PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Rapid screening mutations of first-line-drug-resistant genes in Mycobacterium tuberculosis strains by allele-specific real-time quantitative PCR
items: A set of novel SNP loci for differentiating continental populations and three Chinese populations
items: Understanding the experience of psychopathology after intimate partner violence: the role of personality
items: Using road patrol data to identify factors associated with carnivore roadkill counts
items: IOCBIO Sparks detection and analysis software
items: Comparative analysis and characterization of the gut microbiota of four farmed snakes from southern China
items: Music-performance regulates microRNAs in professional musicians
items: Green potential of Pleurotus spp. in biotechnology
items: Transcriptional factor regulation network and competitive endogenous RNA (ceRNA) network determining response of esophageal squamous cell carcinomas to neoadjuvant chemoradiotherapy
items: Using opportunistic sightings to infer differential spatio-temporal use of western Mediterranean waters by the fin whale

Rapid screening mutations of first-line-drug-resistant genes in Mycobacterium tuberculosis strains by allele-specific real-time quantitative PCR
type: item
type: AcademicArticle
description: Tuberculosis (TB) is a worldwide health, economic, and social burden, especially in developing countries. Drug-resistant TB is the most serious type of this burden. Thus, it is necessary to screen drug-resistant mutations by using a simple and rapid detection method. A total of 32 pairs of allele-specific PCR (AS-PCR) primers were designed to screen mutation and/or wild-type alleles of 16 variations in four first-line drug-resistant genes (katG, rpoB, rpsL, and embB) of TB strains. A pair of primers was designed to amplify 16S rRNA gene and to verify successful amplification. Subsequently, we tested the specificity and sensitivity of these AS-PCR primers. The optimized condition of these AS-PCR primers was first confirmed. All mutations could be screened in general AS-PCR, but only 13 of 16 variations were intuitively investigated by using real-time quantitative PCR (qPCR) and AS-PCR primers. The results of specificity assay suggested that the AS-PCR primers with mutation and/or wildtype alleles could successfully amplify the corresponding allele under optimized PCR conditions. The sensitivity of nine pairs of primers was 500 copy numbers, and the other seven pairs of primers could successfully amplify correct fragments with a template comprising 103 or 104 copy numbers template. An optimized AS-qPCR was established to screen drug-resistant mutations in TB strains with high specificity and sensitivity.
format: application/pdf
format: text/html
creator: Pengpeng Yang
creator: Yuzhu Song
creator: Xueshan Xia
creator: A-Mei Zhang
subject: Drugs and Devices
subject: Pathology
subject: Pharmacology
subject: Respiratory Medicine
subject: Translational Medicine
description: doi:10.7717/peerj.6696
publisher: PeerJ Inc.
rights: © 2019 Yang et al.
abstract: Tuberculosis (TB) is a worldwide health, economic, and social burden, especially in developing countries. Drug-resistant TB is the most serious type of this burden. Thus, it is necessary to screen drug-resistant mutations by using a simple and rapid detection method. A total of 32 pairs of allele-specific PCR (AS-PCR) primers were designed to screen mutation and/or wild-type alleles of 16 variations in four first-line drug-resistant genes (katG, rpoB, rpsL, and embB) of TB strains. A pair of primers was designed to amplify 16S rRNA gene and to verify successful amplification. Subsequently, we tested the specificity and sensitivity of these AS-PCR primers. The optimized condition of these AS-PCR primers was first confirmed. All mutations could be screened in general AS-PCR, but only 13 of 16 variations were intuitively investigated by using real-time quantitative PCR (qPCR) and AS-PCR primers. The results of specificity assay suggested that the AS-PCR primers with mutation and/or wildtype alleles could successfully amplify the corresponding allele under optimized PCR conditions. The sensitivity of nine pairs of primers was 500 copy numbers, and the other seven pairs of primers could successfully amplify correct fragments with a template comprising 103 or 104 copy numbers template. An optimized AS-qPCR was established to screen drug-resistant mutations in TB strains with high specificity and sensitivity.
bibliographic citation: Yang et al. (2019) Rapid screening mutations of first-line-drug-resistant genes in Mycobacterium tuberculosis strains by allele-specific real-time quantitative PCR. PeerJ 7:e6696 https://doi.org/10.7717/peerj.6696
date submitted: 2018-10-29
date accepted: 2019-02-27
issued: 2019-04-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Pengpeng
author list: Agent
  family name: Song
  given name: Yuzhu
author list: Agent
  family name: Xia
  given name: Xueshan
author list: Agent
  family name: Zhang
  given name: A-Mei
doi: 10.7717/peerj.6696
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-01
copyright: © 2019 Yang et al.
attribution name: Yang et al.

