title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1278 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Undesirable immigrants: hobbyist vivaria as a potential source of alien invertebrate species link: https://peerj.com/articles/7617 last-modified: 2019-09-17 description: BackgroundSmall size and large diversity of adaptations make invertebrates a group of animals which can be easily transported by different human activities. Many species can travel as “hitchhikers” with plant material (both on plant surfaces and in the soil), including plants used for decoration in vivaria. Vivaria are often tropical in nature environments, with high temperatures and humidity, suitable for invertebrates from tropical regions. Although many of such invertebrates cannot survive in temperate regions where harsh weather conditions are present, it is also known that some can successfully acclimatise. As a result, their negative impact on local flora and fauna cannot be excluded.Material and methodsTerrestrial invertebrates were collected in several cities of Poland from tropical vivaria where poison dart frogs (Dendrobatidae) and/or orchids (Orchidaceae) were kept by hobbyists. Collecting of the material was preceded by a simple questionnaire placed on the biggest Polish forum devoted to poison dart frogs. Moreover, we contacted some Polish wholesalers offering tropical invertebrates (Isopoda and Collembola), used as the food source for frogs, hoping to receive information about locations where those invertebrates were delivered, over the period of one year. We obtained mtDNA barcodes using the COI marker (cytochrome c oxidase subunit I gene) for seven potential morphospecies.ResultsIn total, 12 taxa classified as Turbellaria, Annelida, Gastropoda, Isopoda, Diplopoda, Chilopoda and Collembola were collected and preserved in pure ethanol. We collected material and/or information from 65 locations, including 56 cities to which exotic isopods and springtails were sold by wholesalers over the period of nine months (average number per month = 18 cities). We obtained 18 COI sequences which were assigned to seven BINs and thus confirmed identification of seven species. The results indicate that the number of species transported with exotic plants is not small and can be observed regularly. Species noted as “hitchhikers” on plant structures and/or as inhabitants of soil in plant pots, originally came from South and Central America, Africa, Asia and possibly from North America or Southern Europe. Three taxa were noted for the first time from Poland, including Rhynchodemus sylvaticus (Rhynchodemidae), Trichorhina sp.1 (Platharthridae), and Guppya gundlachi (Euconulidae).DiscussionThe presented study clearly shows that an exotic hobby such as keeping tropical poison dart frogs and/or orchids may promote fast and uncontrolled dispersion of a high number of invertebrates classified in different taxonomical groups. Plant material (green elements of plants and the soil in which they are planted) used in vivaria can be an important source of such animals. creator: Radomir Jaskuła creator: Anna Sulikowska-Drozd creator: Aleksandra Jabłońska creator: Krzysztof Banaś creator: Tomasz Rewicz uri: https://doi.org/10.7717/peerj.7617 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Jaskuła et al. title: From habitat use to social behavior: natural history of a voiceless poison frog, Dendrobates tinctorius link: https://peerj.com/articles/7648 last-modified: 2019-09-17 description: Descriptive studies of natural history have always been a source of knowledge on which experimental work and scientific progress rely. Poison frogs are a well-studied group of small Neotropical frogs with diverse parental behaviors, distinct calls, and bright colors that warn predators about their toxicity; and a showcase of advances in fundamental biology through natural history observations. The dyeing poison frog, Dendrobates tinctorius, is emblematic of the Guianas region, widespread in the pet trade, and increasingly popular in research. This species shows several unusual behaviors, such as the lack of advertisement calls and the aggregation around tree-fall gaps, which remain poorly described and understood. Here, we summarize our observations from a natural population of D. tinctorius in French Guiana collected over various field trips between 2009 and 2017; our aim is to provide groundwork for future fundamental and applied research spanning parental care, animal dispersal, disease spread, habitat use in relation to color patterns, and intra-specific communication, to name a few. We report sex differences in habitat use and the striking invasion of tree-fall gaps; describe their courtship and aggressive behaviors; document egg development and tadpole transport; and discuss how the knowledge generated by this study could set the grounds for further research