PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Interspecific differences of stridulatory signals in three species of bark beetles from the genus Polygraphus Er. (Coleoptera: Curculionidae, Scolytinae) inhabiting the island of Sakhalin
items: Ambulatory sleep scoring using accelerometers—distinguishing between nonwear and sleep/wake states
items: Basic and target eco-environment water requirements of a dry inland river under typical flow frequencies in China
items: Use of environmental DNA (eDNA) in streams to detect feral swine (Sus scrofa)
items: The fossil record of the genus Varanus from the Southern Caucasus (Armenia, Georgia)
items: A new insight to biomarkers related to resistance in survived-white spot syndrome virus challenged giant tiger shrimp, Penaeus monodon
items: Comparative RNA-sequencing profiled the differential gene expression of liver in response to acetyl-CoA carboxylase inhibitor GS-0976 in a mouse model of NASH
items: Genetic links between endometriosis and cancers in women
items: Evaluation of human-papillomavirus screening for cervical cancer in China’s rural population
items: Systematic evaluation of the gut microbiome of swamp eel (Monopterus albus) by 16S rRNA gene sequencing

Interspecific differences of stridulatory signals in three species of bark beetles from the genus Polygraphus Er. (Coleoptera: Curculionidae, Scolytinae) inhabiting the island of Sakhalin
type: item
type: AcademicArticle
description: Stridulatory signals are involved in conspecific interactions between bark beetles (Coleoptera: Curculionidae, Scolytinae). In this study, we compared the qualitative profiles of acoustic signals in three species from the genus Polygraphus Er. Sympatry can be periodically observed in two of them –P. proximus and P. subopacus. Sporadically they occur on the same plants. P. nigrielytris colonize distinctly different host plant species; however, on the island of Sakhalin it inhabits the same biotopes. The purpose of the study is to identify species-specific parameters and the extent of differences in stridulatory signals of these species. Airborne signals produced during the contact of males of the same species were experimentally recorded. Among tested parameters of stridulatory signals, as the most species-specific were noted: chirp duration, number of tooth-strikes per chirp, and intertooth-strike interval.
format: application/pdf
format: text/html
creator: Ivan Andreevich Kerchev
subject: Animal Behavior
subject: Biophysics
subject: Entomology
subject: Zoology
description: doi:10.7717/peerj.8281
publisher: PeerJ Inc.
rights: © 2020 Kerchev
abstract: Stridulatory signals are involved in conspecific interactions between bark beetles (Coleoptera: Curculionidae, Scolytinae). In this study, we compared the qualitative profiles of acoustic signals in three species from the genus Polygraphus Er. Sympatry can be periodically observed in two of them –P. proximus and P. subopacus. Sporadically they occur on the same plants. P. nigrielytris colonize distinctly different host plant species; however, on the island of Sakhalin it inhabits the same biotopes. The purpose of the study is to identify species-specific parameters and the extent of differences in stridulatory signals of these species. Airborne signals produced during the contact of males of the same species were experimentally recorded. Among tested parameters of stridulatory signals, as the most species-specific were noted: chirp duration, number of tooth-strikes per chirp, and intertooth-strike interval.
bibliographic citation: Kerchev (2020) Interspecific differences of stridulatory signals in three species of bark beetles from the genus Polygraphus Er. (Coleoptera: Curculionidae, Scolytinae) inhabiting the island of Sakhalin. PeerJ 8:e8281 https://doi.org/10.7717/peerj.8281
date submitted: 2019-04-30
date accepted: 2019-11-22
issued: 2020-01-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kerchev
  given name: Ivan Andreevich
doi: 10.7717/peerj.8281
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-02
copyright: ©2020 Kerchev
attribution name: Kerchev

Ambulatory sleep scoring using accelerometers—distinguishing between nonwear and sleep/wake states
type: item
type: AcademicArticle
description: Background Differentiating nonwear time from sleep and wake times is essential for the estimation of sleep duration based on actigraphy data. To efficiently analyze large-scale data sets, an automatic method of identifying these three different states is required. Therefore, we developed a classification algorithm to determine nonwear, sleep and wake periods from accelerometer data. Our work aimed to (I) develop a new pattern recognition algorithm for identifying nonwear periods from actigraphy data based on the influence of respiration rate on the power spectrum of the acceleration signal and implement it in an automatic classification algorithm for nonwear/sleep/wake states; (II) address motion artifacts that occur during nonwear periods and are known to cause misclassification of these periods; (III) adjust the algorithm depending on the sensor position (wrist, chest); and (IV) validate the algorithm on both healthy individuals and patients with sleep disorders. Methods The study involved 98 participants who wore wrist and chest acceleration sensors for one day of measurements. They spent one night in the sleep laboratory and continued to wear the sensors outside of the laboratory for the remainder of the day. The results of the classification algorithm were compared to those of the reference source: polysomnography for wake/sleep and manual annotations for nonwear/wear classification. Results The median kappa values for the two locations were 0.83 (wrist) and 0.84 (chest). The level of agreement did not vary significantly by sleep health (good sleepers vs. subjects with sleep disorders) (p = 0.348, p = 0.118) or by sex (p = 0.442, p = 0.456). The intraclass correlation coefficients of nonwear total time between the reference and the algorithm were 0.92 and 0.97 with the outliers and 0.95 and 0.98 after the outliers were removed for the wrist and chest, respectively. There was no evidence of an association between the mean difference (and 95% limits of agreement)…
format: application/pdf
format: text/html
creator: Amna Barouni
creator: Jörg Ottenbacher
creator: Johannes Schneider
creator: Bernd Feige
creator: Dieter Riemann
creator: Anne Herlan
creator: Driss El Hardouz
creator: Darren McLennan
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.8284
publisher: PeerJ Inc.
