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Search Results: 1 - 10 of 12908 matches for " gene regulation "
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Modeling of gene regulatory networks: A review  [PDF]
Nedumparambathmarath Vijesh, Swarup Kumar Chakrabarti, Janardanan Sreekumar
Journal of Biomedical Science and Engineering (JBiSE) , 2013, DOI: 10.4236/jbise.2013.62A027

Gene regulatory networks play an important role the molecular mechanism underlying biological processes. Modeling of these networks is an important challenge to be addressed in the post genomic era. Several methods have been proposed for estimating gene networks from gene expression data. Computational methods for development of network models and analysis of their functionality have proved to be valuable tools in bioinformatics applications. In this paper we tried to review the different methods for reconstructing gene regulatory networks.

Comparative Assessment of Growth and Gene Regulation between 4 Serotypes of Streptococcus pneumoniae in Broth and Cell Culture  [PDF]
Ben Seabolt, Jeff Brady, Janice Speshock
Advances in Microbiology (AiM) , 2018, DOI: 10.4236/aim.2018.810050
Abstract: Streptococcus pneumoniae is a medically important pathogen capable of causing human infections of pneumonia, bacteremia, otitis media, and meningitis. Although there are vaccinations available, infections with S. pneumoniae still remains a global problem. S. pneumoniae is a highly adaptable bacterial species with numerous serotypes based on capsular polysaccharides. The different serotypes vary in their ability to colonize and causing pathology. Here we compared the regulation of five different virulence factors from four common serotypes of S. pneumoniae that vary in their carriage, morbidity, and mortality rates in the human population using two different in vitro methods, broth and cell culture. We determine that there is variation of virulence factor gene regulation within a serotype using two different culture methods, and variation between the serotypes in the same culture condition. The regulation of genes appeared to have a correlation with the ability of the various serotypes to grow in broth culture, adhere to cultured lung cells, and invade the cultured lung cells, as serotypes that shared similar regulation of virulence factors tended to behave similarly in culture. Many studies with S. pneumoniae rely on the use of one selected serotype, but since there is a wide variation in the growth and regulatory mechanisms of these bacteria. As demonstrated here, future studies should utilize more strains in models before concluding mechanisms of pathobiology.
Circular RNAs: New Players in Gene Regulation  [PDF]
Kalina Andreeva, Nigel G. F. Cooper
Advances in Bioscience and Biotechnology (ABB) , 2015, DOI: 10.4236/abb.2015.66043
Abstract: The existence of circular RNAs (circRNAs) was demonstrated over 30 years ago. They did not gain much interest at the time because they appeared to be relatively rare when compared to the abundance of the canonical linear RNAs. However, more recent evidence suggests that circRNAs are abundant in cells and tissues and possess intriguing biological properties. These recent developments have renewed our interest in this novel class of molecules. This report will provide an overview of circRNAs, discuss how they may modify our understanding of gene regulation and indicate their most likely relevance to health. The circRNAs from viruses, bacteria and archaea are not in the scope of this report, and we focused this review on circRNAs in eukaryotes.
Posttranscriptional Control of Gene Expression and Role of Small RNAs in Streptococcus mutans  [PDF]
Jaros?aw E. Król
Advances in Microbiology (AiM) , 2018, DOI: 10.4236/aim.2018.82010
Abstract: Streptococcus mutansis a key contributor to the formation of biofilms associated with dental caries disease. Living in the oral environment and developing of disease require tight gene regulation. In bacteria, gene expression is most commonly regulated at the level of transcription initiation. This control involved interactions of specific DNA sequences with regulatory proteins. A second mechanism of control of gene expression is mediated at the RNA level by several mechanisms and is generally called posttranscriptional regulation. These mechanisms include cis- and trans-acting small, non-coding RNAs, RNA-binding proteins, riboswitches, thermosensors, RNases, and Type I toxin-antitoxin systems, and may result in changes in RNA stability, efficiency of ribosome binding, translation initiation, and transcript secondary structures. Here I review the posttranscriptional regulation in S. mutans.
