Download or read book Deciphering of Packing Signal Hypothesis in Bacterophage RNA Recognition by the MS2 Capsid Protein in Virus Assembly written by Lokendra Poudel and published by . This book was released on 2018 with total page 131 pages. Available in PDF, EPUB and Kindle. Book excerpt: MS2 is a classical example of a single-stranded RNA virus for which the genomic RNA plays pivotal roles in the virus assembly process. Multiple dispersed RNA sequence/structure motifs, packaging signals (PSs) varying around a central recognition motif, interact with capsid protein in a process referred to as packaging signal mediated assembly. While the discovery and identification of these PSs was based on bioinformatics and geometric approaches, in tandem with sophisticated experimental protocols, we approach this problem by an altogether different philosophy, using a large-scale quantitative ab initio methodology centered on critical aspects of the consensus PS recognition motif. DFT calculations are carried out on four nucleopro tein complexes (PDB IDs: 1ZDI, 1ZDH, 5MSF and 6MSF) that are representative of the phage MS2 PSs. We have calculated atomic partial charge in the models using ab initio DFT based OLCAO method. The calculated partial charge distribution of individual protein and RNA residues indicates that the gross features is the same in CP because they have identical sequences, but there are some important minor differences due to the different RNAs to which they bind. It shows that CP is lost and ssRNA is gained charge in all models. The loss of charge by CP in order of 6MSF>5MSF>1ZDI>1ZDH in CP-RNA complex. We have also calculated strength of the interfacial hydrogen bonding (HB) configurations between protein and RNA. The interfacial HBs enable us to locate the exact binding sites of both nucleoprotein, corresponding to the sites exhibiting the strongest interfacial HBs, here identified to be (TYR85-U−5) in 1ZDI and LYS43 A−4 in 1ZDH, 5MSF and 6MSF. The formation of stronger HBs can be traced to the change in the sequence of the mutated RNA, and three-base loop motif leading to more pronounced HB fit between the amino acids and nucleobases. We have quantify HB with a physical quantum quantity of bond order (BO) and summed up all BO values of interfacial HBs as a total bond order (TBO). This is very important quantum quantity for strength of binding between CP and ssRNA. We found that he interfacial TBO are in order of 6MSF>1ZDI>5MSF>1ZDH. The binding between CP with RNA is higher in three-base loop motif than tetra-base loop motif and the mutate form of RNA has higher binding than wild type RNA. Moreover, simulation provided quantitative information on the strength of CP-RNA interactions with respect to RNA sequences. Finally, our study exemplifying the role that modern computational techniques can play in further advancing the field of physical virology.
Download or read book Cumulated Index Medicus written by and published by . This book was released on 1997 with total page 1860 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Recoding Expansion of Decoding Rules Enriches Gene Expression written by John F. Atkins and published by Springer Science & Business Media. This book was released on 2010-03-10 with total page 473 pages. Available in PDF, EPUB and Kindle. Book excerpt: The literature on recoding is scattered, so this superb book ?lls a need by prov- ing up-to-date, comprehensive, authoritative reviews of the many kinds of recoding phenomena. Between 1961 and 1966 my colleagues and I deciphered the genetic code in Escherichia coli and showed that the genetic code is the same in E. coli, Xenopus laevis, and guinea pig tissues. These results showed that the code has been c- served during evolution and strongly suggested that the code appeared very early during biological evolution, that all forms of life on earth descended from a c- mon ancestor, and thus that all forms of life on this planet are related to one another. The problem of biological time was solved by encoding information in DNA and retrieving the information for each new generation, for it is easier to make a new organism than it is to repair an aging, malfunctioning one. Subsequently, small modi?cations of the standard genetic code were found in certain organisms and in mitochondria. Mitochondrial DNA only encodes about 10–13 proteins, so some modi?cations of the genetic code are tolerated that pr- ably would be lethal if applied to the thousands of kinds of proteins encoded by genomic DNA.
