Computational biology / bioinformatics Books

Book SynopsisA Step-by-Step Guide to Present and Future Uses of Microarray TechnologyMicroarray technology continues to evolve, taking on a variety of forms. From the spotting of cDNA and the in situ synthesis of oligonucleotide arrays now come microarrays comprising proteins, carbohydrates, drugs, tissues, and cells. With contributions from microarray experts in both academia and industry, Microarray Methods and Protocols is a turn-by-turn roadmap through the processes necessary to perform a successful microarray experiment.This easy to use book addresses the fundamental aspects of preparing and processing microarrays and bead arrays, labeling, and detection. It also includes a detailed How it Works section that discusses the underlying principles of a number of techniques. Troubleshooting guides offer additional advice for the successful performance of more than 100 protocols in 10 chapters that cover work iTrade ReviewThe book will be useful for researchers in protein chemistry and biochemistry, molecular biologists, and teachers and students of medical schools and universities specializing in microarray methods.--Doctor of Biological Sciences, G. Ya. Wiederschain. Biochemsitry - Moscow. 2010, VOL 75, No 9,1182Table of ContentsIntroduction to Microarray Technologies. Nucleic Acid Sample Preparation. Solid-Phase Substrates for Nucleic Acid Microarrays. Protein Sample Preparation for Microarrays. Solid-Phase Chemistries for Protein Microarrays. Protein Microarrays: The Link between Genomics and Proteomics. Bead Arrays: An Introduction to Multiplexed Bead-Based Assays for Proteins. Carbohydrate Arrays. Lectin Microarrays. Printing Methods. Appendix A: Microarray Reagent, Materials, and Equipment Sources. Appendix B: Image Analysis. Index.

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Book SynopsisScientists can use molecular profiling microarrays to compare healthy cells with their diseased counterparts and develop gene-specific treatments. Finding the best way to interpret original profiling data into accurate trends, however, continues to drive the development of normalization algorithms and software tools. Methods in Microarray Normalization compiles the most useful and novel techniques for the first time into a single, organized source. Experts in the field provide a diverse view of the mathematical processes that are important in normalizing data and avoiding inherent systematic biases. They also review useful software, including discussions on key algorithms, comparative data, and download locations. The book discusses the use of early normalization techniques for new profiling methods and includes strategies for assessing the utility of various normalization algorithms. It presents the latest microarray innovations from companies such as Agilent, Affymetrix,Trade Review"Methods in Microarray Normalization compiles the most useful and novel techniques for the first time into a single, organized source. Experts in the field provide a diverse view of the mathematical processes that are important in normalizing data and avoiding inherent systematic biases." – In Anticancer Research, July/August 2008, Vol. 28, No. 4ATable of ContentsA comprehensive analysis of the effect of microarray data preprocessing methods on differentially expressed transcript selection. Differentiation detection in microarray normalization. Preprocessing and normalization for affymetrix genechip expression microarrays. Spatial detrending and normalization methods for two-channel DNA and protein microarray data. A survey of cDNA microarray normalization and a comparison by k-NN classification. Technical variation in modeling the joint expression of several genes. Biological interpretation for microarray normalization selection. Methodology of functional analysis for omics data normalization. Exon array analysis for the detection of alternative splicing. Normalization of array CGH data. SNP array-based analysis for detection of chromosomal aberrations and copy number variations. Index.

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Book SynopsisA Step-by-Step Guide to Describing Biomolecular StructureComputational and Visualization Techniques for Structural Bioinformatics Using Chimera shows how to perform computations with Python scripts in the Chimera environment. It focuses on the three core areas needed to study structural bioinformatics: biochemistry, mathematics, and computation.Understand Important Concepts of Structural BioinformaticsThe book covers topics that deal primarily with protein structure and includes many exercises that are grounded in biological problems at the molecular level. The text encourages mathematical analysis by providing a firm foundation for computations. It analyzes numerous Python scripts for the Chimera environment, with the scripts and other material available on a supplementary website.Build Python Scripts to Extend the Capabilities of ChimeraThrough more than 60 exercises that involve the develTrade Review"This book supports an approach to bioinformatics that balances biological problems, mathematical modeling, and computational tools. It breaks down the mathematical complications into manageable parts and augments programming skills while developing biological insight."—L. Ridgway Scott, Louis Block Professor of Computer Science and Mathematics, Member of the Institute for Biophysical Design, Senior Fellow of the Computation Institute, University of Chicago"This book is a useful resource for experienced and newcomer Chimera users alike. It helps extend it programmatically, allowing users to perform any number of useful types of calculations that are often required in conjunction with visualization. From distances to graphs, any way you measure it, Prof. Burkowski’s book is a must have for Chimera users."—Rafael Najmanovich, PhD, Associate Professor, Université de Sherbrooke"Structural bioinformatics is a young science that lies at the crossroads of several synergizing disciplines, including biophysics, structural biology, mathematical modeling, and computational methods. In this context, the book by Forbes Burkowski constitutes a true landmark, enabling the practitioner to implement and exploit computational techniques to test the mathematical models and frame novel hypothesis. This engrossing book is directed at advanced undergraduates and professionals who seek to represent and explore novel structural concepts to describe biomolecular phenomena. Very useful practical applications of the computational techniques presented in the book are likely to emerge, especially in the fields of molecular engineering and structure-based drug design. Thus, I predict that the book will become mandatory for researchers interested in rational design in the pharmaceutical industry and materials science."—Ariel Fernandez, Ph.D., Former Hasselmann Professor of Bioengineering at Rice University and Pioneer of the Wrapping Technology in Drug Design"Students taught with Computational and Visualization Techniques for Structural Bioinformatics Using Chimera will gain not only a thorough understanding of the important concepts of structural bioinformatics, from the basics of protein structure through advanced topics such as molecular mechanics, but also the ability to perform their own analyses using the programming techniques and libraries offered by this book and its supporting materials. The exercises are engaging and vary from problems that can be solved in a few minutes to mini-projects that might require a week of effort. All concepts are clearly described and accompanied by helpful illustrations where needed. This text does an excellent job of turning students into investigators."—Eric Pettersen, UCSF Department of Pharmaceutical ChemistryTable of ContentsIntroduction: Macromolecules and Chimera. Accessing and Displaying Molecular Data with Chimera. Algorithms Dealing with Distance. Algorithms Dealing with Angles. Structure Overlap and Alignment. Potential Energy Functions. Rotamers and Side‑Chain Conformation. Residue Networks. Appendices. Index.

