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https://www.readbyqxmd.com/read/28802167/induction-of-senescence-in-cancer-cells-by-5-aza-2-deoxycytidine-bioinformatics-and-experimental-insights-to-its-targets
#1
Jayarani F Putri, Nashi Widodo, Kazuichi Sakamoto, Sunil C Kaul, Renu Wadhwa
5'-Aza-2'-deoxycytidine (5-Aza-dC) is a demethylating drug that causes genome-wide hypomethylation resulting in the expression of several tumor suppressor genes causing growth arrest of cancer cells. Cancer is well established as a multifactorial disease and requires multi-module therapeutics. Search for new drugs and their approval by FDA takes a long time. Keeping this in view, research on new functions of FDA-approved anticancer drugs is desired to expand the list of multi-module functioning drugs for cancer therapy...
August 2, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28797096/prediction-of-n-linked-glycosylation-sites-using-position-relative-features-and-statistical-moments
#2
Muhammad Aizaz Akmal, Nouman Rasool, Yaser Daanial Khan
Glycosylation is one of the most complex post translation modification in eukaryotic cells. Almost 50% of the human proteome is glycosylated as glycosylation plays a vital role in various biological functions such as antigen's recognition, cell-cell communication, expression of genes and protein folding. It is a significant challenge to identify glycosylation sites in protein sequences as experimental methods are time taking and expensive. A reliable computational method is desirable for the identification of glycosylation sites...
2017: PloS One
https://www.readbyqxmd.com/read/28796060/candidate-genes-investigation-for-severe-nonalcoholic-fatty-liver-disease-based-on-bioinformatics-analysis
#3
Shan Qi, Changhong Wang, Chunfu Li, Pu Wang, Minghui Liu
BACKGROUND: Nonalcoholic fatty liver disease (NAFLD) is the most common chronic liver condition worldwide. However, its etiology and fundamental pathophysiology for the disease process are poorly understood. In this study, we thus used bioinformatics to identify candidate genes potentially causative of severe NAFLD. METHODS: Gene expression profile data GSE49541 were downloaded from the Gene Expression Omnibus database. Tissues samples from 32 severe and 40 mild NAFLD patients were evaluated to identify differentially expressed genes (DEGs) between the 2 groups, followed by analyses of Gene Ontology (GO) functions and Kyoto Encyclopedia of Genes and Genomes pathways...
August 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28796037/functional-prediction-of-mir-3144-5p-in-human-cardiac-myocytes-based-on-transcriptome-sequencing-and-bioinformatics
#4
Lei Ruan, Yi Yang, Yi Huang, Ling Ding, Cuntai Zhang, Xiaofen Wu
BACKGROUND: RAN guanine nucleotide release factor (RANGRF) encoding protein MOG1 plays an important role in cardiac arrhythmia, so we intended to investigate the regulatory miRNA of RANGRF and explore its potential regulatory mechanism in arrhythmogenesis. METHODS: Based on bioinformatic analysis, miR-3144-5p was predicted to be a regulatory miRNA of RANGRF, which were then validated through a dual-luciferase reporter plasmid assay. Subsequently, the expression level of miR-3144-5p in human cardiac myocytes (HCMs) was detected, followed by cell transfection with miR-3144-5p mimics...
August 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28795686/hdl-and-atherosclerotic-cardiovascular-disease-genetic-insights-into-complex-biology
#5
REVIEW
Robert S Rosenson, H Bryan Brewer, Philip J Barter, Johan L M Björkegren, M John Chapman, Daniel Gaudet, Daniel Seung Kim, Eric Niesor, Kerry-Anne Rye, Frank M Sacks, Jean-Claude Tardif, Robert A Hegele
Plasma levels of HDL cholesterol (HDL-C) predict the risk of cardiovascular disease at the epidemiological level, but a direct causal role for HDL in cardiovascular disease remains controversial. Studies in animal models and humans with rare monogenic disorders link only particular HDL-associated mechanisms with causality, including those mechanisms related to particle functionality rather than cholesterol content. Mendelian randomization studies indicate that most genetic variants that affect a range of pathways that increase plasma HDL-C levels are not usually associated with reduced risk of cardiovascular disease, with some exceptions, such as cholesteryl ester transfer protein variants...
