title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1815 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Proteomic profiling analysis reveals that glutathione system plays important roles responding to osmotic stress in wheat (Triticum aestivum L.) roots link: https://peerj.com/articles/2334 last-modified: 2016-08-17 description: Wheat is one of the most important crops in the world, and osmotic stress has become one of the main factors affecting wheat production. Understanding the mechanism of the response of wheat to osmotic stress would be greatly significant. In the present study, isobaric tag for relative and absolute quantification (iTRAQ) was used to analyze the changes of protein expression in the wheat roots exposed to different osmotic stresses. A total of 2,228 expressed proteins, including 81 differentially expressed proteins, between osmotic stress and control, were found. The comprehensive analysis of these differentially expressed proteins revealed that osmotic stress increased the variety of expressed proteins and suppressed the quantity of expressed proteins in wheat roots. Furthermore, the proteins for detoxifying and reactive oxygen species scavenging, especially the glutathione system, played important roles in maintaining organism balance in response to osmotic stress in wheat roots. Thus, the present study comprehensively describes the protein expression changes in wheat roots in response to osmotic stress, providing firmer foundation to further study the mechanism of osmotic resistance in wheat. creator: Jianhui Ma creator: Wen Dong creator: Daijing Zhang creator: Xiaolong Gao creator: Lina Jiang creator: Yun Shao creator: Doudou Tong creator: Chunxi Li uri: https://doi.org/10.7717/peerj.2334 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Ma et al. title: Effects of origin, seasons and storage under different temperatures on germination of Senecio vulgaris (Asteraceae) seeds link: https://peerj.com/articles/2346 last-modified: 2016-08-17 description: Invasive plants colonize new environments, become pests and cause biodiversity loss, economic loss and health damage. Senecio vulgaris L. (Common groundsel, Asteraceae), a widely distributing cosmopolitan weed in the temperate area, is reported with large populations in the north–eastern and south–western part, but not in southern, central, or north-western parts of China. We studied the germination behavior of S. vulgaris to explain the distribution and the biological invasion of this species in China. We used seeds originating from six native and six invasive populations to conduct germination experiments in a climate chamber and under outdoor condition. When incubated in a climate chamber (15 °C), seeds from the majority of the populations showed >90% germination percentage (GP) and the GP was equal for seeds with a native and invasive origin. The mean germination time (MGT) was significantly different among the populations. Under outdoor conditions, significant effects of origin, storage conditions (stored at 4 °C or ambient room temperature, ca. 27 °C) and seasons (in summer or autumn) were observed on the GP while the MGT was only affected by the season. In autumn, the GP (38.6%) was higher and the MGT was slightly longer than that in summer. In autumn, seeds stored at 4 °C showed higher GP than those stored at ambient room temperature (ca.27 °C), and seeds from invasive populations revealed higher GP than those from native populations. The results implied that the high temperature in summer has a negative impact on the germination and might cause viability loss or secondary dormancy to S. vulgaris seeds. Our study offers a clue to exploring what factor limits the distribution of S. vulgaris in China by explaining why, in the cities in South-East China and central China such as Wuhan, S. vulgaris cannot establish natural and viable populations. creator: Noel Ndihokubwayo creator: Viet-Thang Nguyen creator: Dandan Cheng uri: https://doi.org/10.7717/peerj.2346 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Ndihokubwayo et al. title: Selection of a marker gene to construct a reference library for wetland plants, and the application of metabarcoding to analyze the diet of wintering herbivorous waterbirds link: https://peerj.com/articles/2345 last-modified: 2016-08-17 description: Food availability and diet selection are important factors influencing the abundance and distribution of wild waterbirds. In order to better understand changes in waterbird population, it is essential to figure out what they feed on. However, analyzing their diet could be difficult and inefficient using traditional methods such as microhistologic observation. Here, we addressed this gap of knowledge by investigating the diet of greater white-fronted goose Anser albifrons and bean goose Anser fabalis, which are obligate herbivores wintering in China, mostly in the Middle and Lower Yangtze River floodplain. First, we selected a suitable and