on the behavior, ecology, and conservation of this species. creator: Bibiana Rojas creator: Andrius Pašukonis uri: https://doi.org/10.7717/peerj.7648 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Rojas and Pašukonis title: Collisional mechanics of the diagonal gaits of horses over a range of speeds link: https://peerj.com/articles/7689 last-modified: 2019-09-17 description: One of the goals of the neuromotor control system is to minimize the cost of locomotion by reducing mechanical energy losses. Collisional mechanics, which studies the redirection of the downwards motion of the center of mass (COM) by ground reaction forces (GRF) generated by the limbs, represents an important source of energy loss. The primary objective of this study was to compare collisional mechanics and the associated mechanical energy losses in horses performing diagonally-synchronized gaits over a range of speeds. It is to be expected that collisional energy losses will be high when the COM velocity vector is closely aligned with the GRF vector. This condition is achieved in piaffe, an artificial gait performed in dressage competitions that has a diagonal limb coordination pattern similar to trot but performed with little or no forward velocity. Therefore, we hypothesized that collisional energy losses would be higher in piaffe than in trot. Synchronized kinematic and GRF data were collected from three highly-trained horses performing piaffe, passage and trot at a range of speeds. Derived variables were vertical excursion and velocity of the trunk COM, fore and hind limb compression expressed as percentage reduction of standing limb lengths, range of limb pro-retraction, GRF vector magnitude and vector angle, collision angle (Φ), and mechanical cost of motion (CoMotmech). Linear regression was used to investigate the relationship between CoMotmech and speed for each gait. Partial correlation was used to seek relationships between COM excursion and limb mechanics for each gait. Piaffe, passage and trot were clearly separated on the basis of speed. In all gaits the trunk was high at contact and lift off and descended to its lowest point in midstance following the pattern typical of spring mass mechanics. Mechanical cost was significantly (p < .05) and inversely related to speed in trot and piaffe with the value increasing steeply as speed approached zero due to a near vertical orientation of both the COM velocity vector and the GRF vector. Limb compression during stance was significantly (p < .05) linked to trunk COM vertical excursion in all gaits, with a stronger relationship in the forelimb. Hindlimb compression was, however, large in piaffe where the force magnitudes are notably smaller. The study illustrates the potential value of studying artificial gaits to provide data encompassing the entire range of locomotor capabilities. The results supported the experimental hypothesis by showing a threefold increase in collisional energy losses in piaffe compared with trot. In all gaits, dissociation between diagonal limb contacts and lift offs was thought to be an important strategy in reducing in collisional losses. Piaffe, the most costly gait, has similar characteristics to hopping on the spot. It appears that greater hindlimb compliance and a lower step frequency are important energy conservation strategies for piaffe. creator: Sarah Jane Hobbs creator: Hilary M. Clayton uri: https://doi.org/10.7717/peerj.7689 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Hobbs and Clayton title: The co-expression networks of differentially expressed RBPs with TFs and LncRNAs related to clinical TNM stages of cancers link: https://peerj.com/articles/7696 last-modified: 2019-09-17 description: BackgroundRNA-binding proteins (RBPs) play important roles in cellular homeostasis by regulating the expression of thousands of transcripts, which have been reported to be involved in human tumorigenesis. Despite previous reports of the dysregulation of RBPs in cancers, the degree of dysregulation of RBPs in cancers and the intrinsic relevance between dysregulated RBPs and clinical TNM information remains unknown. Furthermore, the co-expressed networks of dysregulated RBPs with transcriptional factors and lncRNAs also require further investigation.ResultsHere, we firstly analyzed the deviations of expression levels of 1,542 RBPs from 20 cancer types and found that (1) RBPs are dysregulated in almost all 20 cancer types, especially in BLCA, COAD, READ, STAD, LUAD, LUSC and GBM with proportion of deviation larger than 300% compared with non-RBPs in normal tissues. (2) Up- and down-regulated RBPs also show opposed patterns of differential expression in cancers and normal tissues. In addition, down-regulated RBPs show a greater degree of dysregulated expression than up-regulated RBPs do. Secondly, we analyzed the intrinsic relevance between dysregulated