Identifying Changes in Punitive Transcriptional Factor Binding Sites Created by PPARα/δ/γ SNPs Associated with Disease  [PDF]
Norman E. Buroker
Journal of Biosciences and Medicines (JBM) , 2017, DOI: 10.4236/jbm.2017.54008
Abstract: Single nucleotide polymorphisms (SNPs) located in the PPARα/δ/γ genes that have been previously found to be significantly associated with human disease or a condition were also found to alter the genes punitive transcriptional factor binding sites (TFBS). Two alleles (C/G) of the PPARα SNP (rs1800206) were found to generate 7 common and 8 unique punitive TFBS. One of the unique TFBS created by the minor G (0.02) allele is for the T-Box 4 (TBX4) transcription factor which is associated with heritable pulmonary arterial hypertension. Two alleles (A/G) of the PPARδ SNP (rs2016520) were found to generate 20 unique punitive TFBS while the two alleles (C/G) of the PPARδ SNP (rs9794) were found to generate 11 common and 11unique punitive TFBS. The alleles of the PPARγ SNPs (rs10865710, rs12629751, rs709158, rs1805192 and rs3856806) were found to generate 15, 12, 16, 2 and 21 common and 9, 4, 12, 4 and 7 unique punitive TFBS, respectively. These changes in TFBS are discussed with relation to alterations in gene expression that may result in disease or change in human condition.
Genetics of Dothistromin Biosynthesis in the Peanut Pathogen Passalora arachidicola
Shuguang Zhang,Yanan Guo,Rosie E. Bradshaw
Toxins , 2010, DOI: 10.3390/toxins2122738
Abstract: The peanut leaf spot pathogen Passalora arachidicola (Mycosphaerella arachidis) is known to produce dothistromin, a mycotoxin related to aflatoxin. This is a feature shared with the pine needle pathogen Dothistroma septosporum (Mycosphaerella pini). Dothistromin biosynthesis in D. septosporum commences at an unusually early stage of growth in culture compared to most other fungal secondary metabolites, and the biosynthetic genes are arranged in fragmented groups, in contrast to aflatoxin gene clusters. Dothistromin biosynthetic genes were identified and studied in P. arachidicola to determine if the attributes described in D. septosporum are shared by another dothistromin-producing species within the Class Dothideomycetes. It was shown that dothistromin biosynthesis is very similar in the two species with regard to gene sequence and gene synteny. Functional complementation of D. septosporum mutants with P. arachidicola dothistromin genes was also possible. These similarities support a vertical mode of dothistromin gene transmission. P. arachidicola also produced dothistromin at an early growth stage in culture, suggesting that this type of regulation pattern may be relevant to the biological role of dothistromin.
Regulación de la expresión génica: cómo operan los mecanismos epigenéticos
Cavagnari,Brian M;
Archivos argentinos de pediatr?-a , 2012, DOI: 10.5546/aap.2012.132
Abstract: cell phenotype does not only depend on the nucleotide sequence, but is determined by those genes that are expressed and those that are not. one way to regulate this gene expression pattern is by modifying the chromatin structure via diverse epigenetic mechanisms. in the present article we present the most important epigenetic mechanisms: deoxyribonucleic acid methylation, histone post-translational modifications, non-coding ribonucleic acid mediated gene-silencing, atp-dependent chromatin remodeling, and polycomb and trithorax group proteins.
