PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Pain neuroscience education on YouTube
items: The transcriptomic response to a short day to long day shift in leaves of the reference legume Medicago truncatula
items: Identification of key genes, pathways and potential therapeutic agents for liver fibrosis using an integrated bioinformatics analysis
items: Relative abundance and molecular evolution of Lake Sinai Virus (Sinaivirus) clades
items: Oceanographic moorings as year-round laboratories for investigating growth performance and settlement dynamics in the Antarctic scallop Adamussium colbecki (E. A. Smith, 1902)
items: Human gut resistome can be country-specific
items: Comparative analysis of the liver transcriptome in the red-eared slider Trachemys scripta elegans under chronic salinity stress
items: Association between herd management practices and antimicrobial resistance in Salmonella spp. from cull dairy cattle in Central California
items: Sea stars of the genus Henricia Gray, 1840 (Echinodermata, Asteroidea) from Vostok Bay, Sea of Japan
items: Spatial near future modeling of land use and land cover changes in the temperate forests of Mexico

Pain neuroscience education on YouTube
type: item
type: AcademicArticle
description: Objectives The Internet in general, and YouTube in particular, is now one of the most popular sources of health-related information. Pain neuroscience education has become a primary tool for managing persistent pain, based in part on the discovery that information about pain can change pain. Our objective was to examine the availability, characteristics, and content of YouTube videos that address the neuroscience of pain. Methods We conducted a systematic review of videos on YouTube using the search terms “pain education”, “what is pain”, and “pain brain” in January 2018. Videos were included if they were in English, were under 10 minutes long, and included information on the neuroscience of pain. Videos were coded for (i) descriptive characteristics (e.g., number of views, duration on YouTube), (ii) source and style, (iii) whether or not they addressed seven pre-determined target concepts of pain neuroscience education (e.g., ‘Pain is not an accurate marker of tissue state’), and (iv) how engaging they were. Results We found 106 unique videos that met the inclusion criteria. The videos ranged from having four views to over five million views (Mdn = 1,163 views), with the three most highly viewed videos accounting for 75% of the total views. Animated videos were much more highly viewed than non-animated videos. Only a small number of videos had been posted by a clearly-identifiable reputable source such as an academic or medical institution (10%), although a number of videos were posted by healthcare professionals and professional medical societies. For a small number of videos (7%), the source was unclear. We found 17 videos that addressed at least one target concept of pain neuroscience science education, only nine of which were considered to be at least somewhat engaging. The target concept ‘Pain is a brain output’ was considered to be well addressed by the most videos (N = 11), followed by ‘Pain is a protector’ (N = 10). We found only one video that adequately a…
format: application/pdf
format: text/html
creator: Lauren C. Heathcote
creator: Joshua W. Pate
creator: Anna L. Park
creator: Hayley B. Leake
creator: G. Lorimer Moseley
creator: Corey A. Kronman
creator: Molly Fischer
creator: Inge Timmers
creator: Laura E. Simons
subject: Neuroscience
subject: Anesthesiology and Pain Management
subject: Psychiatry and Psychology
subject: Science and Medical Education
description: doi:10.7717/peerj.6603
publisher: PeerJ Inc.
rights: © 2019 Heathcote et al.
abstract: Objectives The Internet in general, and YouTube in particular, is now one of the most popular sources of health-related information. Pain neuroscience education has become a primary tool for managing persistent pain, based in part on the discovery that information about pain can change pain. Our objective was to examine the availability, characteristics, and content of YouTube videos that address the neuroscience of pain. Methods We conducted a systematic review of videos on YouTube using the search terms “pain education”, “what is pain”, and “pain brain” in January 2018. Videos were included if they were in English, were under 10 minutes long, and included information on the neuroscience of pain. Videos were coded for (i) descriptive characteristics (e.g., number of views, duration on YouTube), (ii) source and style, (iii) whether or not they addressed seven pre-determined target concepts of pain neuroscience education (e.g., ‘Pain is not an accurate marker of tissue state’), and (iv) how engaging they were. Results We found 106 unique videos that met the inclusion criteria. The videos ranged from having four views to over five million views (Mdn = 1,163 views), with the three most highly viewed videos accounting for 75% of the total views. Animated videos were much more highly viewed than non-animated videos. Only a small number of videos had been posted by a clearly-identifiable reputable source such as an academic or medical institution (10%), although a number of videos were posted by healthcare professionals and professional medical societies. For a small number of videos (7%), the source was unclear. We found 17 videos that addressed at least one target concept of pain neuroscience science education, only nine of which were considered to be at least somewhat engaging. The target concept ‘Pain is a brain output’ was considered to be well addressed by the most videos (N = 11), followed by ‘Pain is a protector’ (N = 10). We found only one video that adequately a…
bibliographic citation: Heathcote et al. (2019) Pain neuroscience education on YouTube. PeerJ 7:e6603 https://doi.org/10.7717/peerj.6603
date submitted: 2018-12-12
date accepted: 2019-02-11
issued: 2019-03-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Heathcote
  given name: Lauren C.
author list: Agent
  family name: Pate
  given name: Joshua W.
author list: Agent
  family name: Park
  given name: Anna L.
author list: Agent
  family name: Leake
  given name: Hayley B.
author list: Agent
  family name: Moseley
  given name: G. Lorimer
author list: Agent
  family name: Kronman
  given name: Corey A.
author list: Agent
  family name: Fischer
  given name: Molly
author list: Agent
  family name: Timmers
  given name: Inge
author list: Agent
  family name: Simons
  given name: Laura E.
doi: 10.7717/peerj.6603
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-22
copyright: ©2019 Heathcote et al.
attribution name: Heathcote et al.