A set of novel SNP loci for differentiating continental populations and three Chinese populations
type: item
type: AcademicArticle
description: In recent years, forensic geneticists have begun to develop some ancestry informative marker (AIM) panels for ancestry analysis of regional populations. In this study, we chose 48 single nucleotide polymorphisms (SNPs) from SPSmart database to infer ancestry origins of continental populations and Chinese subpopulations. Based on the genetic data of four continental populations (African, American, East Asian and European) from the CEPH-HGDP database, the power of these SNPs for differentiating continental populations was assessed. Population genetic structure revealed that distinct ancestry components among these continental populations could be discerned by these SNPs. Another novel population set from 1000 Genomes Phase 3 was treated as testing populations to further validate the efficiency of the selected SNPs. Twenty-two populations from CEPH-HGDP database were classified into three known populations (African, East Asian, and European) based on their biogeographical regions. Principal component analysis and Bayes analysis of testing populations and three known populations indicated these testing populations could be correctly assigned to their corresponding biogeographical origins. For three Chinese populations (Han, Mongolian, and Uygur), multinomial logistic regression analyses indicated that these 48 SNPs could be used to estimate ancestry origins of these populations. Therefore, these SNPs possessed the promising potency in ancestry analysis among continental populations and some Chinese populations, and they could be used in population genetics and forensic research.
format: application/pdf
format: text/html
creator: Xiao-Ye Jin
creator: Yuan-Yuan Wei
creator: Qiong Lan
creator: Wei Cui
creator: Chong Chen
creator: Yu-Xin Guo
creator: Ya-Ting Fang
creator: Bo-Feng Zhu
subject: Bioinformatics
subject: Genetics
subject: Data Science
subject: Population Biology
description: doi:10.7717/peerj.6508
publisher: PeerJ Inc.
rights: © 2019 Jin et al.
abstract: In recent years, forensic geneticists have begun to develop some ancestry informative marker (AIM) panels for ancestry analysis of regional populations. In this study, we chose 48 single nucleotide polymorphisms (SNPs) from SPSmart database to infer ancestry origins of continental populations and Chinese subpopulations. Based on the genetic data of four continental populations (African, American, East Asian and European) from the CEPH-HGDP database, the power of these SNPs for differentiating continental populations was assessed. Population genetic structure revealed that distinct ancestry components among these continental populations could be discerned by these SNPs. Another novel population set from 1000 Genomes Phase 3 was treated as testing populations to further validate the efficiency of the selected SNPs. Twenty-two populations from CEPH-HGDP database were classified into three known populations (African, East Asian, and European) based on their biogeographical regions. Principal component analysis and Bayes analysis of testing populations and three known populations indicated these testing populations could be correctly assigned to their corresponding biogeographical origins. For three Chinese populations (Han, Mongolian, and Uygur), multinomial logistic regression analyses indicated that these 48 SNPs could be used to estimate ancestry origins of these populations. Therefore, these SNPs possessed the promising potency in ancestry analysis among continental populations and some Chinese populations, and they could be used in population genetics and forensic research.
bibliographic citation: Jin et al. (2019) A set of novel SNP loci for differentiating continental populations and three Chinese populations. PeerJ 7:e6508 https://doi.org/10.7717/peerj.6508
date submitted: 2018-10-02
date accepted: 2019-01-22
issued: 2019-03-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jin
  given name: Xiao-Ye
author list: Agent
  family name: Wei
  given name: Yuan-Yuan
author list: Agent
  family name: Lan
  given name: Qiong
author list: Agent
  family name: Cui
  given name: Wei
author list: Agent
  family name: Chen
  given name: Chong
author list: Agent
  family name: Guo
  given name: Yu-Xin
author list: Agent
  family name: Fang
  given name: Ya-Ting
author list: Agent
  family name: Zhu
  given name: Bo-Feng
doi: 10.7717/peerj.6508
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-29
copyright: ©2019 Jin et al.
attribution name: Jin et al.

Understanding the experience of psychopathology after intimate partner violence: the role of personality
type: item
type: AcademicArticle
description: Objective(s) To fully understand the dynamics of Intimate Partner Violence (IPV) it is necessary to understand the role of personality. The current understanding of which personality characteristics are associated with IPV victimization is, however, far from comprehensive. Given this gap in the literature, our objective was to examine the associations between the dimensions of the psychobiological model of personality and psychopathological symptoms in women who had experienced IPV. Methods Using a case-control design, a group of women who had experienced IPV and who were living in shelters (n = 50) were compared to a group of control women who had not experienced IPV (n = 50). All women completed the Temperament and Character Inventory–Revised and the Brief Symptom Inventory. Results Victims of IPV showed significantly higher levels of Harm Avoidance and Self-Transcendence, and lower levels of Reward Dependence and Self-Directedness, than the non-IPV control group. Victims of IPV also reported elevated levels of psychopathological symptoms. Personality dimensions showed a broadly consistent pattern of associations across different psychopathological symptoms. A regression analysis indicated that Novelty Seeking was negatively associated with psychopathological symptoms in victims of IPV, but not significantly associated in non-victims. Conclusions The study highlights the important role of Harm Avoidance and Self-Directedness for understanding psychopathological symptoms. Novelty Seeking appears to play an important role in the expression of individuals’ experiences of IPV. These results have important implications for research and practice, particularly the development and implementation of interventions.
