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Author : Saurabh Vashishtha
Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (13 download)
Download or read book Stochastic Modeling of Eukaryotic Transcription at the Single Nucleotide Level written by Saurabh Vashishtha and published by . This book was released on 2012 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Reba-Jean Murphy
Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (122 download)
Download or read book Stochastic Modeling of the Torpedo Mechanism of Eukaryotic Transcription Termination written by Reba-Jean Murphy and published by . This book was released on 2017 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The torpedo mechanism is a type of eukaryotic transcription termination completed by RNAPII and consists of a chase-down of RNAPII by the exonuclease Xrn2 on the 3' flanking region of the RNA transcript. A biochemical model of the mechanism is detailed. By applying Gillespie simulations and using a one-dimensional biased random walk, the effects of the relative speeds of RNAPII to Xrn2 and the size of the intergenic region on termination via the torpedo mechanism are explored. The success rates of termination in terms of the likelihood of downstream gene interference, the distribution of successful termination times, and the distribution of nucleotides synthesized by RNAPII in the termination region are discussed.
Author : Seyed Hossein Hosseini
Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (122 download)
Download or read book Analytic Solutions for Stochastic Models of Transcription written by Seyed Hossein Hosseini and published by . This book was released on 2016 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The spatio-temporal organization of one RNA polymerase (RNAP) along a DNA strand is explored by studying a kinetic stochastic model for transcription process, the first step in gene expression. An explicit expression for the probability density of one RNAP was found and compared with stochastic simulation results from the corresponding detailed stochastic model. The explicit solution predicts that the movement of RNAP in large genes (genes of a few hundred nucleotides or more) is advective. It provides a justification for the use of delays in gene expression modeling, especially in delay-stochastic models. The kinetic model for the elongation stage of transcription was extended to two bodies, and the related Fokker-Planck equation was developed. This equation describes the evolution of the joint probability density for two RNAPs along the DNA track.
Author : Lisa Amrhein
Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (126 download)
Download or read book Stochastic Modeling of Heterogeneous Low-Input Gene Expression: Linking Single-Cell Probability Distributions to Transcription Mechanisms written by Lisa Amrhein and published by . This book was released on 2021 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Stochastic Modeling of Transcription Factor Binding Fluctuations written by and published by . This book was released on 2004 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Cell populations typically exhibit binary or graded transcriptional responses to external stimuli. Transcription factor interactions with DNA have been hypothesized to account for both of these scenarios. To address this hypothesis, two stochastic models were constructed to describe transcription in simple, engineered eukaryotic systems. In the first system, three transcription factors bind independently to enhancer sites directing production of protein. This system has no regulation in the form of feedback loops, but the system nonetheless exhibits a clear binary response when transcription factor binding fluctuations are slow. The graded response occurs when transcription factor binding fluctuations are rapid. Thus, transcription factor binding fluctuation is an important mechanism underlying and reconciling the graded and binary transcriptional responses. In the second model, the influence of autoregulatory feedback loops on transcription was assessed. Autoregulated systems are capable of exhibiting bistability, a mechanism cited to explain the binary transcriptional response. In this autoregulated system, a dimeric protein acts as a transcription factor to increase its own production. Using biologically realistic parameter values, the system was determined not to be bistable. However, binary transcriptional responses were still observed in stochastic models due to discrete fluctuations in transcription factor binding. The results of both models suggest that transcription factor binding fluctuations play an important, and often overlooked role, in observed patterns of transcriptional activation.
