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https://www.readbyqxmd.com/read/29145093/proteomic-profile-and-toxicity-pathway-analysis-in-zebrafish-embryos-exposed-to-bisphenol-a-and-di-n-butyl-phthalate-at-environmentally-relevant-levels
#1
Xing Dong, Xuchun Qiu, Shunlong Meng, Hai Xu, Xiangyang Wu, Ming Yang
Bisphenol A (BPA) and di-n-butyl phthalate (DBP) are well-known endocrine-disrupting chemicals (EDCs) that have human health risks. Chronic exposure to BPA and DBP increases the occurrence of human disease. Despite the potential for exposure in embryonic development, the mechanism of action of BPA and DBP on vertebrate development and disease still remains unclear. In the present study, we identified proteins and protein networks that are perturbed by BPA and DBP during zebrafish (Danio rerio) development. Zebrafish embryos were exposed to environmentally relevant levels of BPA (10 μg/L) and DBP (50 μg/L) for 96 h...
November 10, 2017: Chemosphere
https://www.readbyqxmd.com/read/29138682/mir-128-is-implicated-in-stress-responses-by-targeting-mafg-in-skeletal-muscle-cells
#2
Rocco Caggiano, Fabio Cattaneo, Ornella Moltedo, Giovanni Esposito, Cinzia Perrino, Bruno Trimarco, Rosario Ammendola, Raffaella Faraonio
MAFG (v-Maf avian musculoaponeurotic fibrosarcoma oncogene homolog G) is a bZIP-type transcriptional regulator that belongs to the small MAF (sMAFs) protein family. By interacting with other bZIP transcription factors, sMAFs can form homo- and heterodimers governing either repressive or activating transcriptional functions. As heterodimeric partner of Nrf2, MAFG positively influences the ARE-dependent antioxidant/xenobiotic pathways, at least in condition of a correct MAFG:Nrf2 balance. MicroRNAs (miRs) participate to different regulatory networks being involved as fine-tuning regulators of gene expression...
2017: Oxidative Medicine and Cellular Longevity
https://www.readbyqxmd.com/read/29138518/predicted-molecular-targets-and-pathways-for-germacrone-curdione-and-furanodiene-in-the-treatment-of-breast-cancer-using-a-bioinformatics-approach
#3
Qi Kong, Yong Ma, Jie Yu, Xiuping Chen
Germacrone, curdione, and furanodiene have been shown to be useful in the treatment of breast cancer but the pharmacological mechanism of action is unclear. In this paper, we explored a new method to study the molecular network and function of Traditional Chinese Medicine (TCM) herbs and their corresponding ingredients with bioinformatics tools, including PubChem Compound Database, BATMAN-TCM, SystemsDock, Coremine Medical, Gene ontology, and KEGG. Eleven targeted genes/proteins, 4 key pathways, and 10 biological processes were identified to participate in the mechanism of action in treating breast cancer with germacrone, curdione, and furanodiene...
November 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29132315/comprehensive-genomic-analysis-of-the-cngc-gene-family-in-brassica-oleracea-novel-insights-into-synteny-structures-and-transcript-profiles
#4
Kaleem U Kakar, Zarqa Nawaz, Khadija Kakar, Essa Ali, Abdulwareth A Almoneafy, Raqeeb Ullah, Xue-Liang Ren, Qing-Yao Shu
BACKGROUND: The cyclic nucleotide-gated ion channel (CNGC) family affects the uptake of cations, growth, pathogen defence, and thermotolerance in plants. However, the systematic identification, origin and function of this gene family has not been performed in Brassica oleracea, an important vegetable crop and genomic model organism. RESULTS: In present study, we identified 26 CNGC genes in B. oleracea genome, which are non-randomly localized on eight chromosomes, and classified into four major (I-IV) and two sub-groups (i...
November 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29132026/integrated-omics-analysis-of-root-preferred-genes-across-diverse-rice-varieties-including-japonica-and-indica-cultivars
#5
Sunok Moon, Anil Kumar Nalini Chandran, Yun-Shil Gho, Sun-A Park, Sung-Ryul Kim, Yo-Han Yoo, Ki-Hong Jung
Plant root systems play essential roles in developmental processes, such as the absorption of water and inorganic nutrients, and structural support. Gene expression is affected by growth conditions and the genetic background of plants. To identify highly conserved root-preferred genes in rice across diverse growth conditions and varieties, we used two independent meta-anatomical expression profiles based on a large collection of Affymetrix and Agilent 44K microarray data sets available for public use. We then identified 684 loci with root-preferred expression, which were validated with in silico analysis using both meta-expression profiles...
