PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Genetic data of museum specimens allow for inferring evolutionary history of the cosmopolitan genus Sirthenea (Heteroptera: Reduviidae)
items: Germination characteristics among different sheepgrass (Leymus chinensis) germplasm during the seed development and after-ripening stages
items: virMine: automated detection of viral sequences from complex metagenomic samples
items: MetaMSD: meta analysis for mass spectrometry data
items: Automated analysis of small RNA datasets with RAPID
items: Decoupling species richness variation and spatial turnover in beta diversity across a fragmented landscape
items: The stimulating role of syringic acid, a plant secondary metabolite, in the microbial degradation of structurally-related herbicide, MCPA
items: Pituitary tissue-specific miR-7a-5p regulates FSH expression in rat anterior adenohypophyseal cells
items: Transcriptional profiling in the livers of rats after hypobaric hypoxia exposure
items: Maturation trade-offs in octopus females and their progeny: energy, digestion and defence indicators

Genetic data of museum specimens allow for inferring evolutionary history of the cosmopolitan genus Sirthenea (Heteroptera: Reduviidae)
type: item
type: AcademicArticle
description: Among the 30 known genera within subfamily Peiratinae, only the genus Sirthenea has a cosmopolitan distribution. The results of our studies are the first comprehensive analysis concerning one of the representatives of mentioned subfamily based on joint phylogenetic analyses of molecular and morphological data as well as molecular dating. A total of 32 species were included into the dataset with all known species of the genus Sirthenea. Material of over 400 dry specimens was examined for the morphological part of this study. The cosmopolitan distribution of Sirthenea and the inaccessibility of specimens preserved in alcohol required the extraction of DNA from the dried skeletal muscles of specimens deposited in 24 entomological collections. The oldest specimens used for the successful extraction and sequencing were collected more than 120 years ago in India. We performed Bayesian Inference analyses of molecular and morphological data separately, as well as combined analysis. The molecular and morphological data obtained during our research verify the correlation of the divergence dates of all known Sirthenea species. Results of the relaxed molecular clock analysis of the molecular data show that, the genus Sirthenea started diverging in the Late Cretaceous into two clades, which subsequently began to branch off in the Paleocene. Our results of phylogenetic analyses suggest that the fossula spongiosa and its development could be one of the most important morphological characters in the evolution of the genus, most likely associated with the ecological niche inhabited by Sirthenea representatives. Confirmation of the results obtained in our studies is the reconciliation of the evolutionary history of Sirthenea with the biogeographical processes that have shaped current global distribution of the genus.
format: application/pdf
format: text/html
creator: Dominik Chłond
creator: Natalia Sawka-Gądek
creator: Dagmara Żyła
subject: Entomology
subject: Evolutionary Studies
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.6640
publisher: PeerJ Inc.
rights: © 2019 Chłond et al.
abstract: Among the 30 known genera within subfamily Peiratinae, only the genus Sirthenea has a cosmopolitan distribution. The results of our studies are the first comprehensive analysis concerning one of the representatives of mentioned subfamily based on joint phylogenetic analyses of molecular and morphological data as well as molecular dating. A total of 32 species were included into the dataset with all known species of the genus Sirthenea. Material of over 400 dry specimens was examined for the morphological part of this study. The cosmopolitan distribution of Sirthenea and the inaccessibility of specimens preserved in alcohol required the extraction of DNA from the dried skeletal muscles of specimens deposited in 24 entomological collections. The oldest specimens used for the successful extraction and sequencing were collected more than 120 years ago in India. We performed Bayesian Inference analyses of molecular and morphological data separately, as well as combined analysis. The molecular and morphological data obtained during our research verify the correlation of the divergence dates of all known Sirthenea species. Results of the relaxed molecular clock analysis of the molecular data show that, the genus Sirthenea started diverging in the Late Cretaceous into two clades, which subsequently began to branch off in the Paleocene. Our results of phylogenetic analyses suggest that the fossula spongiosa and its development could be one of the most important morphological characters in the evolution of the genus, most likely associated with the ecological niche inhabited by Sirthenea representatives. Confirmation of the results obtained in our studies is the reconciliation of the evolutionary history of Sirthenea with the biogeographical processes that have shaped current global distribution of the genus.
bibliographic citation: Chłond et al. (2019) Genetic data of museum specimens allow for inferring evolutionary history of the cosmopolitan genus Sirthenea (Heteroptera: Reduviidae). PeerJ 7:e6640 https://doi.org/10.7717/peerj.6640
date submitted: 2019-01-30
date accepted: 2019-02-18
issued: 2019-04-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chłond
  given name: Dominik
author list: Agent
  family name: Sawka-Gądek
  given name: Natalia
author list: Agent
  family name: Żyła
  given name: Dagmara
doi: 10.7717/peerj.6640
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-10
copyright: © 2019 Chłond et al.
attribution name: Chłond et al.

