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https://www.readbyqxmd.com/read/29025019/differing-molecular-response-of-young-and-advanced-maternal-age-human-oocytes-to-ivm
#1
J M Reyes, E Silva, J L Chitwood, W B Schoolcraft, R L Krisher, P J Ross
STUDY QUESTION: What effect does maternal age have on the human oocyte's molecular response to in vitro oocyte maturation? SUMMARY ANSWER: Although polyadenylated transcript abundance is similar between young and advanced maternal age (AMA) germinal vesicle (GV) oocytes, metaphase II (MII) oocytes exhibit a divergent transcriptome resulting from a differential response to in vitro oocyte maturation. WHAT IS KNOWN ALREADY: Microarray studies considering maternal age or maturation stage have shown that either of these factors will affect oocyte polyadenylated transcript abundance in human oocytes...
September 15, 2017: Human Reproduction
https://www.readbyqxmd.com/read/28987343/comparison-of-gene-co-expression-networks-in-pseudomonas-aeruginosa-and-staphylococcus-aureus-reveals-conservation-in-some-aspects-of-virulence
#2
Nazanin Hosseinkhan, Zaynab Mousavian, Ali Masoudi-Nejad
Pseudomonas aeruginosa and Staphylococcus aureus are two evolutionary distant bacterial species that are frequently isolated from persistent infections such as chronic infectious wounds and severe lung infections in cystic fibrosis patients. To the best of our knowledge no comprehensive genome scale co-expression study has been already conducted on these two species and in most cases only the expression of very few genes has been the subject of investigation. In this study, in order to investigate the level of expressional conservation between these two species, using heterogeneous gene expression datasets the weighted gene co-expression network analysis (WGCNA) approach was applied to study both single and cross species genome scale co-expression patterns of these two species...
October 4, 2017: Gene
https://www.readbyqxmd.com/read/28978801/metabolic-alterations-in-multiple-sclerosis-and-the-impact-of-vitamin-d-supplementation
#3
Pavan Bhargava, Kathryn C Fitzgerald, Peter A Calabresi, Ellen M Mowry
BACKGROUND: Our goal was to identify changes in the metabolome in multiple sclerosis (MS) and how vitamin D supplementation alters metabolic profiles in MS patients and healthy controls. METHODS: We applied global untargeted metabolomics to plasma from a cross-sectional cohort of age- and sex-matched MS patients and controls and a second longitudinal cohort of MS patients and healthy controls who received 5,000 IU cholecalciferol daily for 90 days. We applied partial least squares discriminant analysis, weighted correlation network analysis (WGCNA), and pathway analysis to the metabolomics data...
October 5, 2017: JCI Insight
https://www.readbyqxmd.com/read/28970079/human-kidney-tubule-specific-gene-expression-based-dissection-of-chronic-kidney-disease-traits
#4
Pazit Beckerman, Chengxiang Qiu, Jihwan Park, Nora Ledo, Yi-An Ko, Ae-Seo Deok Park, Sang-Youb Han, Peter Choi, Matthew Palmer, Katalin Susztak
Chronic kidney disease (CKD) has diverse phenotypic manifestations including structural (such as fibrosis) and functional (such as glomerular filtration rate and albuminuria) alterations. Gene expression profiling has recently gained popularity as an important new tool for precision medicine approaches. Here we used unbiased and directed approaches to understand how gene expression captures different CKD manifestations in patients with diabetic and hypertensive CKD. Transcriptome data from ninety-five microdissected human kidney samples with a range of demographics, functional and structural changes were used for the primary analysis...
September 18, 2017: EBioMedicine
https://www.readbyqxmd.com/read/28958131/global-transcriptional-responses-of-denitrifying-bacteria-to-functionalized-single-walled-carbon-nanotubes-revealed-by-weighted-gene-coexpression-network-analysis
#5
Xiong Zheng, Yinglong Su, Yinguang Chen, Haining Huang, Qiuting Shen
Functionalized single-walled carbon nanotubes (f-SWNTs) are widely used in many fields due to the unique structure and the excellent properties. Although these nanomaterials have been reported to enable to cause negative effects on denitrifying bacteria once they enter the environment, the toxic behaviors and regulatory mechanisms of f-SWNTs to denitrification remain unclear. In this study, the denitrification performance of a model denitrifier exposed to pristine and functionalized SWNTs was investigated, and the global transcriptional responses were comprehensively explored by RNA-seq and weighted gene-coexpression network analysis (WGCNA)...