The transcriptomic response to a short day to long day shift in leaves of the reference legume Medicago truncatula
type: item
type: AcademicArticle
description: Photoperiodic flowering aligns plant reproduction to favourable seasons of the year to maximise successful production of seeds and grains. However understanding of this process in the temperate legumes of the Fabaceae family, which are important both agriculturally and ecologically, is incomplete. Previous work in the reference legume Medicago truncatula has shown that the FT-like gene MtFTa1 is a potent floral activator. While MtFTa1 is upregulated by long-day photoperiods (LD) and vernalisation, the molecular basis of this is unknown as functional homologues of key regulatory genes present in other species, notably CONSTANS in A. thaliana, have not been identified. In LD MtFTa1 maintains a near constant diurnal pattern of expression unlike its homologue FT in A. thaliana, which has a notable peak in expression at dusk. This suggests a different manner of regulation. Furthermore, M. truncatula possesses other FT-like genes such as two LD induced MtFTb genes which may also act in the regulation of flowering time. MtFTb genes have a diurnal pattern of expression with peaks at both four and sixteen hours after dawn. This study utilises RNA-Seq to analyse the transcriptome of M. truncatula leaves to identify genes which may regulate or be co-expressed with these FT-like genes following a shift from short-day photoperiods to inductive long-days. Specifically this study focuses on the first four hours of the day in the young leaves, which coincides with the first diurnal peak of the FTb genes. Following differential expression analysis at each timepoint, genes which alter their pattern of expression are distinguished from those which just alter their magnitude of expression (and those that do neither). It goes on to categorise these genes into groups with similar patterns of expression using c-means clustering and identifies a number of potential candidate photoperiod flowering time genes for future studies to consider.
format: application/pdf
format: text/html
creator: Geoffrey Thomson
creator: James Taylor
creator: Joanna Putterill
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.6626
publisher: PeerJ Inc.
rights: © 2019 Thomson et al.
abstract: Photoperiodic flowering aligns plant reproduction to favourable seasons of the year to maximise successful production of seeds and grains. However understanding of this process in the temperate legumes of the Fabaceae family, which are important both agriculturally and ecologically, is incomplete. Previous work in the reference legume Medicago truncatula has shown that the FT-like gene MtFTa1 is a potent floral activator. While MtFTa1 is upregulated by long-day photoperiods (LD) and vernalisation, the molecular basis of this is unknown as functional homologues of key regulatory genes present in other species, notably CONSTANS in A. thaliana, have not been identified. In LD MtFTa1 maintains a near constant diurnal pattern of expression unlike its homologue FT in A. thaliana, which has a notable peak in expression at dusk. This suggests a different manner of regulation. Furthermore, M. truncatula possesses other FT-like genes such as two LD induced MtFTb genes which may also act in the regulation of flowering time. MtFTb genes have a diurnal pattern of expression with peaks at both four and sixteen hours after dawn. This study utilises RNA-Seq to analyse the transcriptome of M. truncatula leaves to identify genes which may regulate or be co-expressed with these FT-like genes following a shift from short-day photoperiods to inductive long-days. Specifically this study focuses on the first four hours of the day in the young leaves, which coincides with the first diurnal peak of the FTb genes. Following differential expression analysis at each timepoint, genes which alter their pattern of expression are distinguished from those which just alter their magnitude of expression (and those that do neither). It goes on to categorise these genes into groups with similar patterns of expression using c-means clustering and identifies a number of potential candidate photoperiod flowering time genes for future studies to consider.
bibliographic citation: Thomson et al. (2019) The transcriptomic response to a short day to long day shift in leaves of the reference legume Medicago truncatula. PeerJ 7:e6626 https://doi.org/10.7717/peerj.6626
date submitted: 2018-11-09
date accepted: 2019-02-15
issued: 2019-03-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Thomson
  given name: Geoffrey
author list: Agent
  family name: Taylor
  given name: James
author list: Agent
  family name: Putterill
  given name: Joanna
doi: 10.7717/peerj.6626
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-22
copyright: ©2019 Thomson et al.
attribution name: Thomson et al.

