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https://www.readbyqxmd.com/read/28209199/making-life-difficult-for-clostridium-difficile-augmenting-the-pathogen-s-metabolic-model-with-transcriptomic-and-codon-usage-data-for-better-therapeutic-target-characterization
#1
Sara Saheb Kashaf, Claudio Angione, Pietro Lió
BACKGROUND: Clostridium difficile is a bacterium which can infect various animal species, including humans. Infection with this bacterium is a leading healthcare-associated illness. A better understanding of this organism and the relationship between its genotype and phenotype is essential to the search for an effective treatment. Genome-scale metabolic models contain all known biochemical reactions of a microorganism and can be used to investigate this relationship. RESULTS: We present icdf834, an updated metabolic network of C...
February 16, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28204845/mirnas-target-databases-developmental-methods-and-target-identification-techniques-with-functional-annotations
#2
REVIEW
Nagendra Kumar Singh
PURPOSE: microRNA (miRNA) regulates diverse biological mechanisms and metabolisms in plants and animals. Thus, the discoveries of miRNA has revolutionized the life sciences and medical research.The miRNA represses and cleaves the targeted mRNA by binding perfect or near perfect or imperfect complementary base pairs by RNA-induced silencing complex (RISC) formation during biogenesis process. One miRNA interacts with one or more mRNA genes and vice versa, hence takes part in causing various diseases...
February 15, 2017: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/28193260/evaluating-the-effect-of-annotation-size-on-measures-of-semantic-similarity
#3
Maxat Kulmanov, Robert Hoehndorf
BACKGROUND: Ontologies are widely used as metadata in biological and biomedical datasets. Measures of semantic similarity utilize ontologies to determine how similar two entities annotated with classes from ontologies are, and semantic similarity is increasingly applied in applications ranging from diagnosis of disease to investigation in gene networks and functions of gene products. RESULTS: Here, we analyze a large number of semantic similarity measures and the sensitivity of similarity values to the number of annotations of entities, difference in annotation size and to the depth or specificity of annotation classes...
February 13, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28191039/elevated-transcriptional-levels-of-aldolase-a-aldoa-associates-with-cell-cycle-related-genes-in-patients-with-nsclc-and-several-solid-tumors
#4
Fan Zhang, Jie-Diao Lin, Xiao-Yu Zuo, Yi-Xuan Zhuang, Chao-Qun Hong, Guo-Jun Zhang, Xiao-Jiang Cui, Yu-Kun Cui
BACKGROUND: Aldolase A (ALDOA) is one of the glycolytic enzymes primarily found in the developing embryo and adult muscle. Recently, a new role of ALDOA in several cancers has been proposed. However, the underlying mechanism remains obscure and inconsistent. In this study, we tried to investigate ALDOA-associated (AA) genes using available microarray datasets to help elucidating the role of ALDOA in cancer. RESULTS: In the dataset of patients with non-small-cell lung cancer (NSCLC, E-GEOD-19188), 3448 differentially expressed genes (DEGs) including ALDOA were identified, in which 710 AA genes were found to be positively associated with ALDOA...
2017: BioData Mining
https://www.readbyqxmd.com/read/28180060/gprc6a-jack-of-all-metabolism-or-master-of-none
#5
REVIEW
Min Pi, Satoru Kenneth Nishimoto, L Darryl Quarles
BACKGROUND: GPRC6A, a widely expressed G-protein coupled receptor, is proposed to be a master regulator of complex endocrine networks and metabolic processes. GPRC6A is activated by multiple ligands, including osteocalcin (Ocn), testosterone (T), basic amino acids, and various cations. SCOPE OF REVIEW: We review the controversy surrounding GPRC6A functions. In mice, GPRC6A is proposed to integrate metabolic functions through the coordinated secretion of hormones, including insulin, GLP-1, T, and IL-6, and direct effects of this receptor to control glucose and fat metabolism in the liver, skeletal muscle, and fat...