September 24, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28944917/application-of-a-co%C3%A2-expression-network-for-the-analysis-of-aggressive-and-non%C3%A2-aggressive-breast-cancer-cell-lines-to-predict-the-clinical-outcome-of-patients
#6
Ling Guo, Kun Zhang, Zhitong Bing
Breast cancer metastasis is a demanding problem in clinical treatment of patients with breast cancer. It is necessary to examine the mechanisms of metastasis for developing therapies. Classification of the aggressiveness of breast cancer is an important issue in biological study and for clinical decisions. Although aggressive and non‑aggressive breast cancer cells can be easily distinguished among different cell lines, it is very difficult to distinguish in clinical practice. The aim of the current study was to use the gene expression analysis from breast cancer cell lines to predict clinical outcomes of patients with breast cancer...
September 25, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28930970/screening-of-critical-genes-and-micrornas-in-blood-samples-of-patients-with-ruptured-intracranial-aneurysms-by-bioinformatic-analysis-of-gene-expression-data
#7
Lijuan Bo, Bo Wei, Zhanfeng Wang, Daliang Kong, Zheng Gao, Zhuang Miao
BACKGROUND This study aimed to identify more potential genes and miRNAs associated with the pathogenesis of intracranial aneurysms (IAs). MATERIAL AND METHODS The dataset of GSE36791 (accession number) was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were screened for in the blood samples from patients with ruptured IAs and controls, followed by functional and pathway enrichment analyses. In addition, gene co-expression network was constructed and significant modules were extracted from the network by WGCNA R package...
September 20, 2017: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/28924976/spontaneous-generation-of-a-novel-foetal-human-retinal-pigment-epithelium-rpe-cell-line-available-for-investigation-on-phagocytosis-and-morphogenesis
#8
Zhihua Shao, Haiyun Wang, Xuejian Zhou, Baosen Guo, Xuehu Gao, Zengrong Xiao, Meng Liu, Jihong Sha, Chunlian Jiang, Yuping Luo, Zhixue Liu, Siguang Li
OBJECTIVES: Primary retinal pigment epithelium (RPE) cells have a limited capacity to re-establish epithelial morphology and to maintain native RPE function in vitro, and all commercially available RPE cell lines have drawbacks of morphology or function; therefore, the establishment of new RPE cell lines with typical characteristics of RPE would be helpful in further understanding of their physiological and pathological mechanisms. Here, we firstly report a new spontaneously generated RPE line, fhRPE-13A, from a 13-week aborted foetus...
September 18, 2017: Cell Proliferation
https://www.readbyqxmd.com/read/28912681/divergence-in-morris-water-maze-based-cognitive-performance-under-chronic-stress-is-associated-with-the-hippocampal-whole-transcriptomic-modification-in-mice
#9
Seung H Jung, Milene L Brownlow, Matteo Pellegrini, Ryan Jankord
Individual susceptibility determines the magnitude of stress effects on cognitive function. The hippocampus, a brain region of memory consolidation, is vulnerable to stressful environments, and the impact of stress on hippocampus may determine individual variability in cognitive performance. Therefore, the purpose of this study was to define the relationship between the divergence in spatial memory performance under chronically unpredictable stress and an associated transcriptomic alternation in hippocampus, the brain region of spatial memory consolidation...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28903352/analysis-of-bos-taurus-and-sus-scrofa-x-and-y-chromosome-transcriptome-highlights-reproductive-driver-genes
#10
Faheem Ahmed Khan, Hui Liu, Hao Zhou, Kai Wang, Muhammad Tahir Ul Qamar, Nuruliarizki Shinta Pandupuspitasari, Zhang Shujun
The biology of sperm, its capability of fertilizing an egg and its role in sex ratio are the major biological questions in reproductive biology. To answer these question we integrated X and Y chromosome transcriptome across different species: Bos taurus and Sus scrofa and identified reproductive driver genes based on Weighted Gene Co-Expression Network Analysis (WGCNA) algorithm. Our strategy resulted in 11007 and 10445 unique genes consisting of 9 and 11 reproductive modules in Bos taurus and Sus scrofa, respectively...
