PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: MazF activation promotes translational heterogeneity of the grcA mRNA in Escherichia coli populations
items: Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity
items: Human agency beliefs influence behaviour during virtual social interactions
items: Taxonomic overview of the hyperdiverse ant genus Tetramorium Mayr (Hymenoptera, Formicidae) in India with descriptions and X-ray microtomography of two new species from the Andaman Islands
items: Evaluation of ddRADseq for reduced representation metagenome sequencing
items: CA1 pyramidal cells have diverse biophysical properties, affected by development, experience, and aging
items: Analysis of drug binding pockets and repurposing opportunities for twelve essential enzymes of ESKAPE pathogens
items: Morning surge in blood pressure and sympathetic activity in Mongolians and Han Chinese: a multimodality investigation of hypertension and dyssomnia
items: Genome-wide identification and characterization of aquaporin gene family in Beta vulgaris
items: Vascular anatomy is a determining factor of successful submental flap raising: a retrospective study of 70 clinical cases

MazF activation promotes translational heterogeneity of the grcA mRNA in Escherichia coli populations
type: item
type: AcademicArticle
description: Bacteria adapt to adverse environmental conditions by altering gene expression patterns. Recently, a novel stress adaptation mechanism has been described that allows Escherichia coli to alter gene expression at the post-transcriptional level. The key player in this regulatory pathway is the endoribonuclease MazF, the toxin component of the toxin-antitoxin module mazEF that is triggered by various stressful conditions. In general, MazF degrades the majority of transcripts by cleaving at ACA sites, which results in the retardation of bacterial growth. Furthermore, MazF can process a small subset of mRNAs and render them leaderless by removing their ribosome binding site. MazF concomitantly modifies ribosomes, making them selective for the translation of leaderless mRNAs. In this study, we employed fluorescent reporter-systems to investigate mazEF expression during stressful conditions, and to infer consequences of the mRNA processing mediated by MazF on gene expression at the single-cell level. Our results suggest that mazEF transcription is maintained at low levels in single cells encountering adverse conditions, such as antibiotic stress or amino acid starvation. Moreover, using the grcA mRNA as a model for MazF-mediated mRNA processing, we found that MazF activation promotes heterogeneity in the grcA reporter expression, resulting in a subpopulation of cells with increased levels of GrcA reporter protein.
format: application/pdf
format: text/html
creator: Nela Nikolic
creator: Zrinka Didara
creator: Isabella Moll
subject: Genetics
subject: Microbiology
description: doi:10.7717/peerj.3830
publisher: PeerJ Inc.
rights: © 2017 Nikolic et al.
abstract: Bacteria adapt to adverse environmental conditions by altering gene expression patterns. Recently, a novel stress adaptation mechanism has been described that allows Escherichia coli to alter gene expression at the post-transcriptional level. The key player in this regulatory pathway is the endoribonuclease MazF, the toxin component of the toxin-antitoxin module mazEF that is triggered by various stressful conditions. In general, MazF degrades the majority of transcripts by cleaving at ACA sites, which results in the retardation of bacterial growth. Furthermore, MazF can process a small subset of mRNAs and render them leaderless by removing their ribosome binding site. MazF concomitantly modifies ribosomes, making them selective for the translation of leaderless mRNAs. In this study, we employed fluorescent reporter-systems to investigate mazEF expression during stressful conditions, and to infer consequences of the mRNA processing mediated by MazF on gene expression at the single-cell level. Our results suggest that mazEF transcription is maintained at low levels in single cells encountering adverse conditions, such as antibiotic stress or amino acid starvation. Moreover, using the grcA mRNA as a model for MazF-mediated mRNA processing, we found that MazF activation promotes heterogeneity in the grcA reporter expression, resulting in a subpopulation of cells with increased levels of GrcA reporter protein.
bibliographic citation: Nikolic et al. (2017) MazF activation promotes translational heterogeneity of the grcA mRNA in Escherichia coli populations. PeerJ 5:e3830 https://doi.org/10.7717/peerj.3830
date submitted: 2017-05-23
date accepted: 2017-08-29
issued: 2017-09-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nikolic
  given name: Nela
author list: Agent
  family name: Didara
  given name: Zrinka
author list: Agent
  family name: Moll
  given name: Isabella
doi: 10.7717/peerj.3830
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-21
copyright: ©2017 Nikolic et al.
attribution name: Nikolic et al.

Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity
type: item
type: AcademicArticle
description: Background Viral metagenomics (viromics) is increasingly used to obtain uncultivated viral genomes, evaluate community diversity, and assess ecological hypotheses. While viromic experimental methods are relatively mature and widely accepted by the research community, robust bioinformatics standards remain to be established. Here we used in silico mock viral communities to evaluate the viromic sequence-to-ecological-inference pipeline, including (i) read pre-processing and metagenome assembly, (ii) thresholds applied to estimate viral relative abundances based on read mapping to assembled contigs, and (iii) normalization methods applied to the matrix of viral relative abundances for alpha and beta diversity estimates. Results Tools specifically designed for metagenomes, specifically metaSPAdes, MEGAHIT, and IDBA-UD, were the most effective at assembling viromes. Read pre-processing, such as partitioning, had virtually no impact on assembly output, but may be useful when hardware is limited. Viral populations with 2–5 × coverage typically assembled well, whereas lesser coverage led to fragmented assembly. Strain heterogeneity within populations hampered assembly, especially when strains were closely related (average nucleotide identity, or ANI ≥97%) and when the most abundant strain represented <50% of the population. Viral community composition assessments based on read recruitment were generally accurate when the following thresholds for detection were applied: (i) ≥10 kb contig lengths to define populations, (ii) coverage defined from reads mapping at ≥90% identity, and (iii) ≥75% of contig length with ≥1 × coverage. Finally, although data are limited to the most abundant viruses in a community, alpha and beta diversity patterns were robustly estimated (±10%) when comparing samples of similar sequencing depth, but more divergent (up to 80%) when sequencing depth was uneven across the dataset. In the latter cases, the use of normalization methods specifically develo…
format: application/pdf
format: text/html
creator: Simon Roux
creator: Joanne B. Emerson
creator: Emiley A. Eloe-Fadrosh
creator: Matthew B. Sullivan
subject: Bioinformatics
subject: Ecology
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.3817
publisher: PeerJ Inc.
rights: © 2017 Roux et al.
abstract: Background Viral metagenomics (viromics) is increasingly used to obtain uncultivated viral genomes, evaluate community diversity, and assess ecological hypotheses. While viromic experimental methods are relatively mature and widely accepted by the research community, robust bioinformatics standards remain to be established. Here we used in silico mock viral communities to evaluate the viromic sequence-to-ecological-inference pipeline, including (i) read pre-processing and metagenome assembly, (ii) thresholds applied to estimate viral relative abundances based on read mapping to assembled contigs, and (iii) normalization methods applied to the matrix of viral relative abundances for alpha and beta diversity estimates. Results Tools specifically designed for metagenomes, specifically metaSPAdes, MEGAHIT, and IDBA-UD, were the most effective at assembling viromes. Read pre-processing, such as partitioning, had virtually no impact on assembly output, but may be useful when hardware is limited. Viral populations with 2–5 × coverage typically assembled well, whereas lesser coverage led to fragmented assembly. Strain heterogeneity within populations hampered assembly, especially when strains were closely related (average nucleotide identity, or ANI ≥97%) and when the most abundant strain represented <50% of the population. Viral community composition assessments based on read recruitment were generally accurate when the following thresholds for detection were applied: (i) ≥10 kb contig lengths to define populations, (ii) coverage defined from reads mapping at ≥90% identity, and (iii) ≥75% of contig length with ≥1 × coverage. Finally, although data are limited to the most abundant viruses in a community, alpha and beta diversity patterns were robustly estimated (±10%) when comparing samples of similar sequencing depth, but more divergent (up to 80%) when sequencing depth was uneven across the dataset. In the latter cases, the use of normalization methods specifically develo…
bibliographic citation: Roux et al. (2017) Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity. PeerJ 5:e3817 https://doi.org/10.7717/peerj.3817
date submitted: 2017-06-24
date accepted: 2017-08-26
issued: 2017-09-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Roux
  given name: Simon
author list: Agent
  family name: Emerson
  given name: Joanne B.
author list: Agent
  family name: Eloe-Fadrosh
  given name: Emiley A.
author list: Agent
  family name: Sullivan
  given name: Matthew B.
doi: 10.7717/peerj.3817
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-21
copyright: ©2017 Roux et al.
attribution name: Roux et al.

Human agency beliefs influence behaviour during virtual social interactions
type: item
type: AcademicArticle
description: In recent years, with the emergence of relatively inexpensive and accessible virtual reality technologies, it is now possible to deliver compelling and realistic simulations of human-to-human interaction. Neuroimaging studies have shown that, when participants believe they are interacting via a virtual interface with another human agent, they show different patterns of brain activity compared to when they know that their virtual partner is computer-controlled. The suggestion is that users adopt an “intentional stance” by attributing mental states to their virtual partner. However, it remains unclear how beliefs in the agency of a virtual partner influence participants’ behaviour and subjective experience of the interaction. We investigated this issue in the context of a cooperative “joint attention” game in which participants interacted via an eye tracker with a virtual onscreen partner, directing each other’s eye gaze to different screen locations. Half of the participants were correctly informed that their partner was controlled by a computer algorithm (“Computer” condition). The other half were misled into believing that the virtual character was controlled by a second participant in another room (“Human” condition). Those in the “Human” condition were slower to make eye contact with their partner and more likely to try and guide their partner before they had established mutual eye contact than participants in the “Computer” condition. They also responded more rapidly when their partner was guiding them, although the same effect was also found for a control condition in which they responded to an arrow cue. Results confirm the influence of human agency beliefs on behaviour in this virtual social interaction context. They further suggest that researchers and developers attempting to simulate social interactions should consider the impact of agency beliefs on user experience in other social contexts, and their effect on the achievement of the application’s goals.