Germination characteristics among different sheepgrass (Leymus chinensis) germplasm during the seed development and after-ripening stages
type: item
type: AcademicArticle
description: Sheepgrass (Leymus chinensis (Trin.) Tzvel) is an important forage grass in the Eurasian steppe. However, little information is available concerning its seed morphological features and germination characteristics during seed development and after-ripening among different germplasm. To clarify the appropriate seed harvest time and the effects of germplasm, seed development and after-ripening on seed germination, 20 germplasm of sheepgrass were selected. Moreover, the seed morphological and physical changes as well as the seed germination and dormancy characteristics of sheepgrass during seed development stages were analyzed using a seven—d gradient of day after pollination (DAP). The results indicated that the seed water content decreased significantly during 35–42 DAP and that the highest seed germination rate of most germplasm was observed at 35–42 DAP. Thus, 35–42 DAP may be the best time to harvest sheepgrass to obtain the maximum seed germination rate and avoid seed shattering. Furthermore, our results indicated that there were six types of germination patterns, including germplasm with increasing germination rates in the developing seed, such as S19 and S13, and germplasm that maintained a consistently low germination rate, such as S10. Moreover, we compared the seed germination rate of eight germplasm during seed development in both 2016 and 2017, and the results indicated that the seed germination patterns of the eight germplasm were highly consistent between the two consecutive years, suggesting that germplasm rather than year is the major factor in determining germination during seed development. The effect of after-ripening on seed germination was different among the germplasm where four types of germination patterns were revealed for 10 germplasm and resulted in various dormancy features. A two-factor ANOVA analysis suggested that the germplasm of the sheepgrass has a large influence on seed germination, whether during seed development or after-ripening. …
format: application/pdf
format: text/html
creator: Weiguang Yang
creator: Shu Liu
creator: Guangxiao Yuan
creator: Panpan Liu
creator: Dongmei Qi
creator: Xiaobing Dong
creator: Hui Liu
creator: Gongshe Liu
creator: Xiaoxia Li
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.6688
publisher: PeerJ Inc.
rights: © 2019 Yang et al.
abstract: Sheepgrass (Leymus chinensis (Trin.) Tzvel) is an important forage grass in the Eurasian steppe. However, little information is available concerning its seed morphological features and germination characteristics during seed development and after-ripening among different germplasm. To clarify the appropriate seed harvest time and the effects of germplasm, seed development and after-ripening on seed germination, 20 germplasm of sheepgrass were selected. Moreover, the seed morphological and physical changes as well as the seed germination and dormancy characteristics of sheepgrass during seed development stages were analyzed using a seven—d gradient of day after pollination (DAP). The results indicated that the seed water content decreased significantly during 35–42 DAP and that the highest seed germination rate of most germplasm was observed at 35–42 DAP. Thus, 35–42 DAP may be the best time to harvest sheepgrass to obtain the maximum seed germination rate and avoid seed shattering. Furthermore, our results indicated that there were six types of germination patterns, including germplasm with increasing germination rates in the developing seed, such as S19 and S13, and germplasm that maintained a consistently low germination rate, such as S10. Moreover, we compared the seed germination rate of eight germplasm during seed development in both 2016 and 2017, and the results indicated that the seed germination patterns of the eight germplasm were highly consistent between the two consecutive years, suggesting that germplasm rather than year is the major factor in determining germination during seed development. The effect of after-ripening on seed germination was different among the germplasm where four types of germination patterns were revealed for 10 germplasm and resulted in various dormancy features. A two-factor ANOVA analysis suggested that the germplasm of the sheepgrass has a large influence on seed germination, whether during seed development or after-ripening. …
bibliographic citation: Yang et al. (2019) Germination characteristics among different sheepgrass (Leymus chinensis) germplasm during the seed development and after-ripening stages. PeerJ 7:e6688 https://doi.org/10.7717/peerj.6688
date submitted: 2018-10-25
date accepted: 2019-02-26
issued: 2019-04-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Weiguang
author list: Agent
  family name: Liu
  given name: Shu
author list: Agent
  family name: Yuan
  given name: Guangxiao
author list: Agent
  family name: Liu
  given name: Panpan
author list: Agent
  family name: Qi
  given name: Dongmei
author list: Agent
  family name: Dong
  given name: Xiaobing
author list: Agent
  family name: Liu
  given name: Hui
author list: Agent
  family name: Liu
  given name: Gongshe
author list: Agent
  family name: Li
  given name: Xiaoxia
doi: 10.7717/peerj.6688
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-10
copyright: © 2019 Yang et al.
attribution name: Yang et al.