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Book SynopsisLearn the data skills necessary for turning large sequencing datasets into reproducible and robust biological findings. With this practical guide, you'll learn how to use freely available open source tools to extract meaning from large complex biological data sets.

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Book SynopsisThis publication is sponsored by the American Association for Medical Systems and Informatics. The Board of AAMSI and the Board of the Society for Computer Medicine, one of AAMSI''s predecessors, agreed that a book on application of medical systems and informatics for the practitioner would help promote high quality health care and they charged the Committee on Standards of the Society for Computer Medicine to write such a text. It is intended as a guide for the field of medical systems and informatics with emphasis on standards, terminology, and coding systems. The text, a result of three years of research and effort, has been reviewed by the Board of Directors of AAMSI and approved by the Publications Committee. We believe that you will find it valuable and hope to revise it from time to time to meet current needs. On behalf of the members of the Association, we congratulate thTable of ContentsI Introduction to Accounting Systems.- 1 Beyond Billing: Some Things You Should Know Before You Begin.- 2 What Sort of Data Should Be Collected and Why?.- 3 The Accounting Module.- II Introduction to Administrative Systems.- 4 The Administration Module.- III Introduction to Health Care Delivery Systems.- 5 How Computers Can Help in Patient Care and Practice (Health Care Delivery).- 6 How Physician Professional Education and Development Can Be Enhanced by Computers.- 7 The Medical Record Summary, Contents, and Utilization.- 8 History Gathering Techniques Via the Computer.- 9 Supervising and Keeping Track of Patient Care.- 10 Quality Assessment and Quality Control of Patient Care.- 11 Patient/Parent/Family Educational Assists.- IV Introduction to Planning, Vendors, and Implementation.- 12 Planning for Automation: The Total Office Practice System.- 13 Be Prepared to Give, Not Receive, the Sales Pitch.- 14 Problems with System Implementation.- 15 Office Computing and the Right to Privacy.- 16 Summary.- Appendices.

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Book SynopsisComputer technology has impacted the practice of medicine in dramatic ways. In many cases, these appli­ cations are limited to administrative functions, e.g., office practice man­ agement, location of hospital patients, appointments, and scheduling.Table of Contentsfor Volume 1.- I. Introduction.- 1. An Overview of Methods for Computer-Assisted Medical Decision Making.- 2. Reasoning Foundations of Medical Diagnosis.- II. Algorithmic Approaches.- 3. Computer-Based Consultation: Electrolyte and Acid-Base Disorders.- 4. Reduction of Digitalis Toxicity by Computer-Assisted Glycoside Dosage Regimens.- 5. A Consultant-Extender System for Breast Cancer Adjuvant Chemotherapy.- III. Statistically Oriented Approaches.- 6. A Mathematical Approach to Medical Diagnosis: Application to Congenital Heart Disease.- 7. Computer-Aided Diagnosis of Acute Abdominal Pain.- 8. Computer-Assisted Diagnosis of Abdominal Pain Using “Estimates” Provided by Clinicians.- 9. Bayes’ Theorem and Conditional Nonindependence of Data in Medical Diagnosis.- 10. Transferability of Medical Decision Support Systems Based on Bayesian Classification.- 11. Experience with a Model of Sequential Diagnosis.- 12. Pattern-Based Interactive Diagnosis of Multiple Disorders: The MEDAS System.- 13. Enhancement of Clinical Predictive Ability by Computer Consultation.- 14. Decision Analysis and Clinical Judgment.

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Book SynopsisIn recent years, owing to the fast development of a variety of sequencing technologies in the post human genome project era, sequencing analysis of a group of target genes, entire protein coding regions of the human genome, and the whole human genome has become a reality.Table of ContentsPart I: Overview.- History of DNA Sequencing Technologies.- Clinical Molecular Diagnostic Techniques: A Brief Review.- Part II: The Technologies and Bioinformatics.- Methods of Gene Enrichment and Massively Parallel Sequencing Technologies.- Sequence Alignment, Analysis, and Bioinformatics Pipelines.- Protein Structural Based Analysis for Variant Interpretation of Missense Variants at the Genomics Era: Using MNGIE Disease as an Example.- Algorithms and Guidelines for Interpretation of DNA Variants.- Part III: Application to Clinical Diagnostics.- NGS-based Clinical Diagnosis of Genetically Heterogeneous Disorders.- Molecular Diagnosis of Congenital Disorders of Glycosylation (CDG).- NGS Improves the Diagnosis of X-Linked Intellectual Disability (XLID).- NGS Analysis of Heterogeneous Retinitis Pigmentosa.- Next Generation Sequencing of the Whole Mitochondrial Genome.- Application of Next-Generation Sequencing of Nuclear Genes for Mitochondrial Disorders.- ​Noninvasive Prenatal Diagnosis Using Next Generation Sequencing.- Part IV: Compliance with CAP/CLIA Regulations.- Guidelines and Approaches to Compliance with Regulatory and Clinical Standards: Quality Control Procedures and Quality Assurance.- Validation of NGS-based Test and Implementation of Quality Control Procedures.- Frequently Asked Questions about the Clinical Utility of Next Generation Sequencing in Molecular Diagnosis of Human Genetic Diseases.- Index.