August 10, 2017: Nature Reviews. Cardiology
https://www.readbyqxmd.com/read/28794466/a-family-of-archaea-like-carboxylesterases-preferentially-expressed-in-the-symbiotic-phase-of-the-mychorrizal-fungus-tuber-melanosporum
#6
Davide Cavazzini, Guido Grossi, Elisabetta Levati, Francesca Vallese, Barbara Montanini, Angelo Bolchi, Giuseppe Zanotti, Simone Ottonello
An increasing number of esterases is being revealed by (meta) genomic sequencing projects, but few of them are functionally/structurally characterized, especially enzymes of fungal origin. Starting from a three-member gene family of secreted putative "lipases/esterases" preferentially expressed in the symbiotic phase of the mycorrhizal fungus Tuber melanosporum ("black truffle"), we show here that these enzymes (TmelEST1-3) are dimeric, heat-resistant carboxylesterases capable of hydrolyzing various short/medium chain p-nitrophenyl esters...
August 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28793249/network-based-genomic-analysis-of-human-oligodendrocyte-progenitor-differentiation
#7
Suyog U Pol, Jessie J Polanco, Richard A Seidman, Melanie A O'Bara, Hani J Shayya, Karen C Dietz, Fraser J Sim
Impaired human oligodendrocyte progenitor cell (hOPC) differentiation likely contributes to failed remyelination in multiple sclerosis. The characterization of molecular pathways that regulate hOPC differentiation will provide means to induce remyelination. In this study, we determined the gene expression profile of PDGFαR(+) hOPCs during initial oligodendrocyte commitment. Weighted gene coexpression network analysis was used to define progenitor and differentiation-specific gene expression modules and functionally important hub genes...
August 8, 2017: Stem Cell Reports
https://www.readbyqxmd.com/read/28790897/regional-specific-evidence-for-memory-load-dependent-activity-in-the-dorsal-subiculum-and-the-lateral-entorhinal-cortex
#8
Shih-Pi Ku, Nozomu H Nakamura, Nicolas Maingret, Liv Mahnke, Motoharu Yoshida, Magdalena M Sauvage
The subiculum and the lateral entorhinal cortex (LEC) are the main output areas of the hippocampus which contribute to spatial and non-spatial memory. The proximal part of the subiculum (bordering CA1) receives heavy projections from the perirhinal cortex and the distal part of CA1 (bordering the subiculum), both known for their ties to object recognition memory. However, the extent to which the proximal subiculum contributes to non-spatial memory is still unclear. Comparatively, the involvement of the LEC in non-spatial information processing is quite well known...
2017: Frontiers in Systems Neuroscience
https://www.readbyqxmd.com/read/28789639/cipher-a-flexible-and-extensive-workflow-platform-for-integrative-next-generation-sequencing-data-analysis-and-genomic-regulatory-element-prediction
#9
Carlos Guzman, Iván D'Orso
BACKGROUND: Next-generation sequencing (NGS) approaches are commonly used to identify key regulatory networks that drive transcriptional programs. Although these technologies are frequently used in biological studies, NGS data analysis remains a challenging, time-consuming, and often irreproducible process. Therefore, there is a need for a comprehensive and flexible workflow platform that can accelerate data processing and analysis so more time can be spent on functional studies. RESULTS: We have developed an integrative, stand-alone workflow platform, named CIPHER, for the systematic analysis of several commonly used NGS datasets including ChIP-seq, RNA-seq, MNase-seq, DNase-seq, GRO-seq, and ATAC-seq data...