rights: © 2020 Barouni et al.
abstract: Background Differentiating nonwear time from sleep and wake times is essential for the estimation of sleep duration based on actigraphy data. To efficiently analyze large-scale data sets, an automatic method of identifying these three different states is required. Therefore, we developed a classification algorithm to determine nonwear, sleep and wake periods from accelerometer data. Our work aimed to (I) develop a new pattern recognition algorithm for identifying nonwear periods from actigraphy data based on the influence of respiration rate on the power spectrum of the acceleration signal and implement it in an automatic classification algorithm for nonwear/sleep/wake states; (II) address motion artifacts that occur during nonwear periods and are known to cause misclassification of these periods; (III) adjust the algorithm depending on the sensor position (wrist, chest); and (IV) validate the algorithm on both healthy individuals and patients with sleep disorders. Methods The study involved 98 participants who wore wrist and chest acceleration sensors for one day of measurements. They spent one night in the sleep laboratory and continued to wear the sensors outside of the laboratory for the remainder of the day. The results of the classification algorithm were compared to those of the reference source: polysomnography for wake/sleep and manual annotations for nonwear/wear classification. Results The median kappa values for the two locations were 0.83 (wrist) and 0.84 (chest). The level of agreement did not vary significantly by sleep health (good sleepers vs. subjects with sleep disorders) (p = 0.348, p = 0.118) or by sex (p = 0.442, p = 0.456). The intraclass correlation coefficients of nonwear total time between the reference and the algorithm were 0.92 and 0.97 with the outliers and 0.95 and 0.98 after the outliers were removed for the wrist and chest, respectively. There was no evidence of an association between the mean difference (and 95% limits of agreement)…
bibliographic citation: Barouni et al. (2020) Ambulatory sleep scoring using accelerometers—distinguishing between nonwear and sleep/wake states. PeerJ 8:e8284 https://doi.org/10.7717/peerj.8284
date submitted: 2018-10-23
date accepted: 2019-11-24
issued: 2020-01-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Barouni
  given name: Amna
author list: Agent
  family name: Ottenbacher
  given name: Jörg
author list: Agent
  family name: Schneider
  given name: Johannes
author list: Agent
  family name: Feige
  given name: Bernd
author list: Agent
  family name: Riemann
  given name: Dieter
author list: Agent
  family name: Herlan
  given name: Anne
author list: Agent
  family name: El Hardouz
  given name: Driss
author list: Agent
  family name: McLennan
  given name: Darren
doi: 10.7717/peerj.8284
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-02
copyright: ©2020 Barouni et al.
attribution name: Barouni et al.

Basic and target eco-environment water requirements of a dry inland river under typical flow frequencies in China
type: item
type: AcademicArticle
description: Analysis of eco-environmental water requirements (EEWRs) and water resource allocation strategies for arid, inland river basins can provide the theoretical basis for sustainable water utilization and management. In this paper, an optimal water resource allocation strategy is proposed for Yarkand River Basin in Xinjiang, China, on the basis of a comprehensive analysis of runoff data collected between 1970 and 2016, three ecological environmental protection goals, basic eco-environmental water requirement (BEEWR) aimed at sustaining aquatic ecosystems within the river, and target eco-environmental water requirements (TEEWR) aimed at protecting various types of riparian vegetation along the river. The results showed that: (1) after the runoff in Kaqun reach subtracting the BEEWR, the annual average river loss (recharge), and the amount of water diversion for irrigation (51.43 × 108 m3) from flows along the Kaqun reach, the remaining water volume during wet years was able to meet all three TEEWRs; (2) during moderately wet years, the remaining water was capable of meeting the second and third TEEWRs; and (3) during dry and extremely dry years, there was little or no residual water available to meet TEEWRs. The proposed optimal water resource allocation strategy, based on the above findings, states that the water diversion requirement for irrigation and domestic use allocated from the total amount of runoff should not exceed the National Water Policy (Three Red Lines) standard first. Then, the BEEWR allocated from the runoff should be met second, and the annual average river loss, third. Depending on the amount of remaining water, the second and third TEEWRs can be fulfilled during wet years, but during moderately wet years, only the third TEEWR can be met. During dry and extremely dry years, only the BEEWR of the river can be met and only during the flood season.