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Book SynopsisThe State of the Art in Transcriptome Analysis RNA sequencing (RNA-seq) data offers unprecedented information about the transcriptome, but harnessing this information with bioinformatics tools is typically a bottleneck. RNA-seq Data Analysis: A Practical Approach enables researchers to examine differential expression at gene, exon, and transcript levels and to discover novel genes, transcripts, and whole transcriptomes.Balanced Coverage of Theory and Practice.Each chapter starts with theoretical background, followed by descriptions of relevant analysis tools and practical examples. Accessible to both bioinformaticians and nonprogramming wet lab scientists, the examples illustrate the use of command-line tools, R, and other open source tools, such as the graphical Chipster software.The Tools and Methods to Get Started in Your Lab. Taking readers through the whole data analysis workflow, this self-contained guide provides a detailed oveTrade Review"Next-generation sequencing (NGS) is without doubt among the last decade’s most important technological advance in molecular biology, and RNA sequencing is its most common application, rapidly becoming an indispensable tool in drug discovery and biomarker identification. Given the complexity and fast-paced evolution of the NGS methodology, it may seem overwhelming to a novice to figure out where to get started. RNA-seq Data Analysis: A Practical Approach solves this problem: the single volume provides the reader with a wealth of details extending from the very fundamentals of NGS technology to comprehensive hands-on instructions on how to interpret your freshly baked sequencing reads. After reading this book, you will have all the necessary information to start putting RNA-seq to work answering your research questions."—Dr. Satu Nahkuri, Pharma Research and Early Development, F. Hoffmann-La Roche Ltd."This is a fantastic book and a real resource for anyone embarking or already working in RNA-seq data analysis. It is a practical guide that provides layers of information to the reader to comprehend the different steps and options when analysing RNA-seq data. The content and style of the book are great and the authors clearly explain and provide well-rounded examples. This book stands out among others since it is very easy to follow and does not require a strong programming or statistical background. It is obvious the authors have experience with explaining and probably teaching others on how to perform RNA-seq analysis. I highly recommend this book to students, researchers, as well as trainers in RNA-seq data analysis."—Dr. Maria Victoria Schneider (Vicky), The Genome Analysis Centre, UK"It is really a very practical book for both wet lab biologists and computer scientists working on RNA-seq projects. The book is clearly written with a general introduction to RNA-seq in Chapter 1 and a brief description to RNA-seq data analysis in Chapter 2. Detailed information of computational methods, analysis pipelines, and software tools are presented in the remaining chapters with some real examples. I believe that this book will serve not only as a textbook for an introductory course of omics data analysis but also as a guideline for researchers working on RNA-seq projects."—Jingchu Luo, Professor, Peking University"RNA-seq is currently the best method for genome-wide transcriptional profiling of cells in about any organism. This book includes all the key steps, in generally the same organization, that we’ve found to be effective when training biologists and bioinformaticians in RNA-seq analysis. It’s a good guide and reference for RNA-seq that can get analysts started (or keep them going) while avoiding much of the time-consuming literature, documentation, and Web searches at each step of the pipeline. It covers a broad (but not overwhelming) selection of popular methods without the typical bias of an author’s research emphasis."—George W. Bell, Ph.D., Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA"In modern life sciences, it is increasingly the bioinformatics aspect that holds the essential key to successful research projects and discoveries, albeit often poorly understood, or even regarded as a ‘black box.’ This is precisely the point at which RNA-seq Data Analysis: A Practical Approach comes in. This book, a brilliant compilation of all different aspects of RNA-sequencing analyses, opens up this ‘black box’ and reveals all of its inner workings. It covers all the basic principles while maintaining a tight focus on the practical aspects of successful analyses, including discussing caveats and possible pitfalls. Following this spirit throughout, it is intuitively structured and easy to read, making it attractive both for researchers who want to quickly deepen their understanding of RNA-seq processing and for use as teaching material in the classroom for the scientists of the future."—Manfred Grabherr, Department of Medical Biochemistry and Microbiology, Uppsala University"I feel that this is a marvelous book and will be of invaluable use to support bioinformaticians, graduate students, and the occasional user of the RNA-seq technology. It has great depth of content and addresses the key areas of designing your study and making sense of the data. It covers the typical scenarios that a services bioinformatician is likely to encounter and I can see this book having a place on desks of scientists across academia and industry."—Stephen Rudd, Head of Computational Biology, University of Queensland"I strongly recommend RNA-seq Data Analysis: A Practical Approach to any scientist who plans to do sequencing experiments, even if he will not analyze the data by himself. The book gives in the first parts very important outlines of the sequencing technology and how it is working. … Going further, the book covers all state-of-the-art techniques of RNA-seq analysis in a very profound yet clear way and will be of great value even for the advanced bioinformatician as a reference work. … a must-have recommendation to everyone working in the molecular biology field … Even as a bioinformatician with over 15 years of experience in this field, I found many valuable details and some yet not known facts about sequencing data analysis."—Oliver Heil, Bioinformatician, German Cancer Research Center (DKFZ)"Many people are interested in applying RNA-seq to examine the transcriptome of their organism of interest but they are finding it difficult to apply it in their own laboratories. … In this book, RNA-seq is introduced by describing the different platforms and then the reader is taken in a systematic way through the process of analyzing RNA-seq data using several free open source tools. This book will be of interest to people starting with RNA-seq."—Dr. Etienne de Villiers, Bioinformatics Group Leader, KEMRI-Wellcome Trust Research Programme (KWTRP), and Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford"Next-generation sequencing (NGS) is without doubt among the last decade’s most important technological advance in molecular biology, and RNA sequencing is its most common application, rapidly becoming an indispensable tool in drug discovery and biomarker identification. Given the complexity and fast-paced evolution of the NGS methodology, it may seem overwhelming to a novice to figure out where to get started. RNA-seq Data Analysis: A Practical Approach solves this problem: the single volume provides the reader with a wealth of details extending from the very fundamentals of NGS technology to comprehensive hands-on instructions on how to interpret your freshly baked sequencing reads. After reading this book, you will have all the necessary information to start putting RNA-seq to work answering your research questions."—Dr. Satu Nahkuri, Pharma Research and Early Development, F. Hoffmann-La Roche Ltd."This is a fantastic book and a real resource for anyone embarking or already working in RNA-seq data analysis. It is a practical guide that provides layers of information to the reader to comprehend the different steps and options when analysing RNA-seq data. The content and style of the book are great and the authors clearly explain and provide well-rounded examples. This book stands out among others since it is very easy to follow and does not require a strong programming or statistical background. It is obvious the authors have experience with explaining and probably teaching others on how to perform RNA-seq analysis. I highly recommend this book to students, researchers, as well as trainers in RNA-seq data analysis."—Dr. Maria Victoria Schneider (Vicky), The Genome Analysis Centre, UK"It is really a very practical book for both wet lab biologists and computer scientists working on RNA-seq projects. The book is clearly written with a general introduction to RNA-seq in Chapter 1 and a brief description to RNA-seq data analysis in Chapter 2. Detailed information of computational methods, analysis pipelines, and software tools are presented in the remaining chapters with some real examples. I believe that this book will serve not only as a textbook for an introductory course of omics data analysis but also as a guideline for researchers working on RNA-seq projects."—Jingchu Luo, Professor, Peking University"RNA-seq is currently the best method for genome-wide transcriptional profiling of cells in about any organism. This book includes all the key steps, in generally the same organization, that we’ve found to be effective when training biologists and bioinformaticians in RNA-seq analysis. It’s a good guide and reference for RNA-seq that can get analysts started (or keep them going) while avoiding much of the time-consuming literature, documentation, and Web searches at each step of the pipeline. It covers a broad (but not overwhelming) selection of popular methods without the typical bias of an author’s research emphasis."—George W. Bell, Ph.D., Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA"In modern life sciences, it is increasingly the bioinformatics aspect that holds the essential key to successful research projects and discoveries, albeit often poorly understood, or even regarded as a ‘black box.’ This is precisely the point at which RNA-seq Data Analysis: A Practical Approach comes in. This book, a brilliant compilation of all different aspects of RNA-sequencing analyses, opens up this ‘black box’ and reveals all of its inner workings. It covers all the basic principles while maintaining a tight focus on the practical aspects of successful analyses, including discussing caveats and possible pitfalls. Following this spirit throughout, it is intuitively structured and easy to read, making it attractive both for researchers who want to quickly deepen their understanding of RNA-seq processing and for use as teaching material in the classroom for the scientists of the future."—Manfred Grabherr, Department of Medical Biochemistry and Microbiology, Uppsala University"I feel that this is a marvelous book and will be of invaluable use to support bioinformaticians, graduate students, and the occasional user of the RNA-seq technology. It has great depth of content and addresses the key areas of designing your study and making sense of the data. It covers the typical scenarios that a services bioinformatician is likely to encounter and I can see this book having a place on desks of scientists across academia and industry."—Stephen Rudd, Head of Computational Biology, University of Queensland"I strongly recommend RNA-seq Data Analysis: A Practical Approach to any scientist who plans to do sequencing experiments, even if he will not analyze the data by himself. The book gives in the first parts very important outlines of the sequencing technology and how it is working. … Going further, the book covers all state-of-the-art techniques of RNA-seq analysis in a very profound yet clear way and will be of great value even for the advanced bioinformatician as a reference work. … a must-have recommendation to everyone working in the molecular biology field … Even as a bioinformatician with over 15 years of experience in this field, I found many valuable details and some yet not known facts about sequencing data analysis."—Oliver Heil, Bioinformatician, German Cancer Research Center (DKFZ)"Many people are interested in applying RNA-seq to examine the transcriptome of their organism of interest but they are finding it difficult to apply it in their own laboratories. … In this book, RNA-seq is introduced by describing the different platforms and then the reader is taken in a systematic way through the process of analyzing RNA-seq data using several free open source tools. This book will be of interest to people starting with RNA-seq."—Dr. Etienne de Villiers, Bioinformatics Group Leader, KEMRI-Wellcome Trust Research Programme (KWTRP), and Centre for Tropical Medicine, Nuffield Department of Medicine, University of OxfordTable of ContentsIntroduction. Quality Control. Mapping, and Assembly. Differential Expression. Analysis of Small Non-Coding RNAs.

