PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Concentrated ambient PM2.5 exposure affects mice sperm quality and testosterone biosynthesis
items: Analysis of miRNA expression profiles in the liver of ClockΔ19 mutant mice
items: The discriminative power of the ReproQ: a client experience questionnaire in maternity care
items: Comparative proteomic analysis of pepper (Capsicum annuum L.) seedlings under selenium stress
items: Intra-individual heteroplasmy in the Gentiana tongolensis plastid genome (Gentianaceae)
items: Field evaluation of Mosq-ovitrap, Ovitrap and a CO2-light trap for Aedes albopictus sampling in Shanghai, China
items: Effects of elevated pCO2 and nutrient enrichment on the growth, photosynthesis, and biochemical compositions of the brown alga Saccharina japonica (Laminariaceae, Phaeophyta)
items: Seasonal variation in apparent conductivity and soil salinity at two Narragansett Bay, RI salt marshes
items: Diatoms as indicators of the effects of river impoundment at multiple spatial scales
items: Evaluation of performance of leading algorithms for variant pathogenicity predictions and designing a combinatory predictor method: application to Rett syndrome variants

Concentrated ambient PM2.5 exposure affects mice sperm quality and testosterone biosynthesis
type: item
type: AcademicArticle
description: Background Studies 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. Methods A 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). Results Exposure 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. Conclus…
format: application/pdf
format: text/html
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
subject: Toxicology
subject: Andrology
subject: Public Health
subject: Ecotoxicology
description: doi:10.7717/peerj.8109
publisher: PeerJ Inc.
rights: © 2019 Yang et al.
abstract: Background Studies 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. Methods A 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). Results Exposure 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. Conclus…
bibliographic citation: Yang et al. (2019) Concentrated ambient PM2.5 exposure affects mice sperm quality and testosterone biosynthesis. PeerJ 7:e8109 https://doi.org/10.7717/peerj.8109
date submitted: 2019-08-20
date accepted: 2019-10-28
issued: 2019-11-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Yingying
author list: Agent
  family name: Yang
  given name: Tingting
author list: Agent
  family name: Liu
  given name: Shengxin
author list: Agent
  family name: Cao
  given name: Zhijuan
author list: Agent
  family name: Zhao
  given name: Yan
author list: Agent
  family name: Su
  given name: Xiujuan
author list: Agent
  family name: Liao
  given name: Zehuan
author list: Agent
  family name: Teng
  given name: Xiaoming
author list: Agent
  family name: Hua
  given name: Jing
doi: 10.7717/peerj.8109
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-28
copyright: © 2019 Yang et al.
attribution name: Yang et al.

Analysis of miRNA expression profiles in the liver of ClockΔ19 mutant mice
type: item
type: AcademicArticle
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.
format: application/pdf
format: text/html
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
subject: Molecular Biology
description: doi:10.7717/peerj.8119
publisher: PeerJ Inc.
rights: © 2019 Wang et al.
abstract: 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.
bibliographic citation: Wang et al. (2019) Analysis of miRNA expression profiles in the liver of ClockΔ19 mutant mice. PeerJ 7:e8119 https://doi.org/10.7717/peerj.8119
date submitted: 2018-10-29
date accepted: 2019-10-29
issued: 2019-11-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Yanli
author list: Agent
  family name: Lv
  given name: Ke
author list: Agent
  family name: Zhao
  given name: Mei
author list: Agent
  family name: Chen
  given name: Hailong
author list: Agent
  family name: Ji
  given name: Guohua
author list: Agent
  family name: Zhang
  given name: Yongliang
author list: Agent
  family name: Wang
  given name: Tingmei
author list: Agent
  family name: Cao
  given name: Hongqing
author list: Agent
  family name: Li
  given name: Yinghui
author list: Agent
  family name: Qu
  given name: Lina
doi: 10.7717/peerj.8119
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-28
copyright: © 2019 Wang et al.
attribution name: Wang et al.

The discriminative power of the ReproQ: a client experience questionnaire in maternity care
type: item
type: AcademicArticle
description: Background The 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. Methods We 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. Results ICCs 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. Conclusions ReproQ, 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.
format: application/pdf
format: text/html
creator: Marisja Scheerhagen
creator: Henk F. van Stel
creator: Arie Franx
creator: Erwin Birnie
creator: Gouke J. Bonsel
subject: Gynecology and Obstetrics
subject: Health Policy
subject: Women’s Health
description: doi:10.7717/peerj.7575
publisher: PeerJ Inc.
rights: © 2019 Scheerhagen et al.
abstract: Background The 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. Methods We 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. Results ICCs 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. Conclusions ReproQ, 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.
bibliographic citation: Scheerhagen et al. (2019) The discriminative power of the ReproQ: a client experience questionnaire in maternity care. PeerJ 7:e7575 https://doi.org/10.7717/peerj.7575
date submitted: 2019-02-07
date accepted: 2019-07-29
issued: 2019-11-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Scheerhagen
  given name: Marisja
author list: Agent
  family name: van Stel
  given name: Henk F.
author list: Agent
  family name: Franx
  given name: Arie
author list: Agent
  family name: Birnie
  given name: Erwin
author list: Agent
  family name: Bonsel
  given name: Gouke J.
doi: 10.7717/peerj.7575
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-27
copyright: ©2019 Scheerhagen et al.
attribution name: Scheerhagen et al.