virMine: automated detection of viral sequences from complex metagenomic samples
type: item
type: AcademicArticle
description: Metagenomics has enabled sequencing of viral communities from a myriad of different environments. Viral metagenomic studies routinely uncover sequences with no recognizable homology to known coding regions or genomes. Nevertheless, complete viral genomes have been constructed directly from complex community metagenomes, often through tedious manual curation. To address this, we developed the software tool virMine to identify viral genomes from raw reads representative of viral or mixed (viral and bacterial) communities. virMine automates sequence read quality control, assembly, and annotation. Researchers can easily refine their search for a specific study system and/or feature(s) of interest. In contrast to other viral genome detection tools that often rely on the recognition of viral signature sequences, virMine is not restricted by the insufficient representation of viral diversity in public data repositories. Rather, viral genomes are identified through an iterative approach, first omitting non-viral sequences. Thus, both relatives of previously characterized viruses and novel species can be detected, including both eukaryotic viruses and bacteriophages. Here we present virMine and its analysis of synthetic communities as well as metagenomic data sets from three distinctly different environments: the gut microbiota, the urinary microbiota, and freshwater viromes. Several new viral genomes were identified and annotated, thus contributing to our understanding of viral genetic diversity in these three environments.
format: application/pdf
format: text/html
creator: Andrea Garretto
creator: Thomas Hatzopoulos
creator: Catherine Putonti
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Microbiology
subject: Virology
description: doi:10.7717/peerj.6695
publisher: PeerJ Inc.
rights: © 2019 Garretto et al.
abstract: Metagenomics has enabled sequencing of viral communities from a myriad of different environments. Viral metagenomic studies routinely uncover sequences with no recognizable homology to known coding regions or genomes. Nevertheless, complete viral genomes have been constructed directly from complex community metagenomes, often through tedious manual curation. To address this, we developed the software tool virMine to identify viral genomes from raw reads representative of viral or mixed (viral and bacterial) communities. virMine automates sequence read quality control, assembly, and annotation. Researchers can easily refine their search for a specific study system and/or feature(s) of interest. In contrast to other viral genome detection tools that often rely on the recognition of viral signature sequences, virMine is not restricted by the insufficient representation of viral diversity in public data repositories. Rather, viral genomes are identified through an iterative approach, first omitting non-viral sequences. Thus, both relatives of previously characterized viruses and novel species can be detected, including both eukaryotic viruses and bacteriophages. Here we present virMine and its analysis of synthetic communities as well as metagenomic data sets from three distinctly different environments: the gut microbiota, the urinary microbiota, and freshwater viromes. Several new viral genomes were identified and annotated, thus contributing to our understanding of viral genetic diversity in these three environments.
bibliographic citation: Garretto et al. (2019) virMine: automated detection of viral sequences from complex metagenomic samples. PeerJ 7:e6695 https://doi.org/10.7717/peerj.6695
date submitted: 2018-11-30
date accepted: 2019-02-26
issued: 2019-04-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Garretto
  given name: Andrea
author list: Agent
  family name: Hatzopoulos
  given name: Thomas
author list: Agent
  family name: Putonti
  given name: Catherine
doi: 10.7717/peerj.6695
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-10
copyright: ©2019 Garretto et al.
attribution name: Garretto et al.

MetaMSD: meta analysis for mass spectrometry data
type: item
type: AcademicArticle
description: Mass spectrometry-based proteomics facilitate disease understanding by providing protein abundance information about disease progression. For the same type of disease studies, multiple mass spectrometry datasets may be generated. Integrating multiple mass spectrometry datasets can provide valuable information that a single dataset analysis cannot provide. In this article, we introduce a meta-analysis software, MetaMSD (Meta Analysis for Mass Spectrometry Data) that is specifically designed for mass spectrometry data. Using Stouffer’s or Pearson’s test, MetaMSD detects significantly more differential proteins than the analysis based on the single best experiment. We demonstrate the performance of MetaMSD using simulated data, urinary proteomic data of kidney transplant patients, and breast cancer proteomic data. Noting the common practice of performing a pilot study prior to a main study, this software will help proteomics researchers fully utilize the benefit of multiple studies (or datasets), thus optimizing biomarker discovery. MetaMSD is a command line tool that automatically outputs various graphs and differential proteins with confidence scores. It is implemented in R and is freely available for public use at https://github.com/soyoungryu/MetaMSD. The user manual and data are available at the site. The user manual is written in such a way that scientists who are not familiar with R software can use MetaMSD.
format: application/pdf
format: text/html
creator: So Young Ryu
creator: George A. Wendt
subject: Bioinformatics
subject: Genomics
description: doi:10.7717/peerj.6699
publisher: PeerJ Inc.
rights: © 2019 Ryu and Wendt
abstract: Mass spectrometry-based proteomics facilitate disease understanding by providing protein abundance information about disease progression. For the same type of disease studies, multiple mass spectrometry datasets may be generated. Integrating multiple mass spectrometry datasets can provide valuable information that a single dataset analysis cannot provide. In this article, we introduce a meta-analysis software, MetaMSD (Meta Analysis for Mass Spectrometry Data) that is specifically designed for mass spectrometry data. Using Stouffer’s or Pearson’s test, MetaMSD detects significantly more differential proteins than the analysis based on the single best experiment. We demonstrate the performance of MetaMSD using simulated data, urinary proteomic data of kidney transplant patients, and breast cancer proteomic data. Noting the common practice of performing a pilot study prior to a main study, this software will help proteomics researchers fully utilize the benefit of multiple studies (or datasets), thus optimizing biomarker discovery. MetaMSD is a command line tool that automatically outputs various graphs and differential proteins with confidence scores. It is implemented in R and is freely available for public use at https://github.com/soyoungryu/MetaMSD. The user manual and data are available at the site. The user manual is written in such a way that scientists who are not familiar with R software can use MetaMSD.
