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Search Results: 1 - 10 of 919 matches for " transcription "
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Identifying species-specific subsequences in bacteria transcription terminators-A machine learning approach  [PDF]
Bao-Hua Gu, Yi Sun
Journal of Biomedical Science and Engineering (JBiSE) , 2009, DOI: 10.4236/jbise.2009.23031
Abstract: Transcription Terminators (TTs) play an impor-tant role in bacterial RNA transcription. Some bacteria are known to have Species-Specific Subsequences (SSS) in their TTs, which are be-lieved containing useful clues to bacterial evolu-tion. The SSS can be identified using biological methods which, however, tend to be costly and time-consuming due to the vast number of sub-sequences to experiment on. In this paper, we study the problem from a computational per-spective and propose a computing method to identify the SSS. Given DNA sequences of a tar-get species, some of which are known to contain a TT while others not, our method uses machine learning techniques and is done in three steps. First, we find all frequent subsequences from the given sequences, and show that this can be effi-ciently done using generalized suffix trees. Sec-ond, we use these subsequences as features to characterize the original DNA sequences and train a classification model using Support Vector Machines (SVM), one of the currently most effec-tive machine learning techniques. Using the pa-rameters of the resulting SVM model, we define a measure called subsequence specificity to rank the frequent subsequences, and output the one with the highest rank as the SSS. Our experi-ments show that the SSS found by the proposed method are very close to those determined by biological experiments. This suggests that our method, though purely computational, can help efficiently locate the SSS by effectively narrowing down the search space.
Regulation and Improvement of Cellulase Production: Recent Advances  [PDF]
Nasir Ali, Muhammad Ammar Athar, Yasir Hayat Khan, Muhammad Idrees, Dawood Ahmad
Natural Resources (NR) , 2014, DOI: 10.4236/nr.2014.514073
Abstract: Cellulases and hemicellulases are the main industrial sources from different microorganisms used to depolymerise plant biomass to simple sugars that are converted to chemical intermediates and biofuels, such as ethanol. Cellulases are formed adaptively, and several positive (xyr1, Ace2, HAP2/3/5) and negative (Ace1, Cre1) components involved in this regulation are now known. In this review, we summarise current knowledge about how cellulase biosynthesis is regulated, and outline recent approaches and suitable strategies for facilitating the targeted improvement of cellulase production by genetic engineering. Trichoderma reesei is the preferred organism for producing industrial cellulases. However, a more efficient heterologous expression system for enzymes from different organism is needed to further improve its cellulase mixture. In addition those optimizations of the promoter and linker for hybrid genes can dramatically improve the efficiency of heterologous expression of cellulase genes.
Triplex DNA: Importance and its medical application
Noori Dalooei M,Mojoodi A
Tehran University Medical Journal , 1998,
Abstract: Back in 1957, when investigators produced a triple-stranded form of DNA while studying synthetic nucleic acids, few researchers paid much attention to the discovery. However, triplex DNA was never entirely forgotton and especially since 1987 its structural and functional importance in biological systems as well as its medical applications and therapeutic potentional have been extensively studied. It was suggested that in triplex DNA, the third strand was hydrogen bonded and positioned in the major groove of the Watson-Crick duplex. Protein binding assays show that triplex formation by HR21ap inhibits Sp1 binding to the Ha-ras promoter. These results suggest that the triplex formation by the Ha-ras promoter targed oligonucleotide may provide a means to specifically inhibit transcription of this oncogene in vivo. Triplex DNA can disrupt gene transcriptions and can be used as of this oncogene in vivo. Triplex DNA can disrupt gene transcriptions and can be used as a new strategy for treating viral diseases, such as AIDS, by blocking virus reproduction. As discussed in this article, for a number of reasons, interest in oligonucleotide designed for triplex helices on dsDNA is being steadily increased (including their potential artificial repressors of gene expression, mediator of site specific DNA cleavage and therapeutic use for genetic diseases, cancer and diseases caused by viruses).
