title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1620 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Characterization of shifts of koala (Phascolarctos cinereus) intestinal microbial communities associated with antibiotic treatment link: https://peerj.com/articles/4452 last-modified: 2018-03-12 description: Koalas (Phascolarctos cinereus) are arboreal marsupials native to Australia that eat a specialized diet of almost exclusively eucalyptus leaves. Microbes in koala intestines are known to break down otherwise toxic compounds, such as tannins, in eucalyptus leaves. Infections by Chlamydia, obligate intracellular bacterial pathogens, are highly prevalent in koala populations. If animals with Chlamydia infections are received by wildlife hospitals, a range of antibiotics can be used to treat them. However, previous studies suggested that koalas can suffer adverse side effects during antibiotic treatment. This study aimed to use 16S rRNA gene sequences derived from koala feces to characterize the intestinal microbiome of koalas throughout antibiotic treatment and identify specific taxa associated with koala health after treatment. Although differences in the alpha diversity were observed in the intestinal flora between treated and untreated koalas and between koalas treated with different antibiotics, these differences were not statistically significant. The alpha diversity of microbial communities from koalas that lived through antibiotic treatment versus those who did not was significantly greater, however. Beta diversity analysis largely confirmed the latter observation, revealing that the overall communities were different between koalas on antibiotics that died versus those that survived or never received antibiotics. Using both machine learning and OTU (operational taxonomic unit) co-occurrence network analyses, we found that OTUs that are very closely related to Lonepinella koalarum, a known tannin degrader found by culture-based methods to be present in koala intestines, was correlated with a koala’s health status. This is the first study to characterize the time course of effects of antibiotics on koala intestinal microbiomes. Our results suggest it may be useful to pursue alternative treatments for Chlamydia infections without the use of antibiotics or the development of Chlamydia-specific antimicrobial compounds that do not broadly affect microbial communities. creator: Katherine E. Dahlhausen creator: Ladan Doroud creator: Alana J. Firl creator: Adam Polkinghorne creator: Jonathan A. Eisen uri: https://doi.org/10.7717/peerj.4452 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Dahlhausen et al. title: Molecular cloning and expression analysis of three ThERFs involved in the response to waterlogging stress of Taxodium ‘Zhongshanshan406’, and subcellular localization of the gene products link: https://peerj.com/articles/4434 last-modified: 2018-03-12 description: As a subfamily of the APETALA 2/ethylene response element binding protein (AP2/EREBP) transcription factor superfamily, the ethylene response factor (ERF) is widely involved in the regulation of growth and response to various abiotic stresses in plants, and has been shown to be the main transcription factor regulating transcription of the genes related to hypoxia and waterlogging stress. In this study, three ThERF genes, with significant differences in expression profile in response to flooding stress, were identified from the transcriptomics data acquired from Taxodium hybrid ‘Zhongshanshan 406’ (T. mucronatum Tenore × T. distichum (L.) Rich) under waterlogging stress: ThERF15, ThERF39 and ThRAP2.3 (GenBank ID: KY463467, KY463468 and KY463470, respectively).The full-length cDNA of each of the three ERFs was obtained using the RACE (rapid amplification cDNA ends) method, and all three were intron-free. Multiple protein sequence alignments indicated that ThERF15, ThERF39 and ThRAP2.3 proteins all had only one AP2-ERF domain and belonged to the ERF subfamily. A transient gene expression assay demonstrated that ThERF15, ThERF39 and ThRAP2.3 were all localized to the nucleus. Real-time quantitative PCR (qPCR) revealed that the expression of ThERF15, ThERF39 and ThRAP2.3 exhibited significant differences, compared with the control, in response to two levels of flooding treatment (half-flooding or total-submergence) of ‘Zhongshanshan 406’. Quantification of ethylene concentration revealed that ethylene was more relevant to the level of expression than the period of flooding treatment. Based on the experimental results above, ThERF15, ThERF39 and ThRAP2.3 