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format: text/html
creator: Paulo A.S. Moreira
creator: Márcia Pinto
creator: C. Robert Cloninger
creator: Daniela Rodrigues
creator: Carlos Fernandes da Silva
subject: Psychiatry and Psychology
subject: Women’s Health
description: doi:10.7717/peerj.6647
publisher: PeerJ Inc.
rights: © 2019 Moreira et al.
abstract: Objective(s) To fully understand the dynamics of Intimate Partner Violence (IPV) it is necessary to understand the role of personality. The current understanding of which personality characteristics are associated with IPV victimization is, however, far from comprehensive. Given this gap in the literature, our objective was to examine the associations between the dimensions of the psychobiological model of personality and psychopathological symptoms in women who had experienced IPV. Methods Using a case-control design, a group of women who had experienced IPV and who were living in shelters (n = 50) were compared to a group of control women who had not experienced IPV (n = 50). All women completed the Temperament and Character Inventory–Revised and the Brief Symptom Inventory. Results Victims of IPV showed significantly higher levels of Harm Avoidance and Self-Transcendence, and lower levels of Reward Dependence and Self-Directedness, than the non-IPV control group. Victims of IPV also reported elevated levels of psychopathological symptoms. Personality dimensions showed a broadly consistent pattern of associations across different psychopathological symptoms. A regression analysis indicated that Novelty Seeking was negatively associated with psychopathological symptoms in victims of IPV, but not significantly associated in non-victims. Conclusions The study highlights the important role of Harm Avoidance and Self-Directedness for understanding psychopathological symptoms. Novelty Seeking appears to play an important role in the expression of individuals’ experiences of IPV. These results have important implications for research and practice, particularly the development and implementation of interventions.
bibliographic citation: Moreira et al. (2019) Understanding the experience of psychopathology after intimate partner violence: the role of personality. PeerJ 7:e6647 https://doi.org/10.7717/peerj.6647
date submitted: 2018-12-13
date accepted: 2019-02-20
issued: 2019-03-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Moreira
  given name: Paulo A.S.
author list: Agent
  family name: Pinto
  given name: Márcia
author list: Agent
  family name: Cloninger
  given name: C. Robert
author list: Agent
  family name: Rodrigues
  given name: Daniela
author list: Agent
  family name: da Silva
  given name: Carlos Fernandes
doi: 10.7717/peerj.6647
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-29
copyright: ©2019 Moreira et al.
attribution name: Moreira et al.

Using road patrol data to identify factors associated with carnivore roadkill counts
type: item
type: AcademicArticle
description: As the global road network expands, roads pose an emerging threat to wildlife populations. One way in which roads can affect wildlife is wildlife-vehicle collisions, which can be a significant cause of mortality through roadkill. In order to successfully mitigate these problems, it is vital to understand the factors that can explain the distribution of roadkill. Collecting the data required to enable this can be expensive and time consuming, but there is significant potential in partnering with organisations that conduct existing road patrols to obtain the necessary data. We assessed the feasibility of using roadkill data collected daily between 2014 and 2017 by road patrol staff from a private road agency on a 410 km length of the N3 road in South Africa. We modelled the relationship between a set of environmental and anthropogenic variables on the number of roadkill carcasses, using serval (Leptailurus serval) as a model species. We recorded 5.24 serval roadkill carcasses/100 km/year. The number of carcasses was related to season, the amount of wetland, and NDVI, but was not related to any of the anthropogenic variables we included. This suggests that roadkill patterns may differ greatly depending on the ecology of species of interest, but targeting mitigation measures where roads pass through wetlands may help to reduce serval roadkill. Partnering with road agencies for data collection offers powerful opportunities to identify factors related to roadkill distribution and reduce the threats posed by roads to wildlife.
format: application/pdf
format: text/html
creator: Samual T. Williams
creator: Wendy Collinson
creator: Claire Patterson-Abrolat
creator: David G. Marneweck
creator: Lourens H. Swanepoel
subject: Conservation Biology
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.6650
publisher: PeerJ Inc.
rights: © 2019 Williams et al.
abstract: As the global road network expands, roads pose an emerging threat to wildlife populations. One way in which roads can affect wildlife is wildlife-vehicle collisions, which can be a significant cause of mortality through roadkill. In order to successfully mitigate these problems, it is vital to understand the factors that can explain the distribution of roadkill. Collecting the data required to enable this can be expensive and time consuming, but there is significant potential in partnering with organisations that conduct existing road patrols to obtain the necessary data. We assessed the feasibility of using roadkill data collected daily between 2014 and 2017 by road patrol staff from a private road agency on a 410 km length of the N3 road in South Africa. We modelled the relationship between a set of environmental and anthropogenic variables on the number of roadkill carcasses, using serval (Leptailurus serval) as a model species. We recorded 5.24 serval roadkill carcasses/100 km/year. The number of carcasses was related to season, the amount of wetland, and NDVI, but was not related to any of the anthropogenic variables we included. This suggests that roadkill patterns may differ greatly depending on the ecology of species of interest, but targeting mitigation measures where roads pass through wetlands may help to reduce serval roadkill. Partnering with road agencies for data collection offers powerful opportunities to identify factors related to roadkill distribution and reduce the threats posed by roads to wildlife.