format: application/pdf
format: text/html
creator: Aihong Fu
creator: Weihong Li
creator: Yi Wang
creator: Yifei Bai
subject: Ecology
subject: Ecohydrology
description: doi:10.7717/peerj.8285
publisher: PeerJ Inc.
rights: © 2020 Fu et al.
abstract: Analysis of eco-environmental water requirements (EEWRs) and water resource allocation strategies for arid, inland river basins can provide the theoretical basis for sustainable water utilization and management. In this paper, an optimal water resource allocation strategy is proposed for Yarkand River Basin in Xinjiang, China, on the basis of a comprehensive analysis of runoff data collected between 1970 and 2016, three ecological environmental protection goals, basic eco-environmental water requirement (BEEWR) aimed at sustaining aquatic ecosystems within the river, and target eco-environmental water requirements (TEEWR) aimed at protecting various types of riparian vegetation along the river. The results showed that: (1) after the runoff in Kaqun reach subtracting the BEEWR, the annual average river loss (recharge), and the amount of water diversion for irrigation (51.43 × 108 m3) from flows along the Kaqun reach, the remaining water volume during wet years was able to meet all three TEEWRs; (2) during moderately wet years, the remaining water was capable of meeting the second and third TEEWRs; and (3) during dry and extremely dry years, there was little or no residual water available to meet TEEWRs. The proposed optimal water resource allocation strategy, based on the above findings, states that the water diversion requirement for irrigation and domestic use allocated from the total amount of runoff should not exceed the National Water Policy (Three Red Lines) standard first. Then, the BEEWR allocated from the runoff should be met second, and the annual average river loss, third. Depending on the amount of remaining water, the second and third TEEWRs can be fulfilled during wet years, but during moderately wet years, only the third TEEWR can be met. During dry and extremely dry years, only the BEEWR of the river can be met and only during the flood season.
bibliographic citation: Fu et al. (2020) Basic and target eco-environment water requirements of a dry inland river under typical flow frequencies in China. PeerJ 8:e8285 https://doi.org/10.7717/peerj.8285
date submitted: 2019-08-15
date accepted: 2019-11-24
issued: 2020-01-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fu
  given name: Aihong
author list: Agent
  family name: Li
  given name: Weihong
author list: Agent
  family name: Wang
  given name: Yi
author list: Agent
  family name: Bai
  given name: Yifei
doi: 10.7717/peerj.8285
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-02
copyright: © 2020 Fu et al.
attribution name: Fu et al.

Use of environmental DNA (eDNA) in streams to detect feral swine (Sus scrofa)
type: item
type: AcademicArticle
description: Invasive feral swine can damage ecosystems, disrupt plant and animal populations, and transmit diseases. Monitoring of feral swine populations requires expensive and labor-intensive techniques such as aerial surveys, field surveys for sign, trail cameras, and verifying landowner reports. Environmental DNA (eDNA) provides an alternative method for locating feral swine. To aid in detection of this harmful invasive species, a novel assay was developed incorporating molecular methods. From August 2017 to April 2018, water samples and stream data were collected along 400 m transects in two different stream types where swine DNA was artificially introduced to investigate potential factors affecting detection. A generalized linear model (family binomial) was used to characterize environmental conditions affecting swine DNA detection; detection was the dependent variable and stream measurements included stream type, distance downstream, water temperature, velocity, turbidity, discharge, and pH as independent variables. Parameters from the generalized linear model were deemed significant if 95% confidence intervals did not overlap 0. Detection probability for swine DNA negatively related to water temperature (β = − 0.21, 95% CI [−0.35 to −0.09]), with the highest detection probability (0.80) at 0 °C and lowest detection probability (0.05) at 17.9 °C water temperature. Results indicate that sampling for swine eDNA in free-flowing stream systems should occur at lower water temperatures to maximize detection probability. This study provides a foundation for further development of field and sampling techniques for utilizing eDNA as a viable alternative to monitoring a terrestrial invasive species in northern regions of the United States.
format: application/pdf
format: text/html
creator: Amberly N. Hauger
creator: Karmen M. Hollis-Etter
creator: Dwayne R. Etter
creator: Gary J. Roloff
creator: Andrew R. Mahon
subject: Ecology
subject: Genetics
subject: Natural Resource Management
description: doi:10.7717/peerj.8287
publisher: PeerJ Inc.
rights: © 2020 Hauger et al.
