Download or read book Determining the Ribosome Binding Footprint in Escherichia Coli to Improve the Ribosome Binding Site Calculator Model of Translation Initiation written by Ashlee Smith and published by . This book was released on 2014 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: In the last 20 years, the technology used to create synthetic DNA has greatly advanced. Today, DNA can now be synthesized 3 times as quickly and costs 5 times less. The availability of recombinant DNA systems provides flexibility for researchers in academia and industry trying to solve metabolic engineering problems and elucidate biological functions. One common metabolic engineering problem is developing a system to control the expression of a protein of interest over a range from very little to very large expression. Instead of generating large combinatorial libraries to find a sequence with a specific function, which is time consuming and inefficient, researchers are rationally altering the DNA sequence to achieve a desired attribute using information gained from biophysical modeling. One such alteration is the design of synthetic ribosome binding sites to improve the rate of translation initiation in order to increase the expression of protein. The Ribosome Binding Site Calculator (RBS) is software that utilizes a biophysical model of translation initiation to allow researchers to predict the translation initiation rate of a particular sequence or generate a synthetic RBS with a specified translation initiation rate. There are many interactions that take place during translation initiation. In order to improve the accuracy of the model's predictions, one such interaction that we studied is the ribosomal footprint. The ribosome must unfold a section of messenger RNA (mRNA) after the start codon and load it into an mRNA channel. This channel can only accommodate single stranded mRNA. The number of nucleotides in the coding section the ribosome must unfold and load into the channel is the ribosomal footprint (FP). We hypothesized that a secondary structure contained in the ribosomal footprint must be unfolded and would greatly decrease protein expression, and that a secondary structure outside of the footprint region would not have to be unfolded and protein expression would be higher. We identified the ribosomal footprint for Escherichia coli by creating a high expressing RBS sequence and a modified coding section appended to the red fluorescent protein (RFP) reporter gene. The modified coding section featured a movable hairpin structure that was moved from immediately after ATG (position 3) to position 39 to show the changes in protein expression. We found that translation initiation gradually increased from very low levels when the hairpin was close to the start codon to over 1000-fold higher after the hairpin had passed the footprint region. The footprint was found to be 13 or 14 nucleotides including the start codon. Discrepancies between the model predictions and the data revealed the free energy the ribosome must expend to load the mRNA into the channel. The average error for constructs with a hairpin located 3 to 10 nucleotides into the coding sequence was determined to be 7.7 kcal/mol. This value represents the free energy cost of secondary structure within the footprint region, [delta]Gload. This information improves the biophysical model by determining the free energy change of loading the mRNA into the channel and will provide researchers with more accurate predictions of translation initiation.
Download or read book Transcription and Translation Initiation in Escherichia Coli written by Lianna M. Munson and published by . This book was released on 1983 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Identification of Ribosome Binding Sites in Escherichia Coli Using Neural Network Models written by David B. Bisant and published by . This book was released on 1994 with total page 234 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Protein Composition of Ribosomal Binding Sites for Initiation Factors in Escherichia Coli written by Ronald Lee Heimark and published by . This book was released on 1976 with total page 356 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book The Development of Equilibrium and Non equilibrium Models of Translation and Riboswitch Regulation written by Amin Espah Borujeni and published by . This book was released on 2015 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Tunable control of protein production inside cells is one of the main challenges in metabolic engineering and pharmaceutical industries. There are many cellular processes that are responsible for altering protein expression levels, including transcription initiation and termination, translation initiation and elongation, and co-translational protein folding. Successful manipulation of each of these processes requires the understanding of their mechanism, and how macromolecular machineries such as RNA polymerases and ribosomes interact with DNAs and mRNAs. In particular, the ribosome's interactions with mRNA govern its translation rate and the effects of post-transcriptional regulation. It has been shown that translation initiation is a rate limiting step in protein production, in which ribosome must efficiently make the first contact with mRNA. Although translation initiation is one of the well-studied processes inside cells, there are still many unanswered questions that puzzled researchers for several decades. For example, what is the role of 5' untranslated regions on protein synthesis rate? How the N-terminal coding section controls ribosome binding to mRNA? How the regulatory components such as small RNAs and ligand-responsive riboswitches alter the ribosome binding rate? Can RNA folding kinetics compete with ribosome binding rate to alter the binding equilibrium between mRNA and ribosome? In this dissertation, we aim to answer these questions by taking a "learn-by-design" approach, in which we first propose a plausible mechanism, and then we conduct specific experiments to test our hypothesis while eliminating other confounding interactions, followed by developing mechanistic models that can explain the experimental observations. Our ultimate goal is to develop simplified yet accurate models that can predict the rate of translation initiation and riboswitch regulation directly from DNA sequence, using kinetics and thermodynamics first principles. These biophysics-based models can be further improved by identifying new interactions, characterizing their effects, and incorporating them into the existing models. Overall, through our biophysical modeling approach, we developed an accurate and comprehensive model of bacterial translation initiation that predicts the rate of translation under both equilibrium and non-equilibrium conditions. In addition, we also developed the first sequence-structure-function relationship for translation-regulating riboswitches that predicts the function of riboswitches from the energetic interactions between mRNA, ligand, and ribosome. Importantly, the incorporation of this biophysics-based model into a web-interface called the Riboswitch Calculator, allows the scientific community to design new generation of high-performance biosensors for diverse applications.