The LysR Transcription Factor, HexS, Is Required for Glucose Inhibition of Prodigiosin Production by Serratia marcescens  [PDF]
Nicholas A. Stella, James E. Fender, Roni M. Lahr, Eric J. Kalivoda, Robert M. Q. Shanks
Advances in Microbiology (AiM) , 2012, DOI: 10.4236/aim.2012.24065
Abstract: Generation of many useful microbe-derived secondary metabolites, including the red pigment prodigiosin of the bacterium Serratia marcescens, is inhibited by glucose. In a previous report, a genetic approach was used to determine that glucose dehydrogenase activity (GDH) is required for inhibiting prodigiosin production and transcription of the prodigiosin biosynthetic operon (pigA-N). However, the transcription factor(s) that regulate this process were not characterized. Here we tested the hypothesis that HexS, a LysR-family transcription factor similar to LrhA of Escherichia coli, is required for inhibition of prodigiosin by growth in glucose. We observed that mutation of the hexS gene in S. marcescens allowed the precocious production of prodigiosin in glucose-rich medium conditions that completely inhibited prodigiosin production by the wild type. Unlike previously described mutants able to generate prodigiosin in glucoserich medium, hexS mutants exhibited GDH activity and medium acidification similar to the wild type. Glucose inhibittion of pigA expression was shown to be dependent upon HexS, suggesting that HexS is a key transcription factor in secondary metabolite regulation in response to medium pH. These data give insight into the prodigiosin regulatory pathway and could be used to enhance the production of secondary metabolites.
Temporal Transcriptional Regulation of IL-10-Induced Anti-Inflammatory Genes in LPS-Triggered Macrophages  [PDF]
Amanda F. Dillow, Leah N. Cardwell, Tyler J. Smith, Brad D. Groppe, Brian A. Peterson, Maxwell A. Sickman, Brian K. Weaver
Open Journal of Immunology (OJI) , 2014, DOI: 10.4236/oji.2014.43013

Interleukin-10 (IL-10) mediates an anti-inflammatory response that is executed through the expression of IL-10-induced genes. Certain IL-10-induced genes, exemplified by TNIP3, are induced by IL-10 only in conjunction with a pro-inflammatory signal. We sought to characterize the mechanism whereby IL-10 and Toll-like receptor signals synergized to induce expression of genes like TNIP3 inmacrophages. Stimulation with IL-10 and lipopolysaccharide (LPS) synergistically induced an increase in the transcription rate of TNIP3, while having no effect on its mRNA stability. This transcriptional mechanism proved to be generalizable to 14 other genes that also were synergistically induced by IL-10 and LPS in monocytes/macrophages. Although all of the genes had this synergistic transcriptional regulation in common, they could be divided into three subsets based on their differential requirements for de novo protein synthesis and kinetics of expression: namely, primary response genes, early secondary response genes, and late secondary response genes. This coordinated and temporal pattern of transcriptional regulation in response to IL-10 and LPS was conserved in both human and mouse monocytes/macrophages, and it was associated with differential dependencies on PI3K and JNK signaling pathways. These results underscore the complex nature of the IL-10-induced transcriptional response that occurs specifically in LPS-triggered macrophages.

Relationships between Translation and Transcription Processes during fMRI Connectivity Scanning and Coded Translation and Transcription in Writing Products after Scanning in Children with and without Transcription Disabilities  [PDF]
Peter Wallis, Todd Richards, Peter Boord, Robert Abbott, Virginia Berninger
Creative Education (CE) , 2017, DOI: 10.4236/ce.2017.85055
Abstract: Students with transcription disabilities (dysgraphia/impaired handwriting, n = 13 or dyslexia/impaired word spelling, n = 16) or without transcription disabilities (controls) completed transcription and translation (idea generating, planning, and creating) writing tasks during fMRI connectivity scanning and compositions after scanning, which were coded for transcription and translation variables. Compositions in both groups showed diversity in genre beyond usual narrative-expository distinction; groups differed in coded transcription but not translation variables. For the control group specific transcription or translation tasks during scanning correlated with corresponding coded transcription or translation skills in composition, but connectivity during scanning was not correlated with coded handwriting during composing in dysgraphia group and connectivity during translating was not correlated with any coded variable during composing in dyslexia group. Results are discussed in reference to the trend in neuroscience to use connectivity from relevant seed points while performing tasks and trends in education to recognize the generativity (creativity) of composing at both the genre and syntax levels.