abstract: Invasive feral swine can damage ecosystems, disrupt plant and animal populations, and transmit diseases. Monitoring of feral swine populations requires expensive and labor-intensive techniques such as aerial surveys, field surveys for sign, trail cameras, and verifying landowner reports. Environmental DNA (eDNA) provides an alternative method for locating feral swine. To aid in detection of this harmful invasive species, a novel assay was developed incorporating molecular methods. From August 2017 to April 2018, water samples and stream data were collected along 400 m transects in two different stream types where swine DNA was artificially introduced to investigate potential factors affecting detection. A generalized linear model (family binomial) was used to characterize environmental conditions affecting swine DNA detection; detection was the dependent variable and stream measurements included stream type, distance downstream, water temperature, velocity, turbidity, discharge, and pH as independent variables. Parameters from the generalized linear model were deemed significant if 95% confidence intervals did not overlap 0. Detection probability for swine DNA negatively related to water temperature (β = − 0.21, 95% CI [−0.35 to −0.09]), with the highest detection probability (0.80) at 0 °C and lowest detection probability (0.05) at 17.9 °C water temperature. Results indicate that sampling for swine eDNA in free-flowing stream systems should occur at lower water temperatures to maximize detection probability. This study provides a foundation for further development of field and sampling techniques for utilizing eDNA as a viable alternative to monitoring a terrestrial invasive species in northern regions of the United States.
bibliographic citation: Hauger et al. (2020) Use of environmental DNA (eDNA) in streams to detect feral swine (Sus scrofa). PeerJ 8:e8287 https://doi.org/10.7717/peerj.8287
date submitted: 2019-05-22
date accepted: 2019-11-24
issued: 2020-01-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hauger
  given name: Amberly N.
author list: Agent
  family name: Hollis-Etter
  given name: Karmen M.
author list: Agent
  family name: Etter
  given name: Dwayne R.
author list: Agent
  family name: Roloff
  given name: Gary J.
author list: Agent
  family name: Mahon
  given name: Andrew R.
doi: 10.7717/peerj.8287
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-02
copyright: ©2020 Hauger et al.
attribution name: Hauger et al.

The fossil record of the genus Varanus from the Southern Caucasus (Armenia, Georgia)
type: item
type: AcademicArticle
description: The Southern Caucasus, with its special geographic position and complex topography, is a well-known biodiversity hotspot. However, the formation of this hotspot remains largely unstudied. To reveal this, a thorough study of the fossil record of the region is necessary. In the present paper, we describe for the first time fossil monitor lizards (Varanus sp.) from two late Miocene localities from the Southern Caucasus (Jradzor, Armenia and Tetri Udabno, Georgia). We suggest that both fossils belong to a small-sized monitor lizard, comparable to the present-day species found in Iran and the Middle East (e.g., Iraq, Saudi Arabian)—the most western part of the extant monitor lizards’ Eurasian distribution range. Our finds show that the genus had a broad distribution in the Eastern Paratethyan region during the late Miocene. In addition, we provide the probable temperature ranges for fossil localities.
format: application/pdf
format: text/html
creator: Davit Vasilyan
creator: Maia Bukhsianidze
subject: Biodiversity
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.8322
publisher: PeerJ Inc.
rights: © 2020 Vasilyan and Bukhsianidze
abstract: The Southern Caucasus, with its special geographic position and complex topography, is a well-known biodiversity hotspot. However, the formation of this hotspot remains largely unstudied. To reveal this, a thorough study of the fossil record of the region is necessary. In the present paper, we describe for the first time fossil monitor lizards (Varanus sp.) from two late Miocene localities from the Southern Caucasus (Jradzor, Armenia and Tetri Udabno, Georgia). We suggest that both fossils belong to a small-sized monitor lizard, comparable to the present-day species found in Iran and the Middle East (e.g., Iraq, Saudi Arabian)—the most western part of the extant monitor lizards’ Eurasian distribution range. Our finds show that the genus had a broad distribution in the Eastern Paratethyan region during the late Miocene. In addition, we provide the probable temperature ranges for fossil localities.
bibliographic citation: Vasilyan et al. (2020) The fossil record of the genus Varanus from the Southern Caucasus (Armenia, Georgia). PeerJ 8:e8322 https://doi.org/10.7717/peerj.8322
date submitted: 2019-09-13
date accepted: 2019-11-30
issued: 2020-01-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vasilyan
  given name: Davit
author list: Agent
  family name: Bukhsianidze
  given name: Maia
doi: 10.7717/peerj.8322
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-02
copyright: ©2020 Vasilyan and Bukhsianidze
attribution name: Vasilyan and Bukhsianidze

A new insight to biomarkers related to resistance in survived-white spot syndrome virus challenged giant tiger shrimp, Penaeus monodon
type: item
type: AcademicArticle
description: The emergence of diseases such as white spot disease has become a threat to Penaeus monodon cultivation. Although there have been a few studies utilizing RNA-Seq, the cellular processes of host-virus interaction in this species remain mostly anonymous. In the present study, P. monodon was challenged with WSSV by intramuscular injection and survived for 12 days. The effect of the host gene expression by WSSV infection in the haemocytes, hepatopancreas and muscle of P. monodon was studied using Illumina HiSeq 2000. The RNA-Seq of cDNA libraries was developed from surviving WSSV-challenged shrimp as well as from normal healthy shrimp as control. A comparison of the transcriptome data of the two groups showed 2,644 host genes to be significantly up-regulated and 2,194 genes significantly down-regulated as a result of the infection with WSSV. Among the differentially expressed genes, our study discovered HMGB, TNFSF and c-Jun in P. monodon as new potential candidate genes for further investigation for the development of potential disease resistance markers. Our study also provided significant data on the differential expression of genes in the survived WSSV infected P. monodon that will help to improve understanding of host-virus interactions in this species.