RBPs and clinical TNM information and found that (3) Clinical TNM information for two cancer types—CHOL and KICH—is shown to be closely related to patterns of differentially expressed RBPs (DE RBPs) by co-expression cluster analysis. Thirdly, we identified ten key RBPs (seven down-regulated and three up-regulated) in CHOL and seven key RBPs (five down-regulated and two up-regulated) in KICH by analyzing co-expression correlation networks. Fourthly, we constructed the co-expression networks of key RBPs between 1,570 TFs and 4,147 lncRNAs for CHOL and KICH, respectively.ConclusionsThese results may provide an insight into the understanding of the functions of RBPs in human carcinogenesis. Furthermore, key RBPs and the co-expressed networks offer useful information for potential prognostic biomarkers and therapeutic targets for patients with cancers at the N and M stages in two cancer types CHOL and KICH. creator: Shuaibin Lian creator: Liansheng Li creator: Yongjie Zhou creator: Zixiao Liu creator: Lei Wang uri: https://doi.org/10.7717/peerj.7696 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Lian et al. title: Characteristics and prognosis of pelvic Ewing sarcoma: a SEER population-based study link: https://peerj.com/articles/7710 last-modified: 2019-09-17 description: BackgroundThe pelvis is one of the primary sites of Ewing sarcoma (ES) and is associated with poorer prognoses than the extremities. Due to the rarity of this disease and limited data available, the prognostic factors of pelvic ES remain controversial. Thus, this study aimed to identify independent prognostic factors, and develop a nomogram for predicting survival rates in patients with pelvic ES.MethodsUsing data provided by the Surveillance, Epidemiology, and End Results (SEER) database, variables including age, sex, race, tumor size, tumor stage, surgery, and radiotherapy were analyzed using the Kaplan–Meier method and Cox proportional hazards regression. Based on the results of multivariate analyses, a nomogram was built to predict the overall survival (OS) of patients with pelvic ES. The performance of the nomogram was evaluated by the concordance index (C-index).ResultsA total of 267 cases diagnosed between 2004 and 2016 were included in the study. Univariate and multivariate analyses showed that patients who were younger, white, had a localized tumor stage, or underwent surgery were associated with improved prognoses, while no significant differences were observed in OS based on sex, tumor size, or radiotherapy. A nomogram was developed and the C-index was 0.728, indicating adequate performance for survival prediction.ConclusionsAge, race, tumor stage, and surgery were identified as independent prognostic factors for the OS of pelvic ES. The nomogram developed in this study can individually predict 3- and 5-year OS in patients with pelvic ES. creator: Li Chen creator: Cheng Long creator: Jiaxin Liu creator: Fei Xing creator: Xin Duan uri: https://doi.org/10.7717/peerj.7710 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Chen et al. title: MYB transcription factors in alfalfa (Medicago sativa): genome-wide identification and expression analysis under abiotic stresses link: https://peerj.com/articles/7714 last-modified: 2019-09-17 description: BackgroundAlfalfa is the most widely cultivated forage legume and one of the most economically valuable crops in the world. Its survival and production are often hampered by environmental changes. However, there are few studies on stress-resistance genes in alfalfa because of its incomplete genomic information and rare expression profile data. The MYB proteins are characterized by a highly conserved DNA-binding domain, which is large, functionally diverse, and represented in all eukaryotes. The role of MYB proteins in plant development is essential; they function in diverse biological processes, including stress and defense responses, and seed and floral development. Studies on the MYB gene family have been reported in several species, but they have not been comprehensively analyzed in alfalfa.MethodsTo identify more comprehensive MYB transcription factor family genes, the sequences of 168 Arabidopsis thaliana, 430 Glycine max, 185 Medicago truncatula, and 130 Oryza sativa MYB proteins were downloaded from the Plant Transcription Factor Database. These sequences were used as queries in a BLAST search against the M. sativa proteome sequences provided by the Noble Research Institute.ResultsIn the present study, a total of 265 MsMYB proteins were obtained, including 50 R1-MYB, 186 R2R3-MYB, 26 R1R2R3-MYB, and three atypical-MYB proteins. These predicted MsMYB proteins were divided into 12 subgroups by phylogenetic analysis, and gene ontology (GO) analysis indicated that most of the MsMYB genes are involved in various biological processes. The expression profiles and quantitative real-time PCR