bibliographic citation: Ryu et al. (2019) MetaMSD: meta analysis for mass spectrometry data. PeerJ 7:e6699 https://doi.org/10.7717/peerj.6699
date submitted: 2018-11-30
date accepted: 2019-03-01
issued: 2019-04-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ryu
  given name: So Young
author list: Agent
  family name: Wendt
  given name: George A.
doi: 10.7717/peerj.6699
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-10
copyright: ©2019 Ryu and Wendt
attribution name: Ryu and Wendt

Automated analysis of small RNA datasets with RAPID
type: item
type: AcademicArticle
description: Understanding the role of short-interfering RNA (siRNA) in diverse biological processes is of current interest and often approached through small RNA sequencing. However, analysis of these datasets is difficult due to the complexity of biological RNA processing pathways, which differ between species. Several properties like strand specificity, length distribution, and distribution of soft-clipped bases are few parameters known to guide researchers in understanding the role of siRNAs. We present RAPID, a generic eukaryotic siRNA analysis pipeline, which captures information inherent in the datasets and automatically produces numerous visualizations as user-friendly HTML reports, covering multiple categories required for siRNA analysis. RAPID also facilitates an automated comparison of multiple datasets, with one of the normalization techniques dedicated for siRNA knockdown analysis, and integrates differential expression analysis using DESeq2. Availability and Implementation RAPID is available under MIT license at https://github.com/SchulzLab/RAPID. We recommend using it as a conda environment available from https://anaconda.org/bioconda/rapid
format: application/pdf
format: text/html
creator: Sivarajan Karunanithi
creator: Martin Simon
creator: Marcel H. Schulz
subject: Bioinformatics
subject: Computational Biology
description: doi:10.7717/peerj.6710
publisher: PeerJ Inc.
rights: © 2019 Karunanithi et al.
abstract: Understanding the role of short-interfering RNA (siRNA) in diverse biological processes is of current interest and often approached through small RNA sequencing. However, analysis of these datasets is difficult due to the complexity of biological RNA processing pathways, which differ between species. Several properties like strand specificity, length distribution, and distribution of soft-clipped bases are few parameters known to guide researchers in understanding the role of siRNAs. We present RAPID, a generic eukaryotic siRNA analysis pipeline, which captures information inherent in the datasets and automatically produces numerous visualizations as user-friendly HTML reports, covering multiple categories required for siRNA analysis. RAPID also facilitates an automated comparison of multiple datasets, with one of the normalization techniques dedicated for siRNA knockdown analysis, and integrates differential expression analysis using DESeq2. Availability and Implementation RAPID is available under MIT license at https://github.com/SchulzLab/RAPID. We recommend using it as a conda environment available from https://anaconda.org/bioconda/rapid
bibliographic citation: Karunanithi et al. (2019) Automated analysis of small RNA datasets with RAPID. PeerJ 7:e6710 https://doi.org/10.7717/peerj.6710
date submitted: 2018-11-29
date accepted: 2019-03-01
issued: 2019-04-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Karunanithi
  given name: Sivarajan
author list: Agent
  family name: Simon
  given name: Martin
author list: Agent
  family name: Schulz
  given name: Marcel H.
doi: 10.7717/peerj.6710
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-10
copyright: ©2019 Karunanithi et al.
attribution name: Karunanithi et al.

Decoupling species richness variation and spatial turnover in beta diversity across a fragmented landscape
type: item
type: AcademicArticle
description: Background How habitat fragmentation affects the relationship between local richness and the variation in community composition across space is important to both ecology and conservation biology, but this effect remains poorly understood. Methods Here, we present an empirical study to address this topic in a fragmented landscape, the Thousand Island Lake (TIL), an artificial land-bridge island system with more than 1,000 islands, which provides an “experimental” fragmented landscape with a homogeneous matrix and similar successional history. We measured species composition and plant functional type (PFT) on 29 islands, and tested the effects of island area and isolation on the relationship between α- and β-diversity. General Linear Models were applied to test the impact of habitat fragmentation. In addition, variation partitioning was used to decouple α-diversity dependent and α-diversity independent spatial turnover in β-diversity of the plant community and across different PFTs. Results We found habitat fragmentation influences β-diversity of plants primarily by modifying local α-diversity, not spatial turnover in the TIL system. We also found area-dependent environmental filtering and differential plant responses across functional types were the most likely underlying driving mechanisms. Discussion These results highlight the importance of hierarchical linkages between components of biodiversity across scales in fragmented landscapes, and have practical conservation implications.
format: application/pdf
format: text/html
creator: Guang Hu
creator: Maxwell C. Wilson
creator: Jianguo Wu
creator: Jingjing Yu
creator: Mingjian Yu
subject: Biodiversity
subject: Ecology
description: doi:10.7717/peerj.6714
publisher: PeerJ Inc.
rights: © 2019 Hu et al.