Bioinformatic screening of the binding transcription sites in the regulatory regions of genes up-regulated in response to oxidative stress  [PDF]
Shkurat TP, Ponomareva NS, Aleksandrova AA, Shkurat MA, Butenko AI, Panich AE
Open Journal of Genetics (OJGen) , 2012, DOI: 10.4236/ojgen.2012.24B001
Abstract: This study focuses on bioinformatics search for new regulatory structures in the non-coding DNA, located around the patterns of gene expression levels changed significantly in response to oxidative stress. Hypothesized that all of the genes increase the expression in response to oxidative stress may have the same motifs in non-coding DNA. To search for motifs created an integrated collection database of transcription binding sites - JASPAR, TRANSFAC, Hocomoco TF Homo sapiens, Uniprobe TF Mus musculus. Two types of regulatory regions: the promoter region and the sequence with the capture of potential cis-regulatory modules. In the regulatory regions of genes increase the expression in response to oxidative stress, in contrast to the gene expression level did not change, families of transcription factors identified SOX (1-30) and HX (A, B, C, D).
Análisis molecular del proceso de transcripción de genes en eucariontes
Cabrejos M.,María Eugenia; Tamayo C.,Evelyn; Maldonado M.,Edio;
Revista chilena de pediatría , 2001, DOI: 10.4067/S0370-41062001000500002
Abstract: the transcription process is highly regulated and requires rna polymerase and additional factors. the enzyme rna polymerase ii is composed of 8 to 14 subunits and transcribes the messenger rna. the largest subunit contains in the amino terminal region a domain which is named ctd. ctd is composed of repetitions of a heptapeptide sequence which is fundamental for the regulation of transcription. although rna polymerase is a multimeric enzyme it is not by itself able to recognize the promoters and initiate specific transcription. it requires auxiliary factors called the general transcription factors, tfiia, tfiib, tfiid, tfiie, tfiif and tfiih. these factors and rna polymerase ii are assembled at the promoter site in a step by step fashion or preassembled with rna polymerase ii. the genes are activated in response to physiological signals by activators which bind to the upstream elements of the promoter site. also for the activation of transcription the med complex is required. this can exist in the free form or bound to the ctd of rna polymerase ii. the dna inside the nucleus is compacted by histones to form chromatin, which restricts the access of the transcription machinery to the promoter site. enzymes called acetylases are able to modify the chromatin structure by acetylation of the n-terminal of the histones, producing a weakening in the dna-histone contacts, thus allowing the transcription machinery access to the promoters and initiate transcription. there exists factors which are able to displace the nucleosomes to allow rna polymerase ii and factors to form a preinitiation complex on the dna promoter site
Tailoring the Models of Transcription
Alena Pance
International Journal of Molecular Sciences , 2013, DOI: 10.3390/ijms14047583
Abstract: Molecular biology is a rapidly evolving field that has led to the development of increasingly sophisticated technologies to improve our capacity to study cellular processes in much finer detail. Transcription is the first step in protein expression and the major point of regulation of the components that determine the characteristics, fate and functions of cells. The study of transcriptional regulation has been greatly facilitated by the development of reporter genes and transcription factor expression vectors, which have become versatile tools for manipulating promoters, as well as transcription factors in order to examine their function. The understanding of promoter complexity and transcription factor structure offers an insight into the mechanisms of transcriptional control and their impact on cell behaviour. This review focuses on some of the many applications of molecular cut-and-paste tools for the manipulation of promoters and transcription factors leading to the understanding of crucial aspects of transcriptional regulation.
Initiation of HIV Reverse Transcription: Is Enzyme Flipping?Required?
Matthias G?tte
Viruses , 2011, DOI: 10.3390/v3040331
Abstract: Liu and colleagues have recently studied dynamic changes in the orientation of HIV reverse transcriptase (RT) on its nucleic acid substrate during initiation of DNA synthesis. The authors employed a single molecule FRET assay and revealed the existence of an equilibrium between polymerase-competent and “flipped” polymerase-incompetent orientations. RT flipping correlates with enzyme pausing during initiation, while the transition to the processive elongation phase correlates with increases in the population of polymerase-competent complexes. The potential biological significance of these findings is discussed in this commentary in lieu of the entire process of reverse transcription.
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