February 2017: Molecular Metabolism
https://www.readbyqxmd.com/read/28177879/comprehensive-analysis-of-differentially-expressed-profiles-of-lncrnas-and-construction-of-mir-133b-mediated-cerna-network-in-colorectal-cancer
#6
Hao Wu, Runliu Wu, Miao Chen, Daojiang Li, Jing Dai, Yi Zhang, Kai Gao, Jun Yu, Gui Hu, Yihang Guo, Changwei Lin, Xiaorong Li
BACKGROUND: Growing evidence suggests that long non-coding RNAs (lncRNAs) play a key role in tumorigenesis. However, the mechanism remains largely unknown. RESULTS: Thousands of significantly dysregulated lncRNAs and mRNAs were identified by microarray. Furthermore, a miR-133b-meditated lncRNA-mRNA ceRNA network was revealed, a subset of which was validated in 14 paired CRC patient tumor/non-tumor samples. Gene set enrichment analysis (GSEA) results demonstrated that lncRNAs ENST00000520055 and ENST00000535511 shared KEGG pathways with miR-133b target genes...
February 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/28176846/prediction-of-biomarkers-of-oral-squamous-cell-carcinoma-using-microarray-technology
#7
Guang Li, Xian Li, Meng Yang, Lvzi Xu, Shixiong Deng, Longke Ran
Microarray data is used to screen the genes of oral squamous cell carcinoma (OSCC). Microarray data of OSCC and normal tissues were downloaded from GEO database and analyzed with Benjamini-Hochberg (BH) method. Differentially expressed genes (DEGs) were then uploaded on DAVID database to process enrichment analysis. Target genes were finally chosen for verification experiment in vitro and in vivo. 78 DEGs were selected from 54676 genes, including 46 up- and 32 down- regulation. GO term showed that these genes were related to epidermal growth (biological processes), extracellular region (cellular components) and cytokines activity (molecular function)...
February 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28174132/traumatic-brain-injury-induces-genome-wide-transcriptomic-methylomic-and-network-perturbations-in-brain-and-blood-predicting-neurological-disorders
#8
Qingying Meng, Yumei Zhuang, Zhe Ying, Rahul Agrawal, Xia Yang, Fernando Gomez-Pinilla
The complexity of the traumatic brain injury (TBI) pathology, particularly concussive injury, is a serious obstacle for diagnosis, treatment, and long-term prognosis. Here we utilize modern systems biology in a rodent model of concussive injury to gain a thorough view of the impact of TBI on fundamental aspects of gene regulation, which have the potential to drive or alter the course of the TBI pathology. TBI perturbed epigenomic programming, transcriptional activities (expression level and alternative splicing), and the organization of genes in networks centered around genes such as Anax2, Ogn, and Fmod...
February 1, 2017: EBioMedicine
https://www.readbyqxmd.com/read/28173844/differential-long-noncoding-rna-mrna-expression-profiling-and-functional-network-analysis-during-osteogenic-differentiation-of-human-bone-marrow-mesenchymal-stem-cells
#9
Wenyuan Zhang, Rui Dong, Shu Diao, Juan Du, Zhipeng Fan, Fu Wang
BACKGROUND: Mesenchymal stem cells (MSCs) are the most promising cell types for bone regeneration and repair due to their osteogenic potential. MSC differentiation is precisely regulated and orchestrated by the mechanical and molecular signals from the extracellular environment, involving complex pathways regulated at both the transcriptional and post-transcriptional levels. However, the potential role of long noncoding RNA (lncRNA) in the osteogenic differentiation of human MSCs remains largely unclear...
February 7, 2017: Stem Cell Research & Therapy
https://www.readbyqxmd.com/read/28158264/recognition-of-prokaryotic-and-eukaryotic-promoters-using-convolutional-deep-learning-neural-networks
#10
Ramzan Kh Umarov, Victor V Solovyev
Accurate computational identification of promoters remains a challenge as these key DNA regulatory regions have variable structures composed of functional motifs that provide gene-specific initiation of transcription. In this paper we utilize Convolutional Neural Networks (CNN) to analyze sequence characteristics of prokaryotic and eukaryotic promoters and build their predictive models. We trained a similar CNN architecture on promoters of five distant organisms: human, mouse, plant (Arabidopsis), and two bacteria (Escherichia coli and Bacillus subtilis)...
2017: PloS One
https://www.readbyqxmd.com/read/28158242/de-novo-characterization-of-micrornas-in-oriental-fruit-moth-grapholita-molesta-and-selection-of-reference-genes-for-normalization-of-microrna-expression
#11
Xiu Wang, Yisong Li, Jing Zhang, Qingwen Zhang, Xiaoxia Liu, Zhen Li
MicroRNAs (miRNAs) are a group of endogenous non-coding small RNAs that have critical regulatory functions in almost all known biological processes at the post-transcriptional level in a variety of organisms. The oriental fruit moth Grapholita molesta is one of the most serious pests in orchards worldwide and threatens the production of Rosacea fruits. In this study, a de novo small RNA library constructed from mixed stages of G. molesta was sequenced through Illumina sequencing platform and a total of 536 mature miRNAs consisting of 291 conserved and 245 novel miRNAs were identified...
2017: PloS One
https://www.readbyqxmd.com/read/28150241/functional-interaction-network-construction-and-analysis-for-disease-discovery
#12
Guanming Wu, Robin Haw
Network-based approaches project seemingly unrelated genes or proteins onto a large-scale network context, therefore providing a holistic visualization and analysis platform for genomic data generated from high-throughput experiments, reducing the dimensionality of data via using network modules and increasing the statistic analysis power. Based on the Reactome database, the most popular and comprehensive open-source biological pathway knowledgebase, we have developed a highly reliable protein functional interaction network covering around 60 % of total human genes and an app called ReactomeFIViz for Cytoscape, the most popular biological network visualization and analysis platform...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28148261/dclk1-a-tumor-stem-cell-marker-regulates-pro-survival-signaling-and-self-renewal-of-intestinal-tumor-cells
#13
Parthasarathy Chandrakesan, Jiannan Yao, Dongfeng Qu, Randal May, Nathaniel Weygant, Yang Ge, Naushad Ali, Sripathi M Sureban, Modhi Gude, Kenneth Vega, Eddie Bannerman-Menson, Lijun Xia, Michael Bronze, Guangyu An, Courtney W Houchen
BACKGROUND: More than 80% of intestinal neoplasia is associated with the adenomatous polyposis coli (APC) mutation. Doublecortin-like kinase 1 (Dclk1), a kinase protein, is overexpressed in colorectal cancer and specifically marks tumor stem cells (TSCs) that self-renew and increased the tumor progeny in Apc (Min/+) mice. However, the role of Dclk1 expression and its contribution to regulating pro-survival signaling for tumor progression in Apc mutant cancer is poorly understood. METHODS: We analyzed DCLK1 and pro-survival signaling gene expression datasets of 329 specimens from TCGA Colon Adenocarcinoma Cancer Data...
February 1, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/28145813/alteration-in-long-non-coding-rna-expression-after-traumatic-brain-injury-in-rats
#14
Chuan-Fang Wang, Cheng-Cheng Zhao, Wei-Ji Weng, Jin Lei, Yong Lin, Qing Mao, Guo-Yi Gao, Jun-Feng Feng, Ji-Yao Jiang
Traumatic brain injury (TBI) causes a primary insult and initiates a secondary injury cascade. The mechanisms underlying the secondary injury are multifactorial and may include the aberrant expression of long non-coding RNA (lncRNA) post-TBI. Here, lncRNA microarray analysis was performed to profile the altered lncRNAs in the rat hippocampus after TBI. A total of 271 lncRNA probe sets and 1046 mRNA probe sets were differentially expressed after TBI. Gene ontology analysis showed that the main components of the most significantly changed categories were inflammation, DNA transcription, apoptosis and necroptosis...
February 1, 2017: Journal of Neurotrauma
https://www.readbyqxmd.com/read/28143760/pretreatment-biomarkers-predicting-ptsd-psychotherapy-outcomes-a-systematic-review
#15
REVIEW
Peter J Colvonen, Lisa H Glassman, Laura D Crocker, Melissa M Buttner, Henry Orff, Dawn M Schiehser, Sonya B Norman, Niloofar Afari
Although our understanding of the relationship between posttraumatic stress disorder (PTSD), brain structure and function, neural networks, stress-related systems, and genetics is growing, there is considerably less attention given to which biological markers predict evidence-based PTSD psychotherapy outcomes. Our systematic PRISMA-informed review of 20 studies examined biomarkers as predictors of evidence-based PTSD psychotherapy outcomes. Results provide preliminary evidence that specific structural and functional neural systems (involved in information processing), glucocorticoid sensitivity and metabolism (part of the hypothalamic-pituitary-adrenal axis and the response to stress), heart rate (involved with fear habituation), gene methylation, and certain genotypes (associated with serotonin and glucocorticoids) predicted positive response to PTSD treatment...
