title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1664 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: MazF activation promotes translational heterogeneity of the grcA mRNA in Escherichia coli populations link: https://peerj.com/articles/3830 last-modified: 2017-09-21 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. creator: Nela Nikolic creator: Zrinka Didara creator: Isabella Moll uri: https://doi.org/10.7717/peerj.3830 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Nikolic et al. title: Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity link: https://peerj.com/articles/3817 last-modified: 2017-09-21 description: BackgroundViral 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.ResultsTools 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 developed for metagenomes provided the best estimates.ConclusionsThese simulations provide benchmarks for selecting analysis cut-offs and establish that an optimized sample-to-ecological-inference viromics pipeline is robust for making ecological inferences from natural viral communities. Continued development to better accessing RNA, rare, and/or diverse viral populations and improved reference viral genome availability will alleviate many of viromics remaining limitations. creator: Simon Roux creator: Joanne B. Emerson creator: Emiley A. Eloe-Fadrosh creator: Matthew B. Sullivan uri: https://doi.org/10.7717/peerj.3817 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Roux et al. title: Human agency beliefs influence behaviour during virtual social interactions link: https://peerj.com/articles/3819 last-modified: 2017-09-20 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. creator: Nathan Caruana creator: Dean Spirou creator: Jon Brock uri: https://doi.org/10.7717/peerj.3819 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Caruana et al. title: 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 link: https://peerj.com/articles/3800 last-modified: 2017-09-20 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. creator: Gaurav Agavekar creator: Francisco Hita Garcia creator: Evan P. Economo uri: https://doi.org/10.7717/peerj.3800 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Agavekar et al. title: Evaluation of ddRADseq for reduced representation metagenome sequencing link: https://peerj.com/articles/3837 last-modified: 2017-09-19 description: BackgroundProfiling 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.MethodsThis 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.ResultsThe 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.DiscussionAlthough 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. 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 uri: https://doi.org/10.7717/peerj.3837 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Liu et al. title: CA1 pyramidal cells have diverse biophysical properties, affected by development, experience, and aging link: https://peerj.com/articles/3836 last-modified: 2017-09-19 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. creator: Erin C. McKiernan creator: Diano F. Marrone uri: https://doi.org/10.7717/peerj.3836 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 McKiernan and Marrone title: Analysis of drug binding pockets and repurposing opportunities for twelve essential enzymes of ESKAPE pathogens link: https://peerj.com/articles/3765 last-modified: 2017-09-19 description: BackgroundThe 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.MethodsNine 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.ResultsHigh 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 derived pocket alignments and distance-based maps provide guidelines for drug discovery and repurposing. In addition they also provide recommendations for the relevant model bacteria that may be used for initial drug testing.DiscussionComparing ligand binding sites through sequence identity calculation could be an effective approach to identify conserved orthologs as drug binding pockets have shown higher level of conservation among various species. By using this approach we could avoid the problems associated with full sequence comparison. We identified essential metabolic enzymes among ESKAPE pathogens that share high sequence identity in their putative drug binding pockets (up to 100%), of which known inhibitors can potentially antagonize these identical pockets in the various species in a similar manner. creator: Sadia Naz creator: Tony Ngo creator: Umar Farooq creator: Ruben Abagyan uri: https://doi.org/10.7717/peerj.3765 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Naz et al. title: Morning surge in blood pressure and sympathetic activity in Mongolians and Han Chinese: a multimodality investigation of hypertension and dyssomnia link: https://peerj.com/articles/3758 last-modified: 2017-09-19 description: BackgroundHypertension 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.MethodsOf 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.ResultsMongolians 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).ConclusionWorsened 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. creator: Guanhua Huang creator: Xiaoming Yang creator: Jing Huang uri: https://doi.org/10.7717/peerj.3758 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Huang et al. title: Genome-wide identification and characterization of aquaporin gene family in Beta vulgaris link: https://peerj.com/articles/3747 last-modified: 2017-09-19 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. creator: Weilong Kong creator: Shaozong Yang creator: Yulu Wang creator: Mohammed Bendahmane creator: Xiaopeng Fu uri: https://doi.org/10.7717/peerj.3747 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Kong et al. title: Vascular anatomy is a determining factor of successful submental flap raising: a retrospective study of 70 clinical cases link: https://peerj.com/articles/3606 last-modified: 2017-09-19 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. 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 uri: https://doi.org/10.7717/peerj.3606 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Lin et al.