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Book SynopsisProtein Design: Method and Applications, Second Edition expands upon the previous edition with current, detailed ideas on how to approach a potential protein design project.Table of Contents1. De novo Design of Stable α-helicesAlexander Yakimov, Georgy Rychkov, and Michael Petukhov 2. Design of Monomeric Water-soluble b-hairpin and β-sheet PeptidesM. Angeles Jiménez 3. Combination of Theoretical and Experimental Approaches for the Design and Study of Fibril-forming Peptides Phanourios Tamamis, Emmanouil Kasotakis, Georgios Archontis, and Anna Mitraki 4. Posttranslational Incorporation of Non-canonical Amino Acids in the RNase S System by Semisynthetic Protein AssemblyMaika Genz and Norbert Sträter 5. Design, Synthesis, and Study of Fluorinated ProteinsBenjamin C. Buer and E. Neil G. Marsh 6. High-Quality Combinatorial Protein Libraries Using the Binary Patterning ApproachLuke H. Bradley 7. Methods for Library-Scale Computational Protein DesignLucas B. Johnson, Thaddaus R. Huber, and Christopher D. Snow 8. Symmetric Protein Architecture in Protein Design: Top-Down Symmetric DeconstructionLiam M. Longo and Michael Blaber 9. Identification of Protein Scaffolds for Enzyme Design using Scaffold SelectionAndré C. Stiel, Kaspar Feldmeier, and Birte Höcker 10. Computational Design of Novel Enzymes without CofactorsMatthew D. Smith, Alexandre Zanghellini, and Daniela Grabs 11. De novo Design of Peptide Scaffolds as Novel Pre-organised Ligands for Metal-ion CoordinationAimee J. Gamble and Anna F. A. Peacock 12. Computational Design of MetalloproteinsAvanish S. Parmar, Douglas Pike, and Vikas Nanda 13. Incorporation of Modified and Artificial Cofactors into Naturally Occurring Protein ScaffoldsKoji Oohor and Takashi Hayashi 14. Computational Redesign of Metalloenzymes for Catalyzing New ReactionsPer Jr. Greisen and Sagar D. Khare

