With the new techniques described in this volume, a new gene can be placed on the linkage map within only a few days. Leading researchers have updated the earlier edition to include the latest versions of DNA-based marker maps for a variety of important crops.

Transcriptome Analysis, by Frank Stahl, Bernd Hitzmann, Kai Mutz, Daniel Landgrebe, Miriam Lubbecke, Cornelia Kasper, Johanna Walter und Thomas Scheper Transcriptome Data Analysis for Cell Culture Processes, by Marlene Castro-Melchor, Huong Le und Wei-Shou Hu Modeling Metabolic Networks for Mammalian Cell Systems: General Considerations, Modeling Strategies, and Available Tools, by Ziomara P. Gerdtzen Metabolic Flux Analysis in Systems Biology of Mammalian Cells, by Jens Niklas und Elmar Heinzle Advancing Biopharmaceutical Process Development by System-Level Data Analysis and Integration of Omics Data, by Jochen Schaub, Christoph Clemens, Hitto Kaufmann und Torsten W. Schulz Protein Glycosylation and Its Impact on Biotechnology, by Markus Berger, Matthias Kaup und Veronique Blanchard Protein Glycosylation Control in Mammalian Cell Culture: Past Precedents and Contemporary Prospects, by Patrick Hossler Modeling of Intracellular Transport and Compartmentation, by Uwe Jandt und An-Ping Zeng Genetic Aspects of Cell Line Development from a Synthetic Biology Perspective, by L. Botezatu, S. Sievers, L. Gama-Norton, R. Schucht, H. