creator: Dong Van Quyen uri: https://doi.org/10.7717/peerj.9502 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Le et al. title: Habitat preferences rather than morphological traits affect the recovery process of Collembola (Arthropoda, Hexapoda) on a bare saline–alkaline land link: https://peerj.com/articles/9519 last-modified: 2020-07-21 description: The Songnen Plain of China was once an important grassland used for sheep grazing, but it has largely been degraded to bare saline-alkaline land (BSAL). BSAL consists of plant-free areas characterized by high soil pH values (up to 10) and salt and alkali (e.g., Na+ and Ca2+) contents, as well as low soil organic matter and water contents; thus, very few soil faunal species can survive on BSAL. The recovery of degraded ecosystems provides a great opportunity to investigate the reconstruction of belowground soil faunal communities. Collembola are a class of widespread and abundant soil fauna that can colonize this harsh environment. Habitat changes on BSAL promote aboveground revegetation, which greatly facilitates the recovery of Collembola. A soil transfer experiment on the BSAL of the Songnen Plain was conducted to study the effects of habitat and Collembola morphological traits on the recovery process of Collembola. Defaunated and with-fauna soil blocks were transferred among three habitats: BSAL, reclaimed arable land, and naturally revegetated grassland. The recovered Collembola in the transferred soil blocks were compared two, seven, and 12 weeks after the start of the experiment. The results showed that (1) the majority of the Collembola, regardless of their morphological traits, recovered in the defaunated soil blocks within 2 weeks; (2) generalists and habitat-preferring species recovered faster than specialists; (3) the average total abundance, species richness, and community composition of Collembola recovered to the natural levels in 2 weeks; and (4) 12 weeks after replacement, the highest average total abundance and species richness of Collembola were found in the arable land. Our results indicate that the majority of Collembola in this study, regardless of their dispersal type, which is related to their morphological traits, are fast dispersers, and their recovery speeds are mainly affected by habitat preferences. We suggest that the reclamation of BSAL to arable land rather than its natural recovery to grassland aids in the recovery of Collembola in degraded grassland systems. creator: Zhen Ni creator: Xiumin Yan creator: Liang Chang creator: Xin Sun creator: Donghui Wu creator: Bing Zhang uri: https://doi.org/10.7717/peerj.9519 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Ni et al.