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Book SynopsisThe structure of DNA varies along its sequence, which can lead to sequence-dependent variations in the fidelity of DNA copying and repair. And because the probability of distinct classes of mutations varies along a DNA sequence, variation that affects fitness will have evolutionary implications, as selection acts on heritable variation. This Annals volume brings together a broad interdisciplinary group of researchers to explore the impact of increasing understanding of DNA structure, repair, replication, and organization on interrelated subjects ranging from evolution, to dependence of the effect of mutagens on environmental and sequence context, to noncanonical forms of information representation in genomes. NOTE: Annals volumes are avaialble for sale as individual books or as a journal. For information on institutional journal subscriptions, please visit http://ordering.onlinelibrary.wiley.com/subs.asp?ref=1749-6632&doi=10.111/(ISSN)1749-6632 ACADEMY MEMBERS: Please contact the New York Academy of Sciences directly to place your order (www.nyas.org). Members of the New York Academy of Science receive full-text access to Annals online and discounts on print volumes. Please visit http://www.nyas.org/MemberCenter/Joun.aspx for more information about becoming a member.Table of ContentsOverview of the creative genome: effects of genome structure and sequence on the generation of variation and evolution 1. Lynn Helena Caporale Genome hyperevolution and the success of a parasite 11. J. David Barry, James P. J. Hall, and Lindsey Plenderleith The tricky path to recombining X and Y chromosomes in meiosis 18. Liisa Kauppi, Maria Jasin, and Scott Keeney Sites of genetic instability in mitosis and cancer 24. Anne M. Casper, Danielle M. Rosen, and Kaveri D. Rajula The genome: an isochore ensemble and it’s evolution 31. Giorgio Bernardi Multiple levels of meaning in DNA sequences, and one more 35. Edward N. Trifonov, Zeev Volkovich, and Zakharia M. Frenkel Evolution of simple sequence repeat-mediated phase variation in bacterial genomes 39. Christopher D. Bayliss and Michael E. Palmer Indirect selection of implicit mutation protocols 45. David G. King G4 motifs in human genes 53. Nancy Maizels Adaptive radiation of venomous marine snail lineages and the accelerated evolution of venom peptide genes 61. Baldomero M. Olivera, Maren Watkins, Pradip Bandyopadhyay, Julita S. Imperial, Edgar P. Heimer de la Cotera, Manual B. Aguilar, Estuardo Lopez Vera, Gisela P. Concepcion, and Arturo Lluisma Integrons and gene cassettes: hotspots of diversity in bacterial genomes 71. Ruth M. Hall Creative deaminases, self-inflicted damage, and genome evolution 79. Silvestro G. Conticello Three-dimensional architecture of the IgH locus facilitates class switch recombination 86. Amy L. Kenter, Scott Feldman, Robert Wuerffel, Ikbel Achour, Lili Wang, and Satyendra Kumar Preaching about the converted: how meiotic gene conversion influences genomic diversity 95. Francesca Cole, Scott Keeney, and Maria Jasin Gross chromosomal rearrangement mediated by DNA replication in stressed cells: evidence from Escherichia coli 103. J.M. Moore, Hallie Wimberly, P.C. Thorton, Susan M. Rosenberg, and P.J. Hastings Implications of genetic heterogeneity in cancer 110. Michael W. Schmitt, Marc J. Prindle, and Lawrence A. Loeb Corrigendum for Ann. N.Y. Acad. Sci. 2009. 1182: 47-57 117.

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Book SynopsisThis book presents the latest research on DNA damage, which due to environmental factors and normal metabolic processes inside the cell, occurs at a rate of 1,000 to 1,000,000 molecular lesions per cell per day. While this constitutes only 0.000165% of the human genome''s approximately 6 billion bases (3 billion base pairs), unrepaired lesions in critical genes (such as tumour suppresser genes) can impede a cell''s ability to carry out its function and appreciably increase the likelihood of tumour formation. The vast majority of DNA damage affects the primary structure of the double helix; that is, the bases themselves are chemically modified. These modifications can in turn disrupt the molecules'' regular helical structure by introducing non-native chemical bonds or bulky adducts that do not fit in the standard double helix. Unlike proteins and RNA, DNA usually lacks tertiary structure and therefore damage or disturbance does not occur at that level. DNA is, however, supercoiled and wound around "packaging" proteins called histones (in eukaryotes), and both superstructures are vulnerable to the effects of DNA damage.

