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https://www.readbyqxmd.com/read/28346469/computational-identifying-and-characterizing-circular-rnas-and-their-associated-genes-in-hepatocellular-carcinoma
#1
Yan Li, Yongcheng Dong, Ziyan Huang, Qifan Kuang, Yiming Wu, Yizhou Li, Menglong Li
Hepatocellular carcinoma (HCC) is currently still a major factor leading to death, lacking of reliable biomarkers. Therefore, deep understanding the pathogenesis for HCC is of great importance. The emergence of circular RNA (circRNA) provides a new way to study the pathogenesis of human disease. Here, we employed the prediction tool to identify circRNAs based on RNA-seq data. Then, to investigate the biological function of the circRNA, the candidate circRNAs were associated with the protein-coding genes (PCGs) by GREAT...
2017: PloS One
https://www.readbyqxmd.com/read/28340487/microrna-4739-regulates-osteogenic-and-adipocytic-differentiation-of-immortalized-human-bone-marrow-stromal-cells-via-targeting-lrp3
#2
Mona Elsafadi, Muthurangan Manikandan, Nehad M Alajez, Rimi Hamam, Raed Abu Dawud, Abdullah Aldahmash, Zafar Iqbal, Musaad Alfayez, Moustapha Kassem, Amer Mahmood
Understanding the regulatory networks underlying lineage differentiation and fate determination of human bone marrow stromal cells (hBMSC) is a prerequisite for their therapeutic use. The goal of the current study was to unravel the novel role of the low-density lipoprotein receptor-related protein 3 (LRP3) in regulating the osteogenic and adipogenic differentiation of immortalized hBMSCs. Gene expression profiling revealed significantly higher LRP3 levels in the highly osteogenic hBMSC clone imCL1 than in the less osteogenic clone imCL2, as well as a significant upregulation of LRP3 during the osteogenic induction of the imCL1 clone...
March 8, 2017: Stem Cell Research
https://www.readbyqxmd.com/read/28334818/chromosomal-dynamics-predicted-by-an-elastic-network-model-explains-genome-wide-accessibility-and-long-range-couplings
#3
Natalie Sauerwald, She Zhang, Carl Kingsford, Ivet Bahar
Understanding the three-dimensional (3D) architecture of chromatin and its relation to gene expression and regulation is fundamental to understanding how the genome functions. Advances in Hi-C technology now permit us to study 3D genome organization, but we still lack an understanding of the structural dynamics of chromosomes. The dynamic couplings between regions separated by large genomic distances (>50 Mb) have yet to be characterized. We adapted a well-established protein-modeling framework, the Gaussian Network Model (GNM), to model chromatin dynamics using Hi-C data...
March 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334268/an-algorithmic-perspective-of-de-novo-cis-regulatory-motif-finding-based-on-chip-seq-data
#4
Bingqiang Liu, Jinyu Yang, Yang Li, Adam McDermaid, Qin Ma
Transcription factors are proteins that bind to specific DNA sequences and play important roles in controlling the expression levels of their target genes. Hence, prediction of transcription factor binding sites (TFBSs) provides a solid foundation for inferring gene regulatory mechanisms and building regulatory networks for a genome. Chromatin immunoprecipitation sequencing (ChIP-seq) technology can generate large-scale experimental data for such protein-DNA interactions, providing an unprecedented opportunity to identify TFBSs (a...
March 8, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28329018/a-unique-microrna-profile-in-end-stage-heart-failure-indicates-alterations-in-specific-cardiovascular-signaling-networks
#5
Sathyamangla V Naga Prasad, Manveen K Gupta, Zhong-Hui Duan, Venkata Suresh K Surampudi, Chang-Gong Liu, Ashwin Kotwal, Christine S Moravec, Randall C Starling, Dianne M Perez, Subha Sen, Qingyu Wu, Edward F Plow, Sadashiva Karnik
It is well established that the gene expression patterns are substantially altered in cardiac hypertrophy and heart failure, however, less is known about the reasons behind such global differences. MicroRNAs (miRNAs) are short non-coding RNAs that can target multiple molecules to regulate wide array of proteins in diverse pathways. The goal of the study was to profile alterations in miRNA expression using end-stage human heart failure samples with an aim to build signaling network pathways using predicted targets for the altered miRNA and to determine nodal molecules regulating individual networks...
