This detailed volume focuses on genotyping and validation in addition to information on how to produce gene edited cells and animals for research. Future advances in biomedical research will benefit greatly from the use of precise gene targeting of transgenes in the genome as CRISPR technology supersedes earlier methods that relied on random transgene integration, which this collection reflects. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step and readily reproducible laboratory protocols, as well as tips for troubleshooting and avoiding known pitfalls. Authoritative and practical, Transgenesis: Methods and Protocols serves as an ideal guide for researchers working with or working on genetically modified models.

This volume provides a collection of protocols from researchers in the statistical genomics field. Chapters focus on integrating genomics with other “omics” data, such as transcriptomics, epigenomics, proteomics, metabolomics, and metagenomics. 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 thorough, Statistical Genomics hopes that by covering these diverse and timely topics researchers are provided insights into future directions and priorities of pan-omics and the precision medicine era.

The book comes during a time of rapid expansion in molecular technology-based selection approaches that are destined to modify or supplement conventional breeding methodology. The new technologies will allow genetic and physiological factors influencing sugar yield and quality to be assessed in great detail and manipulated. These novel techniques will also reduce the dependence of the sugar beet crop on chemical pesticides and fertilizers by using unique and improved resistance mechanisms against the various abiotic stresses and diseases and by producing varieties that use soil resources more efficiently. A whole chapter deals with the current information on the development of these new techniques and their integration into sugar beet breeding.

- The book discusses the recent techniques in NGS data analysis which is the most needed material by biologists (students and researchers) in the wake of numerous genomic projects and the trend toward genomic research. - The book includes both theory and practice for the NGS data analysis. So, readers will understand the concept and learn how to do the analysis using the most recent programs. - The steps of application workflows are written in a manner that can be followed for related projects. - Each chapter includes worked examples with real data available on the NCBI databases. Programming codes and outputs are accompanied with explanation. - The book content is suitable as teaching material for biology and bioinformatics students. Meets the requirements of a complete semester course on Sequencing Data Analysis Covers the latest applications for Next Generation Sequencing Covers data reprocessing, genome assembly, variant discovery, gene profiling, epigenetics, and metagenomics

Genomics, Transcriptomics, Proteomics and Metabolomics of Crop Plants presents current operational methods applied to model crop plants. Including subcellular organelles, DNA fingerprinting and barcoding, sRNA, gene expression, rhizosphere engineering, marker assisted and 5G breeding, plant-microorganism interactions, stress signaling and responses, the book highlights important factors that are often overlooked and explores the latest research. The book also explores cutting-edge approaches for immediate application in new research such as OMICS, genome-wide transcriptome profiling, bioinformatics and database, DNA fingerprinting and barcoding, sRNA, gene expression, genome editing, diagnostics, rhizosphere engineering, marker assisted and 5G breeding, crop plant-microorganism interactions, stress signaling and responses. Additionally, the book describes opportunities to manipulate crop plants genetic and metabolic systems, while also exploring the related bioethical and biosafety issues. These topics are chosen and covered in detail to fill the gap in this understanding of crop molecular biology.

The Fifth Ir Gene Workshop was held at the Chase-Park Plaza Hotel, St. Louis, MO, August 28-31, 1982; 240 scientists participated in the Workshop. The man uscripts compiled in this book describe the state of the art concerning Ir genes. Although the notion of Ir Genes: Past, Present, and Future has not been ad dressed specifically by each author, the reader is certain to get this flavor from the contributions. In this Preface, we have tried to summarize some of the salient ob servations and discussions from the Workshop. The mUltiple genes of the I region have been defined traditionally by serolog ical analysis of intra-H-2 recombinant mice and the pattern of immune responses to certain antigens developed by these recombinant mice. The application of sev eral new techniques, such as gene cloning and DNA sequencing, production of T and B cell hybridomas, and development of cloned T cell lines has changed this tradition and introduced a new phase into the analysis of the I region, Ia antigens, and Ir genes."

The recent progress achieved in aquatic genomics research has important implications in science and aquaculture. Researchers' success in genome sequencing of the fugu has provided a foundation not only for comparative fish genomics but also for genetic studies of other vertebrates. This volume, with contributions by leading scientists from around the world, provides the latest information on genomic studies of a variety of aquatic organisms including fish, crustaceans, and shellfish, with descriptions of such methodologies as genome analysis, gene mapping, DNA markers, and EST analysis. Other topics include regulation of gene expression, stress and immune responses, sex differentiation, hormonal control, and transgenic fish. This book is a valuable resource for all scientists whose work involves aquatic organisms, especially for those in the fields of aquatic genomics, fish immunology, and aquatic biotechnology.

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.