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Book SynopsisRibonucleotide reductase (RNR), a universal enzyme present in essentially all living cells and organisms, has a central role in DNA replication and repair by catalysing production of deoxyribonucleotides from the corresponding ribonucleotides. Three major classes of RNRs are known, differing in their cofactor requirements: class I RNRs (with subclasses Ia and Ib) carry a stable tyrosyl radical and are oxygen-dependent, class II RNRs require the vitamin B12 cofactor 5''-deoxyadenosylcobalamin and are oxygen-independent, and class III RNRs carry a stable glycyl radical and are oxygen-sensitive. Despite these differences, all classes have a similar reaction mechanism and the same highly specific catalytic core structure, indicating that they evolved from a common ancestor. Biochemical studies of RNRs from selected model organisms in combination with the vast number of deduced RNR sequences from publicly available complete genomic sequences show that whereas eukaryotes and their viruses with few exceptions contain only class Ia RNRs, all three major RNR classes are found among prokaryotes and bacteriophages and quite often one organism encodes more than one class of RNR. They are compiled in an open access database, called RNRdb for Ribonucleotide Reductase database that is available at http://rnrdb.molbio.su.se. RNRs are produced in a strictly controlled way depending upon growth phase and environmental cues. The authors describe a comprehensive summary of how the expression of RNR genes is regulated in several eubacterial organisms and in yeast. Due to RNR''s importance for the realisation of DNA replication, it has been recognised as a possible target for antiproliferative therapy. The authors present a comprehensive summary of RNR-specific inhibitors that have reached clinical trials and/or are currently used in clinical therapy.

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Book SynopsisMicroRNAs are involved in crucial biological processes, including developmental timing, cell proliferation, apoptosis, and stress responses. This book presents topical research in the study of microRNAs, including their potential applications in aquaporin associated pathogenesis; microRNAs as novel biomarkers and therapeutic targets for cancer; microRNAs used in regulating EMT and blood circulation metastasis of lung cancer stem cells; the biological functions of microRNAs in animals and the regulation of metabolism, ageing and lifespan by microRNAs.

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Book SynopsisStem cells are cells found in all multi cellular organisms. They are characterised by the ability to renew themselves through mitotic cell division and differentiate into a diverse range of specialised cell types. This book presents and discusses current research in the study of stem cell research, including cancer and prostate stem cells; neural stem cells and taurine; interactions between transplanted neural stem cells and host tissue; retrovirus vector silencing in stem cells and moral and scientific consideration in embryonic stem cell research.

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Book SynopsisThis book examines the peculiarities of the circular dichroism (CD) spectra of the double-stranded (ds) DNA cholesteric liquid-crystalline dispersions (CLCDs). The main physico-chemical properties formed as a result of the phase exclusion of these molecules in water-salt or water-salt-polymer-containing solutions are examined. In addition, the main principles of the theory of optical properties of imperfect, absorbing, cholesteric liquid crystals is discussed.

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Book SynopsisIn this book, the authors present current research in the study of DNA replication and mutation, including connections between BLM and the Fanconi anemia pathway in the repair of replication fork damage; the mutagenic potential of methacrylates used in restorative dentistry; DNA mutation of the progranulin gene in familial frontotemporal lobar degeneration; effect of DNA polymerase a-inhibitor dehydroaltenusin on DNA replication in cultured cells; gel-based methods of DNA-binding zinc II complexes in the detection of DNA mutations and DNA mutations and genetic coding.

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Book SynopsisMiRNA is an extremely fast growing field, and miRNA knowledge is now believed to be a pivotal element of cancer biology. It is already evident that the discovery of miRNA has created a paradigm shift in post-genomics biology, not only for scientists accustomed to traditional central dogma of molecular biology but also for researchers studying human diseases and accustomed to traditional genetics approach of studying one gene at the time. This book provides an introduction to the basic principles of miRNA biology, overview of miRNA significance in the hallmarks of cancer, experimental techniques used in miRNA research, and in special part - miRNAs importance in wide range of solid cancers with a special focus on its potential usage in molecular pathology, predictive oncology or as a novel therapeutic targets.

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Book SynopsisThis book offers an overview of some recent advances in the Computational Bioacoustics methods and technology. In the focus of discussion is the pursuit of scalability, which would facilitate real-world applications of different scope and purpose, such as wildlife monitoring, biodiversity assessment, pest population control, and monitoring the spread of disease transmitting mosquitoes. The various tasks of Computational Bioacoustics are described and a wide range of audio parameterization and recognition tasks related to the automated recognition of species and sound events is discussed. Many of the Computational Bioacoustics methods were originally developed for the needs of speech, audio, or image processing, and afterwards were adapted to the requirements of automated acoustic recognition of species, or were elaborated further to address the challenges of real-world operation in 24/7 mode. The interested reader is encouraged to follow the numerous references and links to web resources for further information and insights. This book is addressed to Software Engineers, IT experts, Computer Science researchers, Bioacousticians, and other practitioners concerned with the creation of new tools and services, aimed at enhancing the technological support to Computational Bioacoustics applications. STTM, Speech Technology and Text Mining in Medicine and Health Care This series demonstrates how the latest advances in speech technology and text mining positively affect patient healthcare and, in a much broader sense, public health at large. New developments in text mining methods have allowed health care providers to monitor a large population of patients at any time and from any location. Employing advanced summarization techniques, patient data can be readily extracted from extensive clinical documents in electronic health records and immediately made available to the physician. These same summarization techniques can also aid the healthcare provider in extracting from the large corpora of medical literature the relevant information for treating the patient. The series topics include the design and acceptance of speech-enabled robots that assist in the operating room, studies of signal processing and acoustic modeling for speech and communication disorders, advanced statistical speech enhancement methods for creating synthetic voice, and technologies for addressing speech and language impairments. Titles in the Series consist of both authored books and edited contributions. All authored books and contributed works are peer-reviewed. The Series is for speech scientists and speech engineers, machine learning experts, biomedical engineers, medical speech pathologists, linguists, and healthcare professionals Table of Contents1. Introduction 2. Why Computational Bioacoustics? 3. Getting to know the problems of automated species recognition 4. Preparation of data 5. Sound production mechanisms 6. Parameterization of bioacoustic signals 7. Machine learning methods 8. Application examples 9. Useful resources 10. Conclusion and outlook