format: application/pdf
format: text/html
creator: Nathan Caruana
creator: Dean Spirou
creator: Jon Brock
subject: Neuroscience
subject: Psychiatry and Psychology
subject: Human-Computer Interaction
description: doi:10.7717/peerj.3819
publisher: PeerJ Inc.
rights: © 2017 Caruana et al.
abstract: In recent years, with the emergence of relatively inexpensive and accessible virtual reality technologies, it is now possible to deliver compelling and realistic simulations of human-to-human interaction. Neuroimaging studies have shown that, when participants believe they are interacting via a virtual interface with another human agent, they show different patterns of brain activity compared to when they know that their virtual partner is computer-controlled. The suggestion is that users adopt an “intentional stance” by attributing mental states to their virtual partner. However, it remains unclear how beliefs in the agency of a virtual partner influence participants’ behaviour and subjective experience of the interaction. We investigated this issue in the context of a cooperative “joint attention” game in which participants interacted via an eye tracker with a virtual onscreen partner, directing each other’s eye gaze to different screen locations. Half of the participants were correctly informed that their partner was controlled by a computer algorithm (“Computer” condition). The other half were misled into believing that the virtual character was controlled by a second participant in another room (“Human” condition). Those in the “Human” condition were slower to make eye contact with their partner and more likely to try and guide their partner before they had established mutual eye contact than participants in the “Computer” condition. They also responded more rapidly when their partner was guiding them, although the same effect was also found for a control condition in which they responded to an arrow cue. Results confirm the influence of human agency beliefs on behaviour in this virtual social interaction context. They further suggest that researchers and developers attempting to simulate social interactions should consider the impact of agency beliefs on user experience in other social contexts, and their effect on the achievement of the application’s goals.
bibliographic citation: Caruana et al. (2017) Human agency beliefs influence behaviour during virtual social interactions. PeerJ 5:e3819 https://doi.org/10.7717/peerj.3819
date submitted: 2017-06-10
date accepted: 2017-08-28
issued: 2017-09-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Caruana
  given name: Nathan
author list: Agent
  family name: Spirou
  given name: Dean
author list: Agent
  family name: Brock
  given name: Jon
doi: 10.7717/peerj.3819
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-20
copyright: ©2017 Caruana et al.
attribution name: Caruana et al.

Taxonomic overview of the hyperdiverse ant genus Tetramorium Mayr (Hymenoptera, Formicidae) in India with descriptions and X-ray microtomography of two new species from the Andaman Islands
type: item
type: AcademicArticle
description: With 600 described species, the ant genus Tetramorium represents one of the most species-rich ant radiations. However, much work remains to fully document the hyperdiversity of this remarkable group. Tetramorium, while globally distributed, is thought to have originated in the Afrotropics and is particularly diverse in the Old World. Here, we focus attention on the Tetramorium fauna of India, a region of high biodiversity value and interest for conservation. We overview Tetramorium diversity in India by providing a species list, accounts of all species groups present, an illustrated identification key to Indian Tetramorium species groups and notes on the Indian Tetramorium fauna. Further, we describe two new species, Tetramorium krishnani sp. n. and Tetramorium jarawa sp. n. from the Andaman Islands archipelago and embed them into currently recognized Tetramorium tonganum and Tetramorium inglebyi species groups. We also provide illustrated species level keys for these groups. Along with detailed species descriptions and high-resolution montage images of types, we provide 3D cybertypes of the new species derived from X-ray micro-computed tomography.
format: application/pdf
format: text/html
creator: Gaurav Agavekar
creator: Francisco Hita Garcia
creator: Evan P. Economo
subject: Biodiversity
subject: Entomology
subject: Taxonomy
description: doi:10.7717/peerj.3800
publisher: PeerJ Inc.
rights: © 2017 Agavekar et al.
abstract: With 600 described species, the ant genus Tetramorium represents one of the most species-rich ant radiations. However, much work remains to fully document the hyperdiversity of this remarkable group. Tetramorium, while globally distributed, is thought to have originated in the Afrotropics and is particularly diverse in the Old World. Here, we focus attention on the Tetramorium fauna of India, a region of high biodiversity value and interest for conservation. We overview Tetramorium diversity in India by providing a species list, accounts of all species groups present, an illustrated identification key to Indian Tetramorium species groups and notes on the Indian Tetramorium fauna. Further, we describe two new species, Tetramorium krishnani sp. n. and Tetramorium jarawa sp. n. from the Andaman Islands archipelago and embed them into currently recognized Tetramorium tonganum and Tetramorium inglebyi species groups. We also provide illustrated species level keys for these groups. Along with detailed species descriptions and high-resolution montage images of types, we provide 3D cybertypes of the new species derived from X-ray micro-computed tomography.