high-resolution marker gene for wetland plants that these geese would consume during the wintering period. Eight candidate genes were included: rbcL, rpoC1, rpoB, matK, trnH-psbA, trnL (UAA), atpF-atpH, and psbK-psbI. The selection was performed via analysis of representative sequences from NCBI and comparison of amplification efficiency and resolution power of plant samples collected from the wintering area. The trnL gene was chosen at last with c/h primers, and a local plant reference library was constructed with this gene. Then, utilizing DNA metabarcoding, we discovered 15 food items in total from the feces of these birds. Of the 15 unique dietary sequences, 10 could be identified at specie level. As for greater white-fronted goose, 73% of sequences belonged to Poaceae spp., and 26% belonged to Carex spp. In contrast, almost all sequences of bean goose belonged to Carex spp. (99%). Using the same samples, microhistology provided consistent food composition with metabarcoding results for greater white-fronted goose, while 13% of Poaceae was recovered for bean goose. In addition, two other taxa were discovered only through microhistologic analysis. Although most of the identified taxa matched relatively well between the two methods, DNA metabarcoding gave taxonomically more detailed information. Discrepancies were likely due to biased PCR amplification in metabarcoding, low discriminating power of current marker genes for monocots, and biases in microhistologic analysis. The diet differences between two geese species might indicate deeper ecological significance beyond the scope of this study. We concluded that DNA metabarcoding provides new perspectives for studies of herbivorous waterbird diets and inter-specific interactions, as well as new possibilities to investigate interactions between herbivores and plants. In addition, microhistologic analysis should be used together with metabarcoding methods to integrate this information. creator: Yuzhan Yang creator: Aibin Zhan creator: Lei Cao creator: Fanjuan Meng creator: Wenbin Xu uri: https://doi.org/10.7717/peerj.2345 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Yang et al. title: MOST: a modified MLST typing tool based on short read sequencing link: https://peerj.com/articles/2308 last-modified: 2016-08-17 description: Multilocus sequence typing (MLST) is an effective method to describe bacterial populations. Conventionally, MLST involves Polymerase Chain Reaction (PCR) amplification of housekeeping genes followed by Sanger DNA sequencing. Public Health England (PHE) is in the process of replacing the conventional MLST methodology with a method based on short read sequence data derived from Whole Genome Sequencing (WGS). This paper reports the comparison of the reliability of MLST results derived from WGS data, comparing mapping and assembly-based approaches to conventional methods using 323 bacterial genomes of diverse species. The sensitivity of the two WGS based methods were further investigated with 26 mixed and 29 low coverage genomic data sets from Salmonella enteridis and Streptococcus pneumoniae. Of the 323 samples, 92.9% (n = 300), 97.5% (n = 315) and 99.7% (n = 322) full MLST profiles were derived by the conventional method, assembly- and mapping-based approaches, respectively. The concordance between samples that were typed by conventional (92.9%) and both WGS methods was 100%. From the 55 mixed and low coverage genomes, 89.1% (n = 49) and 67.3% (n = 37) full MLST profiles were derived from the mapping and assembly based approaches, respectively. In conclusion, deriving MLST from WGS data is more sensitive than the conventional method. When comparing WGS based methods, the mapping based approach was the most sensitive. In addition, the mapping based approach described here derives quality metrics, which are difficult to determine quantitatively using conventional and WGS-assembly based approaches. creator: Rediat Tewolde creator: Timothy Dallman creator: Ulf Schaefer creator: Carmen L. Sheppard creator: Philip Ashton creator: Bruno Pichon creator: Matthew Ellington creator: Craig Swift creator: Jonathan Green creator: Anthony Underwood uri: https://doi.org/10.7717/peerj.2308 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Tewolde et al. title: Detection of a Yersinia pestis gene homologue in rodent samples link: https://peerj.com/articles/2216 last-modified: 2016-08-17 description: A homologue to a widely used genetic marker, pla, for Yersinia pestis has been identified in tissue samples of two species of rat (Rattus rattus and Rattus norvegicus) and of mice (Mus musculus and Apodemus sylvaticus) using a microarray based platform to screen for zoonotic pathogens of interest. Samples were from urban locations in the UK (Liverpool) and Canada (Vancouver). The results indicate the presence of an unknown bacterium that shares a homologue for the pla gene of Yersinia pestis, so caution should be taken when using this gene as a diagnostic