August 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28901407/colon-cancer-recurrence%C3%A2-associated-genes-revealed-by-wgcna-co%C3%A2-expression-network-analysis
#11
Xiaofeng Zhai, Qingfeng Xue, Qun Liu, Yuyu Guo, Zhe Chen
The present study aimed to identify the recurrence‑associated genes in colon cancer, which may provide theoretical evidence for the development of novel methods to prevent tumor recurrence. Colon cancer and matched normal samples microarray data (E‑GEOD‑39582) were downloaded from ArrayExpress. Genes with significant variation were identified, followed by the screening of differentially expressed genes (DEGs). Subsequently, the co‑expression network of DEGs was constructed using the weighted correlation network analysis (WGCNA) method, which was verified using the validation dataset...
August 31, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28886704/differentiated-transcriptional-signatures-in-the-maize-landraces-of-chiapas-mexico
#12
Matthew A Kost, Hugo R Perales, Saranga Wijeratne, Asela J Wijeratne, Eric Stockinger, Kristin L Mercer
BACKGROUND: Landrace farmers are the keepers of crops locally adapted to the environments where they are cultivated. Patterns of diversity across the genome can provide signals of past evolution in the face of abiotic and biotic change. Understanding this rich genetic resource is imperative especially since diversity can provide agricultural security as climate continues to shift. RESULTS: Here we employ RNA sequencing (RNA-seq) to understand the role that conditions that vary across a landscape may have played in shaping genetic diversity in the maize landraces of Chiapas, Mexico...
September 8, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28881601/identification-of-a-rna-seq-based-prognostic-signature-with-five-lncrnas-for-lung-squamous-cell-carcinoma
#13
Rui-Xue Tang, Wen-Jie Chen, Rong-Quan He, Jiang-Hui Zeng, Liang Liang, Shi-Kang Li, Jie Ma, Dian-Zhong Luo, Gang Chen
Long non-coding RNAs (lncRNAs) expression profile signature for survival assessment in lung squamous cell carcinoma (LUSC) are largely inconsistent due to distinct detecting approaches and small sample size. Systematic and integrative investigation of RNA-Seq based data from The Cancer Genome Atlas (TCGA) herein was performed to determine candidate lncRNAs for prognosis evaluation of LUSC. A total of 60483 genes, including 7589 lncRNAs were assessed in a cohort including 478 LUSC cases with follow-up data. Firstly, 4225 differentially expressed lncRNAs were obtained via R packages...
August 1, 2017: Oncotarget
https://www.readbyqxmd.com/read/28872670/tcr-pmhc-encounter-differentially-regulates-transcriptomes-of-tissue-resident-cd8-t%C3%A2-cells
#14
Akihiro Yoshizawa, Kevin Bi, Derin B Keskin, Guanglan Zhang, Bruce Reinhold, Ellis L Reinherz
To investigate the role of TCR-pMHC interaction in regulating lung CD8 tissue-resident T cell (TR ) differentiation, polyclonal responses were compared against NP366-374 /D(b) and PA224-233 /D(b) , two immunodominant epitopes that arise during influenza A infection in mice. Memory niches distinct from iBALTs develop within the lamina propria, supporting CD103(+) and CD103(-) CD8 TR generation and intraepithelial translocation. Gene set enrichment analysis (GSEA) and weighted gene co-expression network analysis (WGCNA) identify dominant TCR, adherens junction, RIG-I-like and NOD-like pattern recognition receptor as well as TGF-β signaling pathways and memory signatures among PA224-233 /D(b) T cells consistent with T resident memory (TRM ) status...
September 5, 2017: European Journal of Immunology
https://www.readbyqxmd.com/read/28857241/coexpression-analysis-reveals-key-gene-modules-and-pathway-of-human-coronary-heart-disease
#15
Yu Tang, Zun-Ping Ke, Yi-Gen Peng, Ping-Tai Cai
Coronary heart disease is a kind of disease which causes great injury to people world-widely. Although gene expression analyses had been performed previously, to our best knowledge, systemic co-expression analysis for this disease is still lacking to date. Microarray data of coronary heart disease was downloaded from NCBI with the accession number of GSE20681. Co-expression modules were constructed by WGCNA. Besides, the connectivity degree of eigengenes was analyzed. Furthermore, GO and KEGG enrichment analysis was performed on these eigengenes in these constructed modules...