bibliographic citation: Williams et al. (2019) Using road patrol data to identify factors associated with carnivore roadkill counts. PeerJ 7:e6650 https://doi.org/10.7717/peerj.6650
date submitted: 2019-01-07
date accepted: 2019-02-15
issued: 2019-03-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Williams
  given name: Samual T.
author list: Agent
  family name: Collinson
  given name: Wendy
author list: Agent
  family name: Patterson-Abrolat
  given name: Claire
author list: Agent
  family name: Marneweck
  given name: David G.
author list: Agent
  family name: Swanepoel
  given name: Lourens H.
doi: 10.7717/peerj.6650
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-29
copyright: ©2019 Williams et al.
attribution name: Williams et al.

IOCBIO Sparks detection and analysis software
type: item
type: AcademicArticle
description: Analysis of calcium sparks in cardiomyocytes can provide valuable information about functional changes of calcium handling in health and disease. As a part of the calcium sparks analysis, sparks detection and characterization is necessary. Here, we describe a new open-source platform for automatic calcium sparks detection from line scan confocal images. The developed software is tailored for detecting only calcium sparks, allowing us to design a graphical user interface specifically for this task. The software enables detecting sparks automatically as well as adding, removing, or adjusting regions of interest marking each spark. The results of the analysis are stored in an SQL database, allowing simple integration with statistical tools. We have analyzed the performance of the algorithm using a large set of synthetic images with varying spark sizes and noise levels and also compared the analysis results with results obtained by software established in the field. The use of our software is illustrated by an analysis of the effect of isoprenaline (ISO) on spark frequency, amplitude, and spatial and temporal characteristics. For that, cardiomyocytes from C57BL/6 mice were used. We demonstrated an increase in spark frequency, tendency of having larger spark amplitudes, sparks with a longer duration, and occurrence of multiple sparks from the same site in the presence of ISO. We also show that the duration and the width of sparks with the same amplitude were similar in the absence and presence of ISO. The software was released as an open source repository and is available for free use and collaborative development.
format: application/pdf
format: text/html
creator: Martin Laasmaa
creator: Niina Karro
creator: Rikke Birkedal
creator: Marko Vendelin
subject: Bioinformatics
subject: Biophysics
subject: Cell Biology
subject: Computational Biology
subject: Cardiology
description: doi:10.7717/peerj.6652
publisher: PeerJ Inc.
rights: © 2019 Laasmaa et al.
abstract: Analysis of calcium sparks in cardiomyocytes can provide valuable information about functional changes of calcium handling in health and disease. As a part of the calcium sparks analysis, sparks detection and characterization is necessary. Here, we describe a new open-source platform for automatic calcium sparks detection from line scan confocal images. The developed software is tailored for detecting only calcium sparks, allowing us to design a graphical user interface specifically for this task. The software enables detecting sparks automatically as well as adding, removing, or adjusting regions of interest marking each spark. The results of the analysis are stored in an SQL database, allowing simple integration with statistical tools. We have analyzed the performance of the algorithm using a large set of synthetic images with varying spark sizes and noise levels and also compared the analysis results with results obtained by software established in the field. The use of our software is illustrated by an analysis of the effect of isoprenaline (ISO) on spark frequency, amplitude, and spatial and temporal characteristics. For that, cardiomyocytes from C57BL/6 mice were used. We demonstrated an increase in spark frequency, tendency of having larger spark amplitudes, sparks with a longer duration, and occurrence of multiple sparks from the same site in the presence of ISO. We also show that the duration and the width of sparks with the same amplitude were similar in the absence and presence of ISO. The software was released as an open source repository and is available for free use and collaborative development.
bibliographic citation: Laasmaa et al. (2019) IOCBIO Sparks detection and analysis software. PeerJ 7:e6652 https://doi.org/10.7717/peerj.6652
date submitted: 2019-01-07
date accepted: 2019-02-19
issued: 2019-03-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Laasmaa
  given name: Martin
author list: Agent
  family name: Karro
  given name: Niina
author list: Agent
  family name: Birkedal
  given name: Rikke
author list: Agent
  family name: Vendelin
  given name: Marko
doi: 10.7717/peerj.6652
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-29
copyright: © 2019 Laasmaa et al.
attribution name: Laasmaa et al.