October 26, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/29131831/substrate-specificity-of-human-metallocarboxypeptidase-d-comparison-of-the-two-active-carboxypeptidase-domains
#6
Javier Garcia-Pardo, Sebastian Tanco, Lucía Díaz, Sayani Dasgupta, Juan Fernandez-Recio, Julia Lorenzo, Francesc X Aviles, Lloyd D Fricker
Metallocarboxypeptidase D (CPD) is a membrane-bound component of the trans-Golgi network that cycles to the cell surface through exocytic and endocytic pathways. Unlike other members of the metallocarboxypeptidase family, CPD is a multicatalytic enzyme with three carboxypeptidase-like domains, although only the first two domains are predicted to be enzymatically active. To investigate the enzymatic properties of each domain in human CPD, a critical active site Glu in domain I and/or II was mutated to Gln and the protein expressed, purified, and assayed with a wide variety of peptide substrates...
2017: PloS One
https://www.readbyqxmd.com/read/29129810/discerning-molecular-interactions-a-comprehensive-review-on-biomolecular-interaction-databases-and-network-analysis-tools
#7
REVIEW
Sravan Kumar Miryala, Anand Anbarasu, Sudha Ramaiah
Computational analysis of biomolecular interaction networks is now gaining a lot of importance to understand the functions of novel genes/proteins. Gene interaction (GI) network analysis and protein-protein interaction (PPI) network analysis play a major role in predicting the functionality of interacting genes or proteins and gives an insight into the functional relationships and evolutionary conservation of interactions among the genes. An interaction network is a graphical representation of gene/protein interactome, where each gene/protein is a node, and interaction between gene/protein is an edge...
November 9, 2017: Gene
https://www.readbyqxmd.com/read/29126202/activedriverdb-human-disease-mutations-and-genome-variation-in-post-translational-modification-sites-of-proteins
#8
Michal Krassowski, Marta Paczkowska, Kim Cullion, Tina Huang, Irakli Dzneladze, B F Francis Ouellette, Joseph T Yamada, Amelie Fradet-Turcotte, Jüri Reimand
Interpretation of genetic variation is needed for deciphering genotype-phenotype associations, mechanisms of inherited disease, and cancer driver mutations. Millions of single nucleotide variants (SNVs) in human genomes are known and thousands are associated with disease. An estimated 21% of disease-associated amino acid substitutions corresponding to missense SNVs are located in protein sites of post-translational modifications (PTMs), chemical modifications of amino acids that extend protein function. ActiveDriverDB is a comprehensive human proteo-genomics database that annotates disease mutations and population variants through the lens of PTMs...
November 8, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29121669/application-and-interpretation-of-functional-data-analysis-techniques-to-differential-scanning-calorimetry-data-from-lupus-patients
#9
Sarah K Kendrick, Qi Zheng, Nichola C Garbett, Guy N Brock
BACKGROUND: DSC is used to determine thermally-induced conformational changes of biomolecules within a blood plasma sample. Recent research has indicated that DSC curves (or thermograms) may have different characteristics based on disease status and, thus, may be useful as a monitoring and diagnostic tool for some diseases. Since thermograms are curves measured over a range of temperature values, they are considered functional data. In this paper we apply functional data analysis techniques to analyze differential scanning calorimetry (DSC) data from individuals from the Lupus Family Registry and Repository (LFRR)...
2017: PloS One
https://www.readbyqxmd.com/read/29121073/diffslc-a-graph-centrality-method-to-detect-essential-proteins-of-a-protein-protein-interaction-network
#10
Divya Mistry, Roger P Wise, Julie A Dickerson
Identification of central genes and proteins in biomolecular networks provides credible candidates for pathway analysis, functional analysis, and essentiality prediction. The DiffSLC centrality measure predicts central and essential genes and proteins using a protein-protein interaction network. Network centrality measures prioritize nodes and edges based on their importance to the network topology. These measures helped identify critical genes and proteins in biomolecular networks. The proposed centrality measure, DiffSLC, combines the number of interactions of a protein and the gene coexpression values of genes from which those proteins were translated, as a weighting factor to bias the identification of essential proteins in a protein interaction network...