were identified as being related to the regulation of downstream flooding- responsive gene expression in ‘Zhongshanshan 406’. ThRAP2.3 is most likely to be a key downstream-response ERF gene to respond to the output of the ethylene signal generated by flooding stress. creator: Wencai Fan creator: Ying Yang creator: Zhiquan Wang creator: Yunlong Yin creator: Chaoguang Yu creator: Qin Shi creator: Jinbo Guo creator: Lei Xuan creator: Jianfeng Hua uri: https://doi.org/10.7717/peerj.4434 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Fan et al. title: Phylogenetic surveys on the newt genus Tylototriton sensu lato (Salamandridae, Caudata) reveal cryptic diversity and novel diversification promoted by historical climatic shifts link: https://peerj.com/articles/4384 last-modified: 2018-03-12 description: Global climatic transitions and Tibetan Plateau uplifts are hypothesized to have profoundly impacted biodiversity in southeastern Asia. To further test the hypotheses related to the impacts of these incidents, we investigated the diversification patterns of the newt genus Tylototriton sensu lato, distributed across the mountain ranges of southeastern Asia. Gene-tree and species-tree analyses of two mitochondrial genes and two nuclear genes revealed five major clades in the genus, and suggested several cryptic species. Dating estimates suggested that the genus originated in the early-to-middle Miocene. Under different species delimitating scenarios, diversification analyses with birth-death likelihood tests indicated that the genus held a higher diversification rate in the late Miocene-to-Pliocene era than that in the Pleistocene. Ancestral area reconstructions indicated that the genus originated from the northern Indochina Peninsula. Accordingly, we hypothesized that the Miocene Climatic Transition triggered the diversification of the genus, and the reinforcement of East Asian monsoons associated with the stepwise uplifts of the Tibetan Plateau promoted the radiation of the genus in southeastern Asia during the Miocene-to-Pliocene period. Quaternary glacial cycles likely had limited effects on speciation events in the genus, but mainly had contributions on their intraspecific differentiations. creator: Bin Wang creator: Kanto Nishikawa creator: Masafumi Matsui creator: Truong Quang Nguyen creator: Feng Xie creator: Cheng Li creator: Janak Raj Khatiwada creator: Baowei Zhang creator: Dajie Gong creator: Yunming Mo creator: Gang Wei creator: Xiaohong Chen creator: Youhui Shen creator: Daode Yang creator: Rongchuan Xiong creator: Jianping Jiang uri: https://doi.org/10.7717/peerj.4384 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Wang et al. title: Out of Asia: mitochondrial evolutionary history of the globally introduced supralittoral isopod Ligia exotica link: https://peerj.com/articles/4337 last-modified: 2018-03-12 description: The native ranges and invasion histories of many marine species remain elusive due to a dynamic dispersal process via marine vessels. Molecular markers can aid in identification of native ranges and elucidation of the introduction and establishment process. The supralittoral isopod Ligia exotica has a wide tropical and subtropical distribution, frequently found in harbors and ports around the globe. This isopod is hypothesized to have an Old World origin, from where it was unintentionally introduced to other regions via wooden ships and solid ballast. Its native range, however, remains uncertain. Recent molecular studies uncovered the presence of two highly divergent lineages of L. exotica in East Asia, and suggest this region is a source of nonindigenous populations. In this study, we conducted phylogenetic analyses (Maximum Likelihood and Bayesian) of a fragment of the mitochondrial 16S ribosomal (r)DNA gene using a dataset of this isopod that greatly expanded previous representation from Asia and putative nonindigenous populations around the world. For a subset of samples, sequences of 12S rDNA and NaK were also obtained and analyzed together with 16S rDNA. Our results show that L. exotica is comprised of several highly divergent genetic lineages, which probably represent different species. Most of the 16S rDNA genetic diversity (48 haplotypes) was detected in East and Southeast Asia. Only seven haplotypes were observed outside this region (in the Americas, Hawai’i, Africa and India), which were identical or closely related to haplotypes found in East and Southeast Asia. Phylogenetic patterns indicate the L. exotica clade originated and diversified in East and Southeast Asia, and only members of