With its modern chapter organization and new Focus on Genomics boxes, iGenetics: A Molecular Approach reflects the increasing molecular emphasis in today's experimental study of genes while helping students develop problem-solving skills and an appreciation for classic experiments. Although molecular topics are presented first, instructors can assign the chapters in any sequence. Pedagogical features such as chapter-opening Key Questions and strategically placed Keynotes help students to efficiently master genetic concepts. The Genetics Place Companion Website contains interactive iActivities and narrated animations that help students visualize and understand processes and concepts that are illustrated in the text.

Scientists and researchers from top labs around the world share their expertise!
This unique text integrates tree transgenesis, functional genomics, and structural genomics to present, for the first time, a unified approach to research on the molecular biology of forest trees. A distinguished panel of scientists, researchers, and educators from around the world have combined their efforts to present the most up-to-date information and make Molecular Genetics and Breeding of Forest Trees an important addition to your professional or teaching collection. Helpful tables and figures make important points easy to access and understand.
To make it easier to find the specific information you're looking for, Molecular Genetics and Breeding of Forest Trees is divided into four sections: Forest Tree Functional Genomics, Molecular Biology of Wood Formation, Forest Tree Transgenesis, and Genome Mapping in Forest Trees. Within these sections, you'll find the most up-to-date information on: functional genomics EST databases proteomics in forest trees genomics of wood formation and in vitro systems for the study of wood formation genetic transformation of forest trees stable expression of foreign genes modification of flowering in forest trees genome mapping in forest trees microsatellite DNA markers in forest trees exploring the transcriptome of the ectomycorrhizal symbiosis in trees

Scientists and researchers from top labs around the world share their expertise!
This unique text integrates tree transgenesis, functional genomics, and structural genomics to present, for the first time, a unified approach to research on the molecular biology of forest trees. A distinguished panel of scientists, researchers, and educators from around the world have combined their efforts to present the most up-to-date information and make Molecular Genetics and Breeding of Forest Trees an important addition to your professional or teaching collection. Helpful tables and figures make important points easy to access and understand.
To make it easier to find the specific information you're looking for, Molecular Genetics and Breeding of Forest Trees is divided into four sections: Forest Tree Functional Genomics, Molecular Biology of Wood Formation, Forest Tree Transgenesis, and Genome Mapping in Forest Trees. Within these sections, you'll find the most up-to-date information on: functional genomics EST databases proteomics in forest trees genomics of wood formation and in vitro systems for the study of wood formation genetic transformation of forest trees stable expression of foreign genes modification of flowering in forest trees genome mapping in forest trees microsatellite DNA markers in forest trees exploring the transcriptome of the ectomycorrhizal symbiosis in trees

In this timely book, expert international authors critically review all of the most important topics in this exciting field. This book is unique in that it is the first to review the area from a molecular biology and genomics perspective. Topics covered include: aerobic and anaerobic biodegradation of aromatic compounds; molecular detection methods (e.g. microautoradiography, mRNA analyses, etc.); genome-based predictive modeling; elucidation of regulatory networks; bioavailability; chemotaxis and transport issues; functional genomic analyses; natural attenuation; community fingerprinting and metagenomics; biotreatment; and biocatalysts engineering. The book will be essential reading for microbial degradation and bioremediation scientists, and of general interest for microbiologists working in field of environmental microbiology.

Man-made carcinogens, natural genotoxic agents in the environment, as well as ionizing and ultraviolet radiation can damage DNA and are a constant threat to genome integrity. Throughout the evolution oflife, complex DNA repair systems have developed in all living organisms to cope with this damage. Unrepaired DNA lesions can promote genetic alterations (mutations) that may be linked to an altered phenotype, and, if growth-controlling genes are involved, these mutations can lead to cell transformation and the development of malignant tumors. Proto oncogenes and tumor suppressor genes may be critical targets for DNA damaging agents. In a number of animal model systems, correlations between exposure to a carcinogen, tumor develop ment, and genetic changes in tumor DNA have been established. To understand mutagenesis processes in more detail at the molecular level, we need to know the type and frequency of DNA adducts within cells, their distribution along genes and specific DNA sequences, as well as the rates at which they are repaired. We also need to know what types of mutations are produced and which gene positions are most prone to mutagenesis. This book provides a collection of techniques that are useful in mutagenesis research. The book is divided into three parts. In Part I, methods for DNA damage and repair analysis are provided."

This volume provides up-to-date and novel techniques for various screening technologies currently used in metagenomics and related areas. Starting with DNA/RNA isolation from environmental samples, the book continues by delving into areas such as current methods used to isolate DNA and construct metagenomic libraries, establishment of metagenome libraries in non-E. coli hosts, and topics like function-driven mining of metagenomic DNA, screening and analyzing protocols for a wide array of different genes encoding enzymes, bacterial viruses and much more. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step and readily reproducible protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Metagenomics: Methods and Protocols, Third Edition provides a comprehensive collection of up-to-date metagenome protocols and tools for the recovery of many major types of biocatalysts and allows for the easy setup of these screens in microbiology laboratories.