August 31, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28851441/parkinson-s-disease-is-associated-with-dna-methylation-levels-in-human-blood-and-saliva
#16
Yu-Hsuan Chuang, Kimberly C Paul, Jeff M Bronstein, Yvette Bordelon, Steve Horvath, Beate Ritz
BACKGROUND: Several articles suggest that DNA methylation levels in blood relate to Parkinson's disease (PD) but there is a need for a large-scale study that involves suitable population based controls. The purposes of the study were: (1) to study whether PD status is associated with DNA methylation levels in blood/saliva; (2) to study whether observed associations relate to blood cell types; and (3) to characterize genome-wide significant markers ("CpGs") and clusters of CpGs (co-methylation modules) in terms of biological pathways...
August 30, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28819298/transcriptome-based-network-analysis-reveals-renal-cell-type-specific-dysregulation-of-hypoxia-associated-transcripts
#17
Natallia Shved, Gregor Warsow, Felix Eichinger, David Hoogewijs, Simone Brandt, Peter Wild, Matthias Kretzler, Clemens D Cohen, Maja T Lindenmeyer
Accumulating evidence suggests that dysregulation of hypoxia-regulated transcriptional mechanisms is involved in development of chronic kidney diseases (CKD). However, it remains unclear how hypoxia-induced transcription factors (HIFs) and subsequent biological processes contribute to CKD development and progression. In our study, genome-wide expression profiles of more than 200 renal biopsies from patients with different CKD stages revealed significant correlation of HIF-target genes with eGFR in glomeruli and tubulointerstitium...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28799567/identification-of-breast-cancer-mechanism-based-on-weighted-gene-coexpression-network-analysis
#18
X Guo, H Xiao, S Guo, L Dong, J Chen
Our gene expression-profiling analysis aimed to explain the mechanism of breast cancer development by identifying key pathways and constructing networks of related transcription factors (TFs) and microRNAs (miRNAs) in breast cancer tissues. Gene expression profiles of normal and breast cancer tissues were downloaded to identify differentially expressed genes (DEGs). Coexpression modules were explored using weighted gene coexpression network analysis (WGCNA). Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were performed to discover the enriched functionally associated gene groups and define pathways in breast cancer, respectively...
August 2017: Cancer Gene Therapy
https://www.readbyqxmd.com/read/28798764/root-transcriptomic-analysis-revealing-the-importance-of-energy-metabolism-to-the-development-of-deep-roots-in-rice-oryza-sativa-l
#19
Qiaojun Lou, Liang Chen, Hanwei Mei, Kai Xu, Haibin Wei, Fangjun Feng, Tiemei Li, Xiaomeng Pang, Caiping Shi, Lijun Luo, Yang Zhong
Drought is the most serious abiotic stress limiting rice production, and deep root is the key contributor to drought avoidance. However, the genetic mechanism regulating the development of deep roots is largely unknown. In this study, the transcriptomes of 74 root samples from 37 rice varieties, representing the extreme genotypes of shallow or deep rooting, were surveyed by RNA-seq. The 13,242 differentially expressed genes (DEGs) between deep rooting and shallow rooting varieties (H vs. L) were enriched in the pathway of genetic information processing and metabolism, while the 1,052 DEGs between the deep roots and shallow roots from each of the plants (D vs...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28782835/identification-and-functional-analysis-of-a-potential-key-lncrna-involved-in-fat-loss-of-cancer-cachexia
#20
Huiquan Liu, Ting Zhou, Bangyan Wang, Lu Li, Dawei Ye, Shiying Yu
Cancer cachexia is a devastating, multifactorial, and irreversible syndrome characterized by skeletal muscle reduction with or without fat loss. Although much attention has been focused on muscle wasting, fat loss may occur earlier and accelerate muscle wasting in cachexia. The cause of 20% of cancer related death makes it urgent to discover molecular mechanisms behind cancer cachexia. Here we applied weighted gene co-expression network analysis (WGCNA) to identify cachexia related gene modules using differentially expressed 3289 genes and 59 long non-coding RNAs based on microarray data of cachectic and non-cachectic subcutaneous adipose tissue...
August 7, 2017: Journal of Cellular Biochemistry
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