The impact of storage conditions on human stool 16S rRNA microbiome composition and diversity
Background Multiple factors can influence stool sample integrity upon sample collection. Preservation of faecal samples for microbiome studies is therefore an important step, particularly in tropical regions where resources are limited and high temperatures may significantly influence microbiota profiles. Freezing is the accepted standard to preserve faecal samples however, cold chain methods are often unfeasible in fieldwork scenarios particularly in low and middle-income countries and alternatives are required. This study therefore aimed to address the impact of different preservative methods, time-to-freezing at ambient tropical temperatures, and stool heterogeneity on stool microbiome diversity and composition under real-life physical environments found in resource-limited fieldwork conditions. Methods Inner and outer stool samples collected from one specimen obtained from three children were stored using different storage preservation methods (raw, ethanol and RNAlater) in a Ugandan field setting. Mixed stool was also stored using these techniques and frozen at different time-to-freezing intervals post-collection from 0–32 h. Metataxonomic profiling was used to profile samples, targeting the V1–V2 regions of 16S rRNA with samples run on a MiSeq platform. Reads were trimmed, combined and aligned to the Greengenes database. Microbial diversity and composition data were generated and analysed using Quantitative Insights Into Microbial Ecology and R software. Results Child donor was the greatest predictor of microbiome variation between the stool samples, with all samples remaining identifiable to their child of origin despite the stool being stored under a variety of conditions. However, significant differences were observed in composition and diversity between preservation techniques, but intra-preservation technique variation was minimal for all preservation methods, and across the time-to-freezing range (0–32 h) used. Stool heterogeneity yielded no apparent microbiome differences. Conclusions Stool collected in a fieldwork setting for comparative microbiome analyses should ideally be stored as consistently as possible using the same preservation method throughout.
Carruthers et al. (2019) The impact of storage conditions on human stool 16S rRNA microbiome composition and diversity. PeerJ 7:e8133 https://doi.org/10.7717/peerj.8133
Propofol inhibits stromatoxin-1-sensitive voltage-dependent K+ channels in pancreatic β-cells and enhances insulin secretion
Background Proper glycemic control is an important goal of critical care medicine, including perioperative patient care that can influence patients’ prognosis. Insulin secretion from pancreatic β-cells is generally assumed to play a critical role in glycemic control in response to an elevated blood glucose concentration. Many animal and human studies have demonstrated that perioperative drugs, including volatile anesthetics, have an impact on glucose-stimulated insulin secretion (GSIS). However, the effects of the intravenous anesthetic propofol on glucose metabolism and insulin sensitivity are largely unknown at present. Methods The effect of propofol on insulin secretion under low glucose or high glucose was examined in mouse MIN6 cells, rat INS-1 cells, and mouse pancreatic β-cells/islets. Cellular oxygen or energy metabolism was measured by Extracellular Flux Analyzer. Expression of glucose transporter 2 (GLUT2), potassium channels, and insulin mRNA was assessed by qRT-PCR. Protein expression of voltage-dependent potassium channels (Kv2) was also assessed by immunoblot. Propofol’s effects on potassium channels including stromatoxin-1-sensitive Kv channels and cellular oxygen and energy metabolisms were also examined. Results We showed that propofol, at clinically relevant doses, facilitates insulin secretion under low glucose conditions and GSIS in MIN6, INS-1 cells, and pancreatic β-cells/islets. Propofol did not affect intracellular ATP or ADP concentrations and cellular oxygen or energy metabolism. The mRNA expression of GLUT2 and channels including the voltage-dependent calcium channels Cav1.2, Kir6.2, and SUR1 subunit of KATP, and Kv2 were not affected by glucose or propofol. Finally, we demonstrated that propofol specifically blocks Kv currents in β-cells, resulting in insulin secretion in the presence of glucose. Conclusions Our data support the hypothesis that glucose induces membrane depolarization at the distal site, leading to KATP channel closure, and that the closure of Kv channels by propofol depolarization in β-cells enhances Ca2+ entry, leading to insulin secretion. Because its activity is dependent on GSIS, propofol and its derivatives are potential compounds that enhance and initiate β-cell electrical activity.