bibliographic citation: Agavekar et al. (2017) Taxonomic overview of the hyperdiverse ant genus Tetramorium Mayr (Hymenoptera, Formicidae) in India with descriptions and X-ray microtomography of two new species from the Andaman Islands. PeerJ 5:e3800 https://doi.org/10.7717/peerj.3800
date submitted: 2017-06-30
date accepted: 2017-08-22
issued: 2017-09-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Agavekar
  given name: Gaurav
author list: Agent
  family name: Hita Garcia
  given name: Francisco
author list: Agent
  family name: Economo
  given name: Evan P.
doi: 10.7717/peerj.3800
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-20
copyright: © 2017 Agavekar et al.
attribution name: Agavekar et al.

Evaluation of ddRADseq for reduced representation metagenome sequencing
type: item
type: AcademicArticle
description: Background Profiling of microbial communities via metagenomic shotgun sequencing has enabled researches to gain unprecedented insight into microbial community structure and the functional roles of community members. This study describes a method and basic analysis for a metagenomic adaptation of the double digest restriction site associated DNA sequencing (ddRADseq) protocol for reduced representation metagenome profiling. Methods This technique takes advantage of the sequence specificity of restriction endonucleases to construct an Illumina-compatible sequencing library containing DNA fragments that are between a pair of restriction sites located within close proximity. This results in a reduced sequencing library with coverage breadth that can be tuned by size selection. We assessed the performance of the metagenomic ddRADseq approach by applying the full method to human stool samples and generating sequence data. Results The ddRADseq data yields a similar estimate of community taxonomic profile as obtained from shotgun metagenome sequencing of the same human stool samples. No obvious bias with respect to genomic G + C content and the estimated relative species abundance was detected. Discussion Although ddRADseq does introduce some bias in taxonomic representation, the bias is likely to be small relative to DNA extraction bias. ddRADseq appears feasible and could have value as a tool for metagenome-wide association studies.
format: application/pdf
format: text/html
creator: Michael Y. Liu
creator: Paul Worden
creator: Leigh G. Monahan
creator: Matthew Z. DeMaere
creator: Catherine M. Burke
creator: Steven P. Djordjevic
creator: Ian G. Charles
creator: Aaron E. Darling
subject: Biodiversity
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.3837
publisher: PeerJ Inc.
rights: © 2017 Liu et al.
abstract: Background Profiling of microbial communities via metagenomic shotgun sequencing has enabled researches to gain unprecedented insight into microbial community structure and the functional roles of community members. This study describes a method and basic analysis for a metagenomic adaptation of the double digest restriction site associated DNA sequencing (ddRADseq) protocol for reduced representation metagenome profiling. Methods This technique takes advantage of the sequence specificity of restriction endonucleases to construct an Illumina-compatible sequencing library containing DNA fragments that are between a pair of restriction sites located within close proximity. This results in a reduced sequencing library with coverage breadth that can be tuned by size selection. We assessed the performance of the metagenomic ddRADseq approach by applying the full method to human stool samples and generating sequence data. Results The ddRADseq data yields a similar estimate of community taxonomic profile as obtained from shotgun metagenome sequencing of the same human stool samples. No obvious bias with respect to genomic G + C content and the estimated relative species abundance was detected. Discussion Although ddRADseq does introduce some bias in taxonomic representation, the bias is likely to be small relative to DNA extraction bias. ddRADseq appears feasible and could have value as a tool for metagenome-wide association studies.
bibliographic citation: Liu et al. (2017) Evaluation of ddRADseq for reduced representation metagenome sequencing. PeerJ 5:e3837 https://doi.org/10.7717/peerj.3837
date submitted: 2017-07-15
date accepted: 2017-08-31
issued: 2017-09-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Michael Y.
author list: Agent
  family name: Worden
  given name: Paul
author list: Agent
  family name: Monahan
  given name: Leigh G.
author list: Agent
  family name: DeMaere
  given name: Matthew Z.
author list: Agent
  family name: Burke
  given name: Catherine M.
author list: Agent
  family name: Djordjevic
  given name: Steven P.
author list: Agent
  family name: Charles
  given name: Ian G.
author list: Agent
  family name: Darling
  given name: Aaron E.
doi: 10.7717/peerj.3837
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-19
copyright: ©2017 Liu et al.
attribution name: Liu et al.