Author : Tamra Lindsey Heberling
Publisher :
ISBN 13 :
Total Pages : 145 pages
Book Rating : 4.:/5 (96 download)
Download or read book Mathematical Modeling for Transcription of DNA with Pausing written by Tamra Lindsey Heberling and published by . This book was released on 2016 with total page 145 pages. Available in PDF, EPUB and Kindle. Book excerpt: In fast-transcribing prokaryotic genes, like an rrn gene in Escherichia coli, many RNA polymerases (RNAPs) transcribe the DNA simultaneously. Active elongation of RNAPs is often interrupted by pauses, which has been observed to cause RNAP traffic jams; yet some studies indicate that elongation seems to be faster in the presence of multiple RNAPs than elongation by a single RNAP. We propose that an interaction between RNAPs via the torque produced by RNAP on helically twisted DNA can explain this apparent paradox. We have incorporated the torque mechanism into a stochastic model and simulated transcription both with and without torque. Simulation results illustrate that the torque causes shorter pause durations and fewer collisions between polymerases. Our results suggest that the torsional interaction of RNAPs is an important mechanism in maintaining fast transcription times, and that transcription should be viewed as a cooperative group effort by multiple polymerases. In an effort to further understand transcription, we investigate the Brownian ratchet model for nucleotide translocation. We model elongation as diffusive particle transport in a tilted periodic potential. To incorporate the RNAP pauses, a second periodic potential is added to the first. We present a formula for the mean escape time from a tilted, periodic potential composed of multiple periodic functions as the product of the mean escape time from each individual periodic function. This formula is extended to an arbitrary finite number of periodic functions. Two examples using truncated Fourier series are presented and analyzed.
Author : Benjamin Lewin
Publisher :
ISBN 13 : 9780763740634
Total Pages : 892 pages
Book Rating : 4.7/5 (46 download)
Download or read book Genes 9 written by Benjamin Lewin and published by . This book was released on 2008 with total page 892 pages. Available in PDF, EPUB and Kindle. Book excerpt: From renowned author Benjamin Lewin comes the newest edition of his classic text, Genes IX. For decades Lewin has provided the teaching community with the most cutting edge presentation of molecular biology and molecular genetics, covering gene structure, sequencing, organization, and expression. The new Ninth Edition boasts a fresh modern design and contemporary art program, as well as a new organization which allows students to focus more sharply on individual topics. Thoroughly updated, including a new chapter on Epigenetic Effects, Genes IX proves to be the most current, comprehensive and student-friendly molecular biology text available!
Author : Bruce Alberts
Publisher :
ISBN 13 : 9780815332183
Total Pages : 0 pages
Book Rating : 4.3/5 (321 download)
Download or read book Molecular Biology of The Cell written by Bruce Alberts and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Ilya Narsky
Publisher : John Wiley & Sons
ISBN 13 : 3527677291
Total Pages : 404 pages
Book Rating : 4.5/5 (276 download)
Download or read book Statistical Analysis Techniques in Particle Physics written by Ilya Narsky and published by John Wiley & Sons. This book was released on 2013-10-24 with total page 404 pages. Available in PDF, EPUB and Kindle. Book excerpt: Modern analysis of HEP data needs advanced statistical tools to separate signal from background. This is the first book which focuses on machine learning techniques. It will be of interest to almost every high energy physicist, and, due to its coverage, suitable for students.
Author : Mark Ptashne
Publisher : CSHL Press
ISBN 13 : 9780879696337
Total Pages : 212 pages
Book Rating : 4.6/5 (963 download)
Download or read book Genes & Signals written by Mark Ptashne and published by CSHL Press. This book was released on 2002 with total page 212 pages. Available in PDF, EPUB and Kindle. Book excerpt: P. 103.