January 28, 2017: Neuroscience and Biobehavioral Reviews
https://www.readbyqxmd.com/read/28139721/therapeutic-properties-of-scutellaria-baicalensis-in-db-db-mice-evaluated-using-connectivity-map-and-network-pharmacology
#16
Bu-Yeo Kim, Kwang Hoon Song, Chi-Yeon Lim, Su-In Cho
We have reported that an extract of Scutellaria baicalensis (ESB) has effects against obesity and hypertriglyceridemia in type 2 diabetic animal model (db/db mouse). In the present study, we tried to explain the pharmacological effects of ESB by integrating gene expression information from db/db mouse liver with that of ESB-treated HepG2 hepatocellular carcinoma cells. Using Connectivity Map (cmap) analysis, we found an inverse relationship in the pharmaceutical profiles based on gene expression between db/db mouse liver and ESB-treated HepG2 cells...
January 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28139702/pancancer-modelling-predicts-the-context-specific-impact-of-somatic-mutations-on-transcriptional-programs
#17
Hatice U Osmanbeyoglu, Eneda Toska, Carmen Chan, José Baselga, Christina S Leslie
Pancancer studies have identified many genes that are frequently somatically altered across multiple tumour types, suggesting that pathway-targeted therapies can be deployed across diverse cancers. However, the same 'actionable mutation' impacts distinct context-specific gene regulatory programs and signalling networks-and interacts with different genetic backgrounds of co-occurring alterations-in different cancers. Here we apply a computational strategy for integrating parallel (phospho)proteomic and mRNA sequencing data across 12 TCGA tumour data sets to interpret the context-specific impact of somatic alterations in terms of functional signatures such as (phospho)protein and transcription factor (TF) activities...
January 31, 2017: Nature Communications
https://www.readbyqxmd.com/read/28137713/hipred-an-integrative-approach-to-predicting-haploinsufficient-genes
#18
Hashem A Shihab, Mark F Rogers, Colin Campbell, Tom R Gaunt
MOTIVATION: A major cause of autosomal dominant disease is haploinsufficiency, whereby a single copy of a gene is not sufficient to maintain the normal function of the gene. A large proportion of existing methods for predicting haploinsufficiency incorporate biological networks, e.g. protein-protein interaction networks, that have recently been shown to introduce study bias. As a result, these methods tend to perform best on well studied genes, but underperform on less studied genes. The advent of large genome sequencing consortia, such as the 1,000 genomes project, NHLBI Exome Sequencing Project (ESP) and the Exome Aggregation Consortium (ExAC) creates an urgent need for unbiased haploinsufficiency prediction methods...
January 30, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28137253/the-integration-of-weighted-human-gene-association-networks-based-on-link-prediction
#19
Jian Yang, Tinghong Yang, Duzhi Wu, Limei Lin, Fan Yang, Jing Zhao
BACKGROUND: Physical and functional interplays between genes or proteins have important biological meaning for cellular functions. Some efforts have been made to construct weighted gene association meta-networks by integrating multiple biological resources, where the weight indicates the confidence of the interaction. However, it is found that these existing human gene association networks share only quite limited overlapped interactions, suggesting their incompleteness and noise. RESULTS: Here we proposed a workflow to construct a weighted human gene association network using information of six existing networks, including two weighted specific PPI networks and four gene association meta-networks...
January 31, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28131833/fluid-shear-stress-stimulates-mate2-k-expression-via-nrf2-pathway-activation
#20
Yasunori Fukuda, Misato Kaishima, Toshiyuki Ohnishi, Kimio Tohyama, Ikumi Chisaki, Yusuke Nakayama, Mari Ogasawara-Shimizu, Yuji Kawamata
Accurate prediction of drug-induced renal toxicity is necessary for development of safer drugs for patients. Cellular assay systems that recapitulate physiologically relevant microenvironments have been proposed for correct estimation of drug responses in the human body. However, establishment of such assay systems for accurate prediction of renal toxicity is challenging because of the lack of readily available in vitro assay systems. In this study, we investigated the cellular response to fluid shear stress, which is a characteristic of the environment in the kidney proximal tubules, using microfluidic devices...
January 25, 2017: Biochemical and Biophysical Research Communications
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