title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1253 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Characterization and expression profiling of the ICE-CBF-COR genes in wheat link: https://peerj.com/articles/8190 last-modified: 2019-11-29 description: Cold stress is one of the major abiotic stresses that limit crop production. The ICE-CBF-COR pathway is associated with cold stress response in a wide variety of crop species. However, the ICE-CBF-COR genes has not been well characterized in wheat (Triticum aestivum). This study identified, characterized and examined the expression profiles of the ICE, CBF and COR genes for cold defense in wheat. Five ICE (inducer of CBF expression) genes, 37 CBF (C-repeat binding factor) genes and 11 COR (cold-responsive or cold-regulated) genes were discovered in the wheat genome database. Phylogenetic trees based on all 53 genes revealed that CBF genes were more diverse than ICE and COR genes. Twenty-two of the 53 genes appeared to include 11 duplicated pairs. Twenty rice (Oryza sativa) genes and 21 sorghum (Sorghum bicolor) and maize (Zea mays) genes showed collinearity with the wheat ICE, CBF and COR genes. Transcriptome data and qRT-PCR analyses revealed tissue-specific expression patterns of the ICE, CBF and COR genes, and identified similarities in the expression pattern of genes from the same family when subjected to drought, heat, drought plus heat, and cold stress. These results provide information for better understanding the biological roles of ICE, CBF, COR genes in wheat. creator: Jie Guo creator: Yongkang Ren creator: Zhaohui Tang creator: Weiping Shi creator: Meixue Zhou uri: https://doi.org/10.7717/peerj.8190 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Guo et al. title: Does bone preparation impact its shape: consequences for comparative analyses of bone shape link: https://peerj.com/articles/7932 last-modified: 2019-11-28 description: Vertebrate osteological collections provide comparative material for morphological analysis. Before being stored in the collection and studied by researchers, specimens are treated by preparators or curators and are cleaned. The preparation protocol employed ideally should not damage the material. Here, we explore the potential deformation of bones due to preparation using geometric morphometric methods. We focus both on intraspecific and interspecific variability. Our data on the scapular girdle of birds show that, at an intraspecific level, the effect of preparation on bone shape cannot be neglected. Paired and unpaired bones did not respond to the preparation process in the same way, possibly due to differences in function and their anatomical characteristics. Moreover, deformations due to preparation can be estimated by looking at the texture of the bone. At the interspecific level, we found no significant differences as the deformations induced by preparation are relatively small compared to differences among species. This study highlights the importance of carefully selecting preparation methods in order to avoid physical damage that could impact the shape of bones, especially for studies at the intraspecific level. creator: Fanny Pagès creator: Anne-Claire Fabre creator: Anick Abourachid uri: https://doi.org/10.7717/peerj.7932 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Pagès et al. title: Invasions of gladiolus rust in North America are caused by a widely-distributed clone of Uromycestransversalis link: https://peerj.com/articles/7986 last-modified: 2019-11-28 description: Uromyces transversalis, the causal agent of Gladiolus rust, is an invasive plant pathogen in the United States and is regulated as a quarantine pathogen in Europe. The aim of this research was to: (i) determine the origin of introductions of U. transversalis to the United States, (ii) track the movement of genotypes, and (iii) understand the worldwide genetic diversity of the species. To develop molecular markers for genotyping, whole genome sequencing was performed on three isolates collected in the United States. Genomes were assembled de novo and searched for microsatellite regions. Primers were developed and tested on ten isolates from the United States resulting in the identification of 24 polymorphic markers. Among 92 isolates collected from Costa Rica, Mexico, New Zealand, Australia, and the United States there were polymorphisms within isolates with no genotypic diversity detected among isolates; however, missing data among the New Zealand and Australia isolates due to either poor amplification of degraded DNA or null alleles as a result of genetic differences made it difficult to generate conclusions about these populations. The microsatellite loci and flanking regions showed high diversity and two divergent genomes within dikaryotic individuals, yet no diversity among individuals, suggesting that the invasive U. transversalis populations from North America are strictly clonal. creator: Jeffery A. DeLong creator: Jane E. Stewart creator: Alberto Valencia-Botín creator: Kerry F. Pedley creator: James W. Buck creator: Marin T. Brewer uri: https://doi.org/10.7717/peerj.7986 