August 8, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28782835/identification-and-functional-analysis-of-a-potential-key-lncrna-involved-in-fat-loss-of-cancer-cachexia
#10
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
https://www.readbyqxmd.com/read/28778080/using-molecular-functional-networks-to-manifest-connections-between-obesity-and-obesity-related-diseases
#11
Jialiang Yang, Jing Qiu, Kejing Wang, Lijuan Zhu, Jingjing Fan, Deyin Zheng, Xiaodi Meng, Jiasheng Yang, Lihong Peng, Yu Fu, Dahan Zhang, Shouneng Peng, Haiyun Huang, Yi Zhang
Obesity is a primary risk factor for many diseases such as certain cancers. In this study, we have developed three algorithms including a random-walk based method OBNet, a shortest-path based method OBsp and a direct-overlap method OBoverlap, to reveal obesity-disease connections at protein-interaction subnetworks corresponding to thousands of biological functions and pathways. Through literature mining, we also curated an obesity-associated disease list, by which we compared the methods. As a result, OBNet outperforms other two methods...
July 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28775366/microrna-143-and-145-modulate-the-phenotype-of-synovial-fibroblasts-in-rheumatoid-arthritis
#12
Bong-Ki Hong, Sungyong You, Seung-Ah Yoo, Dohyun Park, Daehee Hwang, Chul-Soo Cho, Wan-Uk Kim
Fibroblast-like synoviocytes (FLSs) constitute a major cell subset of rheumatoid arthritis (RA) synovia. Dysregulation of microRNAs (miRNAs) has been implicated in activation and proliferation of RA-FLSs. However, the functional association of various miRNAs with their targets that are characteristic of the RA-FLS phenotype has not been globally elucidated. In this study, we performed microarray analyses of miRNAs and mRNAs in RA-FLSs and osteoarthritis FLSs (OA-FLSs), simultaneously, to validate how dysregulated miRNAs may be associated with the RA-FLS phenotype...
August 4, 2017: Experimental & Molecular Medicine
https://www.readbyqxmd.com/read/28774651/microarray-profiling-of-circular-rnas-and-the-potential-regulatory-role-of-hsa_circ_0071410-in-the-activated-human-hepatic-stellate-cell-induced-by-irradiation
#13
Yuhan Chen, Baoying Yuan, Zhifeng Wu, Yinying Dong, Li Zhang, Zhaochong Zeng
Radiation-induced liver fibrosis (RILF) is considered as a major complication of radiation therapy for liver cancer. Circular RNA (circRNA) has been recently identified as a functional noncoding RNA involving in various biological processes. However, the expression pattern and regulatory capacity of circRNA in the irradiated hepatic stellate cell (HSC), the main fibrogenic cell type, still remain unclear. A circRNA microarray was used to identify circRNA expression profiles in irradiated and normal HSC. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) was performed to confirm the dysregulated circRNAs...
July 31, 2017: Gene
https://www.readbyqxmd.com/read/28771859/the-role-of-zip-transporters-and-group-f-bzip-transcription-factors-in-the-zn-deficiency-response-of-wheat-triticum-aestivum
#14
Nicholas P Evens, Peter Buchner, Lorraine E Williams, Malcolm J Hawkesford
Understanding the molecular basis of zinc (Zn) uptake and transport in staple cereal crops is critical for improving both Zn content and tolerance to low Zn soils. This study demonstrates the importance of F-group bZIP transcription factors and ZIP transporters in responses to Zn deficiency in wheat (Triticum aestivum). Seven F group TabZIP genes and fourteen ZIPs with homeologs were identified in hexaploid wheat. Promoter analysis revealed the presence of Zn-deficiency-response elements (ZDREs) in a number of the ZIPs...
August 3, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28768814/construction-and-optimization-of-large-gene-co-expression-network-in-maize-using-rna-seq-data
#15
Ji Huang, Stefania Vendramin Alegre, Lizhen Shi, Karen McGinnis
With the emergence of massively parallel sequencing, genome-wide expression data production has reached an unprecedented level. This abundance of data has greatly facilitated maize research, but may not be amenable to traditional analysis techniques that were optimized for other data types. Using publicly available data, a Gene Co-expression Network (GCN) can be constructed and used for gene function prediction, candidate gene selection and improving understanding of regulatory pathways. Several GCN studies have been done in maize, mostly using microarray datasets...
