title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=1236
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

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.

title: Field evaluation of Mosq-ovitrap, Ovitrap and a CO2-light trap for Aedes albopictus sampling in Shanghai, China
link: https://peerj.com/articles/8031
last-modified: 2019-11-27
description: BackgroundThe Mosq-ovitrap (MOT) is currently used for routine surveillance of container-breeding Aedes in China. However, the effectiveness of monitoring Aedes albopictus using the MOT and other mosquito monitoring methods, such as the Ovitrap (OT) and the CO2-light trap (CLT), have not been extensively compared. Moreover, little is known about the spatial-temporal correlations of eggs with adult Ae. albopictus abundance among these three types of traps.MethodsComparative field evaluation of MOT, OT and CLT for Ae. albopictus monitoring was conducted simultaneously at two city parks and three residential neighborhoods in downtown Shanghai for 8 months from April 21 to December 21, 2017.ResultsSignificantly more Ae. albopictus eggs were collected from both MOTs and OTs when traps remained in the field for 10 d or 7 d compared with 3 d (MOT: 50.16, 34.15 vs. 12.38 per trap, P < 0.001; OT: 3.98, 2.92 vs. 0.63 per trap, P < 0.001). Egg collections of MOTs were significantly greater than OTs for all three exposure durations (Percent positive: X2 = 72.251, 52.420 and 51.429, P value all < 0.001; egg collections: t = 8.068, 8.517 and 10.021, P value all <0.001). Significant temporal correlations were observed between yields of MOT and CLT in all sampling locations and 3 different MOT exposure durations (correlation coefficient r ranged from 0.439 to 0.850, P values all < 0.05). However, great variation was found in the spatial distributions of Ae. albopictus density between MOT and CLT. MOT considerably underestimated Ae. albopictus abundances in areas with high Ae. albopictus density (>25.56 per day ⋅ trap by CLT).ConclusionThe MOT was more efficient than the OT in percent positive scores and egg collections of Ae. albopictus. The minimum length of time that MOTs are deployed in the field should not be less than 7 d, as Ae. albopictus collections during this period were much greater than for 3 d of monitoring. MOT considerably underestimated Ae. albopictus abundance in areas with high Aedes albopictus density compared to CLT. In areas with moderate Aedes albopictus densities, MOT results were significantly correlated with CLT catches.
creator: Qiang Gao
creator: Hui Cao
creator: Jian Fan
creator: Zhendong Zhang
creator: Shuqing Jin
creator: Fei Su
creator: Peien Leng
creator: Chenglong Xiong
uri: https://doi.org/10.7717/peerj.8031
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2019 Gao et al.

title: Effects of elevated pCO2 and nutrient enrichment on the growth, photosynthesis, and biochemical compositions of the brown alga Saccharina japonica (Laminariaceae, Phaeophyta)
link: https://peerj.com/articles/8040
last-modified: 2019-11-27
description: Ocean acidification and eutrophication are two major environmental issues affecting kelp mariculture. In this study, the growth, photosynthesis, and biochemical compositions of adult sporophytes of Saccharina japonica were evaluated at different levels of pCO2 (400 and 800 µatm) and nutrients (nutrient-enriched and non-enriched seawater). The relative growth rate (RGR), net photosynthetic rate, and all tested biochemical contents (including chlorophyll (Chl) a, Chl c, soluble carbohydrates, and soluble proteins) were significantly lower at 800 µatm than at 400 µatm pCO2. The RGR and the contents of Chl a and soluble proteins were significantly higher under nutrient-enriched conditions than under non-enriched conditions. Moreover, the negative effects of the elevated pCO2 level on the RGR, net photosynthetic rate, Chl c and the soluble carbohydrates and proteins contents were synergized by the elevated nutrient availability. These results implied that increased pCO2could suppress the growth and biochemical composition of adult sporophytes of S. japonica. The interactive effects of ocean acidification and eutrophication constitute a great threat to the cultivation of S. japonica due to growth inhibition and a reduction in quality.
creator: Yaoyao Chu
creator: Yan Liu
creator: Jingyu Li
creator: Qingli Gong
uri: https://doi.org/10.7717/peerj.8040
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2019 Chu et al.