Nicotine and acetylcholine lead to distinct modulation of gene regulation
J. Steppan,S. Hofer,S. Lang,T. Brenner
Applied Cardiopulmonary Pathophysiology , 2010,
Abstract: Background: Sepsis is well known to lead to the activation of multiple pro-inflammatory markers, like MCP-1 (Monocyte chemotactic protein 1), TNF-alpha (Tumor necrosis factor alpha), while the underlying genetic changes still remain poorly studied.Methods: We used human umbilical vein endothelial cells to test the reactions to nicotine or acetylcholine/pyridostigmine administration in regards to MCP-1 levels, gene regulation and RNR expression. Results: Pyridostigmine and Acetylcholine (Ach) lead to a significant decrease of MCP-1 levels in TNF-alpha stimulated human umbilical vein endothelial cells, while nicotine had no effect. Interestingly nicotine and acetylcholine lead to different gene expression (nicotine up-regulates epidermal growth factor and down-regulates matrix metalloproteinase-8, while Ach/pyridostigmine up-regulates thioredoxin interacting protein and down-regulates insulin like growth factor 1). Furthermore RNA levels and gene activation were similar after nicotine administration, while changes in RNA levels after Ach/pyridostigmine differed significantly. Conclusions: Our results suggest that the effects of Ach/pyridostigmine and nicotine are modulated by different underlying pathways, despite their common activation of nicotinergic receptors.
Regulation of microRNA expression and function by nuclear receptor signaling
Zhihong Yang, Li Wang
Cell & Bioscience , 2011, DOI: 10.1186/2045-3701-1-31
Abstract: The binding of microRNA (miRNA, or miR) to the 3'-untranslated region of target mRNAs causes transcript degradation or interferes with translation initiation. This posttranscriptional inhibitory mechanism is of critical importance in fundamental cell processes, including development [1], proliferation [2], survival and death. During the past decade, much effort has been focused on elucidating the mechanism of miRNA target gene regulation, however, relatively little is known about the regulation of miRNA genes themselves [3]. A number of large-scale expression profiling studies have shown that the expression of miRNAs is dysregulated under various pathological conditions. Many miRNAs are expressed in a tissue-specific or developmental-stage-specific manner, thereby contributing greatly to cell-type-specific profiles of protein expression [4,5]. Growing evidence suggests that miRNAs can be regulated extensively at the levels of promoter transcription, methylation, miRNA processing, RNA editing, and miRNA-target interactions [6]. Transcriptional regulation by nuclear receptors is the primary level of control for miRNA expression (Table 1). Elucidation of the underlying mechanisms is crucial to understanding the pathways governing the miRNA network [7].miRNAs comprise a class of short (approximately 19-24 nucleotides) single-stranded non-coding RNAs that regulate gene expression through post-transcriptional mechanisms [8]. Since the discovery of RNA interference (RNAi) in 1993, efforts to identify endogenous small RNAs have led to the discovery of thousands of miRNAs in different species [9,10]. The newest database contains 16772 entries representing hairpin precursor miRNAs and expressing 19724 mature miRNA products in 153 species http://www.mirbase.org webcite. Most of the miRNAs are conserved in closely related species and many have homologs in distant species, suggesting that their functions could also be conserved [11]. Accumulating evidence indicates that miRNAs p
Gene expression regulators —MicroRNAs
Fang Chen,James Q. Yin
Chinese Science Bulletin , 2005, DOI: 10.1360/982005-573
Abstract: A large class of non-coding RNAs found in small molecule RNAs are closely associated with the regulation of gene expression, which are called microRNA (miRNA). MiRNAs are coded in intergenic or intronic regions and can be formed into foldback hairpin RNAs. These transcripts are cleaved by Dicer, generating mature miRNAs that can silence their target genes in different modes of action. Now, research on small molecule RNAs has gotten breakthrough advance in biology. To discover miRNA genes and their target genes has become hot topics in RNA research. This review attempts to look back the history of miRNA discovery, to introduce the methods of screening miRNAs, to localize miRNA loci in genome, to seek miRNA target genes and the biological function, and to discuss the working mechanisms of miRNAs. Finally, we will discuss the potential important roles of miRNAs in modulating the genesis, development, growth, and differentiation of organisms. Thus, it can be predicted that a complete understanding of miRNA functions will bring us some new concepts, approaches and strategies for the study of living beings.
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