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https://www.readbyqxmd.com/read/28330294/immuno-hybrid-algorithm-a-novel-hybrid-approach-for-grn-reconstruction
#1
A S Jereesh, V K Govindan
Bio-inspired algorithms are widely used to optimize the model parameters of GRN. In this paper, focus is given to develop improvised versions of bio-inspired algorithm for the specific problem of reconstruction of gene regulatory network. The approach is applied to the data set that was developed by the DNA microarray technology through biological experiments in the lab. This paper introduced a novel hybrid method, which combines the clonal selection algorithm and BFGS Quasi-Newton algorithm. The proposed approach implemented for real world E...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28328153/behavioral-transcriptomic-and-epigenetic-responses-to-social-challenge-in-honey-bees
#2
Hagai Y Shpigler, Michael C Saul, Emma E Murdoch, Amy C Cash-Ahmed, Christopher H Seward, Laura Sloofman, Sriram Chandrasekaran, Saurabh Sinha, Lisa J Stubbs, Gene E Robinson
Understanding how social experiences are represented in the brain and shape future responses is a major challenge in the study of behavior. We addressed this problem by studying behavioral, transcriptomic and epigenetic responses to intrusion in honey bees. Previous research showed that initial exposure to an intruder provokes an immediate attack; we now show that this also leads to longer-term changes in behavior in the response to a second intruder, with increases in the probability of responding aggressively and the intensity of aggression lasting two and one hours, respectively...
March 22, 2017: Genes, Brain, and Behavior
https://www.readbyqxmd.com/read/28327647/microrna-expression-profiles-during-cotton-gossypium-hirsutum-l-fiber-early-development
#3
Min Wang, Runrun Sun, Chao Li, Qinglian Wang, Baohong Zhang
The role of microRNAs (miRNAs) during cotton fiber development remains unclear. Here, a total of 54 miRNAs belonging to 39 families were selected to characterize miRNA regulatory mechanism in eight different fiber development stages in upland cotton cv BM-1. Among 54 miRNAs, 18 miRNAs were involved in cotton fiber initiation and eight miRNAs were related to fiber elongation and secondary wall biosynthesis. Additionally, 3,576 protein-coding genes were candidate target genes of these miRNAs, which are potentially involved in cotton fiber development...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28325216/an-update-on-src-family-of-nonreceptor-tyrosine-kinases-biology
#4
J Espada, J Martín-Pérez
The members of the Src family of nonreceptor tyrosine kinases (SFKs) are implicated in multiple signaling processes that regulate key cellular functions, including proliferation, migration, differentiation, and survival. SFKs are activated by a large number of receptors for growth factors, cytokines, steroid hormones, G protein-coupled receptors, and also by adhesion proteins and other signaling partners. Through their common modular kinase an adapter protein domains, SFKs critically contribute to diversify different signal inputs, weaving a complex and dynamic network of cellular responses...
2017: International Review of Cell and Molecular Biology
https://www.readbyqxmd.com/read/28320951/recurrent-rewiring-and-emergence-of-rna-regulatory-networks
#5
Daniel Wilinski, Natascha Buter, Andrew D Klocko, Christopher P Lapointe, Eric U Selker, Audrey P Gasch, Marvin Wickens
Alterations in regulatory networks contribute to evolutionary change. Transcriptional networks are reconfigured by changes in the binding specificity of transcription factors and their cognate sites. The evolution of RNA-protein regulatory networks is far less understood. The PUF (Pumilio and FBF) family of RNA regulatory proteins controls the translation, stability, and movements of hundreds of mRNAs in a single species. We probe the evolution of PUF-RNA networks by direct identification of the mRNAs bound to PUF proteins in budding and filamentous fungi and by computational analyses of orthologous RNAs from 62 fungal species...
March 20, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28320935/triad-of-human-cellular-proteins-irf2-fam111a-and-rfc3-restrict-replication-of-orthopoxvirus-spi-1-host-range-mutants
#6
Debasis Panda, Daniel J Fernandez, Madhu Lal, Eugen Buehler, Bernard Moss
Viruses and their hosts can reach balanced states of evolution ensuring mutual survival, which makes it difficult to appreciate the underlying dynamics. To uncover hidden interactions, virus mutants that have lost defense genes may be used. Deletion of the gene that encodes serine protease inhibitor 1 (SPI-1) of rabbitpox virus and vaccinia virus, two closely related orthopoxviruses, prevents their efficient replication in human cells, whereas certain other mammalian cells remain fully permissive. Our high-throughput genome-wide siRNA screen identified host factors that prevent reproduction and spread of the mutant viruses in human cells...
