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https://www.readbyqxmd.com/read/29352289/electroacupuncture-at-guanyuan-cv-4-zusanli-st-36-and-baihui-du-20-regulate-the-aging-related-changes-in-gene-expression-profile-of-the-hippocampus-in-sub-acutely-aging-rats
#1
Jianmin Liu, Jing Liu, Guang'an Wang, Guangya Liu, Huanjiao Zhou, Yun Fan, Fengxia Liang, Hua Wang
To investigate the molecular mechanisms of sub-acutely aging and demonstrate the effect of electroacupuncture (EA) at the Guanyuan (CV 4), Zusanli (ST 36) and Baihui (DU 20) acupoint on the sub-acutely aging brain, cDNA microarrays and bioinformatics analyses were carried out. Thirty Sprague-Dawley (SD) male rats were selected and randomly divided into three groups: the control group (C), the sub-acutely aging model group (M) and the electroacupuncture group (M+EA). Sub-acutely aging model rats were obtained by D-galactose s...
2018: PloS One
https://www.readbyqxmd.com/read/29352262/microbial-regulation-of-the-l-cell-transcriptome
#2
Tulika Arora, Rozita Akrami, Ramona Pais, Linda Bergqvist, Bengt R Johansson, Thue W Schwartz, Frank Reimann, Fiona M Gribble, Fredrik Bäckhed
L cells are an important class of enteroendocrine cells secreting hormones such as glucagon like peptide-1 and peptide YY that have several metabolic and physiological effects. The gut is home to trillions of bacteria affecting host physiology, but there has been limited understanding about how the microbiota affects gene expression in L cells. Thus, we rederived the reporter mouse strain, GLU-Venus expressing yellow fluorescent protein under the control of the proglucagon gene, as germ-free (GF). Lpos cells from ileum and colon of GF and conventionally raised (CONV-R) GLU-Venus mice were isolated and subjected to transcriptomic profiling...
January 19, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29351546/accessing-an-expanded-exposure-science-module-at-the-comparative-toxicogenomics-database
#3
Cynthia J Grondin, Allan Peter Davis, Thomas C Wiegers, Jolene A Wiegers, Carolyn J Mattingly
The Comparative Toxicogenomics Database (CTD; http://ctdbase.org) is a free resource that provides manually curated information on chemical, gene, phenotype, and disease relationships to advance understanding of the effect of environmental exposures on human health. Four core content areas are independently curated: chemical-gene interactions, chemical-disease and gene-disease associations, chemical-phenotype interactions, and environmental exposure data (e.g., effects of chemical stressors on humans). Since releasing exposure data in 2015, we have vastly increased our coverage of chemicals and disease/phenotype outcomes; greatly expanded access to exposure content; added search capability by stressors, cohorts, population demographics, and measured outcomes; and created user-specified displays of content...
January 18, 2018: Environmental Health Perspectives
https://www.readbyqxmd.com/read/29351341/labeling-for-big-data-in-radiation-oncology-the-radiation-oncology-structures-ontology
#4
Jean-Emmanuel Bibault, Eric Zapletal, Bastien Rance, Philippe Giraud, Anita Burgun
PURPOSE: Leveraging Electronic Health Records (EHR) and Oncology Information Systems (OIS) has great potential to generate hypotheses for cancer treatment, since they directly provide medical data on a large scale. In order to gather a significant amount of patients with a high level of clinical details, multicenter studies are necessary. A challenge in creating high quality Big Data studies involving several treatment centers is the lack of semantic interoperability between data sources...
2018: PloS One
https://www.readbyqxmd.com/read/29348887/rna-seq-expression-profiling-of-rat-mcao-model-following-reperfusion-orexin-a
#5
Chun-Mei Wang, Yan-You Pan, Ming-Hui Liu, Bao-Hua Cheng, Bo Bai, Jing Chen
Orexin-A is a neuropeptide with potent neuroprotective activity towards cerebral ischemia-reperfusion (I/R) injury, but few studies have attempted to elucidate the mechanism. Herein, we performed global gene expression profiling of the hippocampus following reperfusion with Orexin-A using RNA sequencing (RNA-seq). RNA-seq identified 649 differentially expressed genes (DEGs) in the Orexin-A group compared with saline controls (I/R group), of which 149 were up-regulated and 500 were down-regulated. DEGs were confirmed using qRT-PCR, their molecular functions, biological processes and molecular components were explored using Gene Ontology (GO) analysis and 206 KEGG pathways were associated with Orexin-A treatment...
