title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1406 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Recognizing two new Hippolyte species (Decapoda, Caridea, Hippolytidae) from the South China Sea based on integrative taxonomy link: https://peerj.com/articles/6605 last-modified: 2019-03-14 description: Hippolyte shrimps exhibit abundant biological diversity and display great ecological significance in seaweed bed ecosystems. Dozens of Hippolyte specimens were collected from Hainan Island and the Xisha Islands in the South China Sea. Detailed examination indicates that some of these specimens represent new Hippolyte species. Based on morphological, genetic, and ecological data, Hippolyte chacei sp. nov. and H. nanhaiensis sp. nov. are described. H. chacei sp. nov. was collected from the Sargassum sp. biotope in Hainan Island and is distinguished from congeners by its unique mandible and the dactylus of the third to fifth pereiopods; this species has a basal position in the Indo-West Pacific species clade in the phylogenetic tree which is reconstructed based on 16S rRNA gene. H. nanhaiensis sp. nov. was collected from the biotopes of Galaxaura sp. or Halimeda sp. in the Xisha Islands, and it differs from congeners in a series of characters associated with rostrum, scaphocerite, antennular peduncle, and spines on the dactylus of the third to fifth pereiopods. Additionally, it is sister to H. australiensis in the phylogenetic tree. A key to identifying mature female Hippolyte species of the Indo-West Pacific and neighboring seas is provided. creator: Zhi-Bin Gan creator: Xin-Zheng Li uri: https://doi.org/10.7717/peerj.6605 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Gan and Li title: HOXC6 promotes migration, invasion and proliferation of esophageal squamous cell carcinoma cells via modulating expression of genes involved in malignant phenotypes link: https://peerj.com/articles/6607 last-modified: 2019-03-14 description: BackgroundHOXC6 is a member of the HOX gene family. The elevated expression of this gene occurs in prostate and breast cancers. However, the role of HOXC6 in esophageal squamous cell carcinoma (ESCC) remains largely uninvestigated.MethodsThe expression of HOXC6 was examined by immunohistochemistry, quantitative real-time PCR and immunoblotting assays. The lentivirus-mediated expression of HOXC6 was verified at mRNA and protein levels. Wound healing and Matrigel assays were performed to assess the effect of HOXC6 on the migration and invasion of cancer cells. The growth curving, CCK8, and colony formation assays were utilized to access the proliferation capacities. RNA-seq was performed to evaluate the downstream targets of HOXC6. Bioinformatic tool was used to analyze the gene expression.ResultsHOXC6 was highly expressed in ESCC tissues. HOXC6 overexpression promoted the migration, invasion, and proliferation of both Eca109 and TE10 cells. There were 2,155 up-regulated and 759 down-regulated genes in Eca109-HOXC6 cells and 95 up-regulated and 47 down-regulated genes in TE10-HOXC6 cells compared with the results of control. Interestingly, there were only 20 common genes, including 17 up-regulated and three down-regulated genes with similar changes upon HOXC6 transfection in both cell lines. HOXC6 activated several crucial genes implicated in the malignant phenotype of cancer cells.DiscussionHOXC6 is highly expressed in ESCC and promotes malignant phenotype of ESCC cells. HOXC6 can be used as a new therapeutic target of ESCC. creator: Li Tang creator: Yong Cao creator: Xueqin Song creator: Xiaoyan Wang creator: Yan Li creator: Minglan Yu creator: Mingying Li creator: Xu Liu creator: Fang Huang creator: Feng Chen creator: Haisu Wan uri: https://doi.org/10.7717/peerj.6607 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Tang et al. title: Fatty liver is a risk factor for liver metastasis in Chinese patients with non-small cell lung cancer link: https://peerj.com/articles/6612 last-modified: 2019-03-14 description: BackgroundThe hepatic microenvironment, which may include chronic inflammation and fibrosis, is considered to contribute to the development of liver metastases. Hepatic steatosis (HS) might cause liver inflammation and fibrosis. However, to date, no studies have investigated the impact of HS on liver metastasis in patients with non-small cell lung cancer (NSCLC).MethodsA retrospective cohort study was performed on patients who received NSCLC treatment at two hospitals affiliated