format: application/pdf
format: text/html
creator: Farhana Mohd Ghani
creator: Subha Bhassu
subject: Aquaculture, Fisheries and Fish Science
subject: Bioinformatics
subject: Food Science and Technology
subject: Genomics
subject: Marine Biology
description: doi:10.7717/peerj.8107
publisher: PeerJ Inc.
rights: © 2019 Mohd Ghani and Bhassu
abstract: The emergence of diseases such as white spot disease has become a threat to Penaeus monodon cultivation. Although there have been a few studies utilizing RNA-Seq, the cellular processes of host-virus interaction in this species remain mostly anonymous. In the present study, P. monodon was challenged with WSSV by intramuscular injection and survived for 12 days. The effect of the host gene expression by WSSV infection in the haemocytes, hepatopancreas and muscle of P. monodon was studied using Illumina HiSeq 2000. The RNA-Seq of cDNA libraries was developed from surviving WSSV-challenged shrimp as well as from normal healthy shrimp as control. A comparison of the transcriptome data of the two groups showed 2,644 host genes to be significantly up-regulated and 2,194 genes significantly down-regulated as a result of the infection with WSSV. Among the differentially expressed genes, our study discovered HMGB, TNFSF and c-Jun in P. monodon as new potential candidate genes for further investigation for the development of potential disease resistance markers. Our study also provided significant data on the differential expression of genes in the survived WSSV infected P. monodon that will help to improve understanding of host-virus interactions in this species.
bibliographic citation: Mohd Ghani et al. (2019) A new insight to biomarkers related to resistance in survived-white spot syndrome virus challenged giant tiger shrimp, Penaeus monodon. PeerJ 7:e8107 https://doi.org/10.7717/peerj.8107
date submitted: 2019-02-18
date accepted: 2019-10-27
issued: 2019-12-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mohd Ghani
  given name: Farhana
author list: Agent
  family name: Bhassu
  given name: Subha
doi: 10.7717/peerj.8107
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-20
copyright: ©2019 Mohd Ghani and Bhassu
attribution name: Mohd Ghani and Bhassu

Comparative RNA-sequencing profiled the differential gene expression of liver in response to acetyl-CoA carboxylase inhibitor GS-0976 in a mouse model of NASH
type: item
type: AcademicArticle
description: Background Non-alcoholic steatohepatitis (NASH) is a progressive liver disease characterized by hepatic steatosis, lobular inflammation and fibrosis. Acetyl-CoA carboxylase (ACC) isoform 1 and 2 involved in de novo lipogenesis (DNL) and fatty acid oxidation have been identified as a therapeutic target in NASH. GS-0976, the inhibitor of ACC1 and ACC2, has achieved favorable therapeutic effects in clinical trials with NASH. The purpose of this study was to explore the transcriptional alterations regulated by GS-0976 in NASH. Methods C57BL/6 mice were fed on a choline-deficient, L-amino acid-defined, high-fat diet (CDAHFD) or normal diet for 12 weeks. Mice were treated with or without GS-0976 (3 mg/kg per day) in the last 8 weeks. Oil Red O, Haematoxylin-eosin (H & E), and Sirius Red were used to evaluate hepatic steatosis, inflammation and fibrosis. The comparative RNA-sequencing was conducted to analyse the hepatic gene expression profiles in mice. Reverse transcription–polymerase chain reaction analysis was performed to validate the differential expression of representative genes. Results GS-0976 attenuated the steatosis, inflammation, and fibrosis of NASH in CDAHFD mouse model. High-throughput sequencing and differential gene expression analysis showed that there were 516 up-regulated genes and 525 down-regulated genes after GS-0976 treatment. Genes involved in the metabolic process, extracellular matrix formation, immune response, and angiogenesis were significantly enriched. The “Metabolic pathways” and “ECM-receptor interaction” pathways were the most significantly enriched KEGG pathways in the up-regulated and down-regulated differentially expressed genes (DEGs), respectively. Conclusions Transcriptome analysis showed that GS-0976 could regulate the expression of genes related to metabolism, inflammation and fibrosis in NASH. The global transcriptomic changes in gene expression promote the further understanding for the inhibition mechanisms of GS-0976 in NASH.
format: application/pdf
format: text/html
creator: Ying Lu
creator: Xiaolan Su
creator: Manyu Zhao
creator: Qianru Zhang
creator: Chuang Liu
creator: Qinhuai Lai
creator: Sijia Wu
creator: Aiping Fang
creator: Jinliang Yang
creator: Xiaoxin Chen
creator: Yuqin Yao
subject: Bioinformatics
subject: Molecular Biology
subject: Metabolic Sciences
description: doi:10.7717/peerj.8115
publisher: PeerJ Inc.