Identification of key genes, pathways and potential therapeutic agents for liver fibrosis using an integrated bioinformatics analysis
type: item
type: AcademicArticle
description: Background Liver fibrosis is often a consequence of chronic liver injury, and has the potential to progress to cirrhosis and liver cancer. Despite being an important human disease, there are currently no approved anti-fibrotic drugs. In this study, we aim to identify the key genes and pathways governing the pathophysiological processes of liver fibrosis, and to screen therapeutic anti-fibrotic agents. Methods Expression profiles were downloaded from the Gene Expression Omnibus (GEO), and differentially expressed genes (DEGs) were identified by R packages (Affy and limma). Gene functional enrichments of each dataset were performed on the DAVID database. Protein–protein interaction (PPI) network was constructed by STRING database and visualized in Cytoscape software. The hub genes were explored by the CytoHubba plugin app and validated in another GEO dataset and in a liver fibrosis cell model by quantitative real-time PCR assay. The Connectivity Map L1000 platform was used to identify potential anti-fibrotic agents. Results We integrated three fibrosis datasets of different disease etiologies, incorporating a total of 70 severe (F3–F4) and 116 mild (F0–F1) fibrotic tissue samples. Gene functional enrichment analyses revealed that cell cycle was a pathway uniquely enriched in a dataset from those patients infected by hepatitis B virus (HBV), while the immune-inflammatory response was enriched in both the HBV and hepatitis C virus (HCV) datasets, but not in the nonalcoholic fatty liver disease (NAFLD) dataset. There was overlap between these three datasets; 185 total shared DEGs that were enriched for pathways associated with extracellular matrix constitution, platelet-derived growth-factor binding, protein digestion and absorption, focal adhesion, and PI3K-Akt signaling. In the PPI network, 25 hub genes were extracted and deemed to be essential genes for fibrogenesis, and the expression trends were consistent with GSE14323 (an additional dataset) and liver fibrosis cel…
format: application/pdf
format: text/html
creator: Zhu Zhan
creator: Yuhe Chen
creator: Yuanqin Duan
creator: Lin Li
creator: Kenley Mew
creator: Peng Hu
creator: Hong Ren
creator: Mingli Peng
subject: Bioinformatics
subject: Gastroenterology and Hepatology
subject: Infectious Diseases
description: doi:10.7717/peerj.6645
publisher: PeerJ Inc.
rights: © 2019 Zhan et al.
abstract: Background Liver fibrosis is often a consequence of chronic liver injury, and has the potential to progress to cirrhosis and liver cancer. Despite being an important human disease, there are currently no approved anti-fibrotic drugs. In this study, we aim to identify the key genes and pathways governing the pathophysiological processes of liver fibrosis, and to screen therapeutic anti-fibrotic agents. Methods Expression profiles were downloaded from the Gene Expression Omnibus (GEO), and differentially expressed genes (DEGs) were identified by R packages (Affy and limma). Gene functional enrichments of each dataset were performed on the DAVID database. Protein–protein interaction (PPI) network was constructed by STRING database and visualized in Cytoscape software. The hub genes were explored by the CytoHubba plugin app and validated in another GEO dataset and in a liver fibrosis cell model by quantitative real-time PCR assay. The Connectivity Map L1000 platform was used to identify potential anti-fibrotic agents. Results We integrated three fibrosis datasets of different disease etiologies, incorporating a total of 70 severe (F3–F4) and 116 mild (F0–F1) fibrotic tissue samples. Gene functional enrichment analyses revealed that cell cycle was a pathway uniquely enriched in a dataset from those patients infected by hepatitis B virus (HBV), while the immune-inflammatory response was enriched in both the HBV and hepatitis C virus (HCV) datasets, but not in the nonalcoholic fatty liver disease (NAFLD) dataset. There was overlap between these three datasets; 185 total shared DEGs that were enriched for pathways associated with extracellular matrix constitution, platelet-derived growth-factor binding, protein digestion and absorption, focal adhesion, and PI3K-Akt signaling. In the PPI network, 25 hub genes were extracted and deemed to be essential genes for fibrogenesis, and the expression trends were consistent with GSE14323 (an additional dataset) and liver fibrosis cel…
bibliographic citation: Zhan et al. (2019) Identification of key genes, pathways and potential therapeutic agents for liver fibrosis using an integrated bioinformatics analysis. PeerJ 7:e6645 https://doi.org/10.7717/peerj.6645
date submitted: 2018-12-20
date accepted: 2019-02-17
issued: 2019-03-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhan
  given name: Zhu
author list: Agent
  family name: Chen
  given name: Yuhe
author list: Agent
  family name: Duan
  given name: Yuanqin
author list: Agent
  family name: Li
  given name: Lin
author list: Agent
  family name: Mew
  given name: Kenley
author list: Agent
  family name: Hu
  given name: Peng
author list: Agent
  family name: Ren
  given name: Hong
author list: Agent
  family name: Peng
  given name: Mingli
doi: 10.7717/peerj.6645
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-22
copyright: ©2019 Zhan et al.
attribution name: Zhan et al.

Relative abundance and molecular evolution of Lake Sinai Virus (Sinaivirus) clades
type: item
type: AcademicArticle
description: Lake Sinai Viruses (Sinaivirus) are commonly detected in honey bees (Apis mellifera) but no disease phenotypes or fitness consequences have yet been demonstrated. This viral group is genetically diverse, lacks obvious geographic structure, and multiple lineages can co-infect individual bees. While phylogenetic analyses have been performed, the molecular evolution of LSV has not been studied extensively. Here, I use LSV isolates from GenBank as well as contigs assembled from honey bee Sequence Read Archive (SRA) accessions to better understand the evolutionary history of these viruses. For each ORF, substitution rate variation, codon usage, and tests of positive selection were evaluated. Outlier regions of high or low diversity were sought with sliding window analysis and the role of recombination in creating LSV diversity was explored. Phylogenetic analysis consistently identified two large clusters of sequences that correspond to the current LSV1 and LSV2 nomenclature, however lineages sister to LSV1 were the most frequently detected in honey bee SRA accessions. Different expression levels among ORFs suggested the occurrence of subgenomic transcripts. ORF1 and RNA-dependent RNA polymerase had higher evolutionary rates than the capsid and ORF4. A hypervariable region of the ORF1 protein-coding sequence was identified that had reduced selective constraint, but a site-based model of positive selection was not significantly more likely than a neutral model for any ORF. The only significant recombination signals detected between LSV1 and LSV2 initiated within this hypervariable region, but assumptions of the test (single-frame coding and independence of substitution rate by site) were violated. LSV codon usage differed strikingly from that of honey bees and other common honey-bee viruses, suggesting LSV is not strongly co-evolved with that host. LSV codon usage was significantly correlated with that of Varroa destructor, however, despite the relatively weak codon bias e…
format: application/pdf
format: text/html
creator: Robert S. Cornman
subject: Agricultural Science
subject: Entomology
subject: Genomics
subject: Virology
description: doi:10.7717/peerj.6305
publisher: PeerJ Inc.