Download or read book RNA Phages written by Norton D. Zinder and published by . This book was released on 1975 with total page 448 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Virus Derived Nanoparticles for Advanced Technologies written by Christina Wege and published by Humana Press. This book was released on 2018-06-05 with total page 671 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume details protocols on virus-derived nanoparticles (VNPs) for a number of different applications. Chapters guide readers through the production of VNPs derived from plant, animal and bacterial viruses, prokaryotic and eukaryotic expression systems, encapsulation of heterologous materials within VNPs, and the modification of the outer surface of VNPs and how such modified VNPs can be developed into functional entities. 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, Virus-Derived Nanoparticles for Advanced Technologies: Methods and Protocols aims to ensure successful results in the further study of this vital field.
Download or read book The Bacteriophages written by Richard Calendar and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 607 pages. Available in PDF, EPUB and Kindle. Book excerpt: It has been 10 years since Plenum included a series of reviews on bacte riophages, in Comprehensive Virology. Chapters in that series contained physical-genetic maps but very little DNA sequence information. Now the complete DNA sequence is known for some phages, and the se quences for others will soon follow. During the past 10 years two phages have come into common use as reagents: A phage for cloning single copies of genes, and Ml3 for cloning and DNA sequencing by the dideoxy termi nation method. Also during that period the use of alternative sigma fac tors by RNA polymerase has become established for SPOl and T4. This seems to be a widely used mechanism in bacteria, since it has been implicated in sporulation, heat shock response, and regulation of nitro gen metabolism. The control of transcription by the binding of A phage CII protein to the -35 region of the promoter is a recent finding, and it is not known how widespread this mechanism may be. This rapid progress made me eager to solicit a new series of reviews. These contributions are of two types. Each of the first type deals with an issue that is exemplified by many kinds of phages; chapters of this type should be useful in teaching advanced courses. Chapters of the second type provide comprehensive pictures of individual phage families and should provide valuable information for use in planning experiments.
Download or read book Cryo EM Part B 3 D Reconstruction written by and published by Academic Press. This book was released on 2010-09-30 with total page 472 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume is dedicated to a description of the instruments, samples, protocols, and analyses that belong to cryo-EM. It emphasizes the relatedness of the ideas, instrumentation, and methods underlying all cryo-EM approaches, which allow practitioners to easily move between them. Within each section, the articles are ordered according to the most common symmetry of the sample to which their methods are applied. Includes time-tested core methods and new innovations applicable to any researcher Methods included are useful to both established researchers and newcomers to the field Relevant background and reference information given for procedures can be used as a guide
Download or read book Principles of Molecular Virology written by Alan Cann and published by Elsevier. This book was released on 2005-07-26 with total page 340 pages. Available in PDF, EPUB and Kindle. Book excerpt: "Principles of Molecular Virology, Fourth Edition" provides an essential introduction to modern virology in a clear and concise manner. It is a highly enjoyable and readable text with numerous illustrations that enhance the reader's understanding of important principles. It contains new material on virus structure, virus evolution, zoonoses, bushmeat, SARS and bioterrorism. The standard version includes a CD-ROM with Flash animations, virtual interactive tutorials and experiments, self-assessment questions, useful online resources, along with the glossary, classification of subcellular infectious agents and history of virology.
Download or read book Bacteriophages written by Martha R.J. Clokie and published by Humana Press. This book was released on 2017-11-15 with total page 316 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book expands on the previous volumes with new chapters exploring emerging themes and methodologies in bacterial virus research. The chapters in this book are divided into 4 parts and cover topics such as: iron chloride flocculation of bacteriophages from seawater; encapsulation of Listeria phage A511 by alginate; examining genome termini of bacteriophage through high-throughput sequencing; genome sequencing of dsDNA-containing bacteriophages directly from a single plaque; characterizing bacteriophages by biology, taxonomy, and genome analysis; phage genome annotation using the RAST pipeline; and the use of RP4::mini-Mu for gene transfer. 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. Cutting edge and authoritative, Bacteriophages: Methods and Protocols, Volume III is a valuable resource for both established and novice phage scientists.
