Numerous physical and chemical stress factors, endogenous or exogenous, challenge living organisms. Metabolisation processes generate highly reactive intermediates which can covalently bind to DNA, resulting in bulky addition products called "adducts." DNA adduct formation appears to be a general response of plants to organic chemical exposure, whether in controlled conditions or in the field. In particular, common carcinogenic pollutants and pesticides promote the formation of DNA adducts in plants. The authors of this book examine the development of DNA adducts, as well as the ways in which they can be eliminated due to DNA repair pathways. In this book, the data from in vivo transgenic assays is also examined, which can help to clarify specific pre-mutagenic adducts, DNA repair functions and mutational events that may be involved in the mutagenicity of human carcinogens. Other chapters in this book identify and discuss novel anthracyclines capable of forming DNA adducts, the role of DNA adducts as early biomarkers in the screening and development of marine anticancer drugs, the genotoxicity, such as DNA adduct formation, of air pollutants and its assessment by in vivo mutagenesis and a discussion of oxidative DNA damage, which can play an important role in the carcinogenic processes of PAHs and aromatic amines, in addition to bulky-DNA adducts formation.

This guide covers aspects of designing microarray experiments and analysing the data generated, including information on some of the tools that are available from non--commercial sources. Concepts and principles underpinning gene expression analysis are emphasised and wherever possible, the mathematics has been simplified. The guide is intended for use by graduates and researchers in bioinformatics and the life sciences and is also suitable for statisticians who are interested in the approaches currently used to study gene expression.* Microarrays are an automated way of carrying out thousands of experiments at once, and allows scientists to obtain huge amounts of information very quickly* Short, concise text on this difficult topic area* Clear illustrations throughout* Written by well--known teachers in the subject* Provides insight into how to analyse the data produced from microarrays

The recent expansion in diversity of RNA and DNA editing types has stimulated the development of many unique genetic, molecular, biochemical, and computational approaches to biological issues. In RNA and DNA Editing: Methods and Protocols, leading experts in the field introduce methods developed over the last few years to study editing substrates, mechanisms of specificity, and functions of RNA and DNA editing enzymes and complexes. Sections of the book are dedicated to state-of-the art techniques which enable investigation of uracil insertion/deletion RNA editing in mitochondrion of Trypanosoma brucei, adenosine to inosine RNA editing, cytidine to uracil RNA and DNA editing, as well as tRNA editing and RNA modifications. Written in the highly successful Methods in Molecular Biology (TM) series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, RNA and DNA Editing: Methods and Protocols seeks to inspire the further development of these vital and powerful techniques.

This 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.

As the emerging field of proteomics continues to expand at an extremely rapid rate, the relative quantification of proteins, targeted by their function, becomes its greatest challenge. Complex analytical strategies have been designed that allow comparative analysis of large proteomes, as well as in depth detection of the core proteome or the interaction network of a given protein of interest. In Functional Proteomics: Methods and Protocols, expert researchers describe the latest protocols being developed to address the problems encountered in high-throughput proteomics projects, with emphasis on the factors governing the technical choices for given applications. The case studies within the volume focus on the following three crucial aspects of the experimental design: 1) the strategy used for the selection, purification and preparation of the sample to be analyzed by mass spectrometry, 2) the type of mass spectrometer used and the type of data to be obtained from it, and 3) the method used for the interpretation of the mass spectrometry data and the search engine used for the identification of the proteins in the different types of sequence data banks available. As a part of the highly successful Methods in Molecular Biology (TM) series, the chapters compile step-by-step, readily reproducible laboratory protocols, lists of the necessary materials and reagents, and tips on troubleshooting and avoiding known pitfalls. Comprehensive and cutting-edge, Functional Proteomics: Methods and Protocols is an ideal resource for all scientists pursuing this developing field and its multitudinous data.

Genetic vectors are plasmids, bacteriophages, or viruses used during recombinant DNA techniques that transport foreign genes into recipient cells. Genetic vectors possess a functional replicator site and contain a genetic marker to facilitate their selective recognition. This book presents new and important research from around the globe

This book presents the foundations of key problems in computational molecular biology and bioinformatics. It focuses on computational and statistical principles applied to genomes, and introduces the mathematics and statistics that are crucial for understanding these applications. The book features a free download of the R software statistics package and the text provides great crossover material that is interesting and accessible to students in biology, mathematics, statistics and computer science. More than 100 illustrations and diagrams reinforce concepts and present key results from the primary literature. Exercises are given at the end of chapters.

Recent advances in understanding the thermodynamics of macromolecules, the topological properties of gene networks, the organization and mutation capabilities of genomes, and the structure of populations make it possible to incorporate these key elements into a broader and deeply interdisciplinary view of molecular evolution. This book gives an account of such a new approach, through clear tutorial contributions by leading scientists.