Comparative analysis and characterization of the gut microbiota of four farmed snakes from southern China
type: item
type: AcademicArticle
description: Background The gut microbiota plays an important role in host immunity and metabolic homeostasis. Although analyses of gut microbiotas have been used to assess host health and foster disease prevention and treatment, no comparative comprehensive study, assessing gut microbiotas among several species of farmed snake, is yet available. In this study, we characterized and compared the gut microbiotas of four species of farmed snakes (Naja atra, Ptyas mucosa, Elaphe carinata, and Deinagkistrodon acutus) using high-throughput sequencing of the 16S rDNA gene in southern China and tested whether there was a relationship between gut microbiotal composition and host species. Results A total of 629 operational taxonomic units across 22 samples were detected. The five most abundant phyla were Bacteroidetes, Proteobacteria, Firmicutes, Fusobacteria, and Actinobacteria, while the five most abundant genera were Bacteroides, Cetobacterium, Clostridium, Plesiomonas, and Paeniclostridium. This was the first report of the dominance of Fusobacteria and Cetobacterium in the snake gut. Our phylogenetic analysis recovered a relatively close relationship between Fusobacteria and Bacteroidetes. Alpha diversity analysis indicated that species richness and diversity were highest in the gut microbiota of D. acutus and lowest in that of E. carinata. Significant differences in alpha diversity were detected among the four farmed snake species. The gut microbiotas of conspecifics were more similar to each other than to those of heterospecifics. Conclusion This study provides the first comparative study of gut microbiotas among several species of farmed snakes, and provides valuable data for the management of farmed snakes. In farmed snakes, host species affected the species composition and diversity of the gut microbiota.
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creator: Bing Zhang
creator: Jing Ren
creator: Daode Yang
creator: Shuoran Liu
creator: Xinguo Gong
subject: Bioinformatics
subject: Microbiology
subject: Veterinary Medicine
subject: Zoology
description: doi:10.7717/peerj.6658
publisher: PeerJ Inc.
rights: © 2019 Zhang et al.
abstract: Background The gut microbiota plays an important role in host immunity and metabolic homeostasis. Although analyses of gut microbiotas have been used to assess host health and foster disease prevention and treatment, no comparative comprehensive study, assessing gut microbiotas among several species of farmed snake, is yet available. In this study, we characterized and compared the gut microbiotas of four species of farmed snakes (Naja atra, Ptyas mucosa, Elaphe carinata, and Deinagkistrodon acutus) using high-throughput sequencing of the 16S rDNA gene in southern China and tested whether there was a relationship between gut microbiotal composition and host species. Results A total of 629 operational taxonomic units across 22 samples were detected. The five most abundant phyla were Bacteroidetes, Proteobacteria, Firmicutes, Fusobacteria, and Actinobacteria, while the five most abundant genera were Bacteroides, Cetobacterium, Clostridium, Plesiomonas, and Paeniclostridium. This was the first report of the dominance of Fusobacteria and Cetobacterium in the snake gut. Our phylogenetic analysis recovered a relatively close relationship between Fusobacteria and Bacteroidetes. Alpha diversity analysis indicated that species richness and diversity were highest in the gut microbiota of D. acutus and lowest in that of E. carinata. Significant differences in alpha diversity were detected among the four farmed snake species. The gut microbiotas of conspecifics were more similar to each other than to those of heterospecifics. Conclusion This study provides the first comparative study of gut microbiotas among several species of farmed snakes, and provides valuable data for the management of farmed snakes. In farmed snakes, host species affected the species composition and diversity of the gut microbiota.
bibliographic citation: Zhang et al. (2019) Comparative analysis and characterization of the gut microbiota of four farmed snakes from southern China. PeerJ 7:e6658 https://doi.org/10.7717/peerj.6658
date submitted: 2018-09-11
date accepted: 2019-02-22
issued: 2019-03-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Bing
author list: Agent
  family name: Ren
  given name: Jing
author list: Agent
  family name: Yang
  given name: Daode
author list: Agent
  family name: Liu
  given name: Shuoran
author list: Agent
  family name: Gong
  given name: Xinguo
doi: 10.7717/peerj.6658
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-29
copyright: © 2019 Zhang et al.
attribution name: Zhang et al.

Music-performance regulates microRNAs in professional musicians
type: item
type: AcademicArticle
description: Musical training and performance require precise integration of multisensory and motor centres of the human brain and can be regarded as an epigenetic modifier of brain functions. Numerous studies have identified structural and functional differences between the brains of musicians and non-musicians and superior cognitive functions in musicians. Recently, music-listening and performance has also been shown to affect the regulation of several genes, many of which were identified in songbird singing. MicroRNAs affect gene regulation and studying their expression may give new insights into the epigenetic effect of music. Here, we studied the effect of 2 hours of classical music-performance on the peripheral blood microRNA expressions in professional musicians with respect to a control activity without music for the same duration. As detecting transcriptomic changes in the functional human brain remains a challenge for geneticists, we used peripheral blood to study music-performance induced microRNA changes and interpreted the results in terms of potential effects on brain function, based on the current knowledge about the microRNA function in blood and brain. We identified significant (FDR <0.05) up-regulation of five microRNAs; hsa-miR-3909, hsa-miR-30d-5p, hsa-miR-92a-3p, hsa-miR-222-3p and hsa-miR-30a-5p; and down-regulation of two microRNAs; hsa-miR-6803-3p and hsa-miR-1249-3p. hsa-miR-222-3p and hsa-miR-92a-3p putatively target FOXP2, which was found down-regulated by microRNA regulation in songbird singing. miR-30d and miR-222 corroborate microRNA response observed in zebra finch song-listening/learning. miR-222 is induced by ERK cascade, which is important for memory formation, motor neuron functions and neuronal plasticity. miR-222 is also activated by FOSL1, an immediate early gene from the FOS family of transcriptional regulators which are activated by auditory-motor stimuli. miR-222 and miR-92 promote neurite outgrowth by negatively regulating the neuronal g…
format: application/pdf
format: text/html
creator: Preethy Sasidharan Nair
creator: Tuire Kuusi
creator: Minna Ahvenainen
creator: Anju K. Philips
creator: Irma Järvelä
subject: Genetics
subject: Genomics
subject: Neuroscience
description: doi:10.7717/peerj.6660
publisher: PeerJ Inc.