Download or read book Machine Learning Methodologies To Study Molecular Interactions written by Elif Ozkirimli and published by Frontiers Media SA. This book was released on 2022-01-21 with total page 147 pages. Available in PDF, EPUB and Kindle. Book excerpt: Dr. Elif Ozkirimli is a full time employee of F. Hoffmann-La Roche AG, Switzerland and Dr. Artur Yakimovich is a full time employee of Roche Products Limited, UK. All other Topic Editors declare no competing interests with regards to the Research Topic.
Download or read book Industrial Microorganisms written by Richard H. Baltz and published by ASM Press. This book was released on 1993 with total page 320 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is based on the proceedings of the 5th ASM Conference on the Genetics and Molecular Biology of Industrial Microorganisms held in Bloomington, Indiana in October 1992. The meeting focussed on prokaryotes and lower eukaryotes, with the programme balanced between streptomyces, fungi and yeasts, and other bacteria including Escherichia coli and emerging bacterial systems. The topics of the symposia reflect major trends in research that have immediate and future industrial applications
Download or read book Lasso Peptides written by Yanyan Li and published by Springer. This book was released on 2014-10-21 with total page 113 pages. Available in PDF, EPUB and Kindle. Book excerpt: Lasso peptides form a growing family of fascinating ribosomally-synthesized and post-translationally modified peptides produced by bacteria. They contain 15 to 24 residues and share a unique interlocked topology that involves an N-terminal 7 to 9-residue macrolactam ring where the C-terminal tail is threaded and irreversibly trapped. The ring results from the condensation of the N-terminal amino group with a side-chain carboxylate of a glutamate at position 8 or 9, or an aspartate at position 7, 8 or 9. The trapping of the tail involves bulky amino acids located in the tail below and above the ring and/or disulfide bridges connecting the ring and the tail. Lasso peptides are subdivided into three subtypes depending on the absence (class II) or presence of one (class III) or two (class I) disulfide bridges. The lasso topology results in highly compact structures that give to lasso peptides an extraordinary stability towards both protease degradation and denaturing conditions. Lasso peptides are generally receptor antagonists, enzyme inhibitors and/or antibacterial or antiviral (anti-HIV) agents. The lasso scaffold and the associated biological activities shown by lasso peptides on different key targets make them promising molecules with high therapeutic potential. Their application in drug design has been exemplified by the development of an integrin antagonist based on a lasso peptide scaffold. The biosynthesis machinery of lasso peptides is therefore of high biotechnological interest, especially since such highly compact and stable structures have to date revealed inaccessible by peptide synthesis. Lasso peptides are produced from a linear precursor LasA, which undergoes a maturation process involving several steps, in particular cleavage of the leader peptide and cyclization. The post-translational modifications are ensured by a dedicated enzymatic machinery, which is composed of an ATP-dependent cysteine protease (LasB) and a lactam synthetase (LasC) that form an enzymatic complex called lasso synthetase. Microcin J25, produced by Escherichia coli AY25, is the archetype of lasso peptides and the most extensively studied. To date only around forty lasso peptides have been isolated, but genome mining approaches have revealed that they are widely distributed among Proteobacteria and Actinobacteria, particularly in Streptomyces, making available a rich resource of novel lasso peptides and enzyme machineries towards lasso topologies.