abstract: Background How habitat fragmentation affects the relationship between local richness and the variation in community composition across space is important to both ecology and conservation biology, but this effect remains poorly understood. Methods Here, we present an empirical study to address this topic in a fragmented landscape, the Thousand Island Lake (TIL), an artificial land-bridge island system with more than 1,000 islands, which provides an “experimental” fragmented landscape with a homogeneous matrix and similar successional history. We measured species composition and plant functional type (PFT) on 29 islands, and tested the effects of island area and isolation on the relationship between α- and β-diversity. General Linear Models were applied to test the impact of habitat fragmentation. In addition, variation partitioning was used to decouple α-diversity dependent and α-diversity independent spatial turnover in β-diversity of the plant community and across different PFTs. Results We found habitat fragmentation influences β-diversity of plants primarily by modifying local α-diversity, not spatial turnover in the TIL system. We also found area-dependent environmental filtering and differential plant responses across functional types were the most likely underlying driving mechanisms. Discussion These results highlight the importance of hierarchical linkages between components of biodiversity across scales in fragmented landscapes, and have practical conservation implications.
bibliographic citation: Hu et al. (2019) Decoupling species richness variation and spatial turnover in beta diversity across a fragmented landscape. PeerJ 7:e6714 https://doi.org/10.7717/peerj.6714
date submitted: 2018-06-13
date accepted: 2019-03-05
issued: 2019-04-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hu
  given name: Guang
author list: Agent
  family name: Wilson
  given name: Maxwell C.
author list: Agent
  family name: Wu
  given name: Jianguo
author list: Agent
  family name: Yu
  given name: Jingjing
author list: Agent
  family name: Yu
  given name: Mingjian
doi: 10.7717/peerj.6714
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-10
copyright: © 2019 Hu et al.
attribution name: Hu et al.

The stimulating role of syringic acid, a plant secondary metabolite, in the microbial degradation of structurally-related herbicide, MCPA
type: item
type: AcademicArticle
description: The ability of microorganisms to degrade xenobiotics can be exploited to develop cost-effective and eco-friendly bioremediation technologies. Microorganisms can degrade almost all organic pollutants, but this process might be very slow in some cases. A promising way to enhance removal of recalcitrant xenobiotics from the environment lies in the interactions between plant exudates such as plant secondary metabolites (PSMs) and microorganisms. Although there is a considerable body of evidence that PSMs can alter the microbial community composition and stimulate the microbial degradation of xenobiotics, their mechanisms of action remain poorly understood. With this in mind, our aim was to demonstrate that similarity between the chemical structures of PSMs and xenobiotics results in higher micropollutant degradation rates, and the occurrence of corresponding bacterial degradative genes. To verify this, the present study analyses the influence of syringic acid, a plant secondary metabolite, on the bacterial degradation of an herbicide, 4-chloro-2-methylphenoxyacetic acid (MCPA). In particular, the presence of appropriate MCPA degradative genes, MCPA removal efficiency and changes in samples phytotoxicity have been analyzed. Significant MCPA depletion was achieved in samples enriched with syringic acid. The results confirmed not only greater MCPA removal from the samples upon spiking with syringic acid, and thus decreased phytotoxicity, but also the presence of a greater number of genes responsible for MCPA biodegradation. 16S rRNA gene sequence analysis revealed ubiquitous enrichment of the β-proteobacteria Rhodoferax, Achromobacter, Burkholderia and Cupriavidus. The obtained results provide further confirmation that plant metabolites released into the rhizosphere can stimulate biodegradation of xenobiotics, including MCPA.
format: application/pdf
format: text/html
creator: Magdalena Urbaniak
creator: Elżbieta Mierzejewska
creator: Maciej Tankiewicz
subject: Agricultural Science
subject: Ecology
subject: Genetics
description: doi:10.7717/peerj.6745
publisher: PeerJ Inc.
rights: © 2019 Urbaniak et al.
abstract: The ability of microorganisms to degrade xenobiotics can be exploited to develop cost-effective and eco-friendly bioremediation technologies. Microorganisms can degrade almost all organic pollutants, but this process might be very slow in some cases. A promising way to enhance removal of recalcitrant xenobiotics from the environment lies in the interactions between plant exudates such as plant secondary metabolites (PSMs) and microorganisms. Although there is a considerable body of evidence that PSMs can alter the microbial community composition and stimulate the microbial degradation of xenobiotics, their mechanisms of action remain poorly understood. With this in mind, our aim was to demonstrate that similarity between the chemical structures of PSMs and xenobiotics results in higher micropollutant degradation rates, and the occurrence of corresponding bacterial degradative genes. To verify this, the present study analyses the influence of syringic acid, a plant secondary metabolite, on the bacterial degradation of an herbicide, 4-chloro-2-methylphenoxyacetic acid (MCPA). In particular, the presence of appropriate MCPA degradative genes, MCPA removal efficiency and changes in samples phytotoxicity have been analyzed. Significant MCPA depletion was achieved in samples enriched with syringic acid. The results confirmed not only greater MCPA removal from the samples upon spiking with syringic acid, and thus decreased phytotoxicity, but also the presence of a greater number of genes responsible for MCPA biodegradation. 16S rRNA gene sequence analysis revealed ubiquitous enrichment of the β-proteobacteria Rhodoferax, Achromobacter, Burkholderia and Cupriavidus. The obtained results provide further confirmation that plant metabolites released into the rhizosphere can stimulate biodegradation of xenobiotics, including MCPA.