December 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/29348862/digital-gene-expression-analysis-in-mice-lung-with-coinfection-of-influenza-and-streptococcus-pneumoniae
#6
Jun Luo, Linlin Zhou, Hongren Wang, Zhen Qin, Li Xiang, Jie Zhu, Xiaojun Huang, Yuan Yang, Wanyi Li, Baoning Wang, Mingyuan Li
Influenza A virus (IAV) and Streptococcus pneumoniae (SP) are two major upper respiratory tract pathogens that can also cause infection in polarized bronchial epithelial cells to exacerbate disease in coinfected individuals which may result in significant morbidity. However, the underlying molecular mechanism is poorly understood. Here, we employed BALB/c ByJ mice inflected with SP, IAV, IAV followed by SP (IAV+SP) and PBS (Control) as models to survey the global gene expression using digital gene expression (DGE) profiling...
December 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/29347997/openbiodiv-o-ontology-of-the-openbiodiv-knowledge-management-system
#7
Viktor Senderov, Kiril Simov, Nico Franz, Pavel Stoev, Terry Catapano, Donat Agosti, Guido Sautter, Robert A Morris, Lyubomir Penev
BACKGROUND: The biodiversity domain, and in particular biological taxonomy, is moving in the direction of semantization of its research outputs. The present work introduces OpenBiodiv-O, the ontology that serves as the basis of the OpenBiodiv Knowledge Management System. Our intent is to provide an ontology that fills the gaps between ontologies for biodiversity resources, such as DarwinCore-based ontologies, and semantic publishing ontologies, such as the SPAR Ontologies. We bridge this gap by providing an ontology focusing on biological taxonomy...
January 18, 2018: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/29347969/miro-guidelines-for-minimum-information-for-the-reporting-of-an-ontology
#8
REVIEW
Nicolas Matentzoglu, James Malone, Chris Mungall, Robert Stevens
BACKGROUND: Creation and use of ontologies has become a mainstream activity in many disciplines, in particular, the biomedical domain. Ontology developers often disseminate information about these ontologies in peer-reviewed ontology description reports. There appears to be, however, a high degree of variability in the content of these reports. Often, important details are omitted such that it is difficult to gain a sufficient understanding of the ontology, its content and method of creation...
January 18, 2018: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/29347945/microrna-transcriptome-analysis-of-porcine-vital-organ-responses-to-immunosuppressive-porcine-cytomegalovirus-infection
#9
Xiao Liu, Haoche Wei, Shan Liao, Jianheng Ye, Ling Zhu, Zhiwen Xu
BACKGROUND: Porcine cytomegalovirus (PCMV) is an immunosuppressive virus that mainly inhibits T-lymphocyte and macrophage immune functions; it has significantly damaged the farming industry. Although recent studies have shown that miRNAs play important roles in immune responses, the regulatory mechanisms of miRNAs during immunosuppressive virus infection remain unclear. METHODS: In this study, porcine small-RNA transcriptomes of PCMV-infected and uninfected vital organs were first characterised by high-throughput sequencing...
January 18, 2018: Virology Journal
https://www.readbyqxmd.com/read/29347914/in-depth-proteomic-analysis-of-boar-spermatozoa-through-shotgun-and-gel-based-methods
#10
Jean M Feugang, Shengfa F Liao, Scott T Willard, Peter L Ryan
BACKGROUND: Mature spermatozoa contain numerous epididymal and seminal plasma proteins, which full identification through high-throughput technologies may allow for a better understanding of the sperm biology. Therefore, we conducted a global proteomic analysis of boar spermatozoa through shotgun and gel-based methodologies. RESULTS: The total proteins were extracted from mature spermatozoa and subjecsted to proteome analyses. Functional analyses of gene ontology representations and pathway enrichments were conducted on the shotgun dataset, followed by immunology and gene expression validations...
