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Regulatory network

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https://www.readbyqxmd.com/read/29222758/differential-proteomics-based-on-2d-difference-in-gel-electrophoresis-and-tandem-mass-spectrometry-for-the-elucidation-of-biological-processes-in-antibiotic-producer-bacterial-strains
#1
Giuseppe Gallo, Andrea Scaloni
Proteomics based on 2D-Difference In Gel Electrophoresis (2D-DIGE) coupled with mass spectrometry (MS) procedures can be considered a "gold standard" to determine quantitatively and comparatively protein abundances in cell extracts from different biological sources/conditions according to a gel-based approach. In particular, 2D-DIGE is used for protein specie separation, detection, and relative quantification, whenever tandem MS is used to obtain peptide sequence information that is managed according to bioinformatic procedures to identify the differentially represented protein species...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29222512/improving-gene-regulatory-network-inference-by-incorporating-rates-of-transcriptional-changes
#2
Jigar S Desai, Ryan C Sartor, Lovely Mae Lawas, S V Krishna Jagadish, Colleen J Doherty
Organisms respond to changes in their environment through transcriptional regulatory networks (TRNs). The regulatory hierarchy of these networks can be inferred from expression data. Computational approaches to identify TRNs can be applied in any species where quality RNA can be acquired, However, ChIP-Seq and similar validation methods are challenging to employ in non-model species. Improving the accuracy of computational inference methods can significantly reduce the cost and time of subsequent validation experiments...
December 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29221986/streptococcus-pneumoniae-two-component-regulatory-systems-the-interplay-of-the-pneumococcus-with-its-environment
#3
REVIEW
Alejandro Gómez-Mejia, Gustavo Gámez, Sven Hammerschmidt
Streptococcus pneumoniae is a human pathobiont possessing a diverse array of multifunctional proteins essential for bacterial fitness and virulence. Gene expression is tightly controlled by regulatory components and among the pneumococcal sensorial tools, two‑component regulatory systems (TCS) are the most widespread and conserved. This review aims to provide a comprehensive analysis of original studies on pneumococcal TCS on a functional level. Despite a rather chaotic nomenclature, the current available information on pneumococcal regulation by these systems can be conveniently addressed, according to the regulation of pathophysiological cell processes and the responses to detectable environmental signals...
November 26, 2017: International Journal of Medical Microbiology: IJMM
https://www.readbyqxmd.com/read/29221754/up-regulation-of-ypel1-and-ypel5-and-down-regulation-of-itga2-in-erlotinib-treated-egfr-mutant-non-small-cell-lung-cancer-a-bioinformatic-analysis
#4
Xiaoli Wu
PURPOSE: This study aimed to identify genes with significant alteration following treatment of epidermal growth factor receptor (EGFR)-mutant non-small cell lung cancer (NSCLC) with tyrosine kinase inhibitors (TKIs). METHODS: We downloaded microarray data of GSE67051 from the Gene Expression Omnibus (GEO) database. Genes with differential expression were identified in two groups: erlotinib-treated versus DMSO-treated PC9 cells and erlotinib-treated versus DMSO-treated HCC827 cells...
December 5, 2017: Gene
https://www.readbyqxmd.com/read/29220508/model-based-design-of-bistable-cell-factories-for-metabolic-engineering
#5
Shyam Srinivasan, William R Cluett, Radhakrishnan Mahadevan
Motivation: Metabolism can exhibit dynamic phenomena like bistability due to the presence of regulatory motifs like the positive feedback loop. As cell factories, microorganisms with bistable metabolism can have a high and a low product flux at the two stable steady states, respectively. The exclusion of metabolic regulation and network dynamics limits the ability of pseudo-steady state stoichiometric models to detect the presence of bistability, and reliably assess the outcomes of design perturbations to metabolic networks...