rights: © 2019 Lu et al.
abstract: Background Non-alcoholic steatohepatitis (NASH) is a progressive liver disease characterized by hepatic steatosis, lobular inflammation and fibrosis. Acetyl-CoA carboxylase (ACC) isoform 1 and 2 involved in de novo lipogenesis (DNL) and fatty acid oxidation have been identified as a therapeutic target in NASH. GS-0976, the inhibitor of ACC1 and ACC2, has achieved favorable therapeutic effects in clinical trials with NASH. The purpose of this study was to explore the transcriptional alterations regulated by GS-0976 in NASH. Methods C57BL/6 mice were fed on a choline-deficient, L-amino acid-defined, high-fat diet (CDAHFD) or normal diet for 12 weeks. Mice were treated with or without GS-0976 (3 mg/kg per day) in the last 8 weeks. Oil Red O, Haematoxylin-eosin (H & E), and Sirius Red were used to evaluate hepatic steatosis, inflammation and fibrosis. The comparative RNA-sequencing was conducted to analyse the hepatic gene expression profiles in mice. Reverse transcription–polymerase chain reaction analysis was performed to validate the differential expression of representative genes. Results GS-0976 attenuated the steatosis, inflammation, and fibrosis of NASH in CDAHFD mouse model. High-throughput sequencing and differential gene expression analysis showed that there were 516 up-regulated genes and 525 down-regulated genes after GS-0976 treatment. Genes involved in the metabolic process, extracellular matrix formation, immune response, and angiogenesis were significantly enriched. The “Metabolic pathways” and “ECM-receptor interaction” pathways were the most significantly enriched KEGG pathways in the up-regulated and down-regulated differentially expressed genes (DEGs), respectively. Conclusions Transcriptome analysis showed that GS-0976 could regulate the expression of genes related to metabolism, inflammation and fibrosis in NASH. The global transcriptomic changes in gene expression promote the further understanding for the inhibition mechanisms of GS-0976 in NASH.
bibliographic citation: Lu et al. (2019) Comparative RNA-sequencing profiled the differential gene expression of liver in response to acetyl-CoA carboxylase inhibitor GS-0976 in a mouse model of NASH. PeerJ 7:e8115 https://doi.org/10.7717/peerj.8115
date submitted: 2019-08-16
date accepted: 2019-10-28
issued: 2019-12-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Lu
  given name: Ying
author list: Agent
  family name: Su
  given name: Xiaolan
author list: Agent
  family name: Zhao
  given name: Manyu
author list: Agent
  family name: Zhang
  given name: Qianru
author list: Agent
  family name: Liu
  given name: Chuang
author list: Agent
  family name: Lai
  given name: Qinhuai
author list: Agent
  family name: Wu
  given name: Sijia
author list: Agent
  family name: Fang
  given name: Aiping
author list: Agent
  family name: Yang
  given name: Jinliang
author list: Agent
  family name: Chen
  given name: Xiaoxin
author list: Agent
  family name: Yao
  given name: Yuqin
doi: 10.7717/peerj.8115
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-20
copyright: ©2019 Lu et al.
attribution name: Lu et al.

Genetic links between endometriosis and cancers in women
type: item
type: AcademicArticle
description: Endometriosis is a chronic disease occurring during the reproductive stage of women. Although there is only limited association between endometriosis and gynecological cancers with regard to clinical features, the molecular basis of the relationship between these diseases is unexplored. We conducted a systematic study by integrating literature-based evidence, gene expression and large-scale cancer genomics data in order to reveal any genetic relationships between endometriosis and cancers in women. We curated 984 endometriosis-related genes from 3270 PubMed articles and then conducted a meta-analysis of the two public gene expression profiles related to endometriosis which identified Differential Expression of Genes (DEGs). Following an overlapping analysis, we identified 39 key endometriosis-related genes common in both literature and DEG analysis. Finally, the functional analysis confirmed that all the 39 genes were associated with the vital processes of tumour formation and cancer progression and that two genes (PGR and ESR1) were common to four cancers of women. From network analysis, we identified a novel linker gene, C3AR1, which had not been implicated previously in endometriosis. The shared genetic mechanisms of endometriosis and cancers in women identified in this study provided possible new avenues of multiple disease management and treatments through early diagnosis.
format: application/pdf
format: text/html
creator: Salma Begum Bhyan
creator: Li Zhao
creator: YongKiat Wee
creator: Yining Liu
creator: Min Zhao
subject: Bioinformatics
subject: Genetics
subject: Genomics
subject: Oncology
subject: Women’s Health
description: doi:10.7717/peerj.8135
publisher: PeerJ Inc.
rights: © 2019 Bhyan et al.