Comparative proteomic analysis of pepper (Capsicum annuum L.) seedlings under selenium stress
type: item
type: AcademicArticle
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.
format: application/pdf
format: text/html
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
subject: Agricultural Science
subject: Bioinformatics
subject: Molecular Biology
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
description: doi:10.7717/peerj.8020
publisher: PeerJ Inc.
rights: © 2019 Zhang et al.
abstract: 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.
bibliographic citation: Zhang et al. (2019) Comparative proteomic analysis of pepper (Capsicum annuum L.) seedlings under selenium stress. PeerJ 7:e8020 https://doi.org/10.7717/peerj.8020
date submitted: 2019-04-23
date accepted: 2019-10-09
issued: 2019-11-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Chenghao
author list: Agent
  family name: Xu
  given name: Baoyu
author list: Agent
  family name: Geng
  given name: Wei
author list: Agent
  family name: Shen
  given name: Yunde
author list: Agent
  family name: Xuan
  given name: Dongji
author list: Agent
  family name: Lai
  given name: Qixian
author list: Agent
  family name: Shen
  given name: Chenjia
author list: Agent
  family name: Jin
  given name: Chengwu
author list: Agent
  family name: Yu
  given name: Chenliang
doi: 10.7717/peerj.8020
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-27
copyright: © 2019 Zhang et al.
attribution name: Zhang et al.

Intra-individual heteroplasmy in the Gentiana tongolensis plastid genome (Gentianaceae)
type: item
type: AcademicArticle
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.
format: application/pdf
format: text/html
creator: Shan-Shan Sun
creator: Xiao-Jun Zhou
creator: Zhi-Zhong Li
creator: Hong-Yang Song
creator: Zhi-Cheng Long
creator: Peng-Cheng Fu
subject: Evolutionary Studies
subject: Plant Science
description: doi:10.7717/peerj.8025
publisher: PeerJ Inc.
rights: © 2019 Sun et al.
abstract: 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.
bibliographic citation: Sun et al. (2019) Intra-individual heteroplasmy in the Gentiana tongolensis plastid genome (Gentianaceae). PeerJ 7:e8025 https://doi.org/10.7717/peerj.8025
date submitted: 2019-02-19
date accepted: 2019-10-11
issued: 2019-11-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Shan-Shan
author list: Agent
  family name: Zhou
  given name: Xiao-Jun
author list: Agent
  family name: Li
  given name: Zhi-Zhong
author list: Agent
  family name: Song
  given name: Hong-Yang
author list: Agent
  family name: Long
  given name: Zhi-Cheng
author list: Agent
  family name: Fu
  given name: Peng-Cheng
doi: 10.7717/peerj.8025
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-27
copyright: © 2019 Sun et al.
attribution name: Sun et al.

Field evaluation of Mosq-ovitrap, Ovitrap and a CO2-light trap for Aedes albopictus sampling in Shanghai, China
type: item
type: AcademicArticle
description: Background The 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. Methods Comparative 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. Results Significantly 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). Conclusion The 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 abundan…
format: application/pdf
format: text/html
creator: Qiang Gao
creator: Hui Cao
creator: Jian Fan
creator: Zhendong Zhang
creator: Shuqing Jin
creator: Fei Su
creator: Peien Leng
creator: Chenglong Xiong
subject: Entomology
subject: Parasitology
description: doi:10.7717/peerj.8031
publisher: PeerJ Inc.
rights: © 2019 Gao et al.
abstract: Background The 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. Methods Comparative 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. Results Significantly 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). Conclusion The 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 abundan…
bibliographic citation: Gao et al. (2019) Field evaluation of Mosq-ovitrap, Ovitrap and a CO2-light trap for Aedes albopictus sampling in Shanghai, China. PeerJ 7:e8031 https://doi.org/10.7717/peerj.8031
date submitted: 2019-06-13
date accepted: 2019-10-14
issued: 2019-11-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gao
  given name: Qiang
author list: Agent
  family name: Cao
  given name: Hui
author list: Agent
  family name: Fan
  given name: Jian
author list: Agent
  family name: Zhang
  given name: Zhendong
author list: Agent
  family name: Jin
  given name: Shuqing
author list: Agent
  family name: Su
  given name: Fei
author list: Agent
  family name: Leng
  given name: Peien
author list: Agent
  family name: Xiong
  given name: Chenglong
doi: 10.7717/peerj.8031
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-27
copyright: ©2019 Gao et al.
attribution name: Gao et al.