one of the divergent lineages have spread out of this region, recently, suggesting the potential to become invasive is phylogenetically constrained. creator: Luis A. Hurtado creator: Mariana Mateos creator: Chang Wang creator: Carlos A. Santamaria creator: Jongwoo Jung creator: Valiallah Khalaji-Pirbalouty creator: Won Kim uri: https://doi.org/10.7717/peerj.4337 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Hurtado et al. title: The association between elevated serum uric acid levels and islet β-cell function indexes in newly diagnosed type 2 diabetes mellitus: a cross-sectional study link: https://peerj.com/articles/4515 last-modified: 2018-03-09 description: BackgroundSerum uric acid (UA) has been reported as a risk factor for type 2 diabetes mellitus (T2DM). However, whether serum UA is associated with insulin resistance and insulin secretion, and the effect of gender on it in the case of the existed association, both remain undefined.MethodsA cross-sectional study was designed and performed, which enrolled a total of 403 newly diagnosed T2DM patients (mean age, 50.21 ± 13.34 years (62.5% males)). Clinical characteristics and islet function indexes of all participants were analyzed based on gender-specific tertiles of serum UA levels. In addition, multiple linear regression analysis was conducted to investigate covariates associated with islet function indexes.ResultsThe mean levels of serum UA were 331.05 μmol/L (interquartile range (IQR): 60.6, 400.9 μmol/L) and 267.9 μmol/L (IQR: 204.7, 331.9 μmol/L) in men and women, respectively. The values of insulin secretion indexes involving AUCins30/glu30, AUCins120/glu120 and total insulin disposition index (DI120) in females were significantly higher than those in males. Apart from the homeostasis model assessment insulin resistance of men, serum UA was positively associated with insulin secretion and insulin resistance indexes both in men and women. Multivariable linear regression analysis showed serum UA exerted an independent impact on insulin secretion in females, but not on insulin resistance. In males, islet function was simultaneously affected by serum UA age, body mass index (BMI), and serum lipids.ConclusionSerum UA harbored a positive correlation with insulin secretion and insulin resistance indexes in newly diagnosed T2DM patients, which was influenced by gender, BMI, serum lipids. Hence, serum UA may be considered as a predictor for islet function in clinical practice. creator: Yimeng Hu creator: Jie Liu creator: Huiqiong Li creator: Hui Zhu creator: Linjie Liu creator: Yin Yuan creator: Jing Chen creator: Ye Wang creator: Xuemei Hu creator: Yancheng Xu uri: https://doi.org/10.7717/peerj.4515 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Hu et al. title: Current state of knowledge on Wolbachia infection among Coleoptera: a systematic review link: https://peerj.com/articles/4471 last-modified: 2018-03-09 description: BackgroundDespite great progress in studies on Wolbachia infection in insects, the knowledge about its relations with beetle species, populations and individuals, and the effects of bacteria on these hosts, is still unsatisfactory. In this review we summarize the current state of knowledge about Wolbachia occurrence and interactions with Coleopteran hosts.MethodsAn intensive search of the available literature resulted in the selection of 86 publications that describe the relevant details about Wolbachia presence among beetles. These publications were then examined with respect to the distribution and taxonomy of infected hosts and diversity of Wolbachia found in beetles. Sequences of Wolbachia genes (16S rDNA, ftsZ) were used for the phylogenetic analyses.ResultsThe collected publications revealed that Wolbachia has been confirmed in 204 beetle species and that the estimated average prevalence of this bacteria across beetle species is 38.3% and varies greatly across families and genera (0–88% infected members) and is much lower (c. 13%) in geographic studies. The majority of the examined and infected beetles were from Europe and East Asia. The most intensively studied have been two groups of herbivorous beetles: Curculionidae and Chrysomelidae. Coleoptera harbor Wolbachia belonging to three supergroups: F found in only three species, and A and B found in similar numbers of beetles (including some doubly infected); however the latter two were most prevalent in different families. A total of 59% of species with precise data were found to be totally infected. Single infections were found in 69% of species and others were doubly- or multiply-infected. Wolbachia