This volume provides readers with wide-ranging coverage of CRISPR systems and their applications in various plant species. The chapters in this book discuss topics such as plant DNA repair and genome editing; analysis of CRISPR-induced mutations; multiplexed CRISPR/Cas9 systems; CRISPR-Cas12a (Cpf1) editing systems; and non-agrobacterium based CRISPR delivery systems. 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. Comprehensive and thorough, Plant Genome Editing with CRISPR Systems: Methods and Protocols is a valuable resource for any researcher interested in learning about and using CRISPR systems in plants.

The results obtained from, and techniques used in, different fields of science, such as mathematics, physics and biology are selected, gathered and analyzed to provide an introduction to the developing field of research into the nonlinear physics of DNA. The DNA molecule, which has been traditionally studied by techniques developed through molecular biology, is considered here rather from a physicist's viewpoint, as a nonlinear dynamical system. This is a complimentary way of looking at the molecule, and is arrived at following both a theoretical analysis of interactions and motions in DNA, and as a result of interpretation of experimental data. It is shown that this "nonlinear physics" approach allows one to explain some of the mechanisms of DNA functioning, and that it can offer possibilities in the study and interpretation of genetic codes. This text introduces all those involved in the study of the DNA molecule from a traditional, molecular biology viewpoint, to some of the results and developments which have been realized using a nonlinear physics approach, and should also allow biologists, biochemists and physicists to continue to develop non-traditional techniques of investigating the DNA molecule.

Updated and revised, this thorough volume is organized such that it begins with techniques related to the study of chromatin structure. Protocols for reconstitution of chromatin on solid supports for analysis, preparation of positioned mononucleosomes, techniques to study premature chromatin condensation and the use of comparative genomic hybridization to assess genomic aberration are included as well. Novel techniques for imaging chromatin using atomic force microscopy and the isolation of specific genomic regions using engineered DNA binding molecules generated by CRISPR are then examined. That section is followed by protocols to analyze DNA and histone modifications, while the third section includes methods to study DNA replication and repair, in the context of chromatin. Last but not least, protocols for studying chromatin and its relation with transcriptional regulation are presented in a fourth section. 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 up-to-date, Chromatin Protocols, Third Edition aims to help researchers in facilitating in-depth molecular analysis of various aspects of chromatin structure and function.

This book details the statistical concepts used in gene mapping, first in the experimental context of crosses of inbred lines and then in outbred populations, primarily humans. It presents elementary principles of probability and statistics, which are implemented by computational tools based on the R programming language to simulate genetic experiments and evaluate statistical analyses. Each chapter contains exercises, both theoretical and computational, some routine and others that are more challenging. The R programming language is developed in the text.

The Greek word apoptosis was used first by Hippocrates as a synonym of dislocations of the bones, structural changes related to tissue, by Marcus Aurelius in political and social context as failure and decline. The physician Galen extended the medical meaning of apoptosis to wound healing and inflammation.

Apoptosis, or cell suicide is an integral part of life cycle of plants and animals indicated by the loss of 140-190g (50-70 billion) cells each day in the human adult, amounting to the body weight in one year. The growing interest in apoptosis is indicated by the number of scientific publications since the 1990s which is now more than 140,000 and will exceed 160,000 by the end of 2008.

The unique feature of this book is the use of synhronized and reversibly permeabilized cells allowing to visualize the dynamic nature of chromatin condensation through transitory chromatin and chromosomal forms including changes upon genotoxic treatment, which were not seen earlier. The chromatin condensation process is illustrated from string (DNA) to rope (chromosomes) in more than 160 figures. The interdisciplinary nature of studies summarized in the book facilitate the global view of readers interested in the higher order structure of nucleic acids. The wealth of additional information will attract a wide population of readers. The natural audience engaged in DNA research such as genetics, cell biology, biochemistry, molecular biology will find that it contains essential material.

Introduction The goal of this book is to introduce XML to a bioinformatics audience. It does so by introducing the fundamentals of XML, Document Type De?nitions (DTDs), XML Namespaces, XML Schema, and XML parsing, and illustrating these concepts with speci?c bioinformatics case studies. The book does not assume any previous knowledge of XML and is geared toward those who want a solid introduction to fundamental XML concepts. The book is divided into nine chapters: Chapter 1: Introduction to XML for Bioinformatics. This chapter provides an introduction to XML and describes the use of XML in biological data exchange. A bird's-eye view of our ?rst case study, the Distributed Annotation System (DAS), is provided and we examine a sample DAS XML document. The chapter concludes with a discussion of the pros and cons of using XML in bioinformatic applications. Chapter 2: Fundamentals of XML and BSML. This chapter introduces the fundamental concepts of XML and the Bioinformatic Sequence Markup Language (BSML). We explore the origins of XML, de?ne basic rules for XML document structure, and introduce XML Na- spaces. We also explore several sample BSML documents and visualize these documents in the TM Rescentris Genomic Workspace Viewer.