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Book SynopsisThis book introduces a discrete optimisation technique in four applications: classic Traveller Salesperson Problem (TSP), Multilocus Genetic Mapping, Multilocus Consensus Genetic Mapping, and Physical Mapping. Each of the four sections contains the problem formulation, description of the algorithm, and experimental results. The foregoing problems are solved on the basis of Guided Evolution Strategy (GES) algorithm. The algorithm was implemented in MultiPoint package (http://multiqtl.com). The developed analytical tools were applied in many genome mapping projects.

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Book SynopsisIn somatic cells, DNA is normally wrapped around the histones octamer to forms nucleosomes that eventually give rise to a solenoid DNA structure. Unlike somatic cells, in mammalian sperm, the development of spermatids into mature spermatozoa is accomplished by a series of structural and chemical modifications including a gradual replacement of lysine-rich histones by transition proteins and then by protamines which bind more tightly to DNA than histones, which results in compaction of chromatin in the sperm nucleus, a process which is termed ''sperm chromatin condensation''. This book examines the several techniques that have been devised in order to study chromatin and DNA defects in human spermatozoa.

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Book SynopsisPolyhedra have attracted scientists'' attentions due to their high-symmetric architectures since ancient times, and even served as common modes in natural world. Chemists in the past few centuries have strived to synthesise these polyhedral targets. Despite achievements that have been arrived, there is still a gap between the great varieties of polyhedral shapes observed in nature and the relatively limited molecular polyhedra constructed by small organic molecules. Fortunately, DNA was shown to be an excellent material in molecular construction. The construction of polyhedral structures with DNA improves the development of synthetic chemistry. This book reviews the recent progress made in the theoretical investigation of a new mathematical theory of DNA polyhedra.

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Book SynopsisTelomerase is a ribonucleoprotein enzyme that catalyses the cellular synthesis of telomeric DNA during cellular division, resulting in maintenance of telomere length and increased proliferative potential. Several studies suggest that the telomerase may play an important role in the diagnosis and prognosis of cancer because its expression strongly correlates with the potential tumour progression. Ninety percent of human cancers on different organs have shown high telomerasa activity. This book reviews research in the field of telomerase including functions of telomerase independent of its interaction with telomeres on gene expression and chromatin structure; histone deacetylase inhibition as an anticancer telomerase-targeting strategy and others.

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Book SynopsisNew methods used for the detection of DNA hybridisation process, including electrochemical, optical scattering, surface plasmon resonance, nanogravimetric, and fluorimetric are described and their application in assays assessing DNA damage is discussed in this book. The analyses of damage and alterations for the DNA in solution as well as for the DNA immobilised on core-shell gold nanoparticles and solid electrodes are presented. These methods enable evaluating the degree of DNA damage caused by toxicants and can be applied to studies of the interactions of atrazine and other herbicides and pesticides with DNA.

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Book SynopsisThis book presents the basic results on studies of the interaction of anti-cancer Actinomycin antibiotics with DNA. It focuses on interactions of heterocyclic anti-tumour antibiotics (Actinomycins, as typical example) with DNA, poly-nucleotides, oligonucleotides, and aggregates of purines, using spectroscopic methods. Experimental data, various models of structures of the complexes and their physical and chemical properties are described, and possible approaches for delivery of heterocyclic antibiotics to DNA are also discussed.

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Book SynopsisMicroRNAs are small non-coding RNAs involved in post-transcriptional regulation of gene expression. Thousands of miRNAs have been identified in different organisms including viruses, insects, plants and animals. MiRNAs has emerged as key regulators of important biological processes. The differential expression of miRNAs in various human diseases has made them potential candidates for developing novel therapies and personalized medicines. This book is focused on microRNA let-7, the second miRNA discovered in the year 2000 and one of the most studied miRNA. This book discusses various aspects of miRNA let-7 starting from its discovery, biogenesis, transcriptional and posttranscriptional regulation to its crucial role in various fundamental cellular processes such as development, stem cell maintenance and differentiation, regulation of signalling pathways in cancer, drug resistance and therapeutic potential in different human diseases.

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Book Synopsis

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Book SynopsisThe maintenance of DNA integrity and genome stability is essential for the viability of cells and the life of organisms. The genetic material is constantly under attack from external environmental factors and endogenous metabolic products that can alter its chemical structure and nucleotides sequence. In this book, the authors present topical research in the study of DNA repair including topics such as DNA repair as the primary adaptive function of sex in bacteria and eukaryotes; DNA repair as a therapeutic target in breast cancer; DNA repair in the nervous system; targeting BRCA1 DNA repair pathway for cancer chemotherapy and DNA damage and repair during photodynamic therapy.

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Book SynopsisProline might be the most studied amino acid in nature. Many authors have reviewed its many functions in cell homoeostasis. Not only it is essential in primary metabolism, but it is also involved in cell defence response to a variety of stresses. This book presents topical research data in the study of pro-line functions, including role of pro-line in plant subject to salinity, pro-line cycle and its role in secondary metabolite accumulation, role of pro-line in catalysing the asymmetric reaction, studies of polyproline peptides, structural characteristics and transition mechanisms of proline-rich peptides, functions of proline in behaviour of neonatal chicks and tumour suppressor activities of proline oxidase.