caused numerous effects on its beetle hosts, including selective sweep with host mtDNA (found in 3% of species), cytoplasmic incompatibility (detected in c. 6% of beetles) and other effects related to reproduction or development (like male-killing, possible parthenogenesis or haplodiploidy induction, and egg development). Phylogenetic reconstructions for Wolbachia genes rejected cospeciation between these bacteria and Coleoptera, with minor exceptions found in some Hydraenidae, Curculionidae and Chrysomelidae. In contrast, horizontal transmission of bacteria has been suspected or proven in numerous cases (e.g., among beetles sharing habitats and/or host plants).DiscussionThe present knowledge about Wolbachia infection across beetle species and populations is very uneven. Even the basic data about infection status in species and frequency of infected species across genera and families is very superficial, as only c. 0.15% of all beetle species have been tested so far. Future studies on Wolbachia diversity in Coleoptera should still be based on the Multi-locus Sequence Typing system, and next-generation sequencing technologies will be important for uncovering Wolbachia relations with host evolution and ecology, as well as with other, co-occurring endosymbiotic bacteria. creator: Łukasz Kajtoch creator: Nela Kotásková uri: https://doi.org/10.7717/peerj.4471 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Kajtoch and Kotásková title: Activation of CD4 and CD8 T cell receptors and regulatory T cells in response to human proteins link: https://peerj.com/articles/4462 last-modified: 2018-03-09 description: This study assessed in detail the influence of four different human proteins on the activation of CD4+ and CD8+ T lymphocytes and on the formation of regulatory T cells. Human whole-blood samples were incubated with four different human proteins. The effects of these proteins on the downstream immune-system response, on the expression of extracellular activation markers on and intracellular cytokines in T lymphocytes, and on the number of regulatory T cells (T-reg cells) were investigated via flow cytometry. Incubation with β-actin or glyceraldehyde 3-phosphate dehydrogenase (GAPDH), which are cytoplasmic proteins, increased the expression of both extracellular activation markers (CD69 and HLA-DR) and intracellular cytokines but did not significantly affect the number of T-reg cells. In contrast, incubation with human albumin or insulin, which are serum proteins, reduced both extracellular activation markers and intracellular cytokine expression and subsequently increased the number of T-reg cells. These findings may help to explain the etiological basis of autoimmune diseases. creator: Borros M. Arneth uri: https://doi.org/10.7717/peerj.4462 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Arneth title: First endemic freshwater Gammarus from Crete and its evolutionary history—an integrative taxonomy approach link: https://peerj.com/articles/4457 last-modified: 2018-03-09 description: The Mediterranean islands are known as natural laboratories of evolution with a high level of endemic biodiversity. However, most biodiversity assessments have focused mainly on terrestrial and marine fauna, leaving the freshwater animals aside. Crete is one of the largest islands in the Mediterranean Basin, with a long history of isolation from the continental mainland. Gammarid amphipods are often dominant in macrozoobenthic communities in European inland waters. They are widely used in biomonitoring and exotoxicological studies. Herein, we describe Gammarus plaitisi sp. nov., endemic to Cretan streams, based on morphological characters and a set of molecular species delimitation methods using mitochondrial cytochrome oxidase subunit I and 16S rRNA genes as well as nuclear 28S rDNA, ITS1 and EF1-alpha genes. The divergence of the new species is strongly connected with the geological history of the island supporting its continental origin. creator: Kamil Hupało creator: Tomasz Mamos creator: Weronika Wrzesińska creator: Michał Grabowski uri: https://doi.org/10.7717/peerj.4457 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Hupało et al. title: Curious creatures: a multi-taxa investigation of responses to novelty in a zoo environment link: https://peerj.com/articles/4454 last-modified: 2018-03-08 description: The personality trait of curiosity has been shown to increase welfare in humans. If this positive welfare effect is also true for non-humans, animals with high levels of curiosity may be able to cope better with stressful