January 18, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29346705/effect-of-dys-1-mutation-on-gene-expression-profile-in-space-flown-c-elegans
#11
Dan Xu, Ying Gao, Lin Guo, Chenggang Lin, Yeqing Sun
INTRODUCTION: Dystrophin-like dys-1 gene expression increases in the body-wall muscles of Caenorhabditis elegans (C. elegans) after spaceflight. Here, we utilized a dys-1(cx18) mutant to analyze the molecular adaptive responses of C. elegans to spaceflight. METHODS: DNA microarrays were performed to identify differentially expressed genes between wild-type and dys-1 mutant worms after spaceflight. We performed Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses, predicted human diseases and screened out key genes for human muscle diseases with NextBio...
January 18, 2018: Muscle & Nerve
https://www.readbyqxmd.com/read/29345285/the-epitranscriptome-m6a-writer-mettl3-promotes-chemo-and-radioresistance-in-pancreatic-cancer-cells
#12
Kosuke Taketo, Masamitsu Konno, Ayumu Asai, Jun Koseki, Masayasu Toratani, Taroh Satoh, Yuichiro Doki, Masaki Mori, Hideshi Ishii, Kazuhiko Ogawa
N6-methyladenosine (m6A) is the most abundant epitranscriptome modification in mammalian mRNA. Recent years have seen substantial progress in m6A epitranscriptomics, indicating its crucial roles in the initiation and progression of cancer through regulation of RNA stabilities, mRNA splicing, microRNA processing and mRNA translation. However, by what means m6A is dynamically regulated or written by enzymatic components represented by methyltransferase-like 3 (METTL3) and how m6A is significant for each of the numerous genes remain unclear...
February 2018: International Journal of Oncology
https://www.readbyqxmd.com/read/29344651/identification-of-genes-and-pathways-in-the-synovia-of-women-with-osteoarthritis-by-bioinformatics-analysis
#13
Bobin Mi, Guohui Liu, Wu Zhou, Huijuan Lv, Yi Liu, Jing Liu
Osteoarthritis (OA) has a high prevalence in female patients and sex may be a key factor affecting the progression of OA. The aim of the present study was to identify genetic signatures in the synovial membranes of female patients with OA and to elucidate the potential associated molecular mechanisms. The gene expression profiles of the GSE55457 and GSE55584 datasets were obtained from the Gene Expression Omnibus database. Data of two synovial membranes from normal female individuals (GSM1337306 and GSM1337310) and two synovial membranes from female patients affected by OA (GSM1337327 and GSM1337330) were obtained from the dataset GSE55457, and those of three synovial membranes from female patients affected by OA (GSM1339628, GSM1339629 and GSM1339632) were obtained from the dataset GSE55584...
January 15, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29344379/changes-in-contractile-protein-expression-are-linked-to-ventricular-stiffness-in-infants-with-pulmonary-hypertension-or-right-ventricular-hypertrophy-due-to-congenital-heart-disease
#14
Andrew R Bond, Dominga Iacobazzi, Safa Abdul-Ghani, Mohammed Ghorbel, Kate Heesom, Mariangela Wilson, Christopher Gillett, Sarah J George, Massimo Caputo, Saadeh Suleiman, Robert M R Tulloh
Background: The right ventricle (RV) is not designed to sustain high pressure leading to failure. There are no current medications to help RV contraction, so further information is required on adaption of the RV to such hypertension. Methods: The Right Ventricle in Children (RVENCH) study assessed infants with congenital heart disease undergoing cardiac surgery with hypertensive RV. Clinical and echocardiographic data were recorded, and samples of RV were taken from matched infants, analysed for proteomics and compared between pathologies and with clinical and echocardiographic outcome data...
2018: Open Heart
https://www.readbyqxmd.com/read/29344252/itraq-based-quantitative-proteomic-analysis-and-bioinformatics-study-of-proteins-in-retinoblastoma
#15
Yong Cheng, Qingyu Meng, Lvzhen Huang, Xuan Shi, Jing Hou, Xiaoxin Li, Jianhong Liang
The aim of the present study was to analyze proteins in the aqueous humor (AH) of patients' retinoblastoma (RB), and investigate their potential role in RB using the comparative proteomic technique of isobaric tags for relative and absolute quantitation (iTRAQ) coupled with offline two-dimensional liquid chromatography-tandem mass spectrometry. A total of 0.1 ml AH was collected from 10 children with RB (mean age, 3.8 years; range, 2-5 years) and patients with senile cataracts (mean age, 70.4 years; range, 65-79 years), which was used as the control...