March 20, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28319747/integration-of-in-silico-methods-and-computational-systems-biology-to-explore-endocrine-disrupting-chemical-binding-with-nuclear-hormone-receptors
#7
P Ruiz, A Sack, M Wampole, S Bobst, M Vracko
Thousands of potential endocrine-disrupting chemicals present difficult regulatory challenges. Endocrine-disrupting chemicals can interfere with several nuclear hormone receptors associated with a variety of adverse health effects. The U.S. Environmental Protection Agency (U.S. EPA) has released its reviews of Tier 1 screening assay results for a set of pesticides in the Endocrine Disruptor Screening Program (EDSP), and recently, the Collaborative Estrogen Receptor Activity Prediction Project (CERAPP) data...
March 9, 2017: Chemosphere
https://www.readbyqxmd.com/read/28316886/identification-of-dysregulated-genes-in-rheumatoid-arthritis-based-on-bioinformatics-analysis
#8
Ruihu Hao, Haiwei Du, Lin Guo, Fengde Tian, Ning An, Tiejun Yang, Changcheng Wang, Bo Wang, Zihao Zhou
BACKGROUND: Rheumatoid arthritis (RA) is a chronic auto-inflammatory disorder of joints. The present study aimed to identify the key genes in RA for better understanding the underlying mechanisms of RA. METHODS: The integrated analysis of expression profiling was conducted to identify differentially expressed genes (DEGs) in RA. Moreover, functional annotation, protein-protein interaction (PPI) network and transcription factor (TF) regulatory network construction were applied for exploring the potential biological roles of DEGs in RA...
2017: PeerJ
https://www.readbyqxmd.com/read/28316353/cassava-postharvest-physiological-deterioration-a-complex-phenomenon-involving-calcium-signaling-reactive-oxygen-species-and-programmed-cell-death
#9
REVIEW
Astride S M Djabou, Luiz J C B Carvalho, Qing X Li, Nicolas Niemenak, Songbi Chen
Postharvest physiological deterioration (PPD) of cassava (Manihot esculenta) storage roots is a complex physiological and biochemical process which involve many regulatory networks linked with specific proteins modulation and signaling transduction pathways. However, it is poorly understood regarding biological regulation, and the interactions among protein groups and signals to determine PPD syndrome in cassava storage roots. This review sheds some light on the possible molecular mechanisms involved in reactive oxygen species (ROS), calcium signaling transduction, and programmed cell death (PCD) in cassava PPD syndrome...
2017: Acta Physiologiae Plantarum
https://www.readbyqxmd.com/read/28297929/flexible-dynamics-of-two-quorum-sensing-coupled-repressilators
#10
Edward H Hellen, Evgeny Volkov
Genetic oscillators play important roles in cell life regulation. The regulatory efficiency usually depends strongly on the emergence of stable collective dynamic modes, which requires designing the interactions between genetic networks. We investigate the dynamics of two identical synthetic genetic repressilators coupled by an additional plasmid which implements quorum sensing (QS) in each network thereby supporting global coupling. In a basic genetic ring oscillator network in which three genes inhibit each other in unidirectional manner, QS stimulates the transcriptional activity of chosen genes providing for competition between inhibitory and stimulatory activities localized in those genes...
February 2017: Physical Review. E
https://www.readbyqxmd.com/read/28297900/transient-dynamics-and-their-control-in-time-delay-autonomous-boolean-ring-networks
#11
Johannes Lohmann, Otti D'Huys, Nicholas D Haynes, Eckehard Schöll, Daniel J Gauthier
Biochemical systems with switch-like interactions, such as gene regulatory networks, are well modeled by autonomous Boolean networks. Specifically, the topology and logic of gene interactions can be described by systems of continuous piecewise-linear differential equations, enabling analytical predictions of the dynamics of specific networks. However, most models do not account for time delays along links associated with spatial transport, mRNA transcription, and translation. To address this issue, we have developed an experimental test bed to realize a time-delay autonomous Boolean network with three inhibitory nodes, known as a repressilator, and use it to study the dynamics that arise as time delays along the links vary...
February 2017: Physical Review. E
https://www.readbyqxmd.com/read/28294630/peak-integrating-curated-and-noisy-prior-knowledge-in-gene-regulatory-network-inference
#12
Doaa Altarawy, Fatma-Elzahraa Eid, Lenwood S Heath
With abundance of biological data, computational prediction of gene regulatory networks (GRNs) from gene expression data has become more feasible. Although incorporating other prior knowledge (PK), along with gene expression data, greatly improves prediction accuracy, the overall accuracy is still low. PK in GRN inference can be categorized into noisy and curated. In noisy PK, relations between genes do not necessarily correspond to regulatory relations and are thus considered inaccurate by inference algorithms such as transcription factor binding and protein-protein interactions...
March 15, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28289886/the-pivotal-role-of-small-non-coding-rnas-in-the-regulation-of-seed-development
#13
REVIEW
Andreia S Rodrigues, Célia M Miguel
Seeds represent a crucial stage of the seed plants life cycle. It is during seed development that the foundations of the future plant body, and the ability to give rise to a new plant capable of growing under sometimes adverse environmental conditions, are established. Small non-coding RNAs are major regulators of gene expression both at the post-transcriptional and transcriptional levels and, not surprisingly, these elements play major roles in seed development and germination. We review here the current knowledge about small RNA expression and functions in seed development, going from the morphogenesis phase comprehending embryo development and patterning, to the several steps of the maturation phase, ending in the transition to the germination...