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 DeLong et al. title: Long noncoding RNA MEG3 suppresses podocyte injury in diabetic nephropathy by inactivating Wnt/β-catenin signaling link: https://peerj.com/articles/8016 last-modified: 2019-11-28 description: BackgroundDiabetic nephropathy (DN) is one of the principal complications of diabetes and podocyte injury plays an important role in the DN pathogenesis. Wnt/β-catenin signaling overactivation confers podocyte injury and promotes multiple types of renal disease. However, the underlying mechanism of Wnt/β-catenin signaling activation in DN progression has not been fully elucidated. Long noncoding RNA (lncRNA) is a large class of endogenous RNA molecules lacking functional code capacity and which participates in the pathogenesis of human disease, including DN.MethodA diabetes model was constructed by intraperitoneal injection of Streptozotocin in rats. The MPC5 cells were used to create the in vitro model. Western blot and Quantitative reverse-transcriptase-PCR were used to examine the expression of protein and mRNA. The migrated capacity was analyzed by Transwell migration assay. The cell viability was detected by CCK8.ResultsIn the present study, we revealed the association of lncRNA Maternally Expressed Gene 3 (MEG3) with aberrant activation of Wnt/β-catenin signaling and the role of MEG3/Wnt axis in podocyte injury. We found that high glucose (HG) treatment suppressed MEG3 expression in cultured podocytes, activated Wnt/β-catenin signaling and caused podocyte injury as indicated by the downregulation of podocyte-specific markers (podocin and synaptopodin) and the upregulation of snail1 and α-smooth muscle actin. Overexpression of MEG3 attenuated HG-induced podocyte injury by reducing Wnt/β-catenin activity, repressing cell migration, reactive oxygen species production and increasing the viability of podocytes. Furthermore, we provided evidences that restoration of Wnt/β-catenin signaling by specific agonist impeded the protective effect of MEG3 on podocyte injury. Current results demonstrated that MEG3/Wnt axis plays an important role in fostering podocyte injury and may serve as a potential therapeutic target for the treatment of DN.ConclusionlncRNA MEG3 ameliorates podocyte injury in DN via inactivating Wnt/β-catenin signaling. creator: Xiajing Che creator: Xin Deng creator: Kewei Xie creator: Qin Wang creator: Jiayi Yan creator: Xinghua Shao creator: Zhaohui Ni creator: Liang Ying uri: https://doi.org/10.7717/peerj.8016 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Che et al. title: Multiple ecosystem services from field margin vegetation for ecological sustainability in agriculture: scientific evidence and knowledge gaps link: https://peerj.com/articles/8091 last-modified: 2019-11-28 description: BackgroundField margin and non-crop vegetation in agricultural systems are potential ecosystem services providers because they offer semi-natural habitats for both below and above ground animal groups such as soil organisms, small mammals, birds and arthropods that are service supplying units. They are considered as a target area for enhancing farm biodiversity.MethodologyTo explore the multiple potential benefits of these semi-natural habitats and to identify research trends and knowledge gaps globally, a review was carried out following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. A total of 235 publications from the year 2000 to 2016 in the Scopus and Web of Science databases were reviewed.ResultsThe literature showed an increasing trend in the number of published articles over time with European studies leading in the proportion of studies conducted, followed by North America, Asia, South America, Africa and Australia. Several functional groups of organisms were studied from field margin and non-crop vegetation around agricultural lands including natural enemies (37%), insect pests (22%), birds (17%), pollinators (16%), soil macro fauna (4%) and small mammals (4%). Ecosystem services derived from the field margin included natural pest regulation, pollination, nutrient cycling and reduced offsite erosion. Some field margin plants were reported to host detrimental crop pests, a major ecosystem dis-service, potentially leading to increased pest infestation in the field.ConclusionThe majority of studies revealed the importance of field margin and non-crop vegetation around arable fields in enhancing ecosystem biodiversity. Promotion of field margin plants that selectively enhance the population of beneficial organisms would support sustainable food security rather than simply boosting plant diversity. Our analyses also highlight that agro-ecological studies remain largely overlooked in some regions. creator: Prisila A. Mkenda creator: Patrick A. Ndakidemi creator: Ernest Mbega creator: Philip C. Stevenson creator: Sarah E.J. Arnold creator: Geoff M. Gurr creator: Steven R. Belmain uri: https://doi.org/10.7717/peerj.8091 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Mkenda et al. title: Concentrated ambient PM2.5 exposure affects mice sperm quality and testosterone