Kusunoki et al. (2019) Propofol inhibits stromatoxin-1-sensitive voltage-dependent K+ channels in pancreatic β-cells and enhances insulin secretion. PeerJ 7:e8157 https://doi.org/10.7717/peerj.8157
Global transcriptome analysis of different stages of preimplantation embryo development in river buffalo
Background Water buffalo (Bubalus bubalis) are divided into river buffalo and swamp buffalo subspecies and are essential livestock for agriculture and the local economy. Studies on buffalo reproduction have primarily focused on optimal fertility and embryonic mortality. There is currently limited knowledge on buffalo embryonic development, especially during the preimplantation period. Assembly of the river buffalo genome offers a reference for omics studies and facilitates transcriptomic analysis of preimplantation embryo development (PED). Methods We revealed transcriptomic profile of four stages (2-cell, 8-cell, Morula and Blastocyst) of PED via RNA-seq (Illumina HiSeq4000). Each stage comprised three biological replicates. The data were analyzed according to the basic RNA-seq analysis process. Ingenuity analysis of cell lineage control, especially transcription factor (TF) regulatory networks, was also performed. Results A total of 21,519 expressed genes and 67,298 transcripts were predicted from approximately 81.94 Gb of raw data. Analysis of transcriptome-wide expression, gene coexpression networks, and differentially expressed genes (DEGs) allowed for the characterization of gene-specific expression levels and relationships for each stage. The expression patterns of TFs, such as POU5F1, TEAD4, CDX4 and GATAs, were elucidated across diverse time series; most TF expression levels were increased during the blastocyst stage, during which time cell differentiation is initiated. All of these TFs were involved in the composition of the regulatory networks that precisely specify cell fate. These findings offer a deeper understanding of PED at the transcriptional level in the river buffalo.
Pang et al. (2019) Global transcriptome analysis of different stages of preimplantation embryo development in river buffalo. PeerJ 7:e8185 https://doi.org/10.7717/peerj.8185
Brain structural and functional changes in patients with major depressive disorder: a literature review
Depression is a mental disorder characterized by low mood and anhedonia that involves abnormalities in multiple brain regions and networks. Epidemiological studies demonstrated that depression has become one of the most important diseases affecting human health and longevity. The pathogenesis of the disease has not been fully elucidated. The clinical effect of treatment is not satisfactory in many cases. Neuroimaging studies have provided rich and valuable evidence that psychological symptoms and behavioral deficits in patients with depression are closely related to structural and functional abnormalities in specific areas of the brain. There were morphological differences in several brain regions, including the frontal lobe, temporal lobe, and limbic system, in people with depression compared to healthy people. In addition, people with depression also had abnormal functional connectivity to the default mode network, the central executive network, and the salience network. These findings provide an opportunity to re-understand the biological mechanisms of depression. In the future, magnetic resonance imaging (MRI) may serve as an important auxiliary tool for psychiatrists in the process of early and accurate diagnosis of depression and finding the appropriate treatment target for each patient to optimize clinical response.
Dai et al. (2019) Brain structural and functional changes in patients with major depressive disorder: a literature review. PeerJ 7:e8170 https://doi.org/10.7717/peerj.8170
Stress-induced changes in the expression of antioxidant system genes for rice (Oryza sativa L.) and bread wheat (Triticum aestivum L.)
Background Plant cell metabolism inevitably forms reactive oxygen species (ROS), which can damage cells or lead to their death. The antioxidant system (AOS) evolved to eliminate a high concentration of ROS. For plants, this system consists of the seven classes of antioxidant enzymes and antioxidant compounds. Each enzymatic class contains a various number of genes which may vary from species to species. In such a multi-copy genetic system, the integration of evolutionary characteristics and expression data makes it possible to effectively predict promising breeding targets for the design of highly-yielding cultivars. In the plant cells, ROS production can increase as a result of abiotic stresses. Accordingly, AOS responds to stress by altering the expression of the genes of its components. Expression profiles of AOS enzymes, including their changes under stress, remains incomplete. A comprehensive study of the system behavior in response to stress for different species gives the key to identify the general mechanisms of AOS regulation. In this article, we studied stress-induced changes in the expression of AOS genes in photosynthetic tissues for rice and bread wheat. Methods A meta-analysis of genome-wide transcriptome data on stress-induced changes in expression profiles of antioxidant genes using microarray and next generation sequencing (NGS) experiments from the GEO NCBI database for rice and bread wheat was carried out. Experimental study of expression changes in short (6 h) and prolonged (24 h) cold stress responses for selected AOS genes of bread wheat cultivars Saratovskaya29 and Yanetzkis Probat was conducted using qPCR. Results The large-scale meta-transcriptome and complementary experimental analysis revealed a summary of fold changes in the AOS gene expression in response to cold and water deficiency for rice and bread wheat.