Author : Michel Marie Deza
Publisher : Springer
ISBN 13 : 3662443422
Total Pages : 731 pages
Book Rating : 4.6/5 (624 download)
Download or read book Encyclopedia of Distances written by Michel Marie Deza and published by Springer. This book was released on 2014-10-08 with total page 731 pages. Available in PDF, EPUB and Kindle. Book excerpt: This updated and revised third edition of the leading reference volume on distance metrics includes new items from very active research areas in the use of distances and metrics such as geometry, graph theory, probability theory and analysis. Among the new topics included are, for example, polyhedral metric space, nearness matrix problems, distances between belief assignments, distance-related animal settings, diamond-cutting distances, natural units of length, Heidegger’s de-severance distance, and brain distances. The publication of this volume coincides with intensifying research efforts into metric spaces and especially distance design for applications. Accurate metrics have become a crucial goal in computational biology, image analysis, speech recognition and information retrieval. Leaving aside the practical questions that arise during the selection of a ‘good’ distance function, this work focuses on providing the research community with an invaluable comprehensive listing of the main available distances. As well as providing standalone introductions and definitions, the encyclopedia facilitates swift cross-referencing with easily navigable bold-faced textual links to core entries. In addition to distances themselves, the authors have collated numerous fascinating curiosities in their Who’s Who of metrics, including distance-related notions and paradigms that enable applied mathematicians in other sectors to deploy research tools that non-specialists justly view as arcane. In expanding access to these techniques, and in many cases enriching the context of distances themselves, this peerless volume is certain to stimulate fresh research.
Author : Ron Milo
Publisher : Garland Science
ISBN 13 : 1317230698
Total Pages : 400 pages
Book Rating : 4.3/5 (172 download)
Download or read book Cell Biology by the Numbers written by Ron Milo and published by Garland Science. This book was released on 2015-12-07 with total page 400 pages. Available in PDF, EPUB and Kindle. Book excerpt: A Top 25 CHOICE 2016 Title, and recipient of the CHOICE Outstanding Academic Title (OAT) Award. How much energy is released in ATP hydrolysis? How many mRNAs are in a cell? How genetically similar are two random people? What is faster, transcription or translation?Cell Biology by the Numbers explores these questions and dozens of others provid
Author : Grant Ramsey
Publisher : University of Chicago Press
ISBN 13 : 022640191X
Total Pages : 368 pages
Book Rating : 4.2/5 (264 download)
Download or read book Chance in Evolution written by Grant Ramsey and published by University of Chicago Press. This book was released on 2016-10-25 with total page 368 pages. Available in PDF, EPUB and Kindle. Book excerpt: This illuminating volume explores the effects of chance on evolution, covering diverse perspectives from scientists, philosophers, and historians. The evolution of species, from single-celled organisms to multicellular animals and plants, is the result of a long and highly chancy history. But how profoundly has chance shaped life on earth? And what, precisely, do we mean by chance? Bringing together biologists, philosophers of science, and historians of science, Chance in Evolution is the first book to untangle the far-reaching effects of chance, contingency, and randomness on the evolution of life. The book begins by placing chance in historical context, starting with the ancients and moving through Darwin to contemporary biology. It documents the shifts in our understanding of chance as Darwin’s theory of evolution developed into the modern synthesis, and how the acceptance of chance in Darwinian theory affected theological resistance to it. Other chapters discuss how chance relates to the concepts of genetic drift, mutation, and parallel evolution—as well as recent work in paleobiology and the experimental evolution of microbes. By engaging in collaboration across biology, history, philosophy, and theology, this book offers a comprehensive overview both of the history of chance in evolution and of our current understanding of the impact of chance on life.