2017: PloS One
https://www.readbyqxmd.com/read/28320311/a-receptor-based-analysis-of-local-ecosystems-in-the-human-brain
#6
Skirmantas Janušonis
BACKGROUND: As a complex system, the brain is a self-organizing entity that depends on local interactions among cells. Its regions (anatomically defined nuclei and areas) can be conceptualized as cellular ecosystems, but the similarity of their functional profiles is poorly understood. The study used the Allen Human Brain Atlas to classify 169 brain regions into hierarchically-organized environments based on their expression of 100 G protein-coupled neurotransmitter receptors, with no a priori reference to the regions' positions in the brain's anatomy or function...
March 20, 2017: BMC Neuroscience
https://www.readbyqxmd.com/read/28318762/gene-expression-profiling-reveals-genes-and-transcription-factors-associated-with-dilated-and-ischemic-cardiomyopathies
#7
Aiqing Qiao, Zhenying Zhao, Hui Zhang, Zhenyu Sun, Xiao Cui
AIMS: Dilated cardiomyopathy (DCM) and ischemic cardiomyopathy (ICM) can cause heart failure, and this study aims to identify genes and transcription factors (TFs) associated with DCM and ICM. METHODS: Gene expression dataset GSE42955 was generated from GEO database, and it contained 12 DCM, 12 ICM, and 5 control samples. Differentially expressed genes (DEGs) were identified between DCM (or ICM) and controls. Gene functions were investigated, and their associations were analyzed using Enrichmentmap plugin in Cytoscape...
December 29, 2016: Pathology, Research and Practice
https://www.readbyqxmd.com/read/28302149/identification-and-interaction-analysis-of-key-genes-and-micrornas-in-hepatocellular-carcinoma-by-bioinformatics-analysis
#8
Tong Mou, Di Zhu, Xufu Wei, Tingting Li, Daofeng Zheng, Junliang Pu, Zhen Guo, Zhongjun Wu
BACKGROUND: Hepatocellular carcinoma (HCC) is the most common liver malignancy worldwide. However, present studies of its multiple gene interaction and cellular pathways still could not explain the initiation and development of HCC perfectly. To find the key genes and miRNAs as well as their potential molecular mechanisms in HCC, microarray data GSE22058, GSE25097, and GSE57958 were analyzed. METHODS: The microarray datasets GSE22058, GSE25097, and GSE57958, including mRNA and miRNA profiles, were downloaded from the GEO database and were analyzed using GEO2R...
March 16, 2017: World Journal of Surgical Oncology
https://www.readbyqxmd.com/read/28294056/prediction-of-the-ebola-virus-infection-related-human-genes-using-protein-protein-interaction-network
#9
HuanHuan Cao, YuHang Zhang, Jia Zhao, Liucun Zhu, Yi Wang, JiaRui Li, Yuanming Feng, Ning Zhang
Ebola hemorrhagic fever (EHF) is caused by Ebola virus (EBOV). It is reported that human could be infected by EBOV with a high fatality rate. However, association factors between EBOV and host still tend to be ambiguous. According to the "guilt by association" (GBA) principle, proteins interacting with each other are very likely to function similarly or the same. Based on this assumption, we tried to obtain EBOV infection-related human genes in a protein-protein interaction network using Dijkstra algorithm...
March 10, 2017: Combinatorial Chemistry & High Throughput Screening
https://www.readbyqxmd.com/read/28292833/mesoscale-architecture-shapes-initiation-and-richness-of-spontaneous-network-activity
#10
Samora Okujeni, Steffen Kandler, Ulrich Egert
Spontaneous activity in the absence of external input, including propagating waves of activity, is a robust feature of neuronal networks in vivo and in vitro. The neurophysiological and anatomical requirements for initiation and persistence of such activity, however, are poorly understood, as is their role in the function of neuronal networks. Computational network studies indicate that clustered connectivity may foster the generation, maintenance and richness of spontaneous activity. Since this mesoscale architecture cannot be systematically modified in intact tissue, testing these predictions is impracticable in vivo...
March 14, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/28284064/aberrant-expression-of-microrna-induced-by-high-fructose-diet-implications-in-the-pathogenesis-of-hyperlipidemia-and-hepatic-insulin-resistance
#11
Neetu Sud, Hanyuan Zhang, Kaichao Pan, Xiao Cheng, Juan Cui, Qiaozhu Su
Fructose is a highly lipogenic sugar that can alter energy metabolism and trigger metabolic disorders. In the current study, microRNAs (miRNAs) altered by a high-fructose diet were comprehensively explored to elucidate their significance in the pathogenesis of chronic metabolic disorders. miRNA expression profiling using small noncoding RNA sequencing revealed that 19 miRNAs were significantly upregulated and 26 were downregulated in the livers of high-fructose-fed mice compared to chow-fed mice. Computational prediction and functional analysis identified 10 miRNAs, miR-19b-3p, miR-101a-3p, miR-30a-5p, miR-223-3p, miR-378a-3p, miR-33-5p, miR-145a-3p, miR-128-3p, miR-125b-5p and miR-582-3p, assembled as a regulatory network to potentially target key genes in lipid and lipoprotein metabolism and insulin signaling at multiple levels...