December 6, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29219180/laminar-shear-stress-promotes-mitochondrial-homeostasis-in-endothelial-cells
#6
Li-Hong Wu, Hao-Chun Chang, Pei-Ching Ting, Danny Ling Wang
Vascular endothelial cells (ECs) are constantly subjected to flow-induced shear stress that is crucial for endothelial functions. Laminar shear stress (LSS) exerts atheroprotection to ECs. Mitochondrial homeostasis is essential for cellular survival. However, the effects of LSS on mitochondrial homeostasis in ECs remain unclear. Mitochondrial homeostasis in ECs exposed to LSS was examined. Cultured human umbilical vein ECs were subjected to LSS (12 dynes/cm2 ) generated by a parallel-plate flow chamber system...
December 8, 2017: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/29219084/an-improved-bayesian-network-method-for-reconstructing-gene-regulatory-network-based-on-candidate-auto-selection
#7
Linlin Xing, Maozu Guo, Xiaoyan Liu, Chunyu Wang, Lei Wang, Yin Zhang
BACKGROUND: The reconstruction of gene regulatory network (GRN) from gene expression data can discover regulatory relationships among genes and gain deep insights into the complicated regulation mechanism of life. However, it is still a great challenge in systems biology and bioinformatics. During the past years, numerous computational approaches have been developed for this goal, and Bayesian network (BN) methods draw most of attention among these methods because of its inherent probability characteristics...
November 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29218912/network-analysis-of-pseudogene-gene-relationships-from-pseudogene-evolution-to-their-functional-potentials
#8
Travis S Johnson, Sihong Li, Jonathan R Kho, Kun Huang, Yan Zhang
Pseudogenes are fossil relatives of genes. Pseudogenes have long been thought of as "junk DNAs", since they do not code proteins in normal tissues. Although most of the human pseudogenes do not have noticeable functions, ∼20% of them exhibit transcriptional activity. There has been evidence showing that some pseudogenes adopted functions as lncRNAs and work as regulators of gene expression. Furthermore, pseudogenes can even be "reactivated" in some conditions, such as cancer initiation. Some pseudogenes are transcribed in specific cancer types, and some are even translated into proteins as observed in several cancer cell lines...
2018: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/29218894/mri-to-mgmt-predicting-methylation-status-in-glioblastoma-patients-using-convolutional-recurrent-neural-networks
#9
Lichy Han, Maulik R Kamdar
Glioblastoma Multiforme (GBM), a malignant brain tumor, is among the most lethal of all cancers. Temozolomide is the primary chemotherapy treatment for patients diagnosed with GBM. The methylation status of the promoter or the enhancer regions of the O6-methylguanine methyltransferase (MGMT) gene may impact the efficacy and sensitivity of temozolomide, and hence may affect overall patient survival. Microscopic genetic changes may manifest as macroscopic morphological changes in the brain tumors that can be detected using magnetic resonance imaging (MRI), which can serve as noninvasive biomarkers for determining methylation of MGMT regulatory regions...
2018: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/29218792/complex-selection-on-a-regulator-of-social-cognition-evidence-of-balancing-selection-regulatory-interactions-and-population-differentiation-in-the-prairie-vole-avpr1a-locus
#10
Alejandro Berrio, Rafael F Guerrero, Galina V Aglyamova, Mariam Okhovat, Mikhail V Matz, Steven M Phelps
Adaptive variation in social behavior depends upon standing genetic variation, but we know little about how evolutionary forces shape genetic diversity relevant to brain and behavior. In prairie voles (Microtus ochrogaster), variants at the Avpr1a locus predict expression of the vasopressin 1a receptor in the retrosplenial cortex (RSC), a brain region that mediates spatial and contextual memory; cortical V1aR abundance in turn predicts diversity in space-use and sexual fidelity in the field. To examine the potential contributions of adaptive and neutral forces to variation at the Avpr1a locus, we explore sequence diversity at the Avpr1a locus and throughout the genome in two populations of wild prairie voles...