abstract: Endometriosis is a chronic disease occurring during the reproductive stage of women. Although there is only limited association between endometriosis and gynecological cancers with regard to clinical features, the molecular basis of the relationship between these diseases is unexplored. We conducted a systematic study by integrating literature-based evidence, gene expression and large-scale cancer genomics data in order to reveal any genetic relationships between endometriosis and cancers in women. We curated 984 endometriosis-related genes from 3270 PubMed articles and then conducted a meta-analysis of the two public gene expression profiles related to endometriosis which identified Differential Expression of Genes (DEGs). Following an overlapping analysis, we identified 39 key endometriosis-related genes common in both literature and DEG analysis. Finally, the functional analysis confirmed that all the 39 genes were associated with the vital processes of tumour formation and cancer progression and that two genes (PGR and ESR1) were common to four cancers of women. From network analysis, we identified a novel linker gene, C3AR1, which had not been implicated previously in endometriosis. The shared genetic mechanisms of endometriosis and cancers in women identified in this study provided possible new avenues of multiple disease management and treatments through early diagnosis.
bibliographic citation: Bhyan et al. (2019) Genetic links between endometriosis and cancers in women. PeerJ 7:e8135 https://doi.org/10.7717/peerj.8135
date submitted: 2019-05-31
date accepted: 2019-11-01
issued: 2019-12-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bhyan
  given name: Salma Begum
author list: Agent
  family name: Zhao
  given name: Li
author list: Agent
  family name: Wee
  given name: YongKiat
author list: Agent
  family name: Liu
  given name: Yining
author list: Agent
  family name: Zhao
  given name: Min
doi: 10.7717/peerj.8135
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-20
copyright: ©2019 Bhyan et al.
attribution name: Bhyan et al.

Evaluation of human-papillomavirus screening for cervical cancer in China’s rural population
type: item
type: AcademicArticle
description: Background and Objective Human papillomavirus (HPV) testing has become a preferred cervical cancer screening. However, most HPV infections are harmless and additional tests are required to screen HPV positive women. The objective of this study is to determine the optimal triage strategies for HPV positive women in China’s rural population. Methods A population-based screening was performed at seven rural counties of Jiangxi province, between October 2014 to January 2016. A total of 18,000 women aged 35–64 years were enrolled in this study. The primary screening was performed using CareHPV, HC-2, Cobas ®4,800 or HybriMax. Positive women were further screened with five triage tests: (1) Liquid-based cytology test (LBC); (2) conventional Pap cytology test (Pap smear); (3) HPV16, 18 detection; (4) viral load; and (5) visual inspection with acetic acid and Lugol’s iodine (VIA/VILI). Women who were tested positive were referred for colposcopy. The five triage tests were compared with respect to sensitivity, specificity, referral rate, cost and diagnostic time. Results Complete data were available for 17,782 women. The HPV prevalence was 13.6%. Referral rates for colposcopy were 4.5%, 2.8%, 2.8%, 6.6%, and 3.7% with LBC, Pap smear, HPV16/18, viral load, and VIA/VILI, respectively. The sensitivity of the above triage tests was 65.8%, 51.9%, 86.8%, 73.3%, and 41.7%, respectively. The specificity was 69.8%, 81.0%, 85.8%, 52.2% and 65.3%, respectively. The average time to diagnosis was significantly lower with HPV16/18, viral load and VIA/VILI than LBC and Pap smear. In addition, screening cost that leads to identify one HSIL+ woman was the lowest with viral load. Conclusion Our data indicate that HPV16/18 and viral load are the optimal triage strategies for HPV screening in China’s rural population.
format: application/pdf
format: text/html
creator: Ling Li
creator: Ziwen Zheng
creator: Longyu Li
subject: Infectious Diseases
subject: Oncology
subject: Public Health
description: doi:10.7717/peerj.8152
publisher: PeerJ Inc.
rights: © 2019 Li et al.
abstract: Background and Objective Human papillomavirus (HPV) testing has become a preferred cervical cancer screening. However, most HPV infections are harmless and additional tests are required to screen HPV positive women. The objective of this study is to determine the optimal triage strategies for HPV positive women in China’s rural population. Methods A population-based screening was performed at seven rural counties of Jiangxi province, between October 2014 to January 2016. A total of 18,000 women aged 35–64 years were enrolled in this study. The primary screening was performed using CareHPV, HC-2, Cobas ®4,800 or HybriMax. Positive women were further screened with five triage tests: (1) Liquid-based cytology test (LBC); (2) conventional Pap cytology test (Pap smear); (3) HPV16, 18 detection; (4) viral load; and (5) visual inspection with acetic acid and Lugol’s iodine (VIA/VILI). Women who were tested positive were referred for colposcopy. The five triage tests were compared with respect to sensitivity, specificity, referral rate, cost and diagnostic time. Results Complete data were available for 17,782 women. The HPV prevalence was 13.6%. Referral rates for colposcopy were 4.5%, 2.8%, 2.8%, 6.6%, and 3.7% with LBC, Pap smear, HPV16/18, viral load, and VIA/VILI, respectively. The sensitivity of the above triage tests was 65.8%, 51.9%, 86.8%, 73.3%, and 41.7%, respectively. The specificity was 69.8%, 81.0%, 85.8%, 52.2% and 65.3%, respectively. The average time to diagnosis was significantly lower with HPV16/18, viral load and VIA/VILI than LBC and Pap smear. In addition, screening cost that leads to identify one HSIL+ woman was the lowest with viral load. Conclusion Our data indicate that HPV16/18 and viral load are the optimal triage strategies for HPV screening in China’s rural population.