biosynthesis link: https://peerj.com/articles/8109 last-modified: 2019-11-28 description: BackgroundStudies suggested that PM2.5 exposure could lead to adverse reproductive effects on male animals. However, the underlying mechanism is still not clear. Besides, animals in the majority of previous studies were exposed to PM2.5 through intratracheal instillation which should be improved. In addition, limited amount of research has been conducted in China where the PM2.5 concentration is higher and the PM2.5 components are different. The aim of this work is to explore the effects of concentrated ambient PM2.5 (CAP) on mice sperm quality and testosterone biosynthesis.MethodsA total of 12 male C57BL/6 mice were exposed to filtered air (FA) or CAP for 125 days using the Shanghai Meteorological and Environmental Animal Exposure System. The mice sperm concentration, sperm motility, DNA fragmentation index, high DNA stainability and plasma testosterone were analyzed. Testicular histology and sperm morphology were observed through optical microscope. Testosterone biosynthesis related gene expressions were analyzed using real-time PCR, including cytochrome P450 CHOL side-chain cleavage enzyme (P450scc), steroidogenic acute regulatory protein (StAR), 3β-hydroxysteroid dehydrogenase (3β HSD), 17β-hydroxysteroid dehydrogenase, cytochrome P450 aromatase (P450arom), estrogen receptor (ER), androgen receptor (AR) and follicle stimulating hormone receptor (FSHR).ResultsExposure to CAP resulted in disturbance of various stages of spermatogenesis and significant higher percentage of abnormal sperm (FA vs. CAP: 24.37% vs. 44.83%) in mice testis. CAP exposure significantly decreased sperm concentration (43.00 × 106 vs. 25.33 × 106) and motility (PR: 63.58% vs. 55.15%; PR + NP: 84.00% vs. 77.08%) in epididymis. Plasma testosterone concentration were significantly declined (0.28 ng/ml vs. 0.69 ng/ml) under CAP exposure. Notably, the levels of testosterone biosynthesis related genes, StAR, P450scc, P450arom, ER and FSHR were significantly decreased with CAP exposure.ConclusionConcentrated ambient PM2.5 exposure altered mice sperm concentration, motility and morphology, which might be mediated primarily by the decline in testosterone concentration and testosterone biosynthesis process. creator: Yingying Yang creator: Tingting Yang creator: Shengxin Liu creator: Zhijuan Cao creator: Yan Zhao creator: Xiujuan Su creator: Zehuan Liao creator: Xiaoming Teng creator: Jing Hua uri: https://doi.org/10.7717/peerj.8109 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Yang et al. title: Analysis of miRNA expression profiles in the liver of ClockΔ19 mutant mice link: https://peerj.com/articles/8119 last-modified: 2019-11-28 description: The circadian clock controls the physiological functions of many tissues including the liver via an autoregulatory transcriptional−translational feedback loop, of which CLOCK is a core positive component. In addition, many studies have indicated that microRNAs (miRNAs) regulate liver function. However, how CLOCK-regulated miRNAs are linked to liver function remains largely unknown. In this study, miRNAs expression profiles were performed in the liver of ClockΔ19 mutant mice. Compared to wild type mice, totals of 61 and 57 putative CLOCK-regulated miRNAs were differentially expressed (fold change absolute value ≥2) at zeitgeber time 2 and zeitgeber time 14, respectively. According to the pathway analyses, the target genes of differentially expressed miRNAs were mainly involved in pathways in cancer, the PI3K-Akt signaling pathway and the MAPK signaling pathway. Protein−protein interaction analyses revealed that the hub genes were primarily associated with pathway in cancer and circadian rhythms. Expression validation showed that while the expression levels of miR-195 and miR-340 were up-regulated, the rhythms of these two miRNAs were always maintained. The expression level of nr1d2 mRNA was down-regulated. We identified a number of prospective CLOCK-regulated miRNAs that play roles in the various physiological processes of the liver, providing a reference to better understanding the potential regulatory mechanisms in the liver. creator: Yanli Wang creator: Ke Lv creator: Mei Zhao creator: Hailong Chen creator: Guohua Ji creator: Yongliang Zhang creator: Tingmei Wang creator: Hongqing Cao creator: Yinghui Li creator: Lina Qu uri: https://doi.org/10.7717/peerj.8119 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Wang et al. title: The discriminative power of the ReproQ: a client experience questionnaire in maternity care link: https://peerj.com/articles/7575 last-modified: 2019-11-27 description: BackgroundThe aim of the ReproQuestionnaire (ReproQ) is to measure the client’s experience with maternity care, following WHO’s responsiveness model. To support quality improvement, ReproQ should be able to discriminate best from worst organisational units.MethodsWe sent questionnaires to 27,487 third-trimester pregnant women (response 31%) and to 37,230 women 6 weeks after childbirth (response 39%). For analysis we first summarized the ReproQ domain scores into three