rights: © 2019 Nair et al.
abstract: Musical training and performance require precise integration of multisensory and motor centres of the human brain and can be regarded as an epigenetic modifier of brain functions. Numerous studies have identified structural and functional differences between the brains of musicians and non-musicians and superior cognitive functions in musicians. Recently, music-listening and performance has also been shown to affect the regulation of several genes, many of which were identified in songbird singing. MicroRNAs affect gene regulation and studying their expression may give new insights into the epigenetic effect of music. Here, we studied the effect of 2 hours of classical music-performance on the peripheral blood microRNA expressions in professional musicians with respect to a control activity without music for the same duration. As detecting transcriptomic changes in the functional human brain remains a challenge for geneticists, we used peripheral blood to study music-performance induced microRNA changes and interpreted the results in terms of potential effects on brain function, based on the current knowledge about the microRNA function in blood and brain. We identified significant (FDR <0.05) up-regulation of five microRNAs; hsa-miR-3909, hsa-miR-30d-5p, hsa-miR-92a-3p, hsa-miR-222-3p and hsa-miR-30a-5p; and down-regulation of two microRNAs; hsa-miR-6803-3p and hsa-miR-1249-3p. hsa-miR-222-3p and hsa-miR-92a-3p putatively target FOXP2, which was found down-regulated by microRNA regulation in songbird singing. miR-30d and miR-222 corroborate microRNA response observed in zebra finch song-listening/learning. miR-222 is induced by ERK cascade, which is important for memory formation, motor neuron functions and neuronal plasticity. miR-222 is also activated by FOSL1, an immediate early gene from the FOS family of transcriptional regulators which are activated by auditory-motor stimuli. miR-222 and miR-92 promote neurite outgrowth by negatively regulating the neuronal g…
bibliographic citation: Nair et al. (2019) Music-performance regulates microRNAs in professional musicians. PeerJ 7:e6660 https://doi.org/10.7717/peerj.6660
date submitted: 2018-06-13
date accepted: 2019-02-19
issued: 2019-03-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nair
  given name: Preethy Sasidharan
author list: Agent
  family name: Kuusi
  given name: Tuire
author list: Agent
  family name: Ahvenainen
  given name: Minna
author list: Agent
  family name: Philips
  given name: Anju K.
author list: Agent
  family name: Järvelä
  given name: Irma
doi: 10.7717/peerj.6660
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-29
copyright: © 2019 Nair et al.
attribution name: Nair et al.

Green potential of Pleurotus spp. in biotechnology
type: item
type: AcademicArticle
description: Background The genus Pleurotus is most exploitable xylotrophic fungi, with valuable biotechnological, medical, and nutritional properties. The relevant features of the representatives of this genus to provide attractive low-cost industrial tools have been reported in numerous studies to resolve the pressure of ecological issues. Additionally, a number of Pleurotus species are highly adaptive, do not require any special conditions for growth, and possess specific resistance to contaminating diseases and pests. The unique properties of Pleurotus species widely used in many environmental technologies, such as organic solid waste recycling, chemical pollutant degradation, and bioethanol production. Methodology The literature study encompasses peer-reviewed journals identified by systematic searches of electronic databases such as Google Scholar, NCBI, Springer, ResearchGate, ScienceDirect, and ISI Web of Knowledge. The search scheme was divided into several steps, as described below. Results In this review, we describe studies examining the biotechnological feasibility of Pleurotus spp. to elucidate the importance of this genus for use in green technology. Here, we review areas of application of the genus Pleurotus as a prospective biotechnological tool. Conclusion The incomplete description of some fungal biochemical pathways emphasises the future research goals for this fungal culture.
format: application/pdf
format: text/html
creator: Alona S. Sekan
creator: Olena S. Myronycheva
creator: Olov Karlsson
creator: Andrii P. Gryganskyi
creator: Yaroslav Blume
subject: Agricultural Science
subject: Biotechnology
subject: Molecular Biology
subject: Mycology
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.6664
publisher: PeerJ Inc.
rights: © 2019 Sekan et al.