Download or read book Viral Polymerases written by Satya Prakash Gupta and published by Academic Press. This book was released on 2018-10-29 with total page 496 pages. Available in PDF, EPUB and Kindle. Book excerpt: Viral Polymerases: Structures, Functions and Roles as Antiviral Drug Targets presents in-depth study information on the structure and functions of polymerases and their roles in the lifecycle of viruses, and as drug targets. Viral polymerases constitute a vital component in the lifecycle of many viruses, such as human immunodeficiency virus (HIV), hepatitis viruses, influenza virus, and several others. They are essentially required for the replication of viruses. Thus, the polymerases that can be found in viruses (called viral polymerases) represent favorable targets for the design and development of antiviral drugs. Provides comprehensive, state-of-the-art coverage on virus infections, the virus lifecycle, and mechanisms of polymerase inhibition Analyzes the structure-activity relationships of inhibitors of each viral polymerase Presents a consistent and comprehensive coverage of all aspects of viral polymerases, including structure, function and their role as antiviral drug targets
Download or read book Chemical and Biological Terrorism written by Committee on R&D Needs for Improving Civilian Medical Response to Chemical and Biological Terrorism Incidents and published by National Academies Press. This book was released on 1999-02-26 with total page 303 pages. Available in PDF, EPUB and Kindle. Book excerpt: The threat of domestic terrorism today looms larger than ever. Bombings at the World Trade Center and Oklahoma City's Federal Building, as well as nerve gas attacks in Japan, have made it tragically obvious that American civilians must be ready for terrorist attacks. What do we need to know to help emergency and medical personnel prepare for these attacks? Chemical and Biological Terrorism identifies the R&D efforts needed to implement recommendations in key areas: pre-incident intelligence, detection and identification of chemical and biological agents, protective clothing and equipment, early recognition that a population has been covertly exposed to a pathogen, mass casualty decontamination and triage, use of vaccines and pharmaceuticals, and the psychological effects of terror. Specific objectives for computer software development are also identified. The book addresses the differences between a biological and chemical attack, the distinct challenges to the military and civilian medical communities, and other broader issues. This book will be of critical interest to anyone involved in civilian preparedness for terrorist attack: planners, administrators, responders, medical professionals, public health and emergency personnel, and technology designers and engineers.
Download or read book Flexible Viruses written by Vladimir Uversky and published by John Wiley & Sons. This book was released on 2012-02-07 with total page 532 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides up-to-date information on experimental and computational characterization of the structural and functional properties of viral proteins, which are widely involved in regulatory and signaling processes. With chapters by leading research groups, it features current information on the structural and functional roles of intrinsic disorders in viral proteomes. It systematically addresses the measles, HIV, influenza, potato virus, forest virus, bovine virus, hepatitis, and rotavirus as well as viral genomics. After analyzing the unique features of each class of viral proteins, future directions for research and disease management are presented.