CA1 pyramidal cells have diverse biophysical properties, affected by development, experience, and aging
type: item
type: AcademicArticle
description: Neuron types (e.g., pyramidal cells) within one area of the brain are often considered homogeneous, despite variability in their biophysical properties. Here we review literature demonstrating variability in the electrical activity of CA1 hippocampal pyramidal cells (PCs), including responses to somatic current injection, synaptic stimulation, and spontaneous network-related activity. In addition, we describe how responses of CA1 PCs vary with development, experience, and aging, and some of the underlying ionic currents responsible. Finally, we suggest directions that may be the most impactful in expanding this knowledge, including the use of text and data mining to systematically study cellular heterogeneity in more depth; dynamical systems theory to understand and potentially classify neuron firing patterns; and mathematical modeling to study the interaction between cellular properties and network output. Our goals are to provide a synthesis of the literature for experimentalists studying CA1 PCs, to give theorists an idea of the rich diversity of behaviors models may need to reproduce to accurately represent these cells, and to provide suggestions for future research.
format: application/pdf
format: text/html
creator: Erin C. McKiernan
creator: Diano F. Marrone
subject: Biophysics
subject: Neuroscience
description: doi:10.7717/peerj.3836
publisher: PeerJ Inc.
rights: © 2017 McKiernan and Marrone
abstract: Neuron types (e.g., pyramidal cells) within one area of the brain are often considered homogeneous, despite variability in their biophysical properties. Here we review literature demonstrating variability in the electrical activity of CA1 hippocampal pyramidal cells (PCs), including responses to somatic current injection, synaptic stimulation, and spontaneous network-related activity. In addition, we describe how responses of CA1 PCs vary with development, experience, and aging, and some of the underlying ionic currents responsible. Finally, we suggest directions that may be the most impactful in expanding this knowledge, including the use of text and data mining to systematically study cellular heterogeneity in more depth; dynamical systems theory to understand and potentially classify neuron firing patterns; and mathematical modeling to study the interaction between cellular properties and network output. Our goals are to provide a synthesis of the literature for experimentalists studying CA1 PCs, to give theorists an idea of the rich diversity of behaviors models may need to reproduce to accurately represent these cells, and to provide suggestions for future research.
bibliographic citation: McKiernan et al. (2017) CA1 pyramidal cells have diverse biophysical properties, affected by development, experience, and aging. PeerJ 5:e3836 https://doi.org/10.7717/peerj.3836
date submitted: 2017-07-04
date accepted: 2017-08-31
issued: 2017-09-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: McKiernan
  given name: Erin C.
author list: Agent
  family name: Marrone
  given name: Diano F.
doi: 10.7717/peerj.3836
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-19
copyright: ©2017 McKiernan and Marrone
attribution name: McKiernan and Marrone

Analysis of drug binding pockets and repurposing opportunities for twelve essential enzymes of ESKAPE pathogens
type: item
type: AcademicArticle
description: Background The rapid increase in antibiotic resistance by various bacterial pathogens underlies the significance of developing new therapies and exploring different drug targets. A fraction of bacterial pathogens abbreviated as ESKAPE by the European Center for Disease Prevention and Control have been considered a major threat due to the rise in nosocomial infections. Here, we compared putative drug binding pockets of twelve essential and mostly conserved metabolic enzymes in numerous bacterial pathogens including those of the ESKAPE group and Mycobacterium tuberculosis. The comparative analysis will provide guidelines for the likelihood of transferability of the inhibitors from one species to another. Methods Nine bacterial species including six ESKAPE pathogens, Mycobacterium tuberculosis along with Mycobacterium smegmatis and Eschershia coli, two non-pathogenic bacteria, have been selected for drug binding pocket analysis of twelve essential enzymes. The amino acid sequences were obtained from Uniprot, aligned using ICM v3.8-4a and matched against the Pocketome encyclopedia. We used known co-crystal structures of selected target enzyme orthologs to evaluate the location of their active sites and binding pockets and to calculate a matrix of pairwise sequence identities across each target enzyme across the different species. This was used to generate sequence maps. Results High sequence identity of enzyme binding pockets, derived from experimentally determined co-crystallized structures, was observed among various species. Comparison at both full sequence level and for drug binding pockets of key metabolic enzymes showed that binding pockets are highly conserved (sequence similarity up to 100%) among various ESKAPE pathogens as well as Mycobacterium tuberculosis. Enzymes orthologs having conserved binding sites may have potential to interact with inhibitors in similar way and might be helpful for design of similar class of inhibitors for a particular species. The d…
format: application/pdf
format: text/html
creator: Sadia Naz
creator: Tony Ngo
creator: Umar Farooq
creator: Ruben Abagyan
subject: Bioinformatics
subject: Computational Biology
subject: Microbiology
subject: Pharmacology
description: doi:10.7717/peerj.3765
publisher: PeerJ Inc.
rights: © 2017 Naz et al.