with the Southern Medical University from January 2005 to December 2015. The patients were grouped according to the presence of HS. The clinicopathological features of patients between the two groups were compared. The effect of HS on liver metastasis and overall metastasis was evaluated, adjusting for other confounders using Cox regression analyses.ResultsIn total, 1,873 patients with NSCLC with no distant metastases were included in this study, and 408 (21.8%) patients were diagnosed with HS (at the time of diagnosis or before diagnosis). Liver metastases occurred in 166 (8.9%) patients. Liver metastasis-free survival was significantly worse in the study (HS) group (hazard ratio (HR) 1.42; (95% CI [1.03–1.96]); P = 0.031). Multivariate regression analysis demonstrated that HS was an independent risk factor for liver metastasis (HR 1.43; 95% CI [1.02–2.01]; P = 0.039). However, HS was not associated with overall metastasis of NSCLC (HR 0.99; 95% CI [0.84–1.17]; P = 0.895).ConclusionHepatic steatosis was an independent predictor of liver metastasis from in patients with NSCLC. creator: Wenyu Wu creator: Haiyan Liao creator: Weilin Ye creator: Xi Li creator: Jian Zhang creator: Junguo Bu uri: https://doi.org/10.7717/peerj.6612 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Wu et al. title: Effects of habitat fragmentation and human disturbance on the population dynamics of the Yunnan snub-nosed monkey from 1994 to 2016 link: https://peerj.com/articles/6633 last-modified: 2019-03-14 description: In this study, we integrate data from field investigations, spatial analysis, genetic analysis, and Generalized Linear Models (GLMs) to evaluate the effects of habitat fragmentation on the population dynamics, genetic diversity, and range shifts in the endangered Yunnan snub-nosed monkey (Rhinopithecus bieti). The results indicate that from 1994 to 2016, R. bieti population size increased from less than 2,000 to approximately 3,000 individuals. A primary factor promoting population recovery was the establishment of protected nature reserves. We also found that subpopulation growth rates were uneven, with the groups in some areas, and the formation of new groups. Both the fragmentation index, defined as the ratio of the number of forest patches to the total area of forest patches (e.g., increased fragmentation), and increasing human population size had a negative effect on population growth in R. bieti. We recommend that government conservation plans prioritize the protection of particular R. bieti populations, such as the Baimei and Jisichang populations, which have uncommon haplotypes. In addition, effective conservation strategies need to include an expansion of migration corridors to enable individuals from larger populations such as Guyoulong (Guilong) to serve as a source population to increase the genetic diversity of smaller R. bieti subpopulations. We argue that policies designed to protect endangered primates should not focus solely on total population size but also need to determine the amount of genetic diversity present across different subpopulations and use this information as a measure of the effectiveness of current conservation policies and the basis for new conservation policies. creator: Xumao Zhao creator: Baoping Ren creator: Dayong Li creator: Zuofu Xiang creator: Paul A. Garber creator: Ming Li uri: https://doi.org/10.7717/peerj.6633 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Zhao et al. title: The choice of tree prior and molecular clock does not substantially affect phylogenetic inferences of diversification rates link: https://peerj.com/articles/6334 last-modified: 2019-03-13 description: Comparative methods allow researchers to make inferences about evolutionary processes and patterns from phylogenetic trees. In Bayesian phylogenetics, estimating a phylogeny requires specifying priors on parameters characterizing the branching process and rates of substitution among lineages, in addition to others. Accordingly, characterizing the effect of prior selection on phylogenies is an active area of research. The choice of priors may systematically bias phylogenetic reconstruction and, subsequently, affect conclusions drawn from the resulting phylogeny. Here, we focus on the impact of priors in Bayesian phylogenetic inference and evaluate how they affect the estimation of parameters in macroevolutionary models of lineage diversification. Specifically, we simulate trees under combinations of tree priors