title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1231 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Overexpression of VEGF-C and MMP-9 predicts poor prognosis in Kazakh patients with esophageal squamous cell carcinoma link: https://peerj.com/articles/8182 last-modified: 2019-12-03 description: Vascular endothelial growth factor (VEGF) and Matrix metalloproteinases (MMPs) are believed to participate in infiltration of tumors. High mortality of esophageal squamous cell carcinoma (ESCC) related to its primary infiltration; however, it is not clear whether the expression of VEGF and MMPs is involved in this process. Screening of The Cancer Genome Atlas (TCGA) database showed that among the VEGF family and MMP9, VEGF-A, VEGF-C, and MMP-9 mRNA were overexpression in ESCC. This result was verified using the Oncomine database and in Kazakh patients with ESCC. Overexpression of VEGF-C and MMP-9 and positive association with advanced esophageal cancer and invading ESCC cells (Gene Expression Omnibus (GEO): GSE21293). Immunohistochemical staining revealed that VEGF-C and MMP-9 were overexpressed in Kazakh ESCCs. VEGF-C expression was related to invasive depth, tumor-node-metastasis (TNM) staging, lymphatic, and lymph node metastasis of ESCC. The linear association between them was further confirmed in TCGA database and the specimens from Kazakh patients with ESCC. Patients with both proteins expression had tumors with greater aggressiveness, suffered from poor prognosis compared with patients who did not express either protein or expressed protein alone. Both proteins expression predicted high invasiveness of ESCC, which is related to worse prognosis of Kazakh ESCCs. creator: Jiangfen Li creator: Yufang Xie creator: Xueli Wang creator: Chenhao Jiang creator: Xin Yuan creator: Anzhi Zhang creator: Chunxia Liu creator: Lijuan Pang creator: Feng Li creator: Jianming Hu uri: https://doi.org/10.7717/peerj.8182 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Li et al. title: Comparative genomic analysis of the PAL genes in five Rosaceae species and functional identification of Chinese white pear link: https://peerj.com/articles/8064 last-modified: 2019-12-02 description: Phenylalanine ammonia lyase (PAL) plays an important role in the biosynthesis of secondary metabolites regulating plant growth response. To date, the evolutionary history of the PAL family in Rosaceae plants remains unclear. In this study, we identified 16 PAL homologous genes in five Rosaceae plants (Pyrus bretschneideri, Fragaria vesca, Prunus mume, Prunus persica, and Malus × domestica). We classified these PALs into three categories based on phylogenetic analysis, and all PALs were distributed on 13 chromosomes. We tracked gene duplication events and performed sliding window analysis. These results revealed the evolution of PALs in five Rosaceae plants. We predicted the promoter of the PbPALs by PLANT CARE online software, and found that the promoter region of both PbPAL1 and PbPAL3 have at least one AC element. The results of qRT-PCR analysis found that PbPAL1 and PbPAL2 were highly expressed in the stems and roots, while expression level of PbPAL3 was relatively low in different tissues. The expression of PbPAL1 and PbPAL2 increased firstly and then decreased at different developmental periods of pear fruit. Among them, the expression of PbPAL1 reached the highest level 55 days after flowering. Three PbPALs were induced by abiotic stress to varying degrees. We transfected PbPAL1 and PbPAL2 into Arabidopsis thaliana, which resulted in an increase in lignin content and thickening of the cell walls of intervascular fibres and xylem cells. In summary, this research laid a foundation for better understanding the molecular evolution of PALs in five Rosaceae plants. Furthermore, the present study revealed the role of PbPALs in lignin synthesis, and provided basic data for regulating lignin synthesis and stone cells development in pear plants. creator: Guohui Li creator: Han Wang creator: Xi Cheng creator: Xueqiang Su creator: Yu Zhao creator: Taoshan Jiang creator: Qin Jin creator: Yi Lin creator: Yongping Cai uri: https://doi.org/10.7717/peerj.8064 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Li et al. title: Impact of habitat loss on the diversity and structure of ecological networks between oxyurid nematodes and spur-thighed tortoises (Testudo graeca L.) link: https://peerj.com/articles/8076 last-modified: 2019-12-02 description: Habitat loss and fragmentation are recognized as affecting the nature of biotic interactions, although we still know little about such changes for reptilian herbivores and their hindgut nematodes, in which endosymbiont interactions could range from mutualistic to commensal and parasitic. We investigated the potential cost and benefit of endosymbiont interactions between the spur-thighed tortoise (Testudo graeca L.) and adult oxyurid nematodes (Pharyngodonidae order Oxyurida) in scrublands of southern Spain. For this, we assessed the association between richness and abundance of oxyurid species with tortoises’ growth rates and body traits (weight and carapace length) across levels of habitat loss (low, intermediate and high). Furthermore, by using an intrapopulation ecological network approach, we evaluated the structure and diversity of tortoise–oxyurid interactions by focusing on oxyurid species infesting individual tortoises with different body traits and growth rates across habitats. Overall, tortoise body traits were not related to oxyurid infestation across habitats. Oxyurid richness and abundance however, showed contrasting relationships with growth rates across levels of habitat loss. At low habitat loss, oxyurid infestation was positively associated with growth rates (suggesting a mutualistic oxyurid–tortoise relationship), but the association became negative at high habitat loss (suggesting a parasitic relationship). Furthermore, no