title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1233 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Brain structural and functional changes in patients with major depressive disorder: a literature review link: https://peerj.com/articles/8170 last-modified: 2019-11-29 description: 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. creator: Lisong Dai creator: Hongmei Zhou creator: Xiangyang Xu creator: Zhentao Zuo uri: https://doi.org/10.7717/peerj.8170 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Dai et al. title: Stress-induced changes in the expression of antioxidant system genes for rice (Oryza sativa L.) and bread wheat (Triticum aestivum L.) link: https://peerj.com/articles/7791 last-modified: 2019-11-29 description: BackgroundPlant 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.MethodsA 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.ResultsThe 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. creator: Anton Ermakov creator: Aleksandr Bobrovskikh creator: Ulyana Zubairova creator: Dmitrii Konstantinov creator: Alexey Doroshkov uri: https://doi.org/10.7717/peerj.7791 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Ermakov et al. title: Taxonomic assessment of species of the genus Octopus from the northeastern Pacific via morphological, molecular and morphometric analyses link: https://peerj.com/articles/8118 last-modified: 2019-11-29 description: 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. creator: Mariana Díaz-Santana-Iturrios creator: César Augusto Salinas-Zavala creator: Francisco Javier García-Rodríguez creator: Jasmín Granados-Amores uri: https://doi.org/10.7717/peerj.8118 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Díaz-Santana-Iturrios et al. title: Relationship between the Dark Triad and depressive symptoms link: https://peerj.com/articles/8120 last-modified: 2019-11-29 description: 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. creator: Raquel Gómez-Leal creator: Alberto Megías-Robles creator: María José Gutiérrez-Cobo creator: Rosario Cabello creator: Enrique G. Fernández-Abascal creator: Pablo Fernández-Berrocal uri: https://doi.org/10.7717/peerj.8120 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Gómez-Leal et al. title: Identification of prognostic gene signature associated with microenvironment of lung adenocarcinoma link: https://peerj.com/articles/8128 last-modified: 2019-11-29 description: BackgroundLung 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.MethodsThe 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.ResultsA 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. creator: Cheng Yue creator: Hongtao Ma creator: Yubai Zhou uri: https://doi.org/10.7717/peerj.8128 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Yue et al. title: Characteristics of the vaginal microbiome in cross-border female sex workers in China: a case-control study link: https://peerj.com/articles/8131 last-modified: 2019-11-29 description: BackgroundFemale 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 MethodsA 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.ResultsOne 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.ConclusionThere 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. creator: Xiang Hong creator: Shenghao Fang creator: Kaiping Huang creator: Jiechen Yin creator: Jianshuang Chen creator: Yan Xuan creator: Jing Zhu creator: Jun Ma creator: Pengfei Qin creator: Danhong Peng creator: Ning Wang creator: Bei Wang uri: https://doi.org/10.7717/peerj.8131 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Hong et al. title: Combined effects of body mass index and unhealthy behaviors on disability in older Japanese adults: the Okayama study link: https://peerj.com/articles/8146 last-modified: 2019-11-29 description: BackgroundBody 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.MethodsThis 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.ResultsThe 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).ConclusionIt 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. creator: Yangyang Liu creator: Toshiharu Mitsuhashi creator: Michiyo Yamakawa creator: Megumi Sasai creator: Toshihide Tsuda creator: Hiroyuki Doi creator: Jun Hamada uri: https://doi.org/10.7717/peerj.8146 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Liu et al. title: 1H-NMR spectroscopy identifies potential biomarkers in serum metabolomic signatures for early stage esophageal squamous cell carcinoma link: https://peerj.com/articles/8151 last-modified: 2019-11-29 description: BackgroundEsophageal squamous cell carcinoma (ESCC) is one of the most prevalent types of upper gastrointestinal malignancies. Here, we used 1H nuclear magnetic resonance spectroscopy (1H-NMR) to identify potential serum biomarkers in patients with early stage ESCC.MethodsSixty-five serum samples from early stage ESCC patients (n = 25) and healthy controls (n = 40) were analysed using 1H-NMR spectroscopy. We distinguished between different metabolites through principal component analysis, partial least squares-discriminant analysis, and