Effects of elevated pCO2 and nutrient enrichment on the growth, photosynthesis, and biochemical compositions of the brown alga Saccharina japonica (Laminariaceae, Phaeophyta)
type: item
type: AcademicArticle
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.
format: application/pdf
format: text/html
creator: Yaoyao Chu
creator: Yan Liu
creator: Jingyu Li
creator: Qingli Gong
subject: Ecology
subject: Marine Biology
subject: Plant Science
subject: Synthetic Biology
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.8040
publisher: PeerJ Inc.
rights: © 2019 Chu et al.
abstract: 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.
bibliographic citation: Chu et al. (2019) Effects of elevated pCO2 and nutrient enrichment on the growth, photosynthesis, and biochemical compositions of the brown alga Saccharina japonica (Laminariaceae, Phaeophyta). PeerJ 7:e8040 https://doi.org/10.7717/peerj.8040
date submitted: 2019-07-24
date accepted: 2019-10-15
issued: 2019-11-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chu
  given name: Yaoyao
author list: Agent
  family name: Liu
  given name: Yan
author list: Agent
  family name: Li
  given name: Jingyu
author list: Agent
  family name: Gong
  given name: Qingli
doi: 10.7717/peerj.8040
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-27
copyright: ©2019 Chu et al.
attribution name: Chu et al.

Seasonal variation in apparent conductivity and soil salinity at two Narragansett Bay, RI salt marshes
type: item
type: AcademicArticle
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.
format: application/pdf
format: text/html
creator: Richard McKinney
creator: Alana Hanson
creator: Roxanne Johnson
creator: Michael Charpentier
subject: Ecosystem Science
subject: Soil Science
subject: Aquatic and Marine Chemistry
description: doi:10.7717/peerj.8074
publisher: PeerJ Inc.
rights: ©
abstract: 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.
bibliographic citation: McKinney et al. (2019) Seasonal variation in apparent conductivity and soil salinity at two Narragansett Bay, RI salt marshes. PeerJ 7:e8074 https://doi.org/10.7717/peerj.8074
date submitted: 2019-05-16
date accepted: 2019-10-21
issued: 2019-11-27
is part of: PeerJ
license: https://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: McKinney
  given name: Richard
author list: Agent
  family name: Hanson
  given name: Alana
author list: Agent
  family name: Johnson
  given name: Roxanne
author list: Agent
  family name: Charpentier
  given name: Michael
doi: 10.7717/peerj.8074
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-27

Diatoms as indicators of the effects of river impoundment at multiple spatial scales
type: item
type: AcademicArticle
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 t…
format: application/pdf
format: text/html
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
subject: Freshwater Biology
subject: Ecohydrology
description: doi:10.7717/peerj.8092
publisher: PeerJ Inc.
rights: ©
abstract: 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 t…
bibliographic citation: Krajenbrink et al. (2019) Diatoms as indicators of the effects of river impoundment at multiple spatial scales. PeerJ 7:e8092 https://doi.org/10.7717/peerj.8092
date submitted: 2019-07-08
date accepted: 2019-10-23
issued: 2019-11-27
is part of: PeerJ
license: open-government-licence
author list: Agent
  family name: Krajenbrink
  given name: Hendrik J.
author list: Agent
  family name: Acreman
  given name: Mike
author list: Agent
  family name: Dunbar
  given name: Michael J.
author list: Agent
  family name: Greenway
  given name: Libby
author list: Agent
  family name: Hannah
  given name: David M.
author list: Agent
  family name: Laizé
  given name: Cédric L.R.
author list: Agent
  family name: Ryves
  given name: David B.
author list: Agent
  family name: Wood
  given name: Paul J.
doi: 10.7717/peerj.8092
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-27

Evaluation of performance of leading algorithms for variant pathogenicity predictions and designing a combinatory predictor method: application to Rett syndrome variants
type: item
type: AcademicArticle
description: Background Genomics 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. Methods We 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. Results The 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.
format: application/pdf
format: text/html
creator: Satishkumar Ranganathan Ganakammal
creator: Emil Alexov
subject: Bioinformatics
subject: Computational Biology
subject: Pathology
subject: Medical Genetics
subject: Computational Science
description: doi:10.7717/peerj.8106
publisher: PeerJ Inc.
rights: © 2019 Ganakammal and Alexov
abstract: Background Genomics 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. Methods We 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. Results The 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.
bibliographic citation: Ganakammal et al. (2019) Evaluation of performance of leading algorithms for variant pathogenicity predictions and designing a combinatory predictor method: application to Rett syndrome variants. PeerJ 7:e8106 https://doi.org/10.7717/peerj.8106
date submitted: 2019-07-24
date accepted: 2019-10-27
issued: 2019-11-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ganakammal
  given name: Satishkumar Ranganathan
author list: Agent
  family name: Alexov
  given name: Emil
doi: 10.7717/peerj.8106
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-27
copyright: © 2019 Ganakammal and Alexov
attribution name: Ganakammal and Alexov

PeerJ
type: Periodical
uri: PeerJ
issn: 2167-8359