bibliographic citation: Li et al. (2019) Evaluation of human-papillomavirus screening for cervical cancer in China’s rural population. PeerJ 7:e8152 https://doi.org/10.7717/peerj.8152
date submitted: 2019-01-31
date accepted: 2019-11-04
issued: 2019-12-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Ling
author list: Agent
  family name: Zheng
  given name: Ziwen
author list: Agent
  family name: Li
  given name: Longyu
doi: 10.7717/peerj.8152
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-20
copyright: ©2019 Li et al.
attribution name: Li et al.

Systematic evaluation of the gut microbiome of swamp eel (Monopterus albus) by 16S rRNA gene sequencing
type: item
type: AcademicArticle
description: Background The swamp eel (Monopterus albus) is a commercially important farmed species in China. The dysbiosis and homeostasis of gut microbiota has been suggested to be associated with the swamp eel’s disease pathogenesis and food digestion. Although the contributions of gut microbiome in fish growth and health has been increasingly recognized, little is known about the microbial community in the intestine of the swamp eel (Monopterus albus). Methods The intestinal microbiomes of the five distinct gut sections (midgut content and mucosa, hindgut content and mucosa, and stools) of swamp eel were compared using Illumina MiSeq sequencing of the bacterial 16S rRNA gene sequence and statistical analysis. Results The results showed that the number of observed OTUs in the intestine decreased proximally to distally. Principal coordinate analysis revealed significant separations among samples from different gut sections. There were 54 core OTUs shared by all gut sections and 36 of these core OTUs varied significantly in their abundances. Additionally, we discovered 66 section-specific enriched KEGG pathways. These section-specific enriched microbial taxa (e.g., Bacillus, Lactobacillus) and potential function capacities (e.g., amino acid metabolism, carbohydrate metabolism) might play vital roles in nutrient metabolism, immune modulation and host-microbe interactions of the swamp eel. Conclusions Our results showed that microbial diversity, composition and function capacity varied substantially across different gut sections. The gut section-specific enriched core microbial taxa and function capacities may perform important roles in swamp eel’s nutrient metabolism, immune modulation, and host-microbe interactions. This study should provide insights into the gut microbiome of the swamp eel.
format: application/pdf
format: text/html
creator: Xuan Chen
creator: Shaoming Fang
creator: Lili Wei
creator: Qiwang Zhong
subject: Aquaculture, Fisheries and Fish Science
subject: Microbiology
subject: Freshwater Biology
description: doi:10.7717/peerj.8176
publisher: PeerJ Inc.
rights: © 2019 Chen et al.
abstract: Background The swamp eel (Monopterus albus) is a commercially important farmed species in China. The dysbiosis and homeostasis of gut microbiota has been suggested to be associated with the swamp eel’s disease pathogenesis and food digestion. Although the contributions of gut microbiome in fish growth and health has been increasingly recognized, little is known about the microbial community in the intestine of the swamp eel (Monopterus albus). Methods The intestinal microbiomes of the five distinct gut sections (midgut content and mucosa, hindgut content and mucosa, and stools) of swamp eel were compared using Illumina MiSeq sequencing of the bacterial 16S rRNA gene sequence and statistical analysis. Results The results showed that the number of observed OTUs in the intestine decreased proximally to distally. Principal coordinate analysis revealed significant separations among samples from different gut sections. There were 54 core OTUs shared by all gut sections and 36 of these core OTUs varied significantly in their abundances. Additionally, we discovered 66 section-specific enriched KEGG pathways. These section-specific enriched microbial taxa (e.g., Bacillus, Lactobacillus) and potential function capacities (e.g., amino acid metabolism, carbohydrate metabolism) might play vital roles in nutrient metabolism, immune modulation and host-microbe interactions of the swamp eel. Conclusions Our results showed that microbial diversity, composition and function capacity varied substantially across different gut sections. The gut section-specific enriched core microbial taxa and function capacities may perform important roles in swamp eel’s nutrient metabolism, immune modulation, and host-microbe interactions. This study should provide insights into the gut microbiome of the swamp eel.
bibliographic citation: Chen et al. (2019) Systematic evaluation of the gut microbiome of swamp eel (Monopterus albus) by 16S rRNA gene sequencing. PeerJ 7:e8176 https://doi.org/10.7717/peerj.8176
date submitted: 2018-06-04
date accepted: 2019-11-07
issued: 2019-12-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Xuan
author list: Agent
  family name: Fang
  given name: Shaoming
author list: Agent
  family name: Wei
  given name: Lili
author list: Agent
  family name: Zhong
  given name: Qiwang
doi: 10.7717/peerj.8176
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-20
copyright: © 2019 Chen et al.
attribution name: Chen et al.

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