analysis indicated that some MsMYB genes might play a crucial role in the response to abiotic stresses. Additionally, a total of 170 and 914 predicted protein–protein and protein-DNA interactions were obtained, respectively. The interactions between MsMYB043 and MSAD320162, MsMYB253 and MSAD320162, and MsMYB253 and MSAD308489 were confirmed by a yeast two-hybrid system. This work provides information on the MYB family in alfalfa that was previously lacking and might promote the cultivation of stress-resistant alfalfa. creator: Qiang Zhou creator: Chenglin Jia creator: Wenxue Ma creator: Yue Cui creator: Xiaoyu Jin creator: Dong Luo creator: Xueyang Min creator: Zhipeng Liu uri: https://doi.org/10.7717/peerj.7714 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Zhou et al. title: Ecological networks reveal contrasting patterns of bacterial and fungal communities in glacier-fed streams in Central Asia link: https://peerj.com/articles/7715 last-modified: 2019-09-17 description: Bacterial and fungal communities in biofilms are important components in driving biogeochemical processes in stream ecosystems. Previous studies have well documented the patterns of bacterial alpha diversity in stream biofilms in glacier-fed streams, where, however, beta diversity of the microbial communities has received much less attention especially considering both bacterial and fungal communities. A focus on beta diversity can provide insights into the mechanisms driving community changes associated to large environmental fluctuations and disturbances, such as in glacier-fed streams. Moreover, modularity of co-occurrence networks can reveal more ecological and evolutionary properties of microbial communities beyond taxonomic groups. Here, integrating beta diversity and co-occurrence approach, we explored the network topology and modularity of the bacterial and fungal communities with consideration of environmental variation in glacier-fed streams in Central Asia. Combining results from hydrological modeling and normalized difference of vegetation index, this study highlighted that hydrological variables and vegetation status are major variables determining the environmental heterogeneity of glacier-fed streams. Bacterial communities formed a more complex and connected network, while the fungal communities formed a more clustered network. Moreover, the strong interrelations among the taxonomic dissimilarities of bacterial community (BC) and modules suggest they had common processes in driving diversity and taxonomic compositions across the heterogeneous environment. In contrast, fungal community (FC) and modules generally showed distinct driving processes to each other. Moreover, bacterial and fungal communities also had different driving processes. Furthermore, the variation of BC and modules were strongly correlated with hydrological properties and vegetation status but not with nutrients, while FC and modules (except one module) were not associated with environmental variation. Our results suggest that bacterial and fungal communities had distinct mechanisms in structuring microbial networks, and environmental variation had strong influences on bacterial communities but not on fungal communities. The fungal communities have unique assembly mechanisms and physiological properties which might lead to their insensitive responses to environmental variations compared to bacterial communities. Overall, beyond alpha diversity in previous studies, these results add our knowledge that bacterial and fungal communities have contrasting assembly mechanisms and respond differently to environmental variation in glacier-fed streams. creator: Ze Ren creator: Hongkai Gao uri: https://doi.org/10.7717/peerj.7715 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Ren and Gao title: Urine proteome changes in rats subcutaneously inoculated with approximately ten tumor cells link: https://peerj.com/articles/7717 last-modified: 2019-09-17 description: BackgroundBiomarkers are changes associated with the disease. Urine is not subject to homeostatic control and therefore accumulates very early changes, making it an ideal biomarker source. Usually, we have performed urinary biomarker studies involving at least thousands of tumor cells. However, no tumor starts from a thousand tumor cells. We therefore examined urine proteome changes in rats subcutaneously inoculated with approximately ten tumor cells.MethodsHere, we serially diluted Walker-256 carcinosarcoma cells to a concentration of 102/mL and subcutaneously inoculated 0.1 mL of these cells into nine rats. The urine proteomes on days 0, 13 and 21 were analyzed by liquid chromatography coupled with tandem mass spectrometry.ResultsHierarchical clustering analysis showed that the urine proteome of each sample at three time points were clustered into three clusters, indicating the good consistency of