December 8, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29217535/in-vivo-single-cell-analysis-reveals-gata2-dynamics-in-cells-transitioning-to-hematopoietic-fate
#11
Christina Eich, Jochen Arlt, Chris S Vink, Parham Solaimani Kartalaei, Polynikis Kaimakis, Samanta A Mariani, Reinier van der Linden, Wiggert A van Cappellen, Elaine Dzierzak
Cell fate is established through coordinated gene expression programs in individual cells. Regulatory networks that include the Gata2 transcription factor play central roles in hematopoietic fate establishment. Although Gata2 is essential to the embryonic development and function of hematopoietic stem cells that form the adult hierarchy, little is known about the in vivo expression dynamics of Gata2 in single cells. Here, we examine Gata2 expression in single aortic cells as they establish hematopoietic fate in Gata2Venus mouse embryos...
December 7, 2017: Journal of Experimental Medicine
https://www.readbyqxmd.com/read/29217127/epigenome-in-early-mammalian-development-inheritance-reprogramming-and-establishment
#12
REVIEW
Qianhua Xu, Wei Xie
Drastic epigenetic reprogramming takes place during preimplantation development, leading to the conversion of terminally differentiated gametes to a totipotent embryo. Deficiencies in remodeling of the epigenomes can cause severe developmental defects, including embryonic lethality. However, how chromatin modifications and chromatin organization are reprogrammed upon fertilization in mammals has long remained elusive. Here, we review recent progress in understanding how the epigenome is dynamically regulated during early mammalian development...
December 4, 2017: Trends in Cell Biology
https://www.readbyqxmd.com/read/29215635/mapping-the-small-rna-interactome-in-bacteria-using-ril-seq
#13
Sahar Melamed, Raya Faigenbaum-Romm, Asaf Peer, Niv Reiss, Omer Shechter, Amir Bar, Yael Altuvia, Liron Argaman, Hanah Margalit
Small RNAs (sRNAs) are major post-transcriptional regulators of gene expression in bacteria. To enable transcriptome-wide mapping of bacterial sRNA-target pairs, we developed RIL-seq (RNA interaction by ligation and sequencing). RIL-seq is an experimental-computational methodology for capturing sRNA-target interactions in vivo that takes advantage of the mutual binding of the sRNA and target RNA molecules to the RNA chaperone protein Hfq. The experimental part of the protocol involves co-immunoprecipitation of Hfq and bound RNAs, ligation of RNAs, library preparation and sequencing...
January 2018: Nature Protocols
https://www.readbyqxmd.com/read/29214996/the-role-of-cdx2-as-a-lineage-specific-transcriptional-repressor-for-pluripotent-network-during-the-first-developmental-cell-lineage-segregation
#14
Daosheng Huang, Guoji Guo, Ping Yuan, Amy Ralston, Lingang Sun, Mikael Huss, Tapan Mistri, Luca Pinello, Huck Hui Ng, Guocheng Yuan, Junfeng Ji, Janet Rossant, Paul Robson, Xiaoping Han
The first cellular differentiation event in mouse development leads to the formation of the blastocyst consisting of the inner cell mass (ICM) and trophectoderm (TE). The transcription factor CDX2 is required for proper TE specification, where it promotes expression of TE genes, and represses expression of Pou5f1 (OCT4). However its downstream network in the developing embryo is not fully characterized. Here, we performed high-throughput single embryo qPCR analysis in Cdx2 null embryos to identify CDX2-regulated targets in vivo...
December 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29214180/circulating-microrna-profiles-differ-between-hyperglycemia-and-euglycemia-in-coronary-heart-disease-patients
#15
Yunyao Jiang, Nan Liu, Bingjie Xue, Jincai Hou, Chengren Lin, Jianxun Ren, Jianxun Liu
Coronary heart disease (CHD) has become one of the leading causes of death and functional impairment in the world. Hyperglycemia is associated with an increased risk of cardiovascular disease. It was speculated that miRNAs in peripheral blood were a primary parameter in discriminating CHD. The biological characteristics of coronary heart disease with hyperglycemia (HCHD) and coronary heart disease with euglycemia (ECHD) were investigated in the study. Circulating miRNAs from 26 HCHD patients and 42 ECHD patients were identified by microarrays...