rights: © 2019 Cornman
abstract: Lake Sinai Viruses (Sinaivirus) are commonly detected in honey bees (Apis mellifera) but no disease phenotypes or fitness consequences have yet been demonstrated. This viral group is genetically diverse, lacks obvious geographic structure, and multiple lineages can co-infect individual bees. While phylogenetic analyses have been performed, the molecular evolution of LSV has not been studied extensively. Here, I use LSV isolates from GenBank as well as contigs assembled from honey bee Sequence Read Archive (SRA) accessions to better understand the evolutionary history of these viruses. For each ORF, substitution rate variation, codon usage, and tests of positive selection were evaluated. Outlier regions of high or low diversity were sought with sliding window analysis and the role of recombination in creating LSV diversity was explored. Phylogenetic analysis consistently identified two large clusters of sequences that correspond to the current LSV1 and LSV2 nomenclature, however lineages sister to LSV1 were the most frequently detected in honey bee SRA accessions. Different expression levels among ORFs suggested the occurrence of subgenomic transcripts. ORF1 and RNA-dependent RNA polymerase had higher evolutionary rates than the capsid and ORF4. A hypervariable region of the ORF1 protein-coding sequence was identified that had reduced selective constraint, but a site-based model of positive selection was not significantly more likely than a neutral model for any ORF. The only significant recombination signals detected between LSV1 and LSV2 initiated within this hypervariable region, but assumptions of the test (single-frame coding and independence of substitution rate by site) were violated. LSV codon usage differed strikingly from that of honey bees and other common honey-bee viruses, suggesting LSV is not strongly co-evolved with that host. LSV codon usage was significantly correlated with that of Varroa destructor, however, despite the relatively weak codon bias e…
bibliographic citation: Cornman (2019) Relative abundance and molecular evolution of Lake Sinai Virus (Sinaivirus) clades. PeerJ 7:e6305 https://doi.org/10.7717/peerj.6305
date submitted: 2018-10-22
date accepted: 2018-12-17
issued: 2019-03-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cornman
  given name: Robert S.
doi: 10.7717/peerj.6305
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-21
copyright: © 2019 Cornman
attribution name: Cornman

Oceanographic moorings as year-round laboratories for investigating growth performance and settlement dynamics in the Antarctic scallop Adamussium colbecki (E. A. Smith, 1902)
type: item
type: AcademicArticle
description: Background Oceanographic moorings (OMs) are standard marine platforms composed of wires, buoys, weights and instruments, and are used as in situ observatories to record water column properties. However, OMs are also comprised of hard substrates on which a variety of invertebrates can settle when they encounter these structures along their dispersal routes. In this contribution, we studied the fouling communities found on two OMs deployed in the Ross Sea (Antarctica). Furthermore, a cage containing the Antarctic scallop Adamussium colbecki (E. A. Smith, 1902) was incorporated in the OM. The growth of the caged A. colbecki were evaluated after 1 year and their shells used as biological proxy for seawater temperature and salinity. Methods A variety of settlers were collected from two different OMs deployed in the Ross Sea (Antarctica) and species identified using a combination of morphological and genetic (mainly through DNA barcoding) characteristics. Caged scallops were individually marked with permanent tags and their growth studied in terms of size-increment data (SID). Cages were specifically designed to prevent damage to individuals due to water drag during OM deployment and retrieval. Growth parameters from the caged individuals were applied to the A. colbecki juveniles that had settled on the mooring, to trace the likely settlement period. Results The growth performance of caged A. colbecki was similar to that from previous growth studies of this species. The remarkable survival rate of caged specimens (96.6%) supports the feasibility of caging experiments, even for a species with a fragile shell such as the Antarctic scallop. Some of the new recruits found on the mooring were A. colbecki, the same species we put into special cages fixed to it. The settlement of the A. colbecki juveniles started during the Austral spring with a peak in summer months and, remarkably, coincided with seasonal changes in water temperature and flow direction, which were recorded by …
format: application/pdf
format: text/html
creator: Stefano Schiaparelli
creator: Stefano Aliani
subject: Ecology
subject: Marine Biology
subject: Zoology
subject: Biological Oceanography
description: doi:10.7717/peerj.6373
publisher: PeerJ Inc.