relationship was observed when habitat loss was intermediate (suggesting a commensal relationship). The network analysis showed that the oxyurid community was not randomly assembled but significantly nested, revealing a structured pattern for all levels of habitat loss. The diversity of interactions was lowest at low habitat loss. The intermediate level, however, showed the greatest specialization, which indicates that individuals were infested by fewer oxyurids in this landscape, whereas at high habitat loss individuals were the most generalized hosts. Related to the latter, connectance was greatest at high habitat loss, reflecting a more uniform spread of interactions among oxyurid species. At an individual level, heavier and larger tortoises tended to show a greater number of oxyurid species interactions. We conclude that there is an association between habitat loss and the tortoise–oxyurid interaction. Although we cannot infer causality in their association, we hypothesize that such oxyurids could have negative, neutral and positive consequences for tortoise growth rates. Ecological network analysis can help in the understanding of the nature of such changes in tortoise–oxyurid interactions by showing how generalized or specialized such interactions are under different environmental conditions and how vulnerable endosymbiont interactions might be to further habitat loss. creator: Julieta Benítez-Malvido creator: Andrés Giménez creator: Eva Graciá creator: Roberto Carlos Rodríguez-Caro creator: Rocío Ruiz De Ybáñez creator: Héctor Hugo Siliceo-Cantero creator: Anna Traveset uri: https://doi.org/10.7717/peerj.8076 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Benítez-Malvido et al. title: Co-expression analysis and ceRNA network reveal eight novel potential lncRNA biomarkers in hepatocellular carcinoma link: https://peerj.com/articles/8101 last-modified: 2019-12-02 description: BackgroundHepatocellular carcinoma (HCC) is the most common primary liver cancer in the world, with a high degree of malignancy and recurrence. The influence of the ceRNA network in tumor on the biological function of liver cancer is very important, It has been reported that many lncRNA play a key role in liver cancer development. In our study, integrated data analysis revealed potential eight novel lncRNA biomarkers in hepatocellular carcinoma.MethodsTranscriptome data and clinical data were downloaded from the The Cancer Genome Atlas (TCGA) data portal. Weighted gene co-expression network analysis was performed to identify the expression pattern of genes in liver cancer. Then, the ceRNA network was constructed using transcriptome data.ResultsThe integrated analysis of miRNA and RNAseq in the database show eight novel lncRNAs that may be involved in important biological pathways, including TNM and disease development in liver cancer. We performed function enrichment analysis of mRNAs affected by these lncRNAs.ConclusionsBy identifying the ceRNA network and the lncRNAs that affect liver cancer, we showed that eight novel lncRNAs play an important role in the development and progress of liver cancer. creator: Ren-chao Zou creator: Zhi-tian Shi creator: Shu-feng Xiao creator: Yang Ke creator: Hao-ran Tang creator: Tian-gen Wu creator: Zhi-tang Guo creator: Fan Ni creator: Sanqi An creator: Lin Wang uri: https://doi.org/10.7717/peerj.8101 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zou et al. title: The impact of storage conditions on human stool 16S rRNA microbiome composition and diversity link: https://peerj.com/articles/8133 last-modified: 2019-12-02 description: BackgroundMultiple 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.MethodsInner 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.ResultsChild 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.ConclusionsStool collected in a fieldwork setting for comparative microbiome analyses should ideally be stored as consistently as possible using the same preservation method throughout. creator: Lauren V. Carruthers creator: Arinaitwe Moses creator: Moses Adriko creator: Christina L. Faust creator: Edridah M. Tukahebwa creator: Lindsay J. Hall creator: Lisa C. Ranford-Cartwright creator: Poppy H.L. Lamberton uri: https://doi.org/10.7717/peerj.8133 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Carruthers et al. title: Propofol inhibits stromatoxin-1-sensitive voltage-dependent K+ channels in pancreatic β-cells and enhances insulin secretion link: https://peerj.com/articles/8157 last-modified: 2019-12-02 description: BackgroundProper 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.MethodsThe 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.ResultsWe 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.ConclusionsOur 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. creator: Munenori Kusunoki creator: Mikio Hayashi creator: Tomohiro Shoji creator: Takeo Uba creator: Hiromasa Tanaka creator: Chisato Sumi creator: Yoshiyuki Matsuo creator: Kiichi Hirota uri: https://doi.org/10.7717/peerj.8157 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Kusunoki et al. title: Global transcriptome analysis of different stages of preimplantation embryo development in river buffalo link: https://peerj.com/articles/8185 last-modified: 2019-12-02 description: BackgroundWater 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).MethodsWe 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.ResultsA 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. creator: Chun-Ying Pang creator: Ming-Zhou Bai creator: Chi Zhang creator: Junhui Chen creator: Xing-Rong Lu creator: Ting-Xian Deng creator: Xiao-Ya Ma creator: An-Qin Duan creator: Sha-sha Liang creator: Yun-Qi Huang creator: Zhihui Xiu creator: Xian-Wei Liang uri: https://doi.org/10.7717/peerj.8185 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Pang et al. 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.