Few, if any, genes have had the same level of impact on the field of evolutionary-developmental biology (evo-devo) as the Hox genes. These genes are renowned for their roles in patterning the body plans and development of the animal kingdom. This is complemented by the distinctive organisation of these genes in the genome, with them frequently being found as clusters in which gene position is linked to when and where the individual genes are expressed, particularly during embryogenesis. This book provides the latest overviews of Hox gene organisation and function for major clades of animals from across the animal kingdom. With the rapidly increasing availability of high-quality whole genome sequences from an ever-expanding range of species, it is becoming increasingly evident that there is great diversity in the organisation of Hox genes. These great strides in genome sequencing are wedded to important developments in our ability to detect expression and disrupt gene function in species that are not traditionally genetically-amenable animals. These technical developments are integrated with wide taxon-sampling in this volume to provide new perspectives on the roles of Hox genes in understanding fundamental issues such as embryo patterning, mechanisms of gene regulation, homology, evolvability, evolutionary novelties, phylogeny, the role of gene and genome duplications in evolution, and ancestral states for major clades of animals. Key features Integrative overviews from major animal groups including, arthropods, vertebrates, echinoderms, mollusks and other spiralians. Perspectives gleaned from the latest genome sequence and gene expression data. Individual chapters written by world-leading experts in Hox genes and evo-devo in each animal group. Related Titles Scholtz, G., ed. Evolutionary Developmental Biology of Crustacea (ISBN 978-9-0580-9637-1) Mattick, J. & P. Amaral. RNA, The Epicenter of Genetic Information (ISBN 978-0-3675-6778-1) Bard, J. Evolution: The Origins and Mechanisms of Diversity (ISBN 978-0-3673-5701-6)

Biological markers (biomarkers) are useful tools for understanding the nature and extent of human exposure and risk from environmental toxicants. Biomarkers are classified into three basic categories: exposure, effect, or susceptibility. A marker of exposure is the product of the interaction between a target cell or molecule and a foreign substance (NAS, 1989). These markers can be used to determine the biologically effective dose necessary to elicit a particular physiological change in an organism. A marker of effect is a biochemical or physiological change in an organism that can predict the onset of adverse health effects resulting from a given exposure. Lastly, markers of susceptibility act as indicators of an inherent or acquired tendency of an organism to experience an adverse health effect (NAS, 1989). These markers are already used to detect a variety of diseases and show great promise for developing a better understanding of the mechanicisms of disease. Additionally, biomarkers can be used to establish a more rational basis for quantitative risk extrapolation between species, as weIl as to obtain more precise estimates of the time of critical exposure. These markers can also prove helpful in identifying potentially damaging exposures before the onset of adverse health effects. Biomarkers serve as a valuable exposure assessment tool because they take into account exposure from all routes and integrate exposure from all sources. They have the potential to yield better risk estimates than current monitoring and modeling protocols. In lune 1992, Dr. Travis and Dr.

Biotic stresses cause yield loss of 31-42% in crops in addition to 6-20% during post-harvest stage. Understanding interaction of crop plants to the biotic stresses caused by insects, bacteria, fungi, viruses, and oomycetes, etc. is important to develop resistant crop varieties. Knowledge on the advanced genetic and genomic crop improvement strategies including molecular breeding, transgenics, genomic-assisted breeding and the recently emerging genome editing for developing resistant varieties in technical crops is imperative for addressing FHEE (food, health, energy and environment) security. Whole genome sequencing of these crops followed by genotyping-by-sequencing have facilitated precise information about the genes conferring resistance useful for gene discovery, allele mining and shuttle breeding which in turn opened up the scope for 'designing' crop genomes with resistance to biotic stresses. The 15 chapters dedicated to 13 technical crops and 2 technical crop groups in this volume will deliberate on different types of biotic stress agents and their effects on and interaction with crop plants; will enumerate on the available genetic diversity with regard to biotic stress resistance among available cultivars; illuminate on the potential gene pools for utilization in interspecific gene transfer; will brief on the classical genetics of stress resistance and traditional breeding for transferring them to their cultivated counterparts; will enunciate the success stories of genetic engineering for developing biotic stress resistant varieties; will discuss on molecular mapping of genes and QTLs underlying biotic stress resistance and their marker-assisted introgression into elite varieties; will enunciate on different emerging genomics-aided techniques including genomic selection, allele mining, gene discovery and gene pyramiding for developing resistant crop varieties with higher quantity and quality; and will also elaborate some case studies on genome editing focusing on specific genes for generating disease and insect resistant crops.