bibliographic citation: Urbaniak et al. (2019) The stimulating role of syringic acid, a plant secondary metabolite, in the microbial degradation of structurally-related herbicide, MCPA. PeerJ 7:e6745 https://doi.org/10.7717/peerj.6745
date submitted: 2018-12-20
date accepted: 2019-02-27
issued: 2019-04-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Urbaniak
  given name: Magdalena
author list: Agent
  family name: Mierzejewska
  given name: Elżbieta
author list: Agent
  family name: Tankiewicz
  given name: Maciej
doi: 10.7717/peerj.6745
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-10
copyright: ©2019 Urbaniak et al.
attribution name: Urbaniak et al.

Pituitary tissue-specific miR-7a-5p regulates FSH expression in rat anterior adenohypophyseal cells
type: item
type: AcademicArticle
description: The follicle-stimulating hormone (FSH), which is synthesized and secreted by the anterior pituitary gland, plays an important role in regulating reproductive processes. In this study, using the TargetScan program, we predicted that microRNAs (miRNAs) regulate FSH secretion. Dual-luciferase reporter assays were performed and identified miR-7a-5p. MiR-7a-5p has been reported to regulate diverse cellular functions. However, it is unclear whether miR-7a-5p binds to mRNAs and regulates reproductive functions. Therefore, we constructed a suspension of rat anterior pituitary cells and cultured them under adaptive conditions, transfected miR-7a-5p mimics or inhibitor into the cell suspension and detected expression of the FSHb gene. The results demonstrated that miR-7a-5p downregulated FSHb expression levels, while treatment with miR-7a-5p inhibitors upregulated FSHb expression levels relative to those of negative control groups, as shown by quantitative PCR analysis. The results were confirmed with a subsequent experiment showing that FSH secretion was reduced after treatment with mimics and increased in the inhibitor groups, as shown by enzyme-linked immunosorbent assay. Our results indicated that miR-7a-5p downregulates FSHb expression levels, resulting in decreased FSH synthesis and secretion, which demonstrates the important role of miRNAs in the regulation of FSH and animal reproduction.
format: application/pdf
format: text/html
creator: Chang-Jiang Wang
creator: Hai-Xiang Guo
creator: Dong-Xu Han
creator: Ze-Wen Yu
creator: Yi Zheng
creator: Hao Jiang
creator: Yan Gao
creator: Bao Yuan
creator: Jia-Bao Zhang
subject: Cell Biology
subject: Molecular Biology
subject: Diabetes and Endocrinology
description: doi:10.7717/peerj.6458
publisher: PeerJ Inc.
rights: © 2019 Wang et al.
abstract: The follicle-stimulating hormone (FSH), which is synthesized and secreted by the anterior pituitary gland, plays an important role in regulating reproductive processes. In this study, using the TargetScan program, we predicted that microRNAs (miRNAs) regulate FSH secretion. Dual-luciferase reporter assays were performed and identified miR-7a-5p. MiR-7a-5p has been reported to regulate diverse cellular functions. However, it is unclear whether miR-7a-5p binds to mRNAs and regulates reproductive functions. Therefore, we constructed a suspension of rat anterior pituitary cells and cultured them under adaptive conditions, transfected miR-7a-5p mimics or inhibitor into the cell suspension and detected expression of the FSHb gene. The results demonstrated that miR-7a-5p downregulated FSHb expression levels, while treatment with miR-7a-5p inhibitors upregulated FSHb expression levels relative to those of negative control groups, as shown by quantitative PCR analysis. The results were confirmed with a subsequent experiment showing that FSH secretion was reduced after treatment with mimics and increased in the inhibitor groups, as shown by enzyme-linked immunosorbent assay. Our results indicated that miR-7a-5p downregulates FSHb expression levels, resulting in decreased FSH synthesis and secretion, which demonstrates the important role of miRNAs in the regulation of FSH and animal reproduction.
bibliographic citation: Wang et al. (2019) Pituitary tissue-specific miR-7a-5p regulates FSH expression in rat anterior adenohypophyseal cells. PeerJ 7:e6458 https://doi.org/10.7717/peerj.6458
date submitted: 2018-09-18
date accepted: 2019-01-16
issued: 2019-04-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Chang-Jiang
author list: Agent
  family name: Guo
  given name: Hai-Xiang
author list: Agent
  family name: Han
  given name: Dong-Xu
author list: Agent
  family name: Yu
  given name: Ze-Wen
author list: Agent
  family name: Zheng
  given name: Yi
author list: Agent
  family name: Jiang
  given name: Hao
author list: Agent
  family name: Gao
  given name: Yan
author list: Agent
  family name: Yuan
  given name: Bao
author list: Agent
  family name: Zhang
  given name: Jia-Bao
doi: 10.7717/peerj.6458
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-09
copyright: © 2019 Wang et al.
attribution name: Wang et al.