2017: BioMed Research International
https://www.readbyqxmd.com/read/29214152/identification-of-candidate-casein-kinase-2-substrates-in-mitosis-by-quantitative-phosphoproteomics
#16
Scott F Rusin, Mark E Adamo, Arminja N Kettenbach
Protein phosphorylation is a crucial regulatory mechanism that controls many aspects of cellular signaling. Casein kinase 2 (CK2), a constitutively expressed and active kinase, plays key roles in an array of cellular events including transcription and translation, ribosome biogenesis, cell cycle progression, and apoptosis. CK2 is implicated in cancerous transformation and is a therapeutic target in anti-cancer therapy. The specific and selective CK2 ATP competitive inhibitor, CX-4945 (silmitaseratib), is currently in phase 2 clinical trials...
2017: Frontiers in Cell and Developmental Biology
https://www.readbyqxmd.com/read/29214011/long-non-coding-rna-h19-regulates-e2f1-expression-by-competitively-sponging-endogenous-mir-29a-3p-in-clear-cell-renal-cell-carcinoma
#17
Haowei He, Nana Wang, Xiaoming Yi, Chaopeng Tang, Dong Wang
Background: Numerous recent studies indicate that the long non-coding RNAs (lncRNAs) are frequently abnormal expressed and take critical roles in many cancers. Renal cell carcinoma is the secondary malignant tumors in the urinary system and has high mortality and morbidity. Around 80% of RCCs is clear cell renal cell carcinoma (ccRCC) and is characterized by high metastasis and relapse rate. However, the clinical significances of lncRNAs in ccRCC are still unknown. Methods: The human cancer lncRNA PCR array (Yingbio) was performed to detect the differentially expressed lncRNAs in human ccRCC samples...
2017: Cell & Bioscience
https://www.readbyqxmd.com/read/29212790/the-arp2-3-regulatory-system-and-its-deregulation-in-cancer
#18
REVIEW
Nicolas Molinie, Alexis Gautreau
The Arp2/3 complex is an evolutionary conserved molecular machine that generates branched actin networks. When activated, the Arp2/3 complex contributes the actin branched junction and thus cross-links the polymerizing actin filaments in a network that exerts a pushing force. The different activators initiate branched actin networks at the cytosolic surface of different cellular membranes to promote their protrusion, movement, or scission in cell migration and membrane traffic. Here we review the structure, function, and regulation of all the direct regulators of the Arp2/3 complex that induce or inhibit the initiation of a branched actin network and that controls the stability of its branched junctions...
January 1, 2018: Physiological Reviews
https://www.readbyqxmd.com/read/29212542/a-framework-to-find-the-logic-backbone-of-a-biological-network
#19
Parul Maheshwari, Réka Albert
BACKGROUND: Cellular behaviors are governed by interaction networks among biomolecules, for example gene regulatory and signal transduction networks. An often used dynamic modeling framework for these networks, Boolean modeling, can obtain their attractors (which correspond to cell types and behaviors) and their trajectories from an initial state (e.g. a resting state) to the attractors, for example in response to an external signal. The existing methods however do not elucidate the causal relationships between distant nodes in the network...
December 6, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29212455/comparative-gene-co-expression-network-analysis-of-epithelial-to-mesenchymal-transition-reveals-lung-cancer-progression-stages
#20
Daifeng Wang, John D Haley, Patricia Thompson
BACKGROUND: The epithelial to mesenchymal transition (EMT) plays a key role in lung cancer progression and drug resistance. The dynamics and stability of gene expression patterns as cancer cells transition from E to M at a systems level and relevance to patient outcomes are unknown. METHODS: Using comparative network and clustering analysis, we systematically analyzed time-series gene expression data from lung cancer cell lines H358 and A549 that were induced to undergo EMT...
December 6, 2017: BMC Cancer
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