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Book SynopsisFingerprints have provided a valuable method of personal identification in forensic science and criminal investigations for over 100 years. Fingerprints left at crime scenes generally are latent prints -- unintentional reproductions of the arrangement of ridges on the skin made by the transfer of materials (such as amino acids, proteins, polypeptides, and salts) to a surface. Palms and the soles of feet also have friction ridge skin that can leave latent prints. The examination of a latent print consists of a series of steps involving a comparison of the latent print to a known (or exemplar) print. Courts have accepted latent print evidence for the past century. However, several high-profile cases in the United States and abroad have highlighted the fact that human errors can occur, and litigation and expressions of concern over the evidentiary reliability of latent print examinations and other forensic identification procedures has increased in the last decade. This book discusses latent print examinations in detail, and provides methods to improving the practice through a systems approach.

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Book SynopsisOne of the world's leading experts on genetics unravels one of the most important breakthroughs in modern science and medicine. If our genes are, to a great extent, our destiny, then what would happen if mankind could engineer and alter the very essence of our DNA coding? Millions might be spared the devastating effects of hereditary disease or the challenges of disability, whether it was the pain of sickle-cell anemia to the ravages of Huntington’s disease. But this power to “play God” also raises major ethical questions and poses threats for potential misuse. For decades, these questions have lived exclusively in the realm of science fiction, but as Kevin Davies powerfully reveals in his new book, this is all about to change. Engrossing and page-turning, Editing Humanity takes readers inside the fascinating world of a new gene editing technology called CRISPR, a high-powered genetic toolkit that enables scientists to not only engineer but to edit the DNA of any organism down to the individual building blocks of the genetic code. Davies introduces readers to arguably the most profound scientific breakthrough of our time. He tracks the scientists on the front lines of its research to the patients whose powerful stories bring the narrative movingly to human scale. Though the birth of the “CRISPR babies” in China made international news, there is much more to the story of CRISPR than headlines seemingly ripped from science fiction. In Editing Humanity, Davies sheds light on the implications that this new technology can have on our everyday lives and in the lives of generations to come.

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Book SynopsisTechnology for modifying the genotypes and phenotypes of insects and other arthropods has steadily progressed with the development of more precise and powerful methods, most prominently transgenic modification. For many insect pests, there is now almost unlimited ability to modify phenotypes to benefit human health and agriculture. Precise DNA modifications and gene drive have the power to make wild-type populations less harmful in ways that could never have been performed with previous transgenic approaches. This transition from primarily laboratory science to greater application for field use has also necessitated greater development of modeling, ethical considerations and regulatory oversight. The 2nd Edition of Transgenic Insects contains chapters contributed by experts in the field that cover technologies and applications that are now possible. This edition includes increased attention to associated challenges of risk assessment, regulation, and public engagement. Featuring: Up-to-date analysis of molecular techniques, such as gene editing. Consideration of public attitudes and regulatory aspects associated with transgenic insects. Many examples of the wide range of applications of transgenic insects. This book will be very valuable to students and researchers in entomology, molecular biology, genetics, public health and agriculture, and will also appeal to practitioners who are implementing the technology, and to regulators, stakeholders and ethicists.Table of ContentsChapter 1: Transposon-based Technologies for Insects Chapter 2: Inducible and Repressible Systems for Transgene Expression Chapter 3: Sex-, Tissue- and Stage-Specific Transgene Expression Chapter 4: RNA Interference to Modify Phenotypes in Agriculturally Important Pest and Beneficial Insects: Useful Examples and Future Challenges Chapter 5: Site-specific Recombination for Gene Locus-directed Transgene Integration and Modification Chapter 6: Receptor-Mediated Ovary Transduction of Cargo - ReMOT Control: A Comprehensive Review and Detailed Protocol for Implementation Chapter 7: Site-directed DNA Sequence Modification Using CRISPR-Cas9 Chapter 8: An Introduction to the Molecular Genetics of Gene Drives and Thoughts on Their Gradual Transition to Field Use Chapter 9: Drosophila melanogaster As a Model for Gene Drive Systems Chapter 10: Sex Ratio Manipulation Using Gene Drive for Mosquito Population Control Chapter 11: Population Modification Using Gene Drive for Reduction of Malaria Transmission Chapter 12: Modelling threshold-dependent gene drives Chapter 13: Tsetse Paratransgenesis: a Novel Strategy for Reducing the Spread of African Trypanosomiases Chapter 14: Paratransgenic Control of Chagas Disease Chapter 15: Asaia Paratrangenesis in Mosquitoes Chapter 16: Paratransgenesis in Mosquitoes and Other Insects: Microbial Ecology and Bacterial Genetic Considerations Chapter 17: Transgenic approaches for sterile insect control of dipteran livestock pests and lepidopteran crop pests Chapter 18: Honey bee genome editing Chapter 19: Progress Towards Germline Transformation of Ticks Chapter 20: Silkworm Transgenesis and its Applications Chapter 21: Tephritid Fruit Fly Transgenesis and Applications Chapter 22: Antiviral Effectors for Mosquito Transgenesis Chapter 23: Self-Limiting Insects for Pest Management Chapter 24: Public Acceptability and Stakeholder Engagement for Genetic Control Technologies Chapter 25: Regulation of Transgenic Insects Chapter 26: Economics of Transgenic Insects for Field Release Chapter 27: The Cartagena Protocol on Biosafety and the Regulation of Transboundary Movement of Living Modified Organisms Chapter 28: Risk Analysis of Transgenic Insects

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