rights: © 2019 Schiaparelli and Aliani
abstract: Background Oceanographic moorings (OMs) are standard marine platforms composed of wires, buoys, weights and instruments, and are used as in situ observatories to record water column properties. However, OMs are also comprised of hard substrates on which a variety of invertebrates can settle when they encounter these structures along their dispersal routes. In this contribution, we studied the fouling communities found on two OMs deployed in the Ross Sea (Antarctica). Furthermore, a cage containing the Antarctic scallop Adamussium colbecki (E. A. Smith, 1902) was incorporated in the OM. The growth of the caged A. colbecki were evaluated after 1 year and their shells used as biological proxy for seawater temperature and salinity. Methods A variety of settlers were collected from two different OMs deployed in the Ross Sea (Antarctica) and species identified using a combination of morphological and genetic (mainly through DNA barcoding) characteristics. Caged scallops were individually marked with permanent tags and their growth studied in terms of size-increment data (SID). Cages were specifically designed to prevent damage to individuals due to water drag during OM deployment and retrieval. Growth parameters from the caged individuals were applied to the A. colbecki juveniles that had settled on the mooring, to trace the likely settlement period. Results The growth performance of caged A. colbecki was similar to that from previous growth studies of this species. The remarkable survival rate of caged specimens (96.6%) supports the feasibility of caging experiments, even for a species with a fragile shell such as the Antarctic scallop. Some of the new recruits found on the mooring were A. colbecki, the same species we put into special cages fixed to it. The settlement of the A. colbecki juveniles started during the Austral spring with a peak in summer months and, remarkably, coincided with seasonal changes in water temperature and flow direction, which were recorded by …
bibliographic citation: Schiaparelli et al. (2019) Oceanographic moorings as year-round laboratories for investigating growth performance and settlement dynamics in the Antarctic scallop Adamussium colbecki (E. A. Smith, 1902). PeerJ 7:e6373 https://doi.org/10.7717/peerj.6373
date submitted: 2018-03-19
date accepted: 2018-12-30
issued: 2019-03-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Schiaparelli
  given name: Stefano
author list: Agent
  family name: Aliani
  given name: Stefano
doi: 10.7717/peerj.6373
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-21
copyright: © 2019 Schiaparelli and Aliani
attribution name: Schiaparelli and Aliani

Human gut resistome can be country-specific
type: item
type: AcademicArticle
description: The emergence and spread of antibiotic resistance have become emerging threats to human health. The human gut is a large reservoir for antibiotic resistance genes. The gut resistome may be influenced by many factors, but the consumption of antibiotics at both individual and country level should be one of the most significant factors. Previous studies have suggested that the gut resistome of different populations may vary, but lack quantitative characterization supported with relatively large datasets. In this study, we filled the gap by analyzing a large gut resistome dataset of 1,267 human gut samples of America, China, Denmark, and Spain. We built a stacking machine-learning model to determine whether the gut resistome can act as the sole feature to identify the nationality of an individual reliably. It turned out that the machine learning method could successfully identify American, Chinese, Danish, and Spanish populations with F1 score of 0.964, 0.987, 0.971, and 0.986, respectively. Our finding does highlight the significant differences in the composition of the gut resistome among different nationalities. Our study should be valuable for policy-makers to look into the influences of country-specific factors of the human gut resistome.
format: application/pdf
format: text/html
creator: Yao Xia
creator: Yanshan Zhu
creator: Qier Li
creator: Jiahai Lu
subject: Bioinformatics
subject: Microbiology
subject: Epidemiology
subject: Global Health
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.6389
publisher: PeerJ Inc.
rights: © 2019 Xia et al.
abstract: The emergence and spread of antibiotic resistance have become emerging threats to human health. The human gut is a large reservoir for antibiotic resistance genes. The gut resistome may be influenced by many factors, but the consumption of antibiotics at both individual and country level should be one of the most significant factors. Previous studies have suggested that the gut resistome of different populations may vary, but lack quantitative characterization supported with relatively large datasets. In this study, we filled the gap by analyzing a large gut resistome dataset of 1,267 human gut samples of America, China, Denmark, and Spain. We built a stacking machine-learning model to determine whether the gut resistome can act as the sole feature to identify the nationality of an individual reliably. It turned out that the machine learning method could successfully identify American, Chinese, Danish, and Spanish populations with F1 score of 0.964, 0.987, 0.971, and 0.986, respectively. Our finding does highlight the significant differences in the composition of the gut resistome among different nationalities. Our study should be valuable for policy-makers to look into the influences of country-specific factors of the human gut resistome.
bibliographic citation: Xia et al. (2019) Human gut resistome can be country-specific. PeerJ 7:e6389 https://doi.org/10.7717/peerj.6389
date submitted: 2018-06-28
date accepted: 2019-01-04
issued: 2019-03-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xia
  given name: Yao
author list: Agent
  family name: Zhu
  given name: Yanshan
author list: Agent
  family name: Li
  given name: Qier
author list: Agent
  family name: Lu
  given name: Jiahai
doi: 10.7717/peerj.6389
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-21
copyright: © 2019 Xia et al.
attribution name: Xia et al.