Ermakov et al. (2019) Stress-induced changes in the expression of antioxidant system genes for rice (Oryza sativa L.) and bread wheat (Triticum aestivum L.). PeerJ 7:e7791 https://doi.org/10.7717/peerj.7791
Taxonomic assessment of species of the genus Octopus from the northeastern Pacific via morphological, molecular and morphometric analyses
Species of the genus Octopus from the northeastern Pacific are ecologically and economically important; however, their taxonomy is confusing and has not been comprehensively assessed. In this study, we performed a taxonomic evaluation of these species considering the morphological characteristics of the original descriptions, a molecular analysis of partial COI-gene sequences, and a traditional morphometry analysis of nine body measurements. Several interesting findings were obtained with our results: for instance, we updated the diagnoses of some species by including characters such as the number of lamellae per demibranch and the presence of chromatophores in the visceral sac; we deposited partial COI-gene sequences of species that had not been incorporated into the GenBank repository; and according to the morphometric analysis, we confirmed that the lengths of arms I–IV are relevant to discriminate the species under study. The taxa evaluated were morphologically, molecularly and morphometrically well-delimited; however, features such as funnel organ shape and arm length proportions in regard to dorsal mantle length are either not included in the diagnosis of the genus Octopus or overlap with other genera. Hence, this information, combined with the results obtained from the molecular analysis, supports the generic re-assignation of two of the species evaluated.
Díaz-Santana-Iturrios et al. (2019) Taxonomic assessment of species of the genus Octopus from the northeastern Pacific via morphological, molecular and morphometric analyses. PeerJ 7:e8118 https://doi.org/10.7717/peerj.8118
Relationship between the Dark Triad and depressive symptoms
The Dark Triad (DT) is composed of three closely related personality traits: psychopathy, Machiavellianism and narcissism. These traits have been linked to emotional deficits. The aim of the present study was to analyze the relationship between the DT traits, including sub-dimensions, and depressive symptoms in order to identify those factors most strongly associated with the development of depression in individuals scoring high on DT. For these purposes, a total of 791 adults (M = 35.76 years; 24.91% males) completed a questionnaire battery including DT traits and depression measures. A positive significant correlation was found between psychopathy and Machiavellianism traits (total score and all sub-dimensions) and depressive symptoms. For narcissism, the direction of the correlation was dependent on the sub-dimension assessed. A model explaining 26.2% of the depressive symptoms scores was composed of the callous affect and criminal tendencies sub-dimensions of psychopathy, cynical view of human nature, which is a sub-dimension of Machiavellianism, and entitlement and self-sufficiency, which are sub-dimensions of narcissism. In addition, some of the relationships found between DT sub-dimensions and depressive symptoms appeared to depend on gender. Our results could have implications for detection and intervention programs aimed at decreasing the negative emotional consequences suffered by individuals with high DT scores. Limitations and future lines of research are discussed.
Gómez-Leal et al. (2019) Relationship between the Dark Triad and depressive symptoms. PeerJ 7:e8120 https://doi.org/10.7717/peerj.8120
Identification of prognostic gene signature associated with microenvironment of lung adenocarcinoma
Background Lung cancer has the highest morbidity and mortality worldwide, and lung adenocarcinoma (LADC) is the most common pathological subtype. Accumulating evidence suggests the tumor microenvironment (TME) is correlated with the tumor progress and the patient’s outcome. As the major components of TME, the tumor-infiltrated immune cells and stromal cells have attracted more and more attention. In this study, differentially expressed immune and stromal signature genes were used to construct a TME-related prognostic model for predicting the outcomes of LADC patients. Methods The expression profiles of LADC samples with clinical information were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). The differentially expressed genes (DEGs) related to the TME of LADC were identified using TCGA dataset by Wilcoxon rank sum test. The prognostic effects of TME-related DEGs were analyzed using univariate Cox regression. Then, the least absolute shrinkage and selection operator (LASSO) regression was performed to reduce the overfit and the number of genes for further analysis. Next, the prognostic model was constructed by step multivariate Cox regression and risk score of each sample was calculated. Then, survival and Receiver Operating Characteristic (ROC) analyses were conducted to validate the model using TCGA and GEO datasets, respectively. The Kyoto Encyclopedia of Genes and Genomes analysis of gene signature was performed using Gene Set Enrichment Analysis (GSEA). Finally, the overall immune status, tumor purity and the expression profiles of HLA genes of high- and low-risk samples was further analyzed to reveal the potential mechanisms of prognostic effects of the model. Results A total of 93 TME-related DEGs were identified, of which 23 DEGs were up-regulated and 70 DEGs were down-regulated. The univariate cox analysis indicated that 23 DEGs has the prognostic effects, the hazard ratio ranged from 0.65 to 1.25 (p < 0.05). Then, seven genes were screened out from the 23 DEGs by LASSO regression method and were further analyzed by step multivariate Cox regression. Finally, a three-gene (ADAM12, Bruton Tyrosine Kinase (BTK), ERG) signature was constructed, and ADAM12, BTK can be used as independent prognostic factors. The three-gene signature well stratified the LADC patients in both training (TCGA) and testing (GEO) datasets as high-risk and low-risk groups, the 3-year area under curve (AUC) of ROC curves of three GEO sets were 0.718 (GSE3141), 0.646 (GSE30219) and 0.643 (GSE50081). The GSEA analysis indicated that highly expressed ADAM12, BTK, ERG mainly correlated with the activation of pathways involving in focal adhesion, immune regulation. The immune analysis indicated that the low-risk group has more immune activities and higher expression of HLA genes than that of the high-risk group. In sum, we identified and constructed a three TME-related DEGs signature, which could be used to predict the prognosis of LADC patients.