orthogonal partial least squares-discriminant analysis (OPLS-DA) using SIMCA-P+ version 14.0 software. Receiver operating characteristic (ROC) analysis was conducted to verify potential biomarkers.ResultsUsing OPLS-DA, 31 altered serum metabolites were successfully identified between the groups. Based on the area under the ROC curve (AUROC), and the biomarker panel with AUROC of 0.969, six serum metabolites (α-glucose, choline, glutamine, glutamate, valine, and dihydrothymine) were selected as potential biomarkers for early stage ESCC. Dihydrothymine particularly was selected as a new feasible biomarker associated with tumor occurrence.Conclusions1H-NMR spectroscopy may be a useful tumour detection approach in identifying useful metabolic ESCC biomarkers for early diagnosis and in the exploration of the molecular pathogenesis of ESCC. creator: Yan-Yan Liu creator: Zhong-Xian Yang creator: Li-Min Ma creator: Xu-Qing Wen creator: Huan-Lin Ji creator: Ke Li uri: https://doi.org/10.7717/peerj.8151 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Liu et al. title: Life history response of Echinops gmelinii Turcz. to variation in the rainfall pattern in a temperate desert link: https://peerj.com/articles/8159 last-modified: 2019-11-29 description: BackgroundCurrent and future changes in rainfall amount and frequency may particularly impact annual plants in desert ecosystems. The winter annual Echinops gmelinii Turcz. is widely distributed in the desert habitats of northern China and is a dominant pioneer annual plant following sand stabilization in the Tengger Desert. This species plays a vital role in dune stabilization during spring and early summer, when wind erosion is the most severe and frequent. However, seedling emergence and regeneration in sandy soil are mainly determined by rainfall patterns. Therefore, understanding the life history response of this species to rainfall variation is necessary for understanding the change of population dynamics under the future climate change.MethodsA field simulation rainfall pot experiment using rainout shelter was conducted that included five amounts and five frequencies of rainfall based on historical and predicted values to monitor the life history responses of E. gmelinii in a near-natural habitat.ResultsWe found that rainfall amount and frequency significantly affected seedling survival, growth and reproduction. The plant height, biomass, capitula number, seed number, seed mass and reproductive effort, but not the root/shoot ratio, significantly increased with increasing rainfall. Further, these traits exhibited the greatest response to low-frequency and larger rainfall events, especially the optimal rainfall frequency of 10-day intervals. Offspring seed germination showed increasing trends with decreasing rainfall, suggesting that the maternal effects may have occurred.ConclusionsOur study shows that the plasticity in growth and reproduction of E. gmelinii in response to rainfall variations may help it to gain dominance in the harsh and unpredictable desert environment. Furthermore, population development of this winter annual species should be promoted under the likely future scenarios of large rainfall events and increasing cool-season precipitation in temperate desert. creator: Yanli Wang creator: Xinrong Li creator: Lichao Liu creator: Jiecai Zhao creator: Jingyao Sun uri: https://doi.org/10.7717/peerj.8159 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Wang et al. title: Screening and identification of key candidate genes and pathways in myelodysplastic syndrome by bioinformatic analysis link: https://peerj.com/articles/8162 last-modified: 2019-11-29 description: Myelodysplastic syndrome (MDS) is a heterogeneous hematologic malignancy derived from hematopoietic stem cells and the molecular mechanism of MDS remains unclear. This study aimed to elucidate potential markers of diagnosis and prognosis of MDS. The gene expression profiles GSE19429 and GSE58831 were obtained and downloaded from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) in MDS were screened using GEO2R and overlapped DEGs were obtained with Venn Diagrams. Then, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway functional enrichment analyses, protein–protein interaction network establishment and survival analyses were performed. Functional enrichment analysis indicated that these DEGs were significantly enriched in the interferon signaling pathway, immune response, hematopoietic cell lineage and the FOXO signaling pathway. Four hub genes and four significant modules including 25 module genes were obtained via Cytoscape MCODE. Survival analysis showed that the overall survival of MDS patients having BLNK, IRF4, IFITM1, IFIT1, ISG20, IFI44L alterations were worse than that without alterations. In conclusion, the identification of these genes and pathways helps understand the underlying molecular mechanisms of MDS and provides candidate targets for the diagnosis and prognosis of MDS. creator: Ying Le uri: https://doi.org/10.7717/peerj.8162 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Le