Comparative analysis of the liver transcriptome in the red-eared slider Trachemys scripta elegans under chronic salinity stress
type: item
type: AcademicArticle
description: The red-eared slider (Trachemys scripta elegans), identified as one of the 100 most invasive species in the world, is a freshwater turtle originally from the eastern United States and northeastern Mexico. Field investigations have shown that T. s. elegans can survive and lay eggs in saline habitats. In order to understand the molecular mechanisms of salinity adaptation, high-throughput RNA-Seq was utilized to identify the changes in gene expression profiles in the liver of T. s. elegans in response to elevated salinity. We exposed individuals to 0, 5, or 15 psu (practical salinity units) for 30 days. A total of 157.21 million reads were obtained and assembled into 205138 unigenes with an average length of 620 bp and N50 of 964 bp. Of these, 1019 DEGs (differentially expressed genes) were found in the comparison of 0 vs. 5 psu, 1194 DEGs in 0 vs. 15 psu and 1180 DEGs in 5 vs. 15 psu, which are mainly related to macromolecule metabolic process, ion transport, oxidoreductase activity and generation of precursor metabolites and energy by GO (Gene Ontology) enrichment analyses. T. s. elegans can adapt itself into salinity by balancing the entry of sodium and chloride ions via the up-regulation expression genes of ion transport (potassium voltage-gated channel subfamily H member 5, KCNH5; erine/threonine-protein kinase 32, STK32; salt-inducible kinase 1, SIK1; adiponectin, ACDC), and by accumulating plasma urea and free amino acid via the up-regulation expression genes of amino acid metabolism (ornithine decarboxylase antizyme 3, OAZ3; glutamine synthetase, GLUL; asparaginase-like protein 1b, ASRGL; L-amino-acid oxidase-like, LAAO; sodium-dependent neutral amino acid transporter B, SLC6A15s; amino acid permease, SLC7A9) in response to osmotic regulation. An investment of energy to maintain their homeostatic balance is required to salinity adaptation, therefore, the genes related to energy production and conversion (F-ATPase protein 6, ATP6; cytochrome c oxidase subunit I,…
format: application/pdf
format: text/html
creator: Meiling Hong
creator: Aiping Jiang
creator: Na Li
creator: Weihao Li
creator: Haitao Shi
creator: Kenneth B. Storey
creator: Li Ding
subject: Conservation Biology
subject: Ecology
subject: Genomics
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.6538
publisher: PeerJ Inc.
rights: © 2019 Hong et al.
abstract: The red-eared slider (Trachemys scripta elegans), identified as one of the 100 most invasive species in the world, is a freshwater turtle originally from the eastern United States and northeastern Mexico. Field investigations have shown that T. s. elegans can survive and lay eggs in saline habitats. In order to understand the molecular mechanisms of salinity adaptation, high-throughput RNA-Seq was utilized to identify the changes in gene expression profiles in the liver of T. s. elegans in response to elevated salinity. We exposed individuals to 0, 5, or 15 psu (practical salinity units) for 30 days. A total of 157.21 million reads were obtained and assembled into 205138 unigenes with an average length of 620 bp and N50 of 964 bp. Of these, 1019 DEGs (differentially expressed genes) were found in the comparison of 0 vs. 5 psu, 1194 DEGs in 0 vs. 15 psu and 1180 DEGs in 5 vs. 15 psu, which are mainly related to macromolecule metabolic process, ion transport, oxidoreductase activity and generation of precursor metabolites and energy by GO (Gene Ontology) enrichment analyses. T. s. elegans can adapt itself into salinity by balancing the entry of sodium and chloride ions via the up-regulation expression genes of ion transport (potassium voltage-gated channel subfamily H member 5, KCNH5; erine/threonine-protein kinase 32, STK32; salt-inducible kinase 1, SIK1; adiponectin, ACDC), and by accumulating plasma urea and free amino acid via the up-regulation expression genes of amino acid metabolism (ornithine decarboxylase antizyme 3, OAZ3; glutamine synthetase, GLUL; asparaginase-like protein 1b, ASRGL; L-amino-acid oxidase-like, LAAO; sodium-dependent neutral amino acid transporter B, SLC6A15s; amino acid permease, SLC7A9) in response to osmotic regulation. An investment of energy to maintain their homeostatic balance is required to salinity adaptation, therefore, the genes related to energy production and conversion (F-ATPase protein 6, ATP6; cytochrome c oxidase subunit I,…
bibliographic citation: Hong et al. (2019) Comparative analysis of the liver transcriptome in the red-eared slider Trachemys scripta elegans under chronic salinity stress. PeerJ 7:e6538 https://doi.org/10.7717/peerj.6538
date submitted: 2018-09-21
date accepted: 2019-01-29
issued: 2019-03-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hong
  given name: Meiling
author list: Agent
  family name: Jiang
  given name: Aiping
author list: Agent
  family name: Li
  given name: Na
author list: Agent
  family name: Li
  given name: Weihao
author list: Agent
  family name: Shi
  given name: Haitao
author list: Agent
  family name: Storey
  given name: Kenneth B.
author list: Agent
  family name: Ding
  given name: Li
doi: 10.7717/peerj.6538
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-21
copyright: ©2019 Hong et al.
attribution name: Hong et al.

Association between herd management practices and antimicrobial resistance in Salmonella spp. from cull dairy cattle in Central California
type: item
type: AcademicArticle
description: Background In this study cull dairy cows from six California dairy herds were sampled seasonally over the course of a year. The objectives were to determine the prevalence of antimicrobial resistant (AMR) Salmonella spp. shed in cull cow feces, and the factors associated with fecal shedding of AMR and multidrug resistant (MDR) Salmonella. Methods Six dairy farms located in the San Joaquin Valley of California were identified and enrolled as a convenience sample. On each dairy, and once during each of the four seasons, 10 cull cows were randomly selected for fecal sampling on the day of their removal from the herd. In addition, study personnel completed a survey based on responses of the herd manager to questions related to the previous 4 month’s herd management and the specific cattle sampled. Fecal samples were submitted to the California Animal Health and Food Safety laboratory for Salmonella isolation. Antimicrobial resistance was evaluated using broth microdilution method and a gram-negative assay plate following Clinical Laboratory Standards Institute (CLSI) guidelines and breakpoint references. All statistical models were survey adjusted for number of animals on sampling day. Results A total of 62 Salmonella were isolated from 60 of the 239 fecal samples collected. For 12% (95% confidence interval (CI) [3–20]) of fecal samples a multidrug resistant Salmonella was isolated. The survey-weighted results for the two most common drug classes for which isolates were resistant were tetracycline (39%; 95% CI [27–51]) and ampicillin (18%; 95% CI [9–27]). An important finding was the identification of cephalosporin as the third most common drug class for which isolates were resistant, with ceftriaxone (10%; 95% CI [2–17]) being the most common drug associated with resistance in that class. At the cow-level, reason for culling, prior treatment with antimicrobial drugs as the reason for culling was associated with higher odds of isolating an AMR Salmonella isolate. At the…
format: application/pdf
format: text/html
creator: Richard Pereira
creator: Deniece R. Williams
creator: Paul Rossitto
creator: John Adaska
creator: Emmanuel Okello
creator: John Champagne
creator: Terry W. Lehenbauer
creator: Xunde Li
creator: Jennifer Chase
creator: Tran Nguyen
creator: Alda F. A. Pires
creator: Edward R. Atwill
creator: Sharif S. Aly
subject: Microbiology
subject: Veterinary Medicine
subject: Epidemiology
description: doi:10.7717/peerj.6546
publisher: PeerJ Inc.