This updated volume reflects new and evolved techniques to study detection, profiling, and manipulation of microRNAs (miRNAs) in plants and animals. After overviews of how best to detect, identify, and validate microRNAs, the book continues by exploring state-of-the-art protocols for microRNA detection, approaches to profile the expression level of microRNAs, spatial expression analysis, describe in silico analysis of microRNAs and their targets, as well as protocols for functional analysis of microRNAs and their targets by CRISPR/Cas. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step and readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and up-to-date, MicroRNA Detection and Target Identification: Methods and Protocols, Second Edition aims to ensure successful results in the further study of this vital field.

From Thanksgiving to fast food to anorexia nervosa, Food in the USA brings together essential reading on these topics and is the only substantial collection of essays on food and culture in America. The broad range of essay topics include: the corporate food industry, soup kitchens, meateating, fast food, waitressing, Coca-Cola, Aunt Jemima, the Passover Seder, soul food, diabetes and nutrition. Together, the collection provides a fascinating look at how and why we are what we eat.

The fourth edition of this well-known text provides students, researchers and technicians in the area of medicine, genetics and cell biology with a concise, understandable introduction to the structure and behavior of human chromosomes. It covers both basic and up-to-date material on normal and defective chromosomes, and this new edition is particularly enhanced by the complete revision of the material on the molecular genetics of chromosomes and chromosomal defects.

Computers have become an essential component of modern biology. They help to manage the vast and increasing amount of biological data and continue to play an integral role in the discovery of new biological relationships. This in silico approach to biology has helped to reshape the modern biological sciences. With the biological revolution now among us, it is imperative that each scientist develop and hone today's bioinformatics skills, if only at a rudimentary level. Bioinformatics Methods and Protocols was conceived as part of the Methods in Molecular Biology series to meet this challenge and to provide the experienced user with useful tips and an up-to-date overview of current developments. It builds upon the foundation that was provided in the two-volume set published in 1994 entitled Computer Analysis of Sequence Data. We divided Bioinformatics Methods and Protocols into five parts, including a thorough survey of the basic sequence analysis software packages that are available at most institutions, as well as the design and implemen- tion of an essential introductory Bioinformatics course. In addition, we included sections describing specialized noncommercial software, databases, and other resources available as part of the World Wide Web and a stimul- ing discussion of some of the computational challenges biologists now face and likely future solutions.

Create improved crops with these techniques for plant cell culture This comprehensive book presents the basic concepts and applied techniques of plant cell and tissue culture. More and more, commercial plant breeding and development employs these methods to protect crops from weather, pests, and disease. Covering the history of in vitro breeding as well as emerging research trends, In Vitro Plant Breeding offers specific techniques for crop improvement and breeding. Designed as a text for undergraduate students, In Vitro Plant Breeding presents the theory of tissue culture as well as practical techniques. Its step-by-step instructions and clear illustrations facilitate learning and laboratory work. In Vitro Plant Breeding gives in-depth information and the latest research on the vital concepts and techniques of in vitro breeding, including: applications of plant tissue culture morphogenesis and organogenesis micropropagation producing haploid plants in vitro in vitro pollination and fertilization problems of embryo culture somatic hybridization protoplast technology selection of desirable traits cryopreservation and plant breeding micrograftingThis helpful book is plentifully illustrated with examples, schematic descriptions, and tables to make the concepts clear and easy to learn. In Vitro Plant Breeding is an essential resource.

This volume explores base editors (BEs), an invaluable CRISPR-based genome editing tool with a wide variety of versatile applications. Beginning with an overview of BEs, their diverse variants, and computational tools, the book continues with experimental applications of BEs for disease modeling in mammalian cells and generating mutagenic mice, therapeutic base editing strategies, which covers delivery methods of BE-encoded DNA plasmids, mRNAs, or ribonucleoproteins through viruses or non-viral lipid nanoparticles, and lastly, the use of BEs in plants and bacteria. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step and readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Base Editors: Methods and Protocols serves as an ideal guide for researchers looking to use base editors to continue their studies in an array of fields.

This book presents a comprehensive discussion on the heterogeneity existing between different types of stem cells within the same tissue. As the functions of these stem cells vary, this is very important for the application of stem cells in cell therapy. This book describes the many recent developments that have revealed completely different roles of distinct stem cells within the same organ. Stem Cells Heterogeneity in Different Organs provides a timely update on the current information on stem cells heterogeneity in various tissues. It also provides a solid foundation of the history of stem cells from specific tissues and the current applications of this knowledge in regenerative medicine. Taken with its companion volumes, Stem Cells Heterogeneity: Novel Concepts and Stem Cells Heterogeneity in Cancer, this book is essential reading for advanced cell biology students as well as researchers and clinicians working with stem cells.