these nine rats when inoculated with the same limited tumor cells. Differential proteins on days 13 and 21 were mainly associated with cell adhesion, autophagic cell death, changes in extracellular matrix organization, angiogenesis, and the pentose phosphate pathway. All of these enriched functional processes were reported to contribute to tumor progression and could not be enriched through random allocation analysis.ConclusionsOur results indicated that (1) the urine proteome reflects changes associated with cancer even with only approximately ten tumor cells in the body and that (2) the urine proteome reflects pathophysiological changes in the body with extremely high sensitivity and provides potential for a very early screening process of clinical patients. creator: Jing Wei creator: Wenshu Meng creator: Youhe Gao uri: https://doi.org/10.7717/peerj.7717 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Wei et al. title: Effects of shokyo (Zingiberis Rhizoma) and kankyo (Zingiberis Processum Rhizoma) on prostaglandin E2 production in lipopolysaccharide-treated mouse macrophage RAW264.7 cells link: https://peerj.com/articles/7725 last-modified: 2019-09-17 description: We previously reported that shokyo and kankyo, which are water-extracted fractions of ginger, reduced LPS-induced PGE2 production in human gingival fibroblasts. In this study, we examined the effects of these herbs on LPS-treated mouse macrophage RAW264.7 cells. Both shokyo and kankyo reduced LPS-induced PGE2 production in a concentration-dependent manner. Shokyo and kankyo did not inhibit cyclooxygenase (COX) activity, nor did they alter the expression of molecules in the arachidonic acid cascade. In addition, these herbs did not alter NF-κB p65 translocation into nucleus, or phosphorylation of p65 or ERK. These results suggest that shokyo and kankyo inhibit cPLA2 activity. Although 6-shogaol produced similar results to those of shokyo and kankyo, the concentration of 6-shogaol required for the reduction of PGE2 production were higher than those of 6-shogaol in shokyo and kankyo. Therefore, several gingerols and shogaols other than 6-shogaol may play a role in the reduction of LPS-induced PGE2 production. Thus, 6-shogaol, and other gingerols and shogaols inhibit cPLA2 activity and reduce LPS-induced PGE2 production via a different mechanism from traditional anti-inflammatory drugs. Moreover, kampo medicines that contain shokyo or kankyo are considered to be effective for inflammatory diseases. creator: Toshiaki Ara creator: Masanori Koide creator: Hiroyuki Kitamura creator: Norio Sogawa uri: https://doi.org/10.7717/peerj.7725 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Ara et al. title: Identification of lncRNAs associated with lung squamous cell carcinoma prognosis in the competitive endogenous RNA network link: https://peerj.com/articles/7727 last-modified: 2019-09-17 description: BackgroundLong noncoding RNAs (lncRNAs) play a role in the formation, development, and prognosis of various cancers. Our study aimed to identify prognostic-related lncRNAs in lung squamous cell carcinoma (LUSC), which may provide new perspectives for individualized treatment of patients.Materials and MethodsThe RNA sequencing (lncRNA, microRNA (miRNA), mRNA) data and clinical information related to LUSC were obtained from The Cancer Genome Atlas (TCGA) database. Differentially expressed RNA sequences were used to construct the competitive endogenous RNA (ceRNA) network. In present study, we mainly used two prognostic verification methods, Cox analysis and survival analysis, to identify the prognostic relevance of specific lncRNAs and construct prognostic model of lncRNA.ResultsDatasets on 551 samples of lncRNA and mRNA and 523 miRNA samples were retrieved from the TCGA database. Analysis of the normal and LUSC samples identified 170 DElncRNAs, 331 DEmiRNAs, and 417 DEmRNAs differentially expressed RNAs. The ceRNA network contained 27 lncRNAs, 43 miRNAs, and 11 mRNAs. Furthermore, we identified seven specific lncRNAs (ERVH48-1, HCG9, SEC62-AS1, AC022148.1, LINC00460, C5orf17, LINC00261) as potential prognostic factors after correlation analysis, and five of the seven lncRNAs (AC022148.1, HCG9, LINC00460, C5orf17, LINC00261) constructed a prognostic model of LUSC.ConclusionIn present study, we identified seven lncRNAs in the ceRNA network that are associated with potential prognosis in LUSC patients, and constructed a prognostic model of LUSC which can be used to assess the prognosis risk of clinical patients. Further biological experiments are needed to elucidate the specific molecular mechanisms underlying them. creator: Lingyu Qi creator: Tingting Zhang creator: Yan Yao creator: Jing Zhuang creator: Cun Liu creator: Ruijuan Liu creator: Changgang Sun uri: https://doi.org/10.7717/peerj.7727 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2019 Qi et al.