Epigenetics refers to heritable patterns of gene expression which do not depend on alterations of genomic DNA sequence.

This book provides a state-of-the-art account of a few selected hot spots by scientists at the edge in this extremely active field. It puts special emphasis on two main streams of research. One is the role of post-translational modifications of proteins, mostly histones, on chromatin structure and accessibility. The other one deals with parental genomic imprinting, a process which allows to express a few selected genes from only one of the parental allele while extinguishing the other.

The most influential scientist of the last century, James Watson has been at dead center in the creation of modern molecular biology. This masterful biography brings to life the extraordinary achievements not only of Watson but also all those working on this cutting edge of scientific discovery, such as Walter Gilbert, Francis Crick, Francois Jacob, and David Baltimore. From the ruthless competition in the race to identify the structure of DNA to a near mutiny in the Harvard biology department, to clashes with ethicists over issues in genetics, Watson has left a wake of detractors as well as fans. Victor McElheny probes brilliantly behind the veil of Watson's own invented persona, bringing us close to the relentless genius and scientific impresario who triggered and sustained a revolution in science.

Genetic recombination, in the broadest sense, can be defined as any process in which DNA sequences interact and undergo a transfer of information, producing new "recombinant" sequences that contain information from each of the original molecules. All organisms have the ability to carry out recombination, and this striking universality speaks to the essential role recombination plays in a variety of biological processes fundamentally important to the maintenance of life. Such processes include DNA repair, regulation of gene expression, disease etiology, meiotic chromosome segregation, and evolution. One important aspect of recombination is that it typically occurs only between sequences that display a high degree of sequence identity. The stringent requirement for homology helps to ensure that, under normal circumstances, a cell is protected from deleterious rearrangements since a swap of genetic information between two nearly identical sequences is not expected to dramatically alter a genome. Recombination between dissimilar sequences, which does happen on occasion, may have such harmful consequences as chromosomal translocations, deletions, or inversions. For many organisms, it is also important that recombination rates are not too high lest the genome become destabilized. Curiously, certain organisms, such as the trypanosome parasite, actually use a high rate of recombination at a particular locus in order to switch antigen expression continually and evade the host immune system effectively.

Human Embryos and Preimplantation Genetic Technologies: Ethical, Social, and Public Policy Aspects presents the first holistic analysis of PGD and PGS as it is practiced and regulated worldwide. In addition to scientific and technical aspects, the book provides perspectives on the ethical, legal, religious, policy and social implications of global assisted reproduction technologies, including in Africa, Asia, Europe, North and South America, and Australia. Chapters cover history, ethics, feminism, family dynamics, psychological and interpersonal factors, the current state of PGD and PGS in 20 different sovereign nations and religious communities, and provide an analysis of public policy concerns and future directions.

A Beginner's Guide to Microarrays addresses two audiences - the core facility manager who produces, hybridizes, and scans arrays, and the basic research scientist who will be performing the analysis and interpreting the results. User friendly coverage and detailed protocols are provided for the technical steps and procedures involved in many facets of microarray technology, including:

-Cleaning and coating glass slides,
-Designing oligonucleotide probes,
-Constructing arrays for the detection and quantification of different bacterial species,
-Preparing spotting solutions,
-Troubleshooting spotting problems,
-Setting up and running a core facility,
-Normalizing background signal and controlling for systematic variance,
-Designing experiments for maximum effect,
-Analyzing data with statistical procedures,
-Clustering data with machine-learning protocols.

In the past several years, DNA microarray technology has attracted tremendous interest in both the scientific community and in industry. With its ability to simultaneously measure the activity and interactions of thousands of genes, this modern technology promises unprecedented new insights into mechanisms of living systems. Currently, the primary applications of microarrays include gene discovery, disease diagnosis and prognosis, drug discovery (pharmacogenomics), and toxicological research (toxicogenomics). Typical scientific tasks addressed by microarray experiments include the identification of coexpressed genes, discovery of sample or gene groups with similar expression patterns, identification of genes whose expression patterns are highly differentiating with respect to a set of discerned biological entities (e.g., tumor types), and the study of gene activity patterns under various stress conditions (e.g., chemical treatment). More recently, the discovery, modeling, and simulation of regulatory gene networks, and the mapping of expression data to metabolic pathways and chromosome locations have been added to the list of scientific tasks that are being tackled by microarray technology. Each scientific task corresponds to one or more so-called data analysis tasks. Different types of scientific questions require different sets of data analytical techniques. Broadly speaking, there are two classes of elementary data analysis tasks, predictive modeling and pattern-detection. Predictive modeling tasks are concerned with learning a classification or estimation function, whereas pattern-detection methods screen the available data for interesting, previously unknown regularities or relationships.