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
Download or read book Biofilms in Wastewater Treatment written by Stefan Wuertz and published by IWA Publishing. This book was released on 2003-04-30 with total page 425 pages. Available in PDF, EPUB and Kindle. Book excerpt: The central theme of the book is the flow of information from experimental approaches in biofilm research to simulation and modeling of complex wastewater systems. Probably the greatest challenge in wastewater research lies in using the methods and the results obtained in one scientific discipline to design intelligent experiments in other disciplines, and eventually to improve the knowledge base the practitioner needs to run wastewater treatment plants. The purpose of Biofilms in Wastewater Treatment is to provide engineers with the knowledge needed to apply the new insights gained by researchers. The authors provide an authoritative insight into the function of biofilms on a technical and on a lab-scale, cover some of the exciting new basic microbiological and wastewater engineering research involving molecular biology techniques and microscopy, and discuss recent attempts to predict the development of biofilms. This book is divided into 3 sections: Modeling and Simulation; Architecture, Population Structure and Function; and From Fundamentals to Practical Application, which all start with a scientific question. Individual chapters attempt to answer the question and present different angles of looking at problems. In addition there is an extensive glossary to familiarize the non-expert with unfamiliar terminology used by microbiologists and computational scientists. The colour plate section of this book can be downloaded by clicking here. (PDF Format 1 MB)
Download or read book Biodefense in the Age of Synthetic Biology written by National Academies of Sciences, Engineering, and Medicine and published by National Academies Press. This book was released on 2019-01-05 with total page 189 pages. Available in PDF, EPUB and Kindle. Book excerpt: Scientific advances over the past several decades have accelerated the ability to engineer existing organisms and to potentially create novel ones not found in nature. Synthetic biology, which collectively refers to concepts, approaches, and tools that enable the modification or creation of biological organisms, is being pursued overwhelmingly for beneficial purposes ranging from reducing the burden of disease to improving agricultural yields to remediating pollution. Although the contributions synthetic biology can make in these and other areas hold great promise, it is also possible to imagine malicious uses that could threaten U.S. citizens and military personnel. Making informed decisions about how to address such concerns requires a realistic assessment of the capabilities that could be misused. Biodefense in the Age of Synthetic Biology explores and envisions potential misuses of synthetic biology. This report develops a framework to guide an assessment of the security concerns related to advances in synthetic biology, assesses the levels of concern warranted for such advances, and identifies options that could help mitigate those concerns.
Download or read book Cyanobacterial Biotechnology written by G. Subramanian and published by . This book was released on 1998 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume comprises select papers presented at a symposium held in September, 1996 in India. The contributors used the forum to disseminate their research findings.
Download or read book Genome Data Analysis written by Ju Han Kim and published by Springer. This book was released on 2019-04-30 with total page 367 pages. Available in PDF, EPUB and Kindle. Book excerpt: This textbook describes recent advances in genomics and bioinformatics and provides numerous examples of genome data analysis that illustrate its relevance to real world problems and will improve the reader’s bioinformatics skills. Basic data preprocessing with normalization and filtering, primary pattern analysis, and machine learning algorithms using R and Python are demonstrated for gene-expression microarrays, genotyping microarrays, next-generation sequencing data, epigenomic data, and biological network and semantic analyses. In addition, detailed attention is devoted to integrative genomic data analysis, including multivariate data projection, gene-metabolic pathway mapping, automated biomolecular annotation, text mining of factual and literature databases, and integrated management of biomolecular databases. The textbook is primarily intended for life scientists, medical scientists, statisticians, data processing researchers, engineers, and other beginners in bioinformatics who are experiencing difficulty in approaching the field. However, it will also serve as a simple guideline for experts unfamiliar with the new, developing subfield of genomic analysis within bioinformatics.