marker. creator: Timothy A. Giles creator: Alex D. Greenwood creator: Kyriakos Tsangaras creator: Tom C. Giles creator: Paul A. Barrow creator: Duncan Hannant creator: Abu-Bakr Abu-Median creator: Lisa Yon uri: https://doi.org/10.7717/peerj.2216 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Giles et al. title: Arktocara yakataga, a new fossil odontocete (Mammalia, Cetacea) from the Oligocene of Alaska and the antiquity of Platanistoidea link: https://peerj.com/articles/2321 last-modified: 2016-08-16 description: The diversification of crown cetacean lineages (i.e., crown Odontoceti and crown Mysticeti) occurred throughout the Oligocene, but it remains an ongoing challenge to resolve the phylogenetic pattern of their origins, especially with respect to stem lineages. One extant monotypic lineage, Platanista gangetica (the Ganges and Indus river dolphin), is the sole surviving member of the broader group Platanistoidea, with many fossil relatives that range from Oligocene to Miocene in age. Curiously, the highly threatened Platanista is restricted today to freshwater river systems of South Asia, yet nearly all fossil platanistoids are known globally from marine rocks, suggesting a marine ancestry for this group. In recent years, studies on the phylogenetic relationships in Platanistoidea have reached a general consensus about the membership of different sub-clades and putative extinct groups, although the position of some platanistoid groups (e.g., Waipatiidae) has been contested. Here we describe a new genus and species of fossil platanistoid, Arktocara yakataga, gen. et sp. nov. from the Oligocene of Alaska, USA. The type and only known specimen was collected from the marine Poul Creek Formation, a unit known to include Oligocene strata, exposed in the Yakutat City and Borough of Southeast Alaska. In our phylogenetic analysis of stem and node-based Platanistoidea, Arktocara falls within the node-based sub-clade Allodelphinidae as the sister taxon to Allodelphis pratti. With a geochronologic age between ∼29–24 million years old, Arktocara is among the oldest crown Odontoceti, reinforcing the long-standing view that the diversification for crown lineages must have occurred no later than the early Oligocene. creator: Alexandra T. Boersma creator: Nicholas D. Pyenson uri: https://doi.org/10.7717/peerj.2321 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Boersma and Pyenson title: Ancient phylogenetic divergence of the enigmatic African rodent Zenkerella and the origin of anomalurid gliding link: https://peerj.com/articles/2320 last-modified: 2016-08-16 description: The “scaly-tailed squirrels” of the rodent family Anomaluridae have a long evolutionary history in Africa, and are now represented by two gliding genera (Anomalurus and Idiurus) and a rare and obscure genus (Zenkerella) that has never been observed alive by mammalogists. Zenkerella shows no anatomical adaptations for gliding, but has traditionally been grouped with the glider Idiurus on the basis of craniodental similarities, implying that either the Zenkerella lineage lost its gliding adaptations, or that Anomalurus and Idiurus evolved theirs independently. Here we present the first nuclear and mitochondrial DNA sequences of Zenkerella, based on recently recovered whole-body specimens from Bioko Island (Equatorial Guinea), which show unambiguously that Zenkerella is the sister taxon of Anomalurus and Idiurus. These data indicate that gliding likely evolved only once within Anomaluridae, and that there were no subsequent evolutionary reversals. We combine this new molecular evidence with morphological data from living and extinct anomaluromorph rodents and estimate that the lineage leading to Zenkerella has been evolving independently in Africa since the early Eocene, approximately 49 million years ago. Recently discovered fossils further attest to the antiquity of the lineage leading to Zenkerella, which can now be recognized as a classic example of a “living fossil,” about which we know remarkably little. The osteological markers of gliding are estimated to have evolved along the stem lineage of the Anomalurus–Idiurus clade by the early Oligocene, potentially indicating that this adaptation evolved in response to climatic perturbations at the Eocene–Oligocene boundary (∼34 million years ago). creator: Steven Heritage creator: David Fernández creator: Hesham M. Sallam creator: Drew T. Cronin creator: José Manuel Esara Echube creator: Erik R. Seiffert uri: https://doi.org/10.7717/peerj.2320 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Heritage et al. title: The adder (Vipera berus) in Southern Altay Mountains: population characteristics, distribution, morphology and phylogenetic position link: https://peerj.com/articles/2342 last-modified: 2016-08-16 description: As the most widely distributed snake in Eurasia, the adder (Vipera berus) has been extensively investigated in Europe but poorly understood in Asia. The Southern Altay