summary scores: total score (all eight domains), personal score (four personal domains), and setting score (four setting domains). Second, we estimated the proportion of variance across perinatal units attributable to the ‘actual’ difference across perinatal units using intraclass correlation coefficients (ICCs). Third, we assessed the ability of ReproQ to discriminate between perinatal units based on both a statistical approach using multilevel regression analyses, and a relevance approach based on the minimally important difference (MID). Finally, we compared the domain scores of the best and underperforming units.ResultsICCs ranged between 0.004 and 0.025 for the summary scores, and between 0.002 and 0.125 for the individual domains. ReproQ was able to identify the best and worst performing units with both the statistical and relevance approach. The statistical approach was able to identify four underperforming units during childbirth (total score), while the relevance approach identified 10 underperforming units.ConclusionsReproQ, a valid and efficient measure of client experiences in maternity care, has the ability to discriminate well across perinatal units, and is suitable for benchmarking under routine conditions. creator: Marisja Scheerhagen creator: Henk F. van Stel creator: Arie Franx creator: Erwin Birnie creator: Gouke J. Bonsel uri: https://doi.org/10.7717/peerj.7575 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Scheerhagen et al. title: Comparative proteomic analysis of pepper (Capsicum annuum L.) seedlings under selenium stress link: https://peerj.com/articles/8020 last-modified: 2019-11-27 description: Selenium (Se) is an essential trace element for human and animal health. Se fertilizer has been used to increase the Se content in crops to meet the Se requirements in humans and animals. To address the challenge of Se poisoning in plants, the mechanisms underlying Se-induced stress in plants must be understood. Here, to elucidate the effects of Se stress on the protein levels in pepper, we used an integrated approach involving tandem mass tag labeling, high performance liquid chromatography fractionation, and mass spectrometry-based analysis. A total of 4,693 proteins were identified, 3,938 of which yielded quantitative information. Among them, the expression of 172 proteins was up-regulated, and the expression of 28 proteins was down-regulated in the Se/mock treatment comparison. According to the above data, we performed a systematic bioinformatics analysis of all identified proteins and differentially expressed proteins (DEPs). The DEPs were most strongly associated with the terms “metabolic process,” “posttranslational modification, protein turnover, chaperones,” and “protein processing in endoplasmic reticulum” according to Gene Ontology, eukaryotic orthologous groups classification, and Kyoto Encyclopedia of Genes and Genomes enrichment analysis, respectively. Furthermore, several heat shock proteins were identified as DEPs. These results provide insights that may facilitate further studies on the pepper proteome expressed downstream of the Se stress response. Our data revealed that the responses of pepper to Se stress involve various pathways. creator: Chenghao Zhang creator: Baoyu Xu creator: Wei Geng creator: Yunde Shen creator: Dongji Xuan creator: Qixian Lai creator: Chenjia Shen creator: Chengwu Jin creator: Chenliang Yu uri: https://doi.org/10.7717/peerj.8020 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Zhang et al. title: Intra-individual heteroplasmy in the Gentiana tongolensis plastid genome (Gentianaceae) link: https://peerj.com/articles/8025 last-modified: 2019-11-27 description: Chloroplasts are typically inherited from the female parent and are haploid in most angiosperms, but rare intra-individual heteroplasmy in plastid genomes has been reported in plants. Here, we report an example of plastome heteroplasmy and its characteristics in Gentiana tongolensis (Gentianaceae). The plastid genome of G. tongolensis is 145,757 bp in size and is missing parts of petD gene when compared with other Gentiana species. A total of 112 single nucleotide polymorphisms (SNPs) and 31 indels with frequencies of more than 2% were detected in the plastid genome, and most were located in protein coding regions. Most sites with SNP frequencies of more than 10% were located in six genes in the LSC region. After verification via cloning and Sanger sequencing at three loci, heteroplasmy was identified in different individuals. The cause of heteroplasmy at the nucleotide level in plastome of G. tongolensis is unclear from the present data, although biparental plastid inheritance and transfer of plastid DNA seem to be most likely. This study implies that botanists should reconsider the heredity and evolution of chloroplasts and be cautious with using chloroplasts as genetic markers, especially in Gentiana. creator: Shan-Shan Sun creator: Xiao-Jun Zhou creator: Zhi-Zhong Li creator: Hong-Yang Song creator: Zhi-Cheng Long creator: Peng-Cheng Fu uri: https://doi.org/10.7717/peerj.8025 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Sun et al.