March 13, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/28285833/integrative-proteomics-and-phosphoproteomics-profiling-reveals-dynamic-signaling-networks-and-bioenergetics-pathways-underlying-t-cell-activation
#14
Haiyan Tan, Kai Yang, Yuxin Li, Timothy I Shaw, Yanyan Wang, Daniel Bastardo Blanco, Xusheng Wang, Ji-Hoon Cho, Hong Wang, Sherri Rankin, Cliff Guy, Junmin Peng, Hongbo Chi
The molecular circuits by which antigens activate quiescent T cells remain poorly understood. We combined temporal profiling of the whole proteome and phosphoproteome via multiplexed isobaric labeling proteomics technology, computational pipelines for integrating multi-omics datasets, and functional perturbation to systemically reconstruct regulatory networks underlying T cell activation. T cell receptors activated the T cell proteome and phosphoproteome with discrete kinetics, marked by early dynamics of phosphorylation and delayed ribosome biogenesis and mitochondrial activation...
March 3, 2017: Immunity
https://www.readbyqxmd.com/read/28283057/super-enhancer-mediated-rna-processing-revealed-by-integrative-microrna-network-analysis
#15
Hiroshi I Suzuki, Richard A Young, Phillip A Sharp
Super-enhancers are an emerging subclass of regulatory regions controlling cell identity and disease genes. However, their biological function and impact on miRNA networks are unclear. Here, we report that super-enhancers drive the biogenesis of master miRNAs crucial for cell identity by enhancing both transcription and Drosha/DGCR8-mediated primary miRNA (pri-miRNA) processing. Super-enhancers, together with broad H3K4me3 domains, shape a tissue-specific and evolutionarily conserved atlas of miRNA expression and function...
March 9, 2017: Cell
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
#16
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/28280740/nfp-an-r-package-for-characterizing-and-comparing-of-annotated-biological-networks
#17
Yang Cao, Wenjian Xu, Chao Niu, Xiaochen Bo, Fei Li
Large amounts of various biological networks exist for representing different types of interaction data, such as genetic, metabolic, gene regulatory, and protein-protein relationships. Recent approaches on biological network study are based on different mathematical concepts. It is necessary to construct a uniform framework to judge the functionality of biological networks. We recently introduced a knowledge-based computational framework that reliably characterized biological networks in system level. The method worked by making systematic comparisons to a set of well-studied "basic networks," measuring both the functional and topological similarities...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28280365/downregulation-of-long-noncoding-rna-hotairm1-promotes-monocyte-dendritic-cell-differentiation-through-competitively-binding-to-endogenous-mir-3960
#18
Jiaxuan Xin, Jing Li, Yue Feng, Liyang Wang, Yuan Zhang, Rongcun Yang
Myeloid differentiation is controlled by a multilayered regulatory circuitry consisting of various elements, including histone modifications, transcription factors, and posttranscriptional regulators such as miRNAs, long noncoding RNAs, and circular RNAs. However, the molecular mechanism underlying this biological process remains unclear. In this study, through epigenetic profiling analysis using chromatin immunoprecipitation (ChIP) followed by sequencing (ChIP-seq), we identified an lncRNA, HOTAIRM1, with a critical role in myeloid development...
2017: OncoTargets and Therapy
https://www.readbyqxmd.com/read/28279210/computational-analysis-of-the-mesenchymal-signature-landscape-in-gliomas
#19
Orieta Celiku, Anita Tandle, Joon-Yong Chung, Stephen M Hewitt, Kevin Camphausen, Uma Shankavaram
BACKGROUND: Epithelial to mesenchymal transition, and mimicking processes, contribute to cancer invasion and metastasis, and are known to be responsible for resistance to various therapeutic agents in many cancers. While a number of studies have proposed molecular signatures that characterize the spectrum of such transition, more work is needed to understand how the mesenchymal signature (MS) is regulated in non-epithelial cancers like gliomas, to identify markers with the most prognostic significance, and potential for therapeutic targeting...
March 9, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28273877/protein-kinase-ck2-intricate-relationships-within-regulatory-cellular-networks
#20
REVIEW
Teresa Nuñez de Villavicencio-Diaz, Adam J Rabalski, David W Litchfield
Protein kinase CK2 is a small family of protein kinases that has been implicated in an expanding array of biological processes. While it is widely accepted that CK2 is a regulatory participant in a multitude of fundamental cellular processes, CK2 is often considered to be a constitutively active enzyme which raises questions about how it can be a regulatory participant in intricately controlled cellular processes. To resolve this apparent paradox, we have performed a systematic analysis of the published literature using text mining as well as mining of proteomic databases together with computational assembly of networks that involve CK2...
March 5, 2017: Pharmaceuticals
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