and molecular clocks, simulate sequence data, estimate trees, and estimate diversification parameters (e.g., speciation and extinction rates) from these trees. When substitution rate heterogeneity is large, diversification rate estimates deviate substantially from those estimated under the simulation conditions when not captured by an appropriate choice of relaxed molecular clock. However, in general, we find that the choice of tree prior and molecular clock has relatively little impact on the estimation of diversification rates insofar as the sequence data are sufficiently informative and substitution rate heterogeneity among lineages is low-to-moderate. creator: Brice A.J. Sarver creator: Matthew W. Pennell creator: Joseph W. Brown creator: Sara Keeble creator: Kayla M. Hardwick creator: Jack Sullivan creator: Luke J. Harmon uri: https://doi.org/10.7717/peerj.6334 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Sarver et al. title: Adaptation of metal and antibiotic resistant traits in novel β-Proteobacterium Achromobacter xylosoxidans BHW-15 link: https://peerj.com/articles/6537 last-modified: 2019-03-13 description: Chromosomal co-existence of metal and antibiotic resistance genes in bacteria offers a new perspective to the bacterial resistance proliferation in contaminated environment. In this study, an arsenotrophic bacterium Achromobacter xylosoxidans BHW-15, isolated from Arsenic (As) contaminated tubewell water in the Bogra district of Bangladesh, was analyzed using high throughput Ion Torrent Personal Genome Machine (PGM) complete genome sequencing scheme to reveal its adaptive potentiality. The assembled draft genome of A. xylosoxidans BHW-15 was 6.3 Mbp containing 5,782 functional genes, 1,845 pseudo genes, and three incomplete phage signature regions. Comparative genome study suggested the bacterium to be a novel strain of A. xylosoxidans showing significant dissimilarity with other relevant strains in metal resistance gene islands. A total of 35 metal resistance genes along with arsenite-oxidizing aioSXBA, arsenate reducing arsRCDAB, and mercury resistance merRTPADE operonic gene cluster and 20 broad range antibiotic resistance genes including β-lactams, aminoglycosides, and multiple multidrug resistance (MDR) efflux gene complex with a tripartite system OM-IM-MFP were found co-existed within the genome. Genomic synteny analysis with reported arsenotrophic bacteria revealed the characteristic genetic organization of ars and mer operonic genes, rarely described in β-Proteobacteria. A transposon Tn21 and mobile element protein genes were also detected to the end of mer (mercury) operonic genes, possibly a carrier for the gene transposition. In vitro antibiotic susceptibility assay showed a broad range of resistance against antibiotics belonging to β-lactams, aminoglycosides, cephalosporins (1st, 2nd, and 3rd generations), monobactams and even macrolides, some of the resistome determinants were predicted during in silico analysis. KEGG functional orthology analysis revealed the potential of the bacterium to utilize multiple carbon sources including one carbon pool by folate, innate defense mechanism against multiple stress conditions, motility, a proper developed cell signaling and processing unit and secondary metabolism-combination of all exhibiting a robust feature of the cell in multiple stressed conditions. The complete genome of the strain BHW-15 stands as a genetic basis for the evolutionary adaptation of metal and the antibiotic coexistence phenomenon in an aquatic environment. creator: Arif Istiaq creator: Md. Sadikur Rahman Shuvo creator: Khondaker Md. Jaminur Rahman creator: Mohammad Anwar Siddique creator: M. Anwar Hossain creator: Munawar Sultana uri: https://doi.org/10.7717/peerj.6537 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Istiaq et al. title: Identification of Austwickia chelonae as cause of cutaneous granuloma in endangered crocodile lizards using metataxonomics link: https://peerj.com/articles/6574 last-modified: 2019-03-13 description: The crocodile lizard (Shinisaurus crocodilurus Ahl, 1930) is an endangered reptile species, and in recent years many have died from diseases, especially the rescued and breeding individuals. However, pathogens underlying these diseases are unclear. In this study, we report our effort in rapidly identifying and isolating the pathogen that causes high mortality in crocodile lizards from Guangdong Luokeng Shinisaurus crocodilurus National Nature