2017: PloS One
https://www.readbyqxmd.com/read/29115418/predicting-pathogenic-genes-for-primary-myelofibrosis-based-on-a-system%C3%A2-network-approach
#11
Shu-Cai Xu, Peng Ning
The aim of the present study was to predict pathogenic genes for primary myelofibrosis (PMF) using a system‑network approach by combining protein‑protein interaction (PPI) network and gene expression data with known pathogenic genes. PMF gene expression profiles, known pathogenic genes and protein‑protein interactions were obtained. Using these data, differentially expressed genes (DEGs) were identified between PMF and normal conditions using significance analysis of microarrays, and seed genes were determined based on the intersection of known pathogenic genes and the PMF gene expression profile...
October 20, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29113686/down-regulation-of-mir-26a-5p-in-hepatocellular-carcinoma-a-qrt-pcr-and-bioinformatics-study
#12
Liang Liang, Jiang-Hui Zeng, Jie-Yu Wang, Rong-Quan He, Jie Ma, Gang Chen, Xiao-Yong Cai, Xiao-Hua Hu
BACKGROUND: To practically verify the clinical value of miR-26a-5p and thoroughly explore its target genes as well as its potential functions in hepatocellular carcinoma (HCC). METHODS: HCC and adjacent non-cancerous hepatic tissues of 95 HCC patients were collected for analysis using reverse transcription quantitative real-time PCR (qRT-PCR). For the bioinformatics analysis, we identified potential target genes for miR-26a-5p from differentially expressed genes (DEGs) in Gene Expression Omnibus (GEO) data sets and miRWalk predicted database...
October 10, 2017: Pathology, Research and Practice
https://www.readbyqxmd.com/read/29113181/microrna-profiling-and-bioinformatics-analyses-reveal-the-potential-roles-of-micrornas-in-chordoma
#13
Kangwu Chen, Hao Chen, Kai Zhang, Siwei Sun, Jianqiang Mo, Jian Lu, Zhonglai Qian, Huilin Yang
Chordoma is a rare aggressive bone tumor arising from remnants of the notochord, and patients with chordoma have a poor prognosis. However, the unique expression profiles of microRNAs (miRNAs/miRs) and their downstream signaling pathways in chordoma remain incompletely characterized. The aim of the present study was to delineate the global miRNA expression profile and associated signaling networks in chordoma. miRNA profiling was performed on chordoma and fetal notochord tissues. Differentially expressed miRNAs in chordoma were analyzed using microarrays with hierarchical clustering analysis...
November 2017: Oncology Letters
https://www.readbyqxmd.com/read/29110645/long-intergenic-non-protein-coding-rna-1567-linc01567-acts-as-a-sponge-against-microrna-93-in-regulating-the-proliferation-and-tumorigenesis-of-human-colon-cancer-stem-cells
#14
Xiaofeng Yu, Lin Mi, Jie Dong, Jian Zou
BACKGROUND: Cancer stem cells (CSCs) are considered to be the major factor in tumor initiation, progression, metastasis, recurrence and chemoresistance. Maintaining the stemness and promoting differentiation of these cells involve various factors. Recently, long non-coding RNAs (lncRNAs) have been identified as new regulatory factors in human cancer cells. However, the function of lncRNAs in colon CSCs is still unknown. METHODS: Primary colon cancer cells were maintained in serum-free medium to form spheres and CD133(+)/CD166(+)/CD44(+) spheroid cells were selected using FACS technique...
November 6, 2017: BMC Cancer
https://www.readbyqxmd.com/read/29107989/insight-into-glucocorticoid-receptor-signalling-through-interactome-model-analysis
#15
Emyr Bakker, Kun Tian, Luciano Mutti, Constantinos Demonacos, Jean-Marc Schwartz, Marija Krstic-Demonacos
Glucocorticoid hormones (GCs) are used to treat a variety of diseases because of their potent anti-inflammatory effect and their ability to induce apoptosis in lymphoid malignancies through the glucocorticoid receptor (GR). Despite ongoing research, high glucocorticoid efficacy and widespread usage in medicine, resistance, disease relapse and toxicity remain factors that need addressing. Understanding the mechanisms of glucocorticoid signalling and how resistance may arise is highly important towards improving therapy...