Sequence - Evolution - Function is an introduction to the computational approaches that play a critical role in the emerging new branch of biology known as functional genomics. The book provides the reader with an understanding of the principles and approaches of functional genomics and of the potential and limitations of computational and experimental approaches to genome analysis.

Key topics covered in this textbook are:
*the completed and ongoing genome sequencing projects,
*databases that store and organize genomic data, with their unique advantages and pitfalls,
*principles and methods of genome analysis and annotation,
*ways to automate the searches and increase search sensitivity while minimizing the error rate,
*the first lessons from the Human Genome Project,
*the contribution of comparative genomics to the understanding of hereditary diseases and cancer,
*fundamental and practical applications of comparative genomics,
*the use of complete genomes for evolutionary analysis,
*the application of comparative genomics for identification of potential drug targets in microbial genomes,
*Problems for Further Study, which are designed to be solved by using methods available through the WWW. Sequence - Evolution - Function should help bridge the "digital divide" between biologists and computer scientists, allowing biologists to better grasp the peculiarities of the emerging field of Genome Biology and to learn how to benefit from the enormous amount of sequence data available in the public databases. The book is non-technical with respect to the computer methods for genome analysis and discusses these methods from the user's viewpoint, without addressing mathematical and algorithmic details. Prior practical familiarity with the basic methods for sequence analysis is a major advantage, but a reader without such experience will be able to use the book as an introduction to these methods. This book is perfect for introductory level courses in computational methods for comparative and functional genomics.

DNA from the Beginning (a 3-CD set) is a multimedia primer on the basics of DNA, genes, and heredity. It is an ideal teaching tool for high school students and will also interest adults with a non-technical background who wish to learn more about the impact that DNA science is having on our lives. The content in DNA from the Beginning is built on a progressive series of important but simply stated concepts such as 'Children resemble their parents'. An understanding of the concept is then conveyed in clear, understandable terms with the aid of links to animations, photographs, and video clips, and biographies or interviews featuring key scientists. A wealth of other information and links to web resources are included. Problems and their solutions are included to allow teaching through self-examination. Based on the award-winning web site, the DNA from the Beginning CD-ROM set provides over 72 hours of study time. It runs on Macintosh computers and PCs, and gives immediate access to all the online content, in attractive, uncluttered screens, without the need for network connections. A must for high schools and junior colleges in conjunction with biology classes.

In 1957 two young scientists, Matthew Meselson and Frank Stahl, produced a landmark experiment confirming that DNA replicates as predicted by the double helix structure Watson and Crick had recently proposed. It also gained immediate renown as a "most beautiful" experiment whose beauty was tied to its simplicity. Yet the investigative path that led to the experiment was anything but simple, Frederic L. Holmes shows in this masterful account of Meselson and Stahl's quest. This book vividly reconstructs the complex route that led to the Meselson-Stahl experiment and provides an inside view of day-to-day scientific research--its unpredictability, excitement, intellectual challenge, and serendipitous windfalls, as well as its frustrations, unexpected diversions away from original plans, and chronic uncertainty. Holmes uses research logs, experimental films, correspondence, and interviews with the participants to record the history of Meselson and Stahl's research, from their first thinking about the problem through the publication of their dramatic results. Holmes also reviews the scientific community's reception of the experiment, the experiment's influence on later investigations, and the reasons for its reputation as an exceptionally beautiful experiment.

Proteomics is an introduction to the exciting new field of proteomics, an interdisciplinary science that includes biology, bioinformatics, and protein chemistry. The purpose of this book is to provide the active researcher with an overview of the types of questions being addressed in proteomics studies and the technologies used to address those questions. Key subjects covered in this book include: an assessment of the limitations of this approach and outlines new developments in mass spectrometry that will advance future research high-throughput recombinant DNA cloning methods used to systematically clone all of the open reading frames of an organism into plasmid vectors for large scale protein expression and functional studies such as protein-protein interactions with the two-hybrid system protein structure an overview of large-scale experimental attempts to determine the three-dimensional structures of representative sets of proteins computational approaches to determining the three-dimensional structure of proteins. Proteomics provides a starting point for researchers who would like a theoretical understanding of the new technologies in the field, and obtain a solid grasp of the fundamentals before integrating new tools into their experiments. Written with attention to detail, but without being overwhelmingly technical, Proteomics is a user-friendly guide needed by most biologists today.