Yue et al. (2019) Identification of prognostic gene signature associated with microenvironment of lung adenocarcinoma. PeerJ 7:e8128 https://doi.org/10.7717/peerj.8128
Characteristics of the vaginal microbiome in cross-border female sex workers in China: a case-control study
Background Female sex workers (FSWs) are key groups in the transmission of sexual transmitted infections (STI), and vaginal microbiome variations play an important role in transmission. We aimed to explore the characteristics of vaginal microbiome among FSWs. Materials and Methods A total of 24 cross-border FSWs were randomly selected from a cross-sectional survey for female sex workers in southwest China. Thirty-seven female non-sex workers (FNSWs) were randomly selected from the gynecology clinic and health examination center. Vaginal swabs were collected, bacterial DNA extracted and 16S rRNA genes were sequenced. Differences in the vaginal microbiome between both groups were compared using bioinformatics analysis. Results One DNA sample was excluded due to unqualified concentration, therefore 60 samples were sequenced. FSWs had significantly different vaginal microbiota β diversity, but undifferentiated α diversity when compared with non-sex workers. The average relative abundance of Sneathia, Shigella, Neisseria, Chlamydia, Prevotella, Enterococcus and Ureaplasma among FSWs was higher than FNSWs, and relative abundance of Atopobium in FSWs was lower than FNSWs. The Lactobacillus genus was the major genus in both groups. At the species level, Lactobacllus crispatus, Lactobacllus gasseri and Lactobacllus jensenii, in female sex workers, were lower when compared to FNSWs. Conclusion There were distinct differences in vaginal bacteria variety between FSWs and FNSWs. Some disease-related genus were also more abundant in FSWs. Based on these observations, further research is required to identify microbiome communities related to high STI risks and other diseases in these cohorts.
Hong et al. (2019) Characteristics of the vaginal microbiome in cross-border female sex workers in China: a case-control study. PeerJ 7:e8131 https://doi.org/10.7717/peerj.8131
Combined effects of body mass index and unhealthy behaviors on disability in older Japanese adults: the Okayama study
Background Body mass index (BMI) is a significant predictor of functional disability in older adults. However, when evaluated, the association between BMI and incident functional disability, considering behaviors only as covariates or not, may not be appropriate. The primary purpose of the study was to investigate the combined effects of BMI and unhealthy behaviors on the risk of incident functional disability. Methods This was a retrospective cohort study that took place in Okayama City, Japan. Data on BMI and unhealthy behaviors were obtained using the health check-up questionnaire. The certification of Long-Term Care Insurance was used to measure functional disability. Cox proportional hazard models were used; adjusted hazard ratios (HRs) with 95% confidence interval (CI) were calculated for incidence of functional disability across categories of BMI and number of unhealthy behaviors. Results The relationship between BMI and incident functional disability was U-shaped (HR = 1.18, 95% CI [1.11–1.25], among the underweight range; and 1.26 [1.19–1.34] among the obesity range), and its risk was significantly higher within the normal-to-overweight range of BMI values with co-occurring unhealthy behaviors (with normal weight range and one, 1.17 [1.01–1.21]; two, 1.29 [1.18–1.41]; and three or four unhealthy behaviors 1.38 [1.24–1.54]; as well as among overweight range and one, 1.16 [1.05–1.27]; two, 1.26 [1.15–1.38]; and three or four unhealthy behaviors, 1.47 [1.31–1.64]). In each BMI category, the risk of incident functional disability increased with increasing number of unhealthy behaviors (p < 0.05 for linear tread), with the highest risk (1.87 [1.58–2.20]) occurring in combination with at least three unhealthy behaviors with BMI ≥ 27.5, for both sexes (2.20 [1.64–2.92] in men and 1.66 [1.35–2.04] in women). Conclusion It is necessary to consider the combined effects of BMI and behaviors on incident functional disability. Furthermore, interventions targeting multiple behaviors should be considered as such interventions may offer greater benefits than simple interventions.
Liu et al. (2019) Combined effects of body mass index and unhealthy behaviors on disability in older Japanese adults: the Okayama study. PeerJ 7:e8146 https://doi.org/10.7717/peerj.8146