November 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29104751/conformation-dynamics-of-the-intrinsically-disordered-protein-c-myb-with-the-ff99idps-force-field
#16
Xiang Guo, Jincheng Han, Ray Luo, Hai-Feng Chen
The intrinsically disordered protein c-Myb plays a critical role in cellular proliferation and differentiation. Loss of c-myb function results in embryonic lethality due to failure of fetal hepatic hematopoiesis. The conformation dynamics of the intrinsically disordered c-Myb are still unknown. Here, molecular dynamics (MD) simulations with the intrinsically disordered protein force field ff99IDPs were used to study the conformation dynamics. In comparison with ff99SBildn, ff99IDPs can reproduce more diverse disordered conformers of c-Myb...
2017: RSC Advances
https://www.readbyqxmd.com/read/29101382/deconvolution-of-transcriptional-networks-in-post-traumatic-stress-disorder-uncovers-master-regulators-driving-innate-immune-system-function
#17
Abolfazl Doostparast Torshizi, Kai Wang
Post-Traumatic Stress Disorder (PTSD) is a psychiatric disorder that develops in individuals experiencing a shocking incident, but the underlying disease susceptibility gene networks remain poorly understood. Breen et al. conducted a Weighted Gene Co-expression Network Analysis on PTSD, and identified a dysregulated innate immune module associated with PTSD development. To further identify the Master Regulators (MRs) driving the network function, here we deconvoluted the transcriptional networks on the same datasets using ARACNe (Algorithm for Reconstruction of Accurate Cellular Networks) followed by protein activity analysis...
November 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29097279/mechanical-stress-induced-subcellular-re-localization-of-n-terminally-truncated-tobacco-nt-4-1-protein
#18
Anastasia K Atabekova, Ekaterina A Lazareva, Olga S Strelkova, Andrey G Solovyev, Sergey Y Morozov
The Nicotiana tabacum 4/1 protein (Nt-4/1) of unknown function expressed in plant vasculature has been shown to localize to cytoplasmic bodies associated with endoplasmic reticulum. Here, we analyzed molecular interactions of an Nt-4/1 mutant with a deletion of 90 N-terminal amino acid residues (Nt-4/1d90) having a diffuse GFP-like localization. Upon transient co-expression with VAP27, a membrane protein known to localize to the ER, ER-plasma membrane contact sites and plasmodesmata, Nt-4/1d90 was concentrated around the cortical ER tubules, forming a network matching the shape of the cortical ER...
October 30, 2017: Biochimie
https://www.readbyqxmd.com/read/29093530/sporadic-hirschsprung-disease-mutational-spectrum-and-novel-candidate-genes-revealed-by-next-generation-sequencing
#19
Zhen Zhang, Qi Li, Mei Diao, Na Liu, Wei Cheng, Ping Xiao, Jizhen Zou, Lin Su, Kaihui Yu, Jian Wu, Long Li, Qian Jiang
Hirschsprung disease (HSCR) is a common cause of functional colonic obstruction in children. The currently available genetic testing is often inadequate as it mainly focuses on RET and several other genes, accounting for only 15-20% of cases. To identify novel, potentially pathogenic variants, we isolated a panel of genes from a whole-exome sequencing study and from the published mouse aganglionosis phenotypes, enteric nervous system development, and a literature review. The coding exons of 172 genes were analyzed in 83 sporadic patients using next-generation sequencing...
November 1, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29084214/a-systems-level-approach-to-temporal-expression-dynamics-in-drosophila-reveals-clusters-of-long-term-memory-genes
#20
Julianna Bozler, Balint Z Kacsoh, Hao Chen, William E Theurkauf, Zhiping Weng, Giovanni Bosco
The ability to integrate experiential information and recall it in the form of memory is observed in a wide range of taxa, and is a hallmark of highly derived nervous systems. Storage of past experiences is critical for adaptive behaviors that anticipate both adverse and positive environmental factors. The process of memory formation and consolidation involve many synchronized biological events including gene transcription, protein modification, and intracellular trafficking: However, many of these molecular mechanisms remain illusive...
October 2017: PLoS Genetics
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