abstract: Background The genus Pleurotus is most exploitable xylotrophic fungi, with valuable biotechnological, medical, and nutritional properties. The relevant features of the representatives of this genus to provide attractive low-cost industrial tools have been reported in numerous studies to resolve the pressure of ecological issues. Additionally, a number of Pleurotus species are highly adaptive, do not require any special conditions for growth, and possess specific resistance to contaminating diseases and pests. The unique properties of Pleurotus species widely used in many environmental technologies, such as organic solid waste recycling, chemical pollutant degradation, and bioethanol production. Methodology The literature study encompasses peer-reviewed journals identified by systematic searches of electronic databases such as Google Scholar, NCBI, Springer, ResearchGate, ScienceDirect, and ISI Web of Knowledge. The search scheme was divided into several steps, as described below. Results In this review, we describe studies examining the biotechnological feasibility of Pleurotus spp. to elucidate the importance of this genus for use in green technology. Here, we review areas of application of the genus Pleurotus as a prospective biotechnological tool. Conclusion The incomplete description of some fungal biochemical pathways emphasises the future research goals for this fungal culture.
bibliographic citation: Sekan et al. (2019) Green potential of Pleurotus spp. in biotechnology. PeerJ 7:e6664 https://doi.org/10.7717/peerj.6664
date submitted: 2018-09-07
date accepted: 2019-02-22
issued: 2019-03-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sekan
  given name: Alona S.
author list: Agent
  family name: Myronycheva
  given name: Olena S.
author list: Agent
  family name: Karlsson
  given name: Olov
author list: Agent
  family name: Gryganskyi
  given name: Andrii P.
author list: Agent
  family name: Blume
  given name: Yaroslav
doi: 10.7717/peerj.6664
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-29
copyright: © 2019 Sekan et al.
attribution name: Sekan et al.

Transcriptional factor regulation network and competitive endogenous RNA (ceRNA) network determining response of esophageal squamous cell carcinomas to neoadjuvant chemoradiotherapy
type: item
type: AcademicArticle
description: Background Neoadjuvant chemoradiotherapy (nCRT) followed by surgery benefits survival for patients with esophageal squamous cell carcinomas (ESCC) compared with surgery alone, but the clinical outcomes of nCRT are heterogeneous. This study aimed to elucidate transcriptional factor (TF) regulation network and competitive endogenous RNA (ceRNA) network determining response of ESCC to nCRT. Materials and Methods RNA microarray data of GSE59974 and GSE45670 were analyzed to investigate the significant changes of lincRNAs, miRNAs, mRNAs in responders and non-responders of nCRT in ESCC. Functional and enrichment analyses were conducted by clusterProfiler. The target lincRNAs and mRNAs of miRNAs were predicted by miRWalk. The ceRNA and TF regulatory networks were constructed using Cytoscape. Results Differentially expressed genes between responders and non-responders mainly enriched in biological process including Wnt signaling pathway and regulation of cell development and morphogenesis involved in differentiation. Besides, these genes showed enrichment in molecular function of glycosaminoglycan binding, metalloendopeptidase inhibitor and growth factor activity. KEGG analysis enriched these genes in pathways of neurotrophin signaling pathway, cell adhesion molecules and Wnt signaling pathway. We also constructed ceRNA network and TF network regulating response of ESCC to nCRT. Core regulatory miRNAs were miR-520a, miR-548am, miR-3184, miR-548d, miR-4725, miR-148a, miR-4659a and key regulatory TFs included MBNL1, SLC26A3, BMP4, ZIC1 and ANKRD7. Conclusion We identified significantly altered lincRNAs, miRNAs and mRNAs involved in the nCRT response of ESCC. In addition, the ceRNA regulatory network of lincRNA-miRNA-mRNA and TF regulatory network were constructed, which would elucidate novel molecular mechanisms determining nCRT response of ESCC, thus providing promising clues for clinical therapy.
format: application/pdf
format: text/html
creator: Mingrui Shao
creator: Wenya Li
subject: Oncology
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.6668
publisher: PeerJ Inc.
rights: © 2019 Shao and Li
abstract: Background Neoadjuvant chemoradiotherapy (nCRT) followed by surgery benefits survival for patients with esophageal squamous cell carcinomas (ESCC) compared with surgery alone, but the clinical outcomes of nCRT are heterogeneous. This study aimed to elucidate transcriptional factor (TF) regulation network and competitive endogenous RNA (ceRNA) network determining response of ESCC to nCRT. Materials and Methods RNA microarray data of GSE59974 and GSE45670 were analyzed to investigate the significant changes of lincRNAs, miRNAs, mRNAs in responders and non-responders of nCRT in ESCC. Functional and enrichment analyses were conducted by clusterProfiler. The target lincRNAs and mRNAs of miRNAs were predicted by miRWalk. The ceRNA and TF regulatory networks were constructed using Cytoscape. Results Differentially expressed genes between responders and non-responders mainly enriched in biological process including Wnt signaling pathway and regulation of cell development and morphogenesis involved in differentiation. Besides, these genes showed enrichment in molecular function of glycosaminoglycan binding, metalloendopeptidase inhibitor and growth factor activity. KEGG analysis enriched these genes in pathways of neurotrophin signaling pathway, cell adhesion molecules and Wnt signaling pathway. We also constructed ceRNA network and TF network regulating response of ESCC to nCRT. Core regulatory miRNAs were miR-520a, miR-548am, miR-3184, miR-548d, miR-4725, miR-148a, miR-4659a and key regulatory TFs included MBNL1, SLC26A3, BMP4, ZIC1 and ANKRD7. Conclusion We identified significantly altered lincRNAs, miRNAs and mRNAs involved in the nCRT response of ESCC. In addition, the ceRNA regulatory network of lincRNA-miRNA-mRNA and TF regulatory network were constructed, which would elucidate novel molecular mechanisms determining nCRT response of ESCC, thus providing promising clues for clinical therapy.