December 2017: Oncology Letters
https://www.readbyqxmd.com/read/29344174/expression-profile-of-cytokines-in-gastric-cancer-patients-using-proteomic-antibody-microarray
#16
Xiaoqiang Quan, Yi Ding, Ruo Feng, Xiaoyan Zhu, Qinxian Zhang
Gastric cancer (GC) is often a deadly disease due to the late diagnosis and chemoresistance that characterizes many cases of this disease. The aim of this study was to explore a panel of candidate cytokines as diagnostic and predictive biomarkers for GC. Sixteen tissue samples of GC and adjacent noncancerous mucosa were selected from GC patients (n=8) for antibody microarray analysis. Proteomic chip-based analysis was performed to simultaneously identify 507 cytokines using a cytokine antibody array in the gastric tissues to screen for differential proteins related in cases of GC...
December 2017: Oncology Letters
https://www.readbyqxmd.com/read/29344166/identification-and-functional-analysis-of-risk-related-micrornas-for-the-prognosis-of-patients-with-bladder-urothelial-carcinoma
#17
Ji Gao, Hongyan Li, Lei Liu, Lide Song, Yanting Lv, Yuping Han
The aim of the present study was to investigate risk-related microRNAs (miRs) for bladder urothelial carcinoma (BUC) prognosis. Clinical and microRNA expression data downloaded from the Cancer Genome Atlas were utilized for survival analysis. Risk factor estimation was performed using Cox's proportional regression analysis. A microRNA-regulated target gene network was constructed and presented using Cytoscape. In addition, the Database for Annotation, Visualization and Integrated Discovery was used for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway enrichment, followed by protein-protein interaction (PPI) network analysis...
December 2017: Oncology Letters
https://www.readbyqxmd.com/read/29344147/systematic-analysis-of-the-molecular-mechanism-of-microrna-124-in-hepatoblastoma-cells
#18
Guiming Wang, Hong Liu, Zhigang Wei, Hongyan Jia, Yu Liu, Jiansheng Liu
The present study aimed to identify the molecular mechanisms of microRNA-124 (miRNA-124/miR-124) in hepatoblastoma. The GSE6207 microarray dataset, obtained from the Gene Expression Omnibus database, included samples extracted from HepG2 cells transfected with miR-124 duplex (the experimental group) or negative control (the control group) at 4, 8, 16, 24, 32, 72 and 120 h after transfection. Differentially expressed genes (DEGs) were screened between the two groups. miR-124 activity was inferred based on the expression of its target genes...
December 2017: Oncology Letters
https://www.readbyqxmd.com/read/29344146/integrated-microrna-mrna-analyses-of-distinct-expression-profiles-in-follicular-thyroid-tumors
#19
Jiadong Chi, Xiangqian Zheng, Ming Gao, Jingzhu Zhao, Dapeng Li, Jiansen Li, Li Dong, Xianhui Ruan
MicroRNAs (miRNAs/miRs) are small non-coding RNAs identified in plants, animals and certain viruses; they function in RNA silencing and post-transcriptional regulation of gene expression. miRNAs also serve an important role in the pathogenesis, diagnosis and treatment of tumors. However, few studies have investigated the role of miRNAs in thyroid tumors. In the present study, the expression of miRNA and mRNA was compared between follicular thyroid carcinoma (FTC) and follicular thyroid adenoma (FA) samples, and then miRNA-mRNA regulatory network analysis was performed...
December 2017: Oncology Letters
https://www.readbyqxmd.com/read/29344121/a-five-gene-based-risk-score-with-high-prognostic-value-in-colorectal-cancer
#20
Yida Pan, Hongyang Zhang, Mingming Zhang, Jie Zhu, Jianghong Yu, Bangting Wang, Jigang Qiu, Jun Zhang
Colorectal cancer (CRC) is one of the most frequently occurring malignancies worldwide. The outcomes of patients with similar clinical symptoms or at similar pathological stages remain unpredictable. This inherent clinical diversity is most likely due to the genetic heterogeneity. The present study aimed to create a predicting tool to evaluate patient survival based on genetic profile. Firstly, three Gene Expression Omnibus (GEO) datasets (GSE9348, GSE44076 and GSE44861) were utilized to identify and validate differentially expressed genes (DEGs) in CRC...
December 2017: Oncology Letters
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