abstract: Background The rapid increase in antibiotic resistance by various bacterial pathogens underlies the significance of developing new therapies and exploring different drug targets. A fraction of bacterial pathogens abbreviated as ESKAPE by the European Center for Disease Prevention and Control have been considered a major threat due to the rise in nosocomial infections. Here, we compared putative drug binding pockets of twelve essential and mostly conserved metabolic enzymes in numerous bacterial pathogens including those of the ESKAPE group and Mycobacterium tuberculosis. The comparative analysis will provide guidelines for the likelihood of transferability of the inhibitors from one species to another. Methods Nine bacterial species including six ESKAPE pathogens, Mycobacterium tuberculosis along with Mycobacterium smegmatis and Eschershia coli, two non-pathogenic bacteria, have been selected for drug binding pocket analysis of twelve essential enzymes. The amino acid sequences were obtained from Uniprot, aligned using ICM v3.8-4a and matched against the Pocketome encyclopedia. We used known co-crystal structures of selected target enzyme orthologs to evaluate the location of their active sites and binding pockets and to calculate a matrix of pairwise sequence identities across each target enzyme across the different species. This was used to generate sequence maps. Results High sequence identity of enzyme binding pockets, derived from experimentally determined co-crystallized structures, was observed among various species. Comparison at both full sequence level and for drug binding pockets of key metabolic enzymes showed that binding pockets are highly conserved (sequence similarity up to 100%) among various ESKAPE pathogens as well as Mycobacterium tuberculosis. Enzymes orthologs having conserved binding sites may have potential to interact with inhibitors in similar way and might be helpful for design of similar class of inhibitors for a particular species. The d…
bibliographic citation: Naz et al. (2017) Analysis of drug binding pockets and repurposing opportunities for twelve essential enzymes of ESKAPE pathogens. PeerJ 5:e3765 https://doi.org/10.7717/peerj.3765
date submitted: 2017-04-08
date accepted: 2017-08-15
issued: 2017-09-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Naz
  given name: Sadia
author list: Agent
  family name: Ngo
  given name: Tony
author list: Agent
  family name: Farooq
  given name: Umar
author list: Agent
  family name: Abagyan
  given name: Ruben
doi: 10.7717/peerj.3765
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-19
copyright: ©2017 Naz et al.
attribution name: Naz et al.

Morning surge in blood pressure and sympathetic activity in Mongolians and Han Chinese: a multimodality investigation of hypertension and dyssomnia
type: item
type: AcademicArticle
description: Background Hypertension and dyssomnia are increasing significantly in Mongolians, and the related factors of ethnic differences in hypertension and dyssomnia between Mongolians and Han Chinese are unclear. This study examined the relationship of morning surge in blood pressure (MBP) with ethnicity, sleep situation, and sympathetic activity throughout the day. Methods Of 692 hypertensive patients screened, 202 subjects with dyssomnia were selected. They were then divided into Mongolian (n = 87) and Han (n = 115) groups. The differences in dyssomnia, 24-h blood pressure, and urinary catecholamine were analyzed in all subjects; they were then further divided according to the degree of dyssomnia (low, moderate, and severe) to determine the differences in blood pressure and catecholamine. Results Mongolians had a lower history of smoking, daytime dysfunction, nocturnal heart rates, and dopamine levels, but their body mass index, triglyceride, fasting glucose, morning surge in systolic blood pressure (MSBP), nocturnal systolic blood pressure (NSBP), nocturnal diastolic blood pressure, daytime systolic blood pressure, daytime heart rates, and dopamine level (D-DA) were higher than those of Han Chinese. With the aggravation of dyssomnia, MSBP, NSBP, D-NE, daytime epinephrine, and D-DA of Mongolians and Han Chinese increased gradually, but the rate of increase was faster in the latter (p < 0.05). D-DA was entered into the MSBP regression model of Mongolians (intercept, 157 mmHg), whereas D-DA and D-NE were entered into the MSBP regression model of Han Chinese (intercept, 142 mmHg). Conclusion Worsened dyssomnia induces higher MSBP and augments sympathetic excitability in Mongolians and Han Chinese. Mongolians with hypertension and dyssomnia had higher MSBP baseline and D-DA but lower N-DA. With an increase in D-DA, MSBP in Han and Mongolian patients increased gradually.
format: application/pdf
format: text/html
creator: Guanhua Huang
creator: Xiaoming Yang
creator: Jing Huang
subject: Cardiology
subject: Global Health
subject: Public Health
description: doi:10.7717/peerj.3758
publisher: PeerJ Inc.
rights: © 2017 Huang et al.