Reserve. The typical symptom is cutaneous granuloma in the infected crocodile lizards. Metagenomic next-generation sequencing (mNGS) is a comprehensive approach for sequence-based identification of pathogenic microbes. In this study, 16S rDNA based mNGS was used for rapid identification of pathogens, and microscopy and microbe isolation were used to confirm the results. Austwickia chelonae was identified to be the dominant pathogen in the granuloma using 16S rDNA based mNGS. Chinese skinks were used as an animal model to verify the pathogenicity of A. chelonae to fulfill Koch’s postulates. As expected, subcutaneous inoculation of A. chelonae induced granulomas in the healthy Chinese skinks and the A. chelonae was re-isolated from the induced granulomas. Therefore, A. chelonae was the primary pathogen that caused this high mortality disease, cutaneous granuloma, in crocodile lizards from Guangdong Luokeng Shinisaurus crocodilurus National Nature Reserve. Antibiotics analysis demonstrated that A. chelonae was sensitive to cephalothin, minocycline and ampicillin, but not to kanamycin, gentamicin, streptomycin and clarithromycin, suggesting a possible treatment for the infected crocodile lizards. However, surgical resection of the nodules as early as possible was recommended. This study is the first report of pathogenic analysis in crocodile lizards and provides a reference for disease control and conservations of the endangered crocodile lizards and other reptiles. In addition, this study indicated that mNGS of lesions could be used to detect the pathogens in animals with benefits in speed and convenient. creator: Haiying Jiang creator: Xiujuan Zhang creator: Linmiao Li creator: Jinge Ma creator: Nan He creator: Haiyang Liu creator: Richou Han creator: Huiming Li creator: Zhengjun Wu creator: Jinping Chen uri: https://doi.org/10.7717/peerj.6574 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Jiang et al. title: Geochemical characteristics of dissolved heavy metals in Zhujiang River, Southwest China: spatial-temporal distribution, source, export flux estimation, and a water quality assessment link: https://peerj.com/articles/6578 last-modified: 2019-03-13 description: To investigate the sources and spatial-temporal distribution of dissolved heavy metals in river water, and to evaluate the water quality, a total of 162 water samples were collected from 81 key sampling points in high and low flow seasons separately in the Zhujiang River, Southwest China. Ten dissolved heavy metals (V, Cr, Mn, Co, Ni, Cu, Mo, Cd, Ba, and Pb) in the Zhujiang River water exhibit little variation at temporal scale, but vary with a significant spatial heterogeneity. Furthermore, different metals present different variation trends along the main channel of the Zhujiang River. Our results suggest that Ba (14.72 μg L−1 in low flow season and 12.50 μg L−1 in high flow season) and Cr (6.85 μg L−1 in low flow season and 7.52 μg L−1 in high flow season) are consistently the most abundant metals in the two sampling periods. According to the water quality index (WQI values ranged from 1.3 to 43.9) and health risk assessment, metals investigated in Zhujiang River are below the hazard level (all hazard index (HI) < 1). Application of statistical approaches, including correlation matrix and principal component analysis (PCA), identify three principal components that account for 61.74% of the total variance, the results conclude that the anthropogenic heavy metals (V, Cr, Ni, and Cu) are greatly impacted by the dilution effect, and the heavy metals in Zhujiang River are mainly presented a natural sources signature from the perspective of entire basin. Moreover, our results reveal that the estimated export budget of several heavy metals including V (735.6 t year−1), Cr (1,561.1 t year−1), Ni (498.2 t year−1), and Mo (118.9 t year−1) to the ocean are higher than the world average. creator: Jie Zeng creator: Guilin Han creator: Qixin Wu creator: Yang Tang uri: https://doi.org/10.7717/peerj.6578 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Zeng et al. title: Just a small bunch of flowers: the botanical knowledge of students and the positive effects of courses in plant identification at German universities link: https://peerj.com/articles/6581 last-modified: 2019-03-13 description: BackgroundIn the light of the ongoing loss of species the knowledge about and the ability to identify species becomes increasingly important for effective monitoring and conservation