August 2, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28765971/identification-of-key-genes-and-pathways-in-parkinson-s-disease-through-integrated-analysis
#16
Jingru Wang, Yining Liu, Tuanzhi Chen
Parkinson's disease (PD) is a progressive, degene-rative neurological disease, typically characterized by tremors and muscle rigidity. The present study aimed to identify differe-ntially expressed genes (DEGs) between patients with PD and healthy patients, and clarify their association with additional biological processes that may regulate factors that lead to PD. An integrated analysis of publicly available Gene Expression Omnibus datasets of PD was performed. DEGs were identified between PD and normal blood samples...
July 31, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28765929/characterization-and-predicted-role-of-microrna-expression-profiles-associated-with-early-childhood-obesity
#17
Shengrong Ouyang, Renqiao Tang, Zhuo Liu, Feifei Ma, Yuanyuan Li, Jianxin Wu
MicroRNAs (miRNAs) are implicated in the pathogenesis of obesity. The aim of the present study was to characterize the miRNA profile associated with early childhood obesity in peripheral blood mononuclear cells (PBMCs). A total of 12 children (6 obese and 6 lean controls) aged 36 months old to 48 months old were recruited. The miRNA expression profile from PBMCs was detected using the multiplexed NanoString nCounter system. Bioinformatics was employed to detect target genes and miRNA‑regulated biological function...
July 31, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28765921/mir-198-induced-upregulation-of-livin-may-be-associated-with-the-prognosis-and-contribute-to-the-oncogenesis-of-lung-adenocarcinoma
#18
Yicheng Liang, Hetan Wang, Yuanyuan Sun, Sheng Chen, Haoyou Wang, Rong Huang, Xinyi Zhao, Weineng Fu, Chunlu Yang
Livin, a member of the inhibitor of apoptosis protein (IAP) family, is expressed at a high level in lung adenocarcinoma and influences the progression of cancer, and its response to chemotherapy and radiotherapy. Aberrant microRNA (miRNA) expression has also been associated with cancer initiation and development. However, the clinical significance of Livin and its relationship with miRNAs in lung adenocarcinoma are still unclear. In the present study, the expression level of Livin in 90 pairs of lung adenocarcinoma and their adjacent tissues were detected by immunohistochemistry staining...
August 1, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28761373/chronic-constriction-injury-of-sciatic-nerve-changes-circular-rna-expression-in-rat-spinal-dorsal-horn
#19
Song Cao, Wenwen Deng, Ying Li, Bangyong Qin, Lin Zhang, Shouyang Yu, Peng Xie, Zhi Xiao, Tian Yu
BACKGROUND: Mechanisms of neuropathic pain are still largely unknown. Molecular changes in spinal dorsal horn may contribute to the initiation and development of neuropathic pain. Circular RNAs (circRNAs) have been identified as microRNA sponges and involved in various biological processes, but whether their expression profile changes in neuropathic pain condition is not reported. METHODS: To test whether neuropathic pain influences circRNA expression, we developed a sciatic chronic constriction injury (CCI) model in rats...
2017: Journal of Pain Research
https://www.readbyqxmd.com/read/28759592/pcsf-an-r-package-for-network-based-interpretation-of-high-throughput-data
#20
Murodzhon Akhmedov, Amanda Kedaigle, Renan Escalante Chong, Roberto Montemanni, Francesco Bertoni, Ernest Fraenkel, Ivo Kwee
With the recent technological developments a vast amount of high-throughput data has been profiled to understand the mechanism of complex diseases. The current bioinformatics challenge is to interpret the data and underlying biology, where efficient algorithms for analyzing heterogeneous high-throughput data using biological networks are becoming increasingly valuable. In this paper, we propose a software package based on the Prize-collecting Steiner Forest graph optimization approach. The PCSF package performs fast and user-friendly network analysis of high-throughput data by mapping the data onto a biological networks such as protein-protein interaction, gene-gene interaction or any other correlation or coexpression based networks...
July 2017: PLoS Computational Biology
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