Download or read book Brenner s Encyclopedia of Genetics written by Stanley Maloy and published by Academic Press. This book was released on 2013-03-03 with total page 4360 pages. Available in PDF, EPUB and Kindle. Book excerpt: The explosion of the field of genetics over the last decade, with the new technologies that have stimulated research, suggests that a new sort of reference work is needed to keep pace with such a fast-moving and interdisciplinary field. Brenner's Encyclopedia of Genetics, Second Edition, Seven Volume Set, builds on the foundation of the first edition by addressing many of the key subfields of genetics that were just in their infancy when the first edition was published. The currency and accessibility of this foundational content will be unrivalled, making this work useful for scientists and non-scientists alike. Featuring relatively short entries on genetics topics written by experts in that topic, Brenner's Encyclopedia of Genetics, Second Edition, Seven Volume Set provides an effective way to quickly learn about any aspect of genetics, from Abortive Transduction to Zygotes. Adding to its utility, the work provides short entries that briefly define key terms, and a guide to additional reading and relevant websites for further study. Many of the entries include figures to explain difficult concepts. Key terms in related areas such as biochemistry, cell, and molecular biology are also included, and there are entries that describe historical figures in genetics, providing insights into their careers and discoveries. This 7-volume set represents a 25% expansion from the first edition, with over 1600 articles encompassing this burgeoning field Thoroughly up-to-date, with many new topics and subfields covered that were in their infancy or not inexistence at the time of the first edition. Timely coverage of emergent areas such as epigenetics, personalized genomic medicine, pharmacogenetics, and genetic enhancement technologies Interdisciplinary and global in its outlook, as befits the field of genetics Brief articles, written by experts in the field, which not only discuss, define, and explain key elements of the field, but also provide definition of key terms, suggestions for further reading, and biographical sketches of the key people in the history of genetics
Download or read book Industrialization of Biology written by National Research Council and published by National Academies Press. This book was released on 2015-06-29 with total page 158 pages. Available in PDF, EPUB and Kindle. Book excerpt: The tremendous progress in biology over the last half century - from Watson and Crick's elucidation of the structure of DNA to today's astonishing, rapid progress in the field of synthetic biology - has positioned us for significant innovation in chemical production. New bio-based chemicals, improved public health through improved drugs and diagnostics, and biofuels that reduce our dependency on oil are all results of research and innovation in the biological sciences. In the past decade, we have witnessed major advances made possible by biotechnology in areas such as rapid, low-cost DNA sequencing, metabolic engineering, and high-throughput screening. The manufacturing of chemicals using biological synthesis and engineering could expand even faster. A proactive strategy - implemented through the development of a technical roadmap similar to those that enabled sustained growth in the semiconductor industry and our explorations of space - is needed if we are to realize the widespread benefits of accelerating the industrialization of biology. Industrialization of Biology presents such a roadmap to achieve key technical milestones for chemical manufacturing through biological routes. This report examines the technical, economic, and societal factors that limit the adoption of bioprocessing in the chemical industry today and which, if surmounted, would markedly accelerate the advanced manufacturing of chemicals via industrial biotechnology. Working at the interface of synthetic chemistry, metabolic engineering, molecular biology, and synthetic biology, Industrialization of Biology identifies key technical goals for next-generation chemical manufacturing, then identifies the gaps in knowledge, tools, techniques, and systems required to meet those goals, and targets and timelines for achieving them. This report also considers the skills necessary to accomplish the roadmap goals, and what training opportunities are required to produce the cadre of skilled scientists and engineers needed.
Download or read book Synthetic Metabolic Pathways written by Michael Krogh Jensen and published by Humana Press. This book was released on 2017-11-24 with total page 354 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume outlines key steps associated with the design, building, and testing of synthetic metabolic pathways for optimal cell factory performance and robustness, and illustrates how data-driven learning from these steps can be used for rational cost-effective engineering of cell factories with improved performance. Chapters are divided into four sections focusing on the four steps of the iterative design-build-test-learn cycle related to modern cell factory engineering. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Synthetic Metabolic Pathways: Methods and Protocols aims to ensure successful results in the further study of this vital field.
Download or read book Biology for the IB Diploma Coursebook written by Brenda Walpole and published by Cambridge University Press. This book was released on 2011-03-24 with total page 609 pages. Available in PDF, EPUB and Kindle. Book excerpt: This text offers an in-depth analysis of all topics covered in the IB syllabus, preparing students with the skills needed to succeed in the examination. Features include: clearly stated learning objectives at the start of each section; quick questions throughout each chapter and accessible language for students at all levels.