Download or read book Phage Display of Peptides and Proteins written by Brian K. Kay and published by Elsevier. This book was released on 1996-10-23 with total page 369 pages. Available in PDF, EPUB and Kindle. Book excerpt: Both novices and experts will benefit from this insightful step-by-step discussion of phage display protocols.Phage Display of Peptides and Proteins: A Laboratory Manual reviews the literature and outlines the strategies for maximizing the successful application of phage display technology to one's research. It contains the most up-to-date protocols for preparing peptide affinity reagents, monclonal antibodies, and evolved proteins. Prepared by experts in the field Provides proven laboratory protocols, troubleshooting, and tips Includes maps, sequences, and sample data Contains extensive and up-to-date references
Download or read book PCR for Clinical Microbiology written by Ian W.J. Carter and published by Springer Science & Business Media. This book was released on 2010-07-03 with total page 420 pages. Available in PDF, EPUB and Kindle. Book excerpt: Not another textbook, but a valuable tool for doctors and microbiologists wanting to know how to set up a PCR diagnostic microbiology laboratory according to current regulatory standards and perform assays supplied with patient clinical diagnostic criteria and easy to follow protocols. Whether laboratories are using commercial kits or in-house methods developed in their own laboratories or adopted from published methods, all clinical microbiology laboratories need to be able to understand, critically evaluate, perform and interpret these tests according to rigorous and clinically appropriate standards and international guidelines. The cost and effort of development and evaluation of in-house tests is considerable and many laboratories do not have the resources to do so. This compendium is a vehicle to improve and maintain the clinical relevance and high quality of diagnostic PCR. It is a unique collection of; guidelines for PCR laboratory set up and quality control, test selection criteria, methods and detailed step by step protocols for a diagnostic assays in the field of molecular microbiology. The structure of the book provides the PCR fundamentals and describes the clinical aspects and diagnosis of infectious disease. This is followed by protocols divided into; bacteria, virus, fungi and parasites, and susceptibility screens. The inclusion of medical criteria and interpretation adds value to the compendium and benefits clinicians, scientists, researchers and students of clinical diagnostic microbiology
Download or read book Desk Encyclopedia of Microbiology written by Moselio Schaechter and published by Academic Press. This book was released on 2010-04-19 with total page 1277 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Desk Encyclopedia of Microbiology, Second Edition is a single-volume comprehensive guide to microbiology for the advanced reader. Derived from the six volume e-only Encyclopedia of Microbiology, Third Edition, it bridges the gap between introductory texts and specialized reviews. Covering topics ranging from the basic science of microbiology to the current "hot" topics in the field, it will be invaluable for obtaining background information on a broad range of microbiological topics, preparing lectures and preparing grant applications and reports. The most comprehensive single-volume source providing an overview of microbiology to non-specialists Bridges the gap between introductory texts and specialized reviews Provides concise and general overviews of important topics within the field making it a helpful resource when preparing for lectures, writing reports, or drafting grant applications
Download or read book RNA protein Interactions written by Kiyoshi Nagai and published by Oxford University Press, USA. This book was released on 1994 with total page 302 pages. Available in PDF, EPUB and Kindle. Book excerpt: The study of RNA-protein interactions is crucial to understanding the mechanisms and control of gene expression and protein synthesis. The realization that RNAs are often far more biologically active than was previously appreciated has stimulated a great deal of new research in this field. Uniquely, in this book, the world's leading researchers have collaborated to produce a comprehensive and current review of RNA-protein interactions for all scientists working in this area. Timely, comprehensive, and authoritative, this new Frontiers title will be invaluable for all researchers in molecular biology, biochemistry and structural biology.
Download or read book Innovations and Implementations of Computer Aided Drug Discovery Strategies in Rational Drug Design written by Sanjeev Kumar Singh and published by Springer Nature. This book was released on 2021-02-02 with total page 334 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents various computer-aided drug discovery methods for the design and development of ligand and structure-based drug molecules. A wide variety of computational approaches are now being used in various stages of drug discovery and development, as well as in clinical studies. Yet, despite the rapid advances in computer software and hardware, combined with the exponential growth in the available biological information, there are many challenges that still need to be addressed, as this book shows. In turn, it shares valuable insights into receptor-ligand interactions in connection with various biological functions and human diseases. The book discusses a wide range of phylogenetic methods and highlights the applications of Molecular Dynamics Simulation in the drug discovery process. It also explores the application of quantum mechanics in order to provide better accuracy when calculating protein-ligand binding interactions and predicting binding affinities. In closing, the book provides illustrative descriptions of major challenges associated with computer-aided drug discovery for the development of therapeutic drugs. Given its scope, it offers a valuable asset for life sciences researchers, medicinal chemists and bioinformaticians looking for the latest information on computer-aided methodologies for drug development, together with their applications in drug discovery.