rights: © 2019 Pereira et al.
abstract: Background In this study cull dairy cows from six California dairy herds were sampled seasonally over the course of a year. The objectives were to determine the prevalence of antimicrobial resistant (AMR) Salmonella spp. shed in cull cow feces, and the factors associated with fecal shedding of AMR and multidrug resistant (MDR) Salmonella. Methods Six dairy farms located in the San Joaquin Valley of California were identified and enrolled as a convenience sample. On each dairy, and once during each of the four seasons, 10 cull cows were randomly selected for fecal sampling on the day of their removal from the herd. In addition, study personnel completed a survey based on responses of the herd manager to questions related to the previous 4 month’s herd management and the specific cattle sampled. Fecal samples were submitted to the California Animal Health and Food Safety laboratory for Salmonella isolation. Antimicrobial resistance was evaluated using broth microdilution method and a gram-negative assay plate following Clinical Laboratory Standards Institute (CLSI) guidelines and breakpoint references. All statistical models were survey adjusted for number of animals on sampling day. Results A total of 62 Salmonella were isolated from 60 of the 239 fecal samples collected. For 12% (95% confidence interval (CI) [3–20]) of fecal samples a multidrug resistant Salmonella was isolated. The survey-weighted results for the two most common drug classes for which isolates were resistant were tetracycline (39%; 95% CI [27–51]) and ampicillin (18%; 95% CI [9–27]). An important finding was the identification of cephalosporin as the third most common drug class for which isolates were resistant, with ceftriaxone (10%; 95% CI [2–17]) being the most common drug associated with resistance in that class. At the cow-level, reason for culling, prior treatment with antimicrobial drugs as the reason for culling was associated with higher odds of isolating an AMR Salmonella isolate. At the…
bibliographic citation: Pereira et al. (2019) Association between herd management practices and antimicrobial resistance in Salmonella spp. from cull dairy cattle in Central California. PeerJ 7:e6546 https://doi.org/10.7717/peerj.6546
date submitted: 2018-06-19
date accepted: 2019-01-30
issued: 2019-03-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pereira
  given name: Richard
author list: Agent
  family name: Williams
  given name: Deniece R.
author list: Agent
  family name: Rossitto
  given name: Paul
author list: Agent
  family name: Adaska
  given name: John
author list: Agent
  family name: Okello
  given name: Emmanuel
author list: Agent
  family name: Champagne
  given name: John
author list: Agent
  family name: Lehenbauer
  given name: Terry W.
author list: Agent
  family name: Li
  given name: Xunde
author list: Agent
  family name: Chase
  given name: Jennifer
author list: Agent
  family name: Nguyen
  given name: Tran
author list: Agent
  family name: Pires
  given name: Alda F. A.
author list: Agent
  family name: Atwill
  given name: Edward R.
author list: Agent
  family name: Aly
  given name: Sharif S.
doi: 10.7717/peerj.6546
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-21
copyright: © 2019 Pereira et al.
attribution name: Pereira et al.

Sea stars of the genus Henricia Gray, 1840 (Echinodermata, Asteroidea) from Vostok Bay, Sea of Japan
type: item
type: AcademicArticle
description: We report seven species of the genus Henricia Gray, 1840 that were found in Vostok Bay, and two species from adjacent area, known from museum collection or seen in underwater footage. while existing literature reported no confirmed species from this area. Most of these species: H. djakonovi, H. alexeyi, H. densispina, H. hayashii, H. granulifera, H. pacifica, H. asiatica, and H. oculata robusta were reported from the Sea of Japan previously. H. nipponica, known from Japan, is reported from Russian seas for the first time. All studied taxa are re-described here using a range of morphological characters and partial 16S rRNA nucleotide sequences, life colorations of several species are reported for the first time, and an identification key is provided. Lectotype designations are fixed for studied series of species described by AM Djakonov.
format: application/pdf
format: text/html
creator: Anton Chichvarkhin
creator: Olga Chichvarkhina
creator: Daiki Wakita
subject: Biodiversity
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.6585
publisher: PeerJ Inc.
rights: © 2019 Chichvarkhin et al.