Transcriptional profiling in the livers of rats after hypobaric hypoxia exposure
type: item
type: AcademicArticle
description: Ascent to high altitude feels uncomfortable in part because of a decreased partial pressure of oxygen due to the decrease in barometric pressure. The molecular mechanisms causing injury in liver tissue after exposure to a hypoxic environment are widely unknown. The liver must physiologically and metabolically change to improve tolerance to altitude-induced hypoxia. Since the liver is the largest metabolic organ and regulates many physiological and metabolic processes, it plays an important part in high altitude adaptation. The cellular response to hypoxia results in changes in the gene expression profile. The present study explores these changes in a rat model. To comprehensively investigate the gene expression and physiological changes under hypobaric hypoxia, we used genome-wide transcription profiling. Little is known about the genome-wide transcriptional response to acute and chronic hypobaric hypoxia in the livers of rats. In this study, we carried out RNA-Sequencing (RNA-Seq) of liver tissue from rats in three groups, normal control rats (L), rats exposed to acute hypobaric hypoxia for 2 weeks (W2L) and rats chronically exposed to hypobaric hypoxia for 4 weeks (W4L), to explore the transcriptional profile of acute and chronic mountain sickness in a mammal under a controlled time-course. We identified 497 differentially expressed genes between the three groups. A principal component analysis revealed large differences between the acute and chronic hypobaric hypoxia groups compared with the control group. Several immune-related and metabolic pathways, such as cytokine-cytokine receptor interaction and galactose metabolism, were highly enriched in the KEGG pathway analysis. Similar results were found in the Gene Ontology analysis. Cogena analysis showed that the immune-related pathways were mainly upregulated and enriched in the acute hypobaric hypoxia group.
format: application/pdf
format: text/html
creator: Zhenguo Xu
creator: Zhilong Jia
creator: Jinlong Shi
creator: Zeyu Zhang
creator: Xiaojian Gao
creator: Qian Jia
creator: Bohan Liu
creator: Jixuan Liu
creator: Chunlei Liu
creator: Xiaojing Zhao
creator: Kunlun He
subject: Bioinformatics
subject: Genetics
subject: Anatomy and Physiology
subject: Gastroenterology and Hepatology
description: doi:10.7717/peerj.6499
publisher: PeerJ Inc.
rights: © 2019 Xu et al.
abstract: Ascent to high altitude feels uncomfortable in part because of a decreased partial pressure of oxygen due to the decrease in barometric pressure. The molecular mechanisms causing injury in liver tissue after exposure to a hypoxic environment are widely unknown. The liver must physiologically and metabolically change to improve tolerance to altitude-induced hypoxia. Since the liver is the largest metabolic organ and regulates many physiological and metabolic processes, it plays an important part in high altitude adaptation. The cellular response to hypoxia results in changes in the gene expression profile. The present study explores these changes in a rat model. To comprehensively investigate the gene expression and physiological changes under hypobaric hypoxia, we used genome-wide transcription profiling. Little is known about the genome-wide transcriptional response to acute and chronic hypobaric hypoxia in the livers of rats. In this study, we carried out RNA-Sequencing (RNA-Seq) of liver tissue from rats in three groups, normal control rats (L), rats exposed to acute hypobaric hypoxia for 2 weeks (W2L) and rats chronically exposed to hypobaric hypoxia for 4 weeks (W4L), to explore the transcriptional profile of acute and chronic mountain sickness in a mammal under a controlled time-course. We identified 497 differentially expressed genes between the three groups. A principal component analysis revealed large differences between the acute and chronic hypobaric hypoxia groups compared with the control group. Several immune-related and metabolic pathways, such as cytokine-cytokine receptor interaction and galactose metabolism, were highly enriched in the KEGG pathway analysis. Similar results were found in the Gene Ontology analysis. Cogena analysis showed that the immune-related pathways were mainly upregulated and enriched in the acute hypobaric hypoxia group.
bibliographic citation: Xu et al. (2019) Transcriptional profiling in the livers of rats after hypobaric hypoxia exposure. PeerJ 7:e6499 https://doi.org/10.7717/peerj.6499
date submitted: 2018-10-26
date accepted: 2019-01-21
issued: 2019-04-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xu
  given name: Zhenguo
author list: Agent
  family name: Jia
  given name: Zhilong
author list: Agent
  family name: Shi
  given name: Jinlong
author list: Agent
  family name: Zhang
  given name: Zeyu
author list: Agent
  family name: Gao
  given name: Xiaojian
author list: Agent
  family name: Jia
  given name: Qian
author list: Agent
  family name: Liu
  given name: Bohan
author list: Agent
  family name: Liu
  given name: Jixuan
author list: Agent
  family name: Liu
  given name: Chunlei
author list: Agent
  family name: Zhao
  given name: Xiaojing
author list: Agent
  family name: He
  given name: Kunlun
doi: 10.7717/peerj.6499
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-09
copyright: ©2019 Xu et al.
attribution name: Xu et al.