measures. Learning about identifying biodiversity is a central task for future biologists and biology teachers and universities play an important role in educating future experts and multipliers. It builds one basis for conservation literacy.MethodsWe analyzed undergraduate students’ prior knowledge on plant species, identification and their knowledge gain from introductory plant identification courses at eight German universities. Using the Visual Classification Method—a combination of a presentation and standardized questionnaires—we evaluated the learning success of more than 500 students regarding (a) ‘declarative species knowledge’ of plant species names and (b) ‘taxonomic concept knowledge’, which is seen as knowledge on a higher level of complexity. From comparison of paired pre- and post-tests we calculated the individual knowledge gain. Using Linear Mixed Effects Models (LMMs) we analyzed effects of knowledge levels, learner-specific resources and learning environment on the knowledge gain.ResultsWe found that university course instructors have to start teaching at an almost zero level with respect to undergraduates’ prior knowledge: on average 2.6 of 32 common plant species were known. Overall, the introductory courses resulted in a significant but weak knowledge gain. We detected a higher knowledge gain in ‘taxonomic concept knowledge’ than in ‘declarative species knowledge’. We showed that the learning success was influenced by learner-specific resources, such as prior knowledge or aspects of motivation towards the subject matter, and by learning environment such as teaching methodology.DiscussionWe discuss didactical demands and aspects of teaching methodologies that could facilitate learning the complex task of plant identification in university courses. Plant identification should be taught and supervised by experienced, highly motivated course instructors with profound expertise and outstanding didactical skills. In order to qualify future generations of biologists, biology teachers, or conservationists universities should aim at and encourage high-quality teaching. creator: Thorsten Buck creator: Ines Bruchmann creator: Pascale Zumstein creator: Claudia Drees uri: https://doi.org/10.7717/peerj.6581 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Buck et al. title: Coral-algal interactions at Weizhou Island in the northern South China Sea: variations by taxa and the exacerbating impact of sediments trapped in turf algae link: https://peerj.com/articles/6590 last-modified: 2019-03-13 description: Competitive interactions between corals and benthic algae are increasingly frequent on degrading coral reefs, but the processes and mechanisms surrounding the interactions, as well as the exacerbating effects of sediments trapped in turf algae, are poorly described. We surveyed the frequency, proportion, and outcomes of interactions between benthic algae (turf algae and macroalgae) and 631 corals (genera: Porites, Favites, Favia, Platygyra, and Pavona) on a degenerating reef in the northern South China Sea, with a specific focus on the negative effects of algal contact on corals. Our data indicated that turf algae were the main algal competitors for each surveyed coral genus and the proportion of algal contact along the coral edges varied significantly among the coral genera and the algal types. The proportions of algal wins between corals and turf algae or macroalgae differed significantly among coral genera. Compared to macroalgae, turf algae consistently yielded more algal wins and fewer coral wins on all coral genera. Amongst the coral genera, Porites was the most easily damaged by algal competition. The proportions of turf algal wins on the coral genera increased 1.1–1.9 times in the presence of sediments. Furthermore, the proportions of algal wins on massive and encrusting corals significantly increased with the combination of sediments and turf algae as the algal type. However, the variation in proportions of algal wins between massive and encrusting corals disappeared as sediments became trapped in turf algae. Sediments bound within turf algae further induced damage to corals and reduced the competitive advantage of the different coral growth forms in their competitive interactions with adjacent turf algae. creator: Zhiheng Liao creator: Kefu Yu creator: Yinghui Wang creator: Xueyong Huang creator: Lijia Xu uri: https://doi.org/10.7717/peerj.6590 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Liao et al.