Author : Kal Renganathan Sharma
Publisher : McGraw Hill Professional
ISBN 13 : 0071593071
Total Pages : 338 pages
Book Rating : 4.0/5 (715 download)
Download or read book Bioinformatics: Sequence Alignment and Markov Models written by Kal Renganathan Sharma and published by McGraw Hill Professional. This book was released on 2008-09-29 with total page 338 pages. Available in PDF, EPUB and Kindle. Book excerpt: GET FULLY UP-TO-DATE ON BIOINFORMATICS-THE TECHNOLOGY OF THE 21ST CENTURY Bioinformatics showcases the latest developments in the field along with all the foundational information you'll need. It provides in-depth coverage of a wide range of autoimmune disorders and detailed analyses of suffix trees, plus late-breaking advances regarding biochips and genomes. Featuring helpful gene-finding algorithms, Bioinformatics offers key information on sequence alignment, HMMs, HMM applications, protein secondary structure, microarray techniques, and drug discovery and development. Helpful diagrams accompany mathematical equations throughout, and exercises appear at the end of each chapter to facilitate self-evaluation. This thorough, up-to-date resource features: Worked-out problems illustrating concepts and models End-of-chapter exercises for self-evaluation Material based on student feedback Illustrations that clarify difficult math problems A list of bioinformatics-related websites Bioinformatics covers: Sequence representation and alignment Hidden Markov models Applications of HMMs Gene finding Protein secondary structure prediction Microarray techniques Drug discovery and development Internet resources and public domain databases
Author : Lucy W. Barrett
Publisher : Springer Science & Business Media
ISBN 13 : 3034806795
Total Pages : 63 pages
Book Rating : 4.0/5 (348 download)
Download or read book Untranslated Gene Regions and Other Non-coding Elements written by Lucy W. Barrett and published by Springer Science & Business Media. This book was released on 2013-06-26 with total page 63 pages. Available in PDF, EPUB and Kindle. Book excerpt: There is now compelling evidence that the complexity of higher organisms correlates with the relative amount of non-coding RNA rather than the number of protein-coding genes. Previously dismissed as “junk DNA”, it is the non-coding regions of the genome that are responsible for regulation, facilitating complex temporal and spatial gene expression through the combinatorial effect of numerous mechanisms and interactions working together to fine-tune gene expression. The major regions involved in regulation of a particular gene are the 5’ and 3’ untranslated regions and introns. In addition, pervasive transcription of complex genomes produces a variety of non-coding transcripts that interact with these regions and contribute to regulation. This book discusses recent insights into the regulatory roles of the untranslated gene regions and non-coding RNAs in the control of complex gene expression, as well as the implications of this in terms of organism complexity and evolution.
Author : James C. Blackstock
Publisher : Butterworth-Heinemann
ISBN 13 : 148318367X
Total Pages : 268 pages
Book Rating : 4.4/5 (831 download)
Download or read book Guide to Biochemistry written by James C. Blackstock and published by Butterworth-Heinemann. This book was released on 2014-06-28 with total page 268 pages. Available in PDF, EPUB and Kindle. Book excerpt: Guide to Biochemistry provides a comprehensive account of the essential aspects of biochemistry. This book discusses a variety of topics, including biological molecules, enzymes, amino acids, nucleic acids, and eukaryotic cellular organizations. Organized into 19 chapters, this book begins with an overview of the construction of macromolecules from building-block molecules. This text then discusses the strengths of some weak acids and bases and explains the interaction of acids and bases involving the transfer of a proton from an acid to a base. Other chapters consider the effectiveness of enzymes, which can be appreciated through the comparison of spontaneous chemical reactions and enzyme-catalyzed reactions. This book discusses as well structure and function of lipids. The final chapter deals with the importance and applications of gene cloning in the fundamental biological research, which lies in the preparation of DNA fragments containing a specific gene. This book is a valuable resource for biochemists and students.
Author : Edgar Wingender
Publisher : Wiley-Blackwell
ISBN 13 :
Total Pages : 452 pages
Book Rating : 4.3/5 (91 download)
Download or read book Gene Regulation in Eukaryotes written by Edgar Wingender and published by Wiley-Blackwell. This book was released on 1993 with total page 452 pages. Available in PDF, EPUB and Kindle. Book excerpt: A much-needed guide through the overwhelming amount of literature in the field. Comprehensive and detailed, this book combines background information with the most recentinsights. It introduces current concepts, emphasizing the transcriptional control of genetic information. Moreover, it links data on the structure of regulatory proteins with basic cellular processes. Both advanced students and experts will find answers to such intriguing questions as: - How are programs of specific gene repertoires activated and controlled? - Which genes drive and control morphogenesis? - Which genes govern tissue-specific tasks? - How do hormones control gene expression in coordinating the activities of different tissues? An abundant number of clearly presented glossary terms facilitates understanding of the biological background. Speacial feature: over 2200 (!) literature references.