Maturation trade-offs in octopus females and their progeny: energy, digestion and defence indicators
type: item
type: AcademicArticle
description: Sexual maturation and reproduction influence the status of a number of physiological processes and consequently the ecology and behaviour of cephalopods. Using Octopus mimus as a study model, the present work was focused in the changes in biochemical compound and activity that take place during gonadal maturation of females and its consequences in embryo and hatchlings characteristics. To do that, a total of 31 adult females of O. mimus were sampled to follow metabolites (ovaries and digestive gland) and digestive enzyme activities (alkaline and acidic proteases) during physiological and functional maturation. Levels of protein (Prot), triacylglyceride (TG), cholesterol (Chol), glucose (Glu), and glycogen (Gly) were evaluated. Groups of eggs coming from mature females were also sampled along development and after hatching (paralarvae of 1 and 3 days old) to track metabolites (Prot, TG, Glu, Gly, TG, Chol), digestive enzymes activity (Lipase, alkaline proteases, and acidic proteases), and antioxidant/detoxification defence indicators with embryos development. Based on the data obtained, we hypothesized that immature females store Chol in their ovaries, probably from the food they ingested, but switch to TG reserves at the beginning of the maturation processes. At the same time, results suggest that these processes were energetically supported by Glu, obtained probably from Gly breakdown by gluconeogenic pathways. Also, was observed that embryos metabolites and enzyme activities (digestive and antioxidant/detoxification enzymes) where maintained without significant changes and in a low activity during the whole organogenesis, meaning that organogenesis is relatively not energetically costly. In contrast, after organogenesis, a mobilization of nutrients and activation of the metabolic and digestive enzymes was observed, together with increments in consumption of yolk and Gly, and reduction in lipid peroxidation. Derived from our results, we also have the hypothesis tha…
format: application/pdf
format: text/html
creator: Alberto Olivares
creator: Gabriela Rodríguez-Fuentes
creator: Maite Mascaró
creator: Ariadna Sanchez Arteaga
creator: Karen Ortega
creator: Claudia Caamal Monsreal
creator: Nelly Tremblay
creator: Carlos Rosas
subject: Aquaculture, Fisheries and Fish Science
subject: Developmental Biology
subject: Marine Biology
description: doi:10.7717/peerj.6618
publisher: PeerJ Inc.
rights: © 2019 Olivares et al.
abstract: Sexual maturation and reproduction influence the status of a number of physiological processes and consequently the ecology and behaviour of cephalopods. Using Octopus mimus as a study model, the present work was focused in the changes in biochemical compound and activity that take place during gonadal maturation of females and its consequences in embryo and hatchlings characteristics. To do that, a total of 31 adult females of O. mimus were sampled to follow metabolites (ovaries and digestive gland) and digestive enzyme activities (alkaline and acidic proteases) during physiological and functional maturation. Levels of protein (Prot), triacylglyceride (TG), cholesterol (Chol), glucose (Glu), and glycogen (Gly) were evaluated. Groups of eggs coming from mature females were also sampled along development and after hatching (paralarvae of 1 and 3 days old) to track metabolites (Prot, TG, Glu, Gly, TG, Chol), digestive enzymes activity (Lipase, alkaline proteases, and acidic proteases), and antioxidant/detoxification defence indicators with embryos development. Based on the data obtained, we hypothesized that immature females store Chol in their ovaries, probably from the food they ingested, but switch to TG reserves at the beginning of the maturation processes. At the same time, results suggest that these processes were energetically supported by Glu, obtained probably from Gly breakdown by gluconeogenic pathways. Also, was observed that embryos metabolites and enzyme activities (digestive and antioxidant/detoxification enzymes) where maintained without significant changes and in a low activity during the whole organogenesis, meaning that organogenesis is relatively not energetically costly. In contrast, after organogenesis, a mobilization of nutrients and activation of the metabolic and digestive enzymes was observed, together with increments in consumption of yolk and Gly, and reduction in lipid peroxidation. Derived from our results, we also have the hypothesis tha…
bibliographic citation: Olivares et al. (2019) Maturation trade-offs in octopus females and their progeny: energy, digestion and defence indicators. PeerJ 7:e6618 https://doi.org/10.7717/peerj.6618
date submitted: 2018-06-04
date accepted: 2019-02-14
issued: 2019-04-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Olivares
  given name: Alberto
author list: Agent
  family name: Rodríguez-Fuentes
  given name: Gabriela
author list: Agent
  family name: Mascaró
  given name: Maite
author list: Agent
  family name: Sanchez Arteaga
  given name: Ariadna
author list: Agent
  family name: Ortega
  given name: Karen
author list: Agent
  family name: Caamal Monsreal
  given name: Claudia
author list: Agent
  family name: Tremblay
  given name: Nelly
author list: Agent
  family name: Rosas
  given name: Carlos
doi: 10.7717/peerj.6618
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-09
copyright: © 2019 Olivares et al.
attribution name: Olivares et al.

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