Mountains represent the adder’s southern distribution limit in Central Asia, whereas its population status has never been assessed. We conducted, for the first time, field surveys for the adder at two areas of Southern Altay Mountains using a combination of line transects and random searches. We also described the morphological characteristics of the collected specimens and conducted analyses of external morphology and molecular phylogeny. The results showed that the adder distributed in both survey sites and we recorded a total of 34 sightings. In Kanas river valley, the estimated encounter rate over a total of 137 km transects was 0.15 ± 0.05 sightings/km. The occurrence of melanism was only 17%. The small size was typical for the adders in Southern Altay Mountains in contrast to other geographic populations of the nominate subspecies. A phylogenetic tree obtained by Bayesian Inference based on DNA sequences of the mitochondrial cytochrome b (1,023 bp) grouped them within the Northern clade of the species but failed to separate them from the subspecies V. b. sachalinensis. Our discovery extends the distribution range of V. berus and provides a basis for further researches. We discuss the hypothesis that the adder expands its distribution border to the southwest along the mountains’ elevation gradient, but the population abundance declines gradually due to a drying climate. creator: Shaopeng Cui creator: Xiao Luo creator: Daiqiang Chen creator: Jizhou Sun creator: Hongjun Chu creator: Chunwang Li creator: Zhigang Jiang uri: https://doi.org/10.7717/peerj.2342 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Cui et al. title: Evolution of morphological and climatic adaptations in Veronica L. (Plantaginaceae) link: https://peerj.com/articles/2333 last-modified: 2016-08-16 description: Perennials and annuals apply different strategies to adapt to the adverse environment, based on ‘tolerance’ and ‘avoidance’, respectively. To understand lifespan evolution and its impact on plant adaptability, we carried out a comparative study of perennials and annuals in the genus Veronica from a phylogenetic perspective. The results showed that ancestors of the genus Veronicawere likely to be perennial plants. Annual life history of Veronica has evolved multiple times and subtrees with more annual species have a higher substitution rate. Annuals can adapt to more xeric habitats than perennials. This indicates that annuals are more drought-resistant than their perennial relatives. Due to adaptation to similar selective pressures, parallel evolution occurs in morphological characters among annual species of Veronica. creator: Jian-Cheng Wang creator: Bo-Rong Pan creator: Dirk C. Albach uri: https://doi.org/10.7717/peerj.2333 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Wang et al. title: The health care and life sciences community profile for dataset descriptions link: https://peerj.com/articles/2331 last-modified: 2016-08-16 description: Access to consistent, high-quality metadata is critical to finding, understanding, and reusing scientific data. However, while there are many relevant vocabularies for the annotation of a dataset, none sufficiently captures all the necessary metadata. This prevents uniform indexing and querying of dataset repositories. Towards providing a practical guide for producing a high quality description of biomedical datasets, the W3C Semantic Web for Health Care and the Life Sciences Interest Group (HCLSIG) identified Resource Description Framework (RDF) vocabularies that could be used to specify common metadata elements and their value sets. The resulting guideline covers elements of description, identification, attribution, versioning, provenance, and content summarization. This guideline reuses existing vocabularies, and is intended to meet key functional requirements including indexing, discovery, exchange, query, and retrieval of datasets, thereby enabling the publication of FAIR data. The resulting metadata profile is generic and could be used by other domains with an interest in providing machine readable descriptions of versioned datasets. creator: Michel Dumontier creator: Alasdair J.G. Gray creator: M. Scott Marshall creator: Vladimir Alexiev creator: Peter Ansell creator: Gary Bader creator: Joachim Baran creator: Jerven T. Bolleman creator: Alison Callahan creator: José Cruz-Toledo creator: Pascale Gaudet creator: Erich A. Gombocz creator: Alejandra N. Gonzalez-Beltran creator: Paul Groth creator: Melissa Haendel creator: Maori Ito creator: Simon Jupp creator: Nick Juty creator: Toshiaki Katayama creator: Norio Kobayashi creator: Kalpana Krishnaswami creator: Camille Laibe creator: Nicolas Le Novère creator: Simon Lin creator: James Malone creator: Michael Miller creator: Christopher J. Mungall creator: Laurens Rietveld creator: Sarala M. Wimalaratne creator: Atsuko Yamaguchi uri: https://doi.org/10.7717/peerj.2331 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Dumontier et al.