abstract: We report seven species of the genus Henricia Gray, 1840 that were found in Vostok Bay, and two species from adjacent area, known from museum collection or seen in underwater footage. while existing literature reported no confirmed species from this area. Most of these species: H. djakonovi, H. alexeyi, H. densispina, H. hayashii, H. granulifera, H. pacifica, H. asiatica, and H. oculata robusta were reported from the Sea of Japan previously. H. nipponica, known from Japan, is reported from Russian seas for the first time. All studied taxa are re-described here using a range of morphological characters and partial 16S rRNA nucleotide sequences, life colorations of several species are reported for the first time, and an identification key is provided. Lectotype designations are fixed for studied series of species described by AM Djakonov.
bibliographic citation: Chichvarkhin et al. (2019) Sea stars of the genus Henricia Gray, 1840 (Echinodermata, Asteroidea) from Vostok Bay, Sea of Japan. PeerJ 7:e6585 https://doi.org/10.7717/peerj.6585
date submitted: 2018-03-06
date accepted: 2019-02-08
issued: 2019-03-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chichvarkhin
  given name: Anton
author list: Agent
  family name: Chichvarkhina
  given name: Olga
author list: Agent
  family name: Wakita
  given name: Daiki
doi: 10.7717/peerj.6585
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-21
copyright: ©2019 Chichvarkhin et al.
attribution name: Chichvarkhin et al.

Spatial near future modeling of land use and land cover changes in the temperate forests of Mexico
type: item
type: AcademicArticle
description: The loss of temperate forests of Mexico has continued in recent decades despite wide recognition of their importance to maintaining biodiversity. This study analyzes land use/land cover change scenarios, using satellite images from the Landsat sensor. Images corresponded to the years 1990, 2005 and 2017. The scenarios were applied for the temperate forests with the aim of getting a better understanding of the patterns in land use/land cover changes. The Support Vector Machine (SVM) multispectral classification technique served to determine the land use/land cover types, which were validated through the Kappa Index. For the simulation of land use/land cover dynamics, a model developed in Dinamica-EGO was used, which uses stochastic models of Markov Chains, Cellular Automata and Weight of Evidences. For the study, a stationary, an optimistic and a pessimistic scenario were proposed. The projections based on the three scenarios were simulated for the year 2050. Five types of land use/land cover were identified and evaluated. They were primary forest, secondary forest, human settlements, areas without vegetation and water bodies. Results from the land use/land cover change analysis show a substantial gain for the secondary forest. The surface area of the primary forest was reduced from 55.8% in 1990 to 37.7% in 2017. Moreover, the three projected scenarios estimate further losses of the surface are for the primary forest, especially under the stationary and pessimistic scenarios. This highlights the importance and probably urgent implementation of conservation and protection measures to preserve these ecosystems and their services. Based on the accuracy obtained and on the models generated, results from these methodologies can serve as a decision tool to contribute to the sustainable management of the natural resources of a region.
format: application/pdf
format: text/html
creator: Jesús A. Prieto-Amparán
creator: Federico Villarreal-Guerrero
creator: Martin Martínez-Salvador
creator: Carlos Manjarrez-Domínguez
creator: Griselda Vázquez-Quintero
creator: Alfredo Pinedo-Alvarez
subject: Ecology
subject: Natural Resource Management
subject: Forestry
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.6617
publisher: PeerJ Inc.
rights: © 2019 Prieto-Amparán et al.
abstract: The loss of temperate forests of Mexico has continued in recent decades despite wide recognition of their importance to maintaining biodiversity. This study analyzes land use/land cover change scenarios, using satellite images from the Landsat sensor. Images corresponded to the years 1990, 2005 and 2017. The scenarios were applied for the temperate forests with the aim of getting a better understanding of the patterns in land use/land cover changes. The Support Vector Machine (SVM) multispectral classification technique served to determine the land use/land cover types, which were validated through the Kappa Index. For the simulation of land use/land cover dynamics, a model developed in Dinamica-EGO was used, which uses stochastic models of Markov Chains, Cellular Automata and Weight of Evidences. For the study, a stationary, an optimistic and a pessimistic scenario were proposed. The projections based on the three scenarios were simulated for the year 2050. Five types of land use/land cover were identified and evaluated. They were primary forest, secondary forest, human settlements, areas without vegetation and water bodies. Results from the land use/land cover change analysis show a substantial gain for the secondary forest. The surface area of the primary forest was reduced from 55.8% in 1990 to 37.7% in 2017. Moreover, the three projected scenarios estimate further losses of the surface are for the primary forest, especially under the stationary and pessimistic scenarios. This highlights the importance and probably urgent implementation of conservation and protection measures to preserve these ecosystems and their services. Based on the accuracy obtained and on the models generated, results from these methodologies can serve as a decision tool to contribute to the sustainable management of the natural resources of a region.
bibliographic citation: Prieto-Amparán et al. (2019) Spatial near future modeling of land use and land cover changes in the temperate forests of Mexico. PeerJ 7:e6617 https://doi.org/10.7717/peerj.6617
date submitted: 2018-09-28
date accepted: 2019-02-11
issued: 2019-03-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Prieto-Amparán
  given name: Jesús A.
author list: Agent
  family name: Villarreal-Guerrero
  given name: Federico
author list: Agent
  family name: Martínez-Salvador
  given name: Martin
author list: Agent
  family name: Manjarrez-Domínguez
  given name: Carlos
author list: Agent
  family name: Vázquez-Quintero
  given name: Griselda
author list: Agent
  family name: Pinedo-Alvarez
  given name: Alfredo
doi: 10.7717/peerj.6617
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-21
copyright: ©2019 Prieto-Amparán et al.
attribution name: Prieto-Amparán et al.

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