bibliographic citation: Shao et al. (2019) Transcriptional factor regulation network and competitive endogenous RNA (ceRNA) network determining response of esophageal squamous cell carcinomas to neoadjuvant chemoradiotherapy. PeerJ 7:e6668 https://doi.org/10.7717/peerj.6668
date submitted: 2018-10-17
date accepted: 2019-02-21
issued: 2019-03-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shao
  given name: Mingrui
author list: Agent
  family name: Li
  given name: Wenya
doi: 10.7717/peerj.6668
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-29
copyright: ©2019 Shao and Li
attribution name: Shao and Li

Using opportunistic sightings to infer differential spatio-temporal use of western Mediterranean waters by the fin whale
type: item
type: AcademicArticle
description: The fin whale (Balaenoptera physalus) is a cosmopolitan species with a resident population in the Mediterranean Sea. Due to its habitat, open seas often far from ports and airfields, and its long-distance migratory behaviour, studying and monitoring its distribution is costly. Currently, many opportunistic sightings (OS) reports are available, which provide a source of potentially useful, low-cost information about the spatio-temporal distribution of this species. Since 1993, the Spanish Institute of Oceanography has compiled a dataset comprising 874 records of OS of nine species of cetaceans in the western Mediterranean Sea and adjacent waters. The aim of this study was to use this dataset to investigate the differential use of these waters by the fin whale when compared with other cetaceans. We compared the presence of fin whales with the presence of any other cetacean species in the dataset. Binary logistic regression was then used to model these occurrences according to several spatio-temporal variables expected to reflect their habitat use. Several significant models reveal that fin whales are more prone than other cetaceans to use the waters over the slope of the Gulf of Lion in summer. This finding confirms that the Gulf of Lion is an area of importance for this species and suggests that the slope of the continental shelf could be particularly important. Our study shows how OS can be a source of useful information when appropriately analyzed.
format: application/pdf
format: text/html
creator: Estefanía Torreblanca
creator: Juan Antonio Camiñas
creator: David Macías
creator: Salvador García-Barcelona
creator: Raimundo Real
creator: José Carlos Báez
subject: Biogeography
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.6673
publisher: PeerJ Inc.
rights: © 2019 Torreblanca et al.
abstract: The fin whale (Balaenoptera physalus) is a cosmopolitan species with a resident population in the Mediterranean Sea. Due to its habitat, open seas often far from ports and airfields, and its long-distance migratory behaviour, studying and monitoring its distribution is costly. Currently, many opportunistic sightings (OS) reports are available, which provide a source of potentially useful, low-cost information about the spatio-temporal distribution of this species. Since 1993, the Spanish Institute of Oceanography has compiled a dataset comprising 874 records of OS of nine species of cetaceans in the western Mediterranean Sea and adjacent waters. The aim of this study was to use this dataset to investigate the differential use of these waters by the fin whale when compared with other cetaceans. We compared the presence of fin whales with the presence of any other cetacean species in the dataset. Binary logistic regression was then used to model these occurrences according to several spatio-temporal variables expected to reflect their habitat use. Several significant models reveal that fin whales are more prone than other cetaceans to use the waters over the slope of the Gulf of Lion in summer. This finding confirms that the Gulf of Lion is an area of importance for this species and suggests that the slope of the continental shelf could be particularly important. Our study shows how OS can be a source of useful information when appropriately analyzed.
bibliographic citation: Torreblanca et al. (2019) Using opportunistic sightings to infer differential spatio-temporal use of western Mediterranean waters by the fin whale. PeerJ 7:e6673 https://doi.org/10.7717/peerj.6673
date submitted: 2018-06-07
date accepted: 2019-02-23
issued: 2019-03-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Torreblanca
  given name: Estefanía
author list: Agent
  family name: Camiñas
  given name: Juan Antonio
author list: Agent
  family name: Macías
  given name: David
author list: Agent
  family name: García-Barcelona
  given name: Salvador
author list: Agent
  family name: Real
  given name: Raimundo
author list: Agent
  family name: Báez
  given name: José Carlos
doi: 10.7717/peerj.6673
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-29
copyright: © 2019 Torreblanca et al.
attribution name: Torreblanca et al.

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