February 20, 2017: Journal of Nutritional Biochemistry
https://www.readbyqxmd.com/read/28281877/comprehensive-analysis-of-interaction-networks-of-telomerase-reverse-transcriptase-with-multiple-bioinformatic-approach-deep-mining-the-potential-functions-of-telomere-and-telomerase
#12
Chunyu Hou, Fei Wang, Xuewen Liu, Guangming Chang, Feng Wang, Xin Geng
Telomerase reverse transcriptase (TERT)is the protein component of telomerase complex. Evidence has accumulated showing that the non-telomeric functions of TERT are independent of telomere elongation. However, the mechanisms governing the interaction between TERT and its target genes are not revealed clear. The biological functions of TERT are not fully elucidated and have thus far been underestimated. To further explore these functions, we investigated TERT interaction networks using multiple bioinformatic databases, including BioGRID, STRING, DAVID, GeneCards, GeneMANIA, PANTHER, miRWalk, mirTarBase, miRNet, miRDB and TargetScan...
March 6, 2017: Rejuvenation Research
https://www.readbyqxmd.com/read/28273854/overexpression-of-transforming-acidic-coiled-coil%C3%A2-containing-protein-3-reflects-malignant-characteristics-and-poor-prognosis-of-glioma
#13
Ying Sun, Yu Tian, Guang-Zhi Wang, Shi-Hong Zhao, Bo Han, Yong-Li Li, Chuan-Lu Jiang
Gliomas are malignant primary brain tumors with poor prognosis. Recently, research was indicative of a tight connection between tumor malignancy and genetic alterations. Here, we propose an oncogenic implication of transforming acidic coiled-coil-containing protein 3 (TACC3) in gliomas. By comprehensively analyzing the Chinese glioma genome atlas (CGGA) and publicly available data, we demonstrated that TACC3 were overexpressed along with glioma grade and served as an independent negative prognostic biomarker for glioma patients...
March 4, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28270809/functional-diversity-of-transcriptional-regulators-in-the-cyanobacterium-synechocystis-sp-pcc-6803
#14
Mengliang Shi, Xiaoqing Zhang, Guangsheng Pei, Lei Chen, Weiwen Zhang
Functions of transcriptional regulators (TRs) are still poorly understood in the model cyanobacterium Synechocystis sp. PCC 6803. To address the issue, we constructed knockout mutants for 32 putative TR-encoding genes of Synechocystis, and comparatively analyzed their phenotypes under autotrophic growth condition and metabolic profiles using liquid chromatography-mass spectrometry-based metabolomics. The results showed that only four mutants of TR genes, sll1872 (lytR), slr0741 (phoU), slr0395 (ntcB), and slr1871 (pirR), showed differential growth patterns in BG11 medium when compared with the wild type; however, in spite of no growth difference observed for the remaining TR mutants, metabolomic profiling showed that they were different at the metabolite level, suggesting significant functional diversity of TRs in Synechocystis...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28266596/bioinformatics-analysis-of-the-proteins-interacting-with-lasp-1-and-their-association-with-hbv-related-hepatocellular-carcinoma
#15
Fan-Yun Kong, Ting Zhu, Nan Li, Yun-Fei Cai, Kai Zhou, Xiao Wei, Yan-Bo Kou, Hong-Juan You, Kui-Yang Zheng, Ren-Xian Tang
LIM and SH3 domain protein (LASP-1) is responsible for the development of several types of human cancers via the interaction with other proteins; however, the precise biological functions of proteins interacting with LASP-1 are not fully clarified. Although the role of LASP-1 in hepatocarcinogenesis has been reported, the implication of LASP-1 interactors in HBV-related hepatocellular carcinoma (HCC) is not clearly evaluated. We obtained information regarding LASP-1 interactors from public databases and published studies...