title: Seasonal variation in apparent conductivity and soil salinity at two Narragansett Bay, RI salt marshes
link: https://peerj.com/articles/8074
last-modified: 2019-11-27
description: Measurement of the apparent conductivity of salt marsh sediments using electromagnetic induction (EMI) is a rapid alternative to traditional methods of salinity determination that can be used to map soil salinity across a marsh surface. Soil salinity measures can provide information about marsh processes, since salinity is important in determining the structure and function of tidally influenced marsh communities. While EMI has been shown to accurately reflect salinity to a specified depth, more information is needed on the potential for spatial and temporal variability in apparent conductivity measures that may impact the interpretation of salinity data. In this study we mapped soil salinity at two salt marshes in the Narragansett Bay, RI estuary monthly over the course of several years to examine spatial and temporal trends in marsh salinity. Mean monthly calculated salinity was 25.8 ± 5.5 ppt at Narrow River marsh (NAR), located near the mouth of the Bay, and 17.7 ± 5.3 ppt at Passeonkquis marsh (PAS) located in the upper Bay. Salinity varied seasonally with both marshes, showing the lowest values (16.3 and 8.3 ppt, respectively) in April and highest values (35.4 and 26.2 ppt, respectively) in August. Contour plots of calculated salinities showed that while the mean whole-marsh calculated salinity at both sites changed over time, within-marsh patterns of higher versus lower salinity were maintained at NAR but changed over time at PAS. Calculated salinity was significantly negatively correlated with elevation at NAR during a sub-set of 12 sample events, but not at PAS. Best-supported linear regression models for both sites included one-month and 6-month cumulative rainfall, and tide state as potential factors driving observed changes in calculated salinity. Mapping apparent conductivity of salt marsh sediments may be useful both identifying within-marsh micro-habitats, and documenting marsh-wide changes in salinity over time.
creator: Richard McKinney
creator: Alana Hanson
creator: Roxanne Johnson
creator: Michael Charpentier
uri: https://doi.org/10.7717/peerj.8074
license: https://creativecommons.org/publicdomain/zero/1.0/
rights: 

title: Diatoms as indicators of the effects of river impoundment at multiple spatial scales
link: https://peerj.com/articles/8092
last-modified: 2019-11-27
description: River impoundment constitutes one of the most important anthropogenic impacts on the World’s rivers. An increasing number of studies have tried to quantify the effects of river impoundment on riverine ecosystems over the past two decades, often focusing on the effects of individual large reservoirs. This study is one of the first to use a large-scale, multi-year diatom dataset from a routine biomonitoring network to analyse sample sites downstream of a large number of water supply reservoirs (n = 77) and to compare them with paired unregulated control sites. We analysed benthic diatom assemblage structure and a set of derived indices, including ecological guilds, in tandem with multiple spatio-temporal variables to disclose patterns of ecological responses to reservoirs beyond the site-specific scale. Diatom assemblage structure at sites downstream of water supply reservoirs was significantly different to control sites, with the effect being most evident at the regional scale. We found that regional influences were important drivers of differences in assemblage structure at the national scale, although this effect was weaker at downstream sites, indicating the homogenising effect of river impoundment on diatom assemblages. Sites downstream of reservoirs typically exhibited a higher taxonomic richness, with the strongest increases found within the motile guild. In addition, Trophic Diatom Index (TDI) values were typically higher at downstream sites. Water quality gradients appeared to be an important driver of diatom assemblages, but the influence of other abiotic factors could not be ruled out and should be investigated further. Our results demonstrate the value of diatom assemblage data from national-scale biomonitoring networks to detect the effects of water supply reservoirs on instream communities at large spatial scales. This information may assist water resource managers with the future implementation of mitigation measures such as setting environmental flow targets.
creator: Hendrik J. Krajenbrink
creator: Mike Acreman
creator: Michael J. Dunbar
creator: Libby Greenway
creator: David M. Hannah
creator: Cédric L.R. Laizé
creator: David B. Ryves
creator: Paul J. Wood
uri: https://doi.org/10.7717/peerj.8092
license: http://www.nationalarchives.gov.uk/doc/open-government-licence/
rights: 

title: Evaluation of performance of leading algorithms for variant pathogenicity predictions and designing a combinatory predictor method: application to Rett syndrome variants
link: https://peerj.com/articles/8106
last-modified: 2019-11-27
description: BackgroundGenomics diagnostic tests are done for a wide spectrum of complex genetics conditions such as autism and cancer. The growth of technology has not only aided in successfully decoding the genetic variants that causes or trigger these disorders. However, interpretation of these variants is not a trivial task even at a level of distinguish pathogenic vs benign variants.MethodsWe used the clinically significant variants from ClinVar database to evaluate the performance of 14 most popular in-silico predictors using supervised learning methods. We implemented a feature selection and random forest classification algorithm to identify the best combination of predictors to evaluate the pathogenicity of a variant. Finally, we have also utilized this combination of predictors to reclassify the variants of unknown significance in MeCP2 gene that are associated with the Rett syndrome.ResultsThe results from analysis shows an optimized selection of prediction algorithm and developed a combinatory predictor method. Our combinatory approach of using both best performing independent and ensemble predictors reduces any algorithm biases in variant characterization. The reclassification of variants (such as VUS) in MECP2 gene associated with RETT syndrome suggest that the combinatory in-silico predictor approach had a higher success rate in categorizing their pathogenicity.
creator: Satishkumar Ranganathan Ganakammal
creator: Emil Alexov
uri: https://doi.org/10.7717/peerj.8106
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2019 Ganakammal and Alexov