abstract: Background Hypertension and dyssomnia are increasing significantly in Mongolians, and the related factors of ethnic differences in hypertension and dyssomnia between Mongolians and Han Chinese are unclear. This study examined the relationship of morning surge in blood pressure (MBP) with ethnicity, sleep situation, and sympathetic activity throughout the day. Methods Of 692 hypertensive patients screened, 202 subjects with dyssomnia were selected. They were then divided into Mongolian (n = 87) and Han (n = 115) groups. The differences in dyssomnia, 24-h blood pressure, and urinary catecholamine were analyzed in all subjects; they were then further divided according to the degree of dyssomnia (low, moderate, and severe) to determine the differences in blood pressure and catecholamine. Results Mongolians had a lower history of smoking, daytime dysfunction, nocturnal heart rates, and dopamine levels, but their body mass index, triglyceride, fasting glucose, morning surge in systolic blood pressure (MSBP), nocturnal systolic blood pressure (NSBP), nocturnal diastolic blood pressure, daytime systolic blood pressure, daytime heart rates, and dopamine level (D-DA) were higher than those of Han Chinese. With the aggravation of dyssomnia, MSBP, NSBP, D-NE, daytime epinephrine, and D-DA of Mongolians and Han Chinese increased gradually, but the rate of increase was faster in the latter (p < 0.05). D-DA was entered into the MSBP regression model of Mongolians (intercept, 157 mmHg), whereas D-DA and D-NE were entered into the MSBP regression model of Han Chinese (intercept, 142 mmHg). Conclusion Worsened dyssomnia induces higher MSBP and augments sympathetic excitability in Mongolians and Han Chinese. Mongolians with hypertension and dyssomnia had higher MSBP baseline and D-DA but lower N-DA. With an increase in D-DA, MSBP in Han and Mongolian patients increased gradually.
bibliographic citation: Huang et al. (2017) Morning surge in blood pressure and sympathetic activity in Mongolians and Han Chinese: a multimodality investigation of hypertension and dyssomnia. PeerJ 5:e3758 https://doi.org/10.7717/peerj.3758
date submitted: 2017-05-17
date accepted: 2017-08-13
issued: 2017-09-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Guanhua
author list: Agent
  family name: Yang
  given name: Xiaoming
author list: Agent
  family name: Huang
  given name: Jing
doi: 10.7717/peerj.3758
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-19
copyright: ©2017 Huang et al.
attribution name: Huang et al.

Genome-wide identification and characterization of aquaporin gene family in Beta vulgaris
type: item
type: AcademicArticle
description: Aquaporins (AQPs) are essential channel proteins that execute multi-functions throughout plant growth and development, including water transport, uncharged solutes uptake, stress response, and so on. Here, we report the first genome-wide identification and characterization AQP (BvAQP) genes in sugar beet (Beta vulgaris), an important crop widely cultivated for feed, for sugar production and for bioethanol production. Twenty-eight sugar beet AQPs (BvAQPs) were identified and assigned into five subfamilies based on phylogenetic analyses: seven of plasma membrane (PIPs), eight of tonoplast (TIPs), nine of NOD26-like (NIPs), three of small basic (SIPs), and one of x-intrinsic proteins (XIPs). BvAQP genes unevenly mapped on all chromosomes, except on chromosome 4. Gene structure and motifs analyses revealed that BvAQP have conserved exon-intron organization and that they exhibit conserved motifs within each subfamily. Prediction of BvAQPs functions, based on key protein domains conservation, showed a remarkable difference in substrate specificity among the five subfamilies. Analyses of BvAQPs expression, by mean of RNA-seq, in different plant organs and in response to various abiotic stresses revealed that they were ubiquitously expressed and that their expression was induced by heat and salt stresses. These results provide a reference base to address further the function of sugar beet aquaporins and to explore future applications for plants growth and development improvements as well as in response to environmental stresses.
format: application/pdf
format: text/html
creator: Weilong Kong
creator: Shaozong Yang
creator: Yulu Wang
creator: Mohammed Bendahmane
creator: Xiaopeng Fu
subject: Agricultural Science
subject: Bioinformatics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.3747
publisher: PeerJ Inc.
rights: © 2017 Kong et al.
abstract: Aquaporins (AQPs) are essential channel proteins that execute multi-functions throughout plant growth and development, including water transport, uncharged solutes uptake, stress response, and so on. Here, we report the first genome-wide identification and characterization AQP (BvAQP) genes in sugar beet (Beta vulgaris), an important crop widely cultivated for feed, for sugar production and for bioethanol production. Twenty-eight sugar beet AQPs (BvAQPs) were identified and assigned into five subfamilies based on phylogenetic analyses: seven of plasma membrane (PIPs), eight of tonoplast (TIPs), nine of NOD26-like (NIPs), three of small basic (SIPs), and one of x-intrinsic proteins (XIPs). BvAQP genes unevenly mapped on all chromosomes, except on chromosome 4. Gene structure and motifs analyses revealed that BvAQP have conserved exon-intron organization and that they exhibit conserved motifs within each subfamily. Prediction of BvAQPs functions, based on key protein domains conservation, showed a remarkable difference in substrate specificity among the five subfamilies. Analyses of BvAQPs expression, by mean of RNA-seq, in different plant organs and in response to various abiotic stresses revealed that they were ubiquitously expressed and that their expression was induced by heat and salt stresses. These results provide a reference base to address further the function of sugar beet aquaporins and to explore future applications for plants growth and development improvements as well as in response to environmental stresses.