situations than their conspecifics. Before discoveries can be made regarding the effect of curiosity on an animal’s ability to cope in their environment, a way of measuring curiosity across species in different environments must be created to standardise testing. To determine the suitability of novel objects in testing curiosity, species from different evolutionary backgrounds with sufficient sample sizes were chosen. Barbary sheep (Ammotragus lervia) n = 12, little penguins (Eudyptula minor) n = 10, ringtail lemurs (Lemur catta) n = 8, red tailed black cockatoos (Calyptorhynchus banksia) n = 7, Indian star tortoises (Geochelone elegans) n = 5 and red kangaroos (Macropus rufus) n = 5 were presented with a stationary object, a moving object and a mirror. Having objects with different characteristics increased the likelihood individuals would find at least one motivating. Conspecifics were all assessed simultaneously for time to first orientate towards object (s), latency to make contact (s), frequency of interactions, and total duration of interaction (s). Differences in curiosity were recorded in four of the six species; the Barbary sheep and red tailed black cockatoos did not interact with the novel objects suggesting either a low level of curiosity or that the objects were not motivating for these animals. Variation in curiosity was seen between and within species in terms of which objects they interacted with and how long they spent with the objects. This was determined by the speed in which they interacted, and the duration of interest. By using the measure of curiosity towards novel objects with varying characteristics across a range of zoo species, we can see evidence of evolutionary, husbandry and individual influences on their response. Further work to obtain data on multiple captive populations of a single species using a standardised method could uncover factors that nurture the development of curiosity. In doing so, it would be possible to isolate and modify sub-optimal husbandry practices to improve welfare in the zoo environment. creator: Belinda A. Hall creator: Vicky Melfi creator: Alicia Burns creator: David M. McGill creator: Rebecca E. Doyle uri: https://doi.org/10.7717/peerj.4454 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Hall et al. title: Validation and application of the Chinese version of the Perceived Stress Questionnaire (C-PSQ) in nursing students link: https://peerj.com/articles/4503 last-modified: 2018-03-08 description: ObjectiveTo translate the Perceived Stress Questionnaire (PSQ) into Chinese, validate its reliability and validity in nursing students and investigate the perceived stress level of nursing students.MethodForward- and back-translation combined with expert assessment and cross-cultural adaptations were used to construct the Chinese version of the PSQ (C-PSQ). This research adopted a stratified sampling method among 1,519 nursing students in 30 classes of Ningbo College of Health Sciences to assess the reliability and validity of the C-PSQ. Among them, we used the Recent C-PSQ (only the last month).ResultsThe C-PSQ retained all 30 items of the original scale. Principal component analysis extracted five factors that explained 52.136% of the total variance. The S-CVI/Ave was 0.913. Concurrent validity was 0.525 and 0.567 for anxiety and depression respectively. The results of the confirmatory factor analysis were as follows: χ2/df = 4.376, RMR = 0.023, GFI = 0.921, AGFI = 0.907, CFI = 0.916, RMSEA = 0.048, PNFI = 0.832, PGFI = 0.782, CN = 342 and AIC/CAIC = 0.809. The scale’s Cronbach’s alpha was 0.922, and Cronbach’s α of each dimension was 0.899 (worries/tension), 0.821 (joy), 0.688 (overload), 0.703 (conflict), 0.523 (self-realization). The correlation coefficient between the first and second test, the first and third test and the second and third test was 0.725, 0.787 and 0.731, respectively. Mean values and distribution of overall PSQ index in nursing students was 0.399 ± 0.138. Different demographic factors were significantly associated with the perceived stress of nursing students.ConclusionThe C-PSQ has an appropriate reliability and validity, which means that the scale can be used as a universal tool for psychosomatic studies. The perceived stress of nursing students was relatively high. Further studies are needed. creator: Yi Luo creator: Boxiong Gong creator: Runtang Meng creator: Xiaoping Cao creator: Shuang Tang creator: Hongzhi Fang creator: Xing Zhao creator: Bing Liu uri: https://doi.org/10.7717/peerj.4503 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Luo et al.