March 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28264060/whole-exome-sequencing-implicates-eye-development-the-unfolded-protein-response-and-plasma-membrane-homeostasis-in-primary-open-angle-glaucoma
#16
Tiger Zhou, Emmanuelle Souzeau, Shiwani Sharma, John Landers, Richard Mills, Ivan Goldberg, Paul R Healey, Stuart Graham, Alex W Hewitt, David A Mackey, Anna Galanopoulos, Robert J Casson, Jonathan B Ruddle, Jonathan Ellis, Paul Leo, Matthew A Brown, Stuart MacGregor, David J Lynn, Kathryn P Burdon, Jamie E Craig
PURPOSE: To identify biological processes associated with POAG and its subtypes, high-tension (HTG) and normal-tension glaucoma (NTG), by analyzing rare potentially damaging genetic variants. METHODS: A total of 122 and 65 unrelated HTG and NTG participants, respectively, with early onset advanced POAG, 103 non-glaucoma controls and 993 unscreened ethnicity-matched controls were included in this study. Study participants without myocilin disease-causing variants and non-glaucoma controls were subjected to whole exome sequencing on an Illumina HiSeq2000...
2017: PloS One
https://www.readbyqxmd.com/read/28263559/coordination-driven-syntheses-of-compact-supramolecular-metallacycles-toward-extended-metallo-organic-stacked-supramolecular-assemblies
#17
Christophe Lescop
One important concept associated with supramolecular chemistry is supramolecular self-assembly, which deals with the way discrete individual components interact via intermolecular interactions in order to build, upon their spontaneous association, high order functional assemblies. The accumulation of these very simple and localized noncovalent interactions (such as H-bonding, dipole-dipole, hydrophobic/hydrophilic, van der Waals, π-π, π-CH, etc.) is ubiquitous in the complexity of natural systems (such as DNA, proteins, membranes, micelles, etc...
March 6, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28260664/ultrasonic-disruption-of-pseudomonas-putida-for-the-release-of-arginine-deiminase-kinetics-and-predictive-models
#18
Mahesh D Patil, Manoj J Dev, Sujit Tangadpalliwar, Gopal Patel, Prabha Garg, Yusuf Chisti, Uttam Chand Banerjee
The responses of the ultrasound-mediated disruption of Pseudomonas putida KT2440 were modelled as the function of biomass concentration in the cell suspension; the treatment time of sonication; the duty cycle and the acoustic power of the sonicator. For the experimental data, the response surface (RSM), the artificial neural network (ANN) and the support vector machine (SVM) models were compared for their ability to predict the performance parameters. The satisfactory prediction of the unseen data of the responses implied the proficient generalization capabilities of ANN...
February 20, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28260060/bioinformatics-analysis-on-the-differentiation-of-bone-mesenchymal-stem-cells-into-osteoblasts-and-adipocytes
#19
Xiaoyuan Xu, He Jiang, Xingnuan Li, Ping Wu, Jianyun Liu, Tao Wang, Xiaoou Zhou, Jianjun Xiong, Weidong Li
The present study aimed to screen several differentially expressed genes (DEGs) and differentially expressed microRNAs (miRNAs) for two types of mesenchymal stem cell (MSC) differentiation. Bone morphogenetic protein 6 (BMP‑6) and dexamethasone were used to induce MSCs towards osteoblastic differentiation or adipocytic differentiation. The t‑test in the Bioconductor bioinformatics software tool was used to screen DEGs and differentially expressed miRNAs in the two samples. Subsequent gene ontology (GO) and pathway analyses on the DEGs were performed using the GO and Kyoto Encyclopedia of Genes and Genomes databases, respectively; potential target genes for the screened miRNAs were predicted using the TargetScan database...
February 8, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28260035/screening-of-potential-gene-markers-for-predicting-carotid-atheroma-plaque-formation-using-bioinformatics-approaches
#20
Guiming Wang, Dong Kuai, Yudong Yang, Gaochao Yang, Zhigang Wei, Wenbo Zhao
The present study aimed to investigate potential gene markers for predicting the formation of carotid atheroma plaques using high‑throughput bioinformatics methods. The GSE43292 gene expression profile was downloaded from the Gene Expression Omnibus database. Following data processing, differentially expressed genes (DEGs) were screened using a paired t‑test in the Linear Models for Microarray Data package with the criteria of a false discovery rate of P<0.05 and |log2 fold‑change| ≥0.58, followed by functional enrichment, protein‑protein interaction (PPI) network construction, key node and module analysis, and prediction of transcription factors (TFs) targeting genes in the significant modules...
March 1, 2017: Molecular Medicine Reports
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