bibliographic citation: Kong et al. (2017) Genome-wide identification and characterization of aquaporin gene family in Beta vulgaris. PeerJ 5:e3747 https://doi.org/10.7717/peerj.3747
date submitted: 2017-04-13
date accepted: 2017-08-08
issued: 2017-09-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kong
  given name: Weilong
author list: Agent
  family name: Yang
  given name: Shaozong
author list: Agent
  family name: Wang
  given name: Yulu
author list: Agent
  family name: Bendahmane
  given name: Mohammed
author list: Agent
  family name: Fu
  given name: Xiaopeng
doi: 10.7717/peerj.3747
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-19
copyright: ©2017 Kong et al.
attribution name: Kong et al.

Vascular anatomy is a determining factor of successful submental flap raising: a retrospective study of 70 clinical cases
type: item
type: AcademicArticle
description: The vascular anatomy of submental flaps (SFs) represents a determining factor in successful SF raising. However, little attention has been focused on the venous return of SFs. Thus, the present study aimed to investigate SF venous return. This study enrolled patients who underwent SF reconstructive surgery in a tertiary referral center between November 2009 and October 2016. The drainage pathway of the SF venous return was routinely identified during the course of our operations to prevent damage during head and neck surgery. The venous return data of 70 patients were reviewed. The size of the flaps ranged from 15 to 84 cm2, and total flap loss was not observed in the case series. All of the submental arteries originated from the facial artery; however, the submental veins of 70 patients returned to either the internal jugular vein (IJV, 72.9%) or the external jugular vein (EJV, 27.1%). Our data suggest that drainage of the submental vein into the EJV, which has been previously overlooked, should receive greater attention during SF surgeries. The results support mandatory preservation of the EJV and IJV and indicate that vascular anatomy is a determining factor for successful SF raising.
format: application/pdf
format: text/html
creator: Hung-Che Lin
creator: Yuahn-Sieh Huang
creator: Yueng-Hsiang Chu
creator: Shao-Cheng Liu
creator: Wei-Chuan Shangkuan
creator: Wen-Sen Lai
creator: Jinn-Moon Yang
creator: Yaoh-Shiang Lin
creator: Kuo-Hsing Ma
creator: Jih-Chin Lee
subject: Anatomy and Physiology
subject: Otorhinolaryngology
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.3606
publisher: PeerJ Inc.
rights: © 2017 Lin et al.
abstract: The vascular anatomy of submental flaps (SFs) represents a determining factor in successful SF raising. However, little attention has been focused on the venous return of SFs. Thus, the present study aimed to investigate SF venous return. This study enrolled patients who underwent SF reconstructive surgery in a tertiary referral center between November 2009 and October 2016. The drainage pathway of the SF venous return was routinely identified during the course of our operations to prevent damage during head and neck surgery. The venous return data of 70 patients were reviewed. The size of the flaps ranged from 15 to 84 cm2, and total flap loss was not observed in the case series. All of the submental arteries originated from the facial artery; however, the submental veins of 70 patients returned to either the internal jugular vein (IJV, 72.9%) or the external jugular vein (EJV, 27.1%). Our data suggest that drainage of the submental vein into the EJV, which has been previously overlooked, should receive greater attention during SF surgeries. The results support mandatory preservation of the EJV and IJV and indicate that vascular anatomy is a determining factor for successful SF raising.
bibliographic citation: Lin et al. (2017) Vascular anatomy is a determining factor of successful submental flap raising: a retrospective study of 70 clinical cases. PeerJ 5:e3606 https://doi.org/10.7717/peerj.3606
date submitted: 2017-04-12
date accepted: 2017-07-02
issued: 2017-09-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lin
  given name: Hung-Che
author list: Agent
  family name: Huang
  given name: Yuahn-Sieh
author list: Agent
  family name: Chu
  given name: Yueng-Hsiang
author list: Agent
  family name: Liu
  given name: Shao-Cheng
author list: Agent
  family name: Shangkuan
  given name: Wei-Chuan
author list: Agent
  family name: Lai
  given name: Wen-Sen
author list: Agent
  family name: Yang
  given name: Jinn-Moon
author list: Agent
  family name: Lin
  given name: Yaoh-Shiang
author list: Agent
  family name: Ma
  given name: Kuo-Hsing
author list: Agent
  family name: Lee
  given name: Jih-Chin
doi: 10.7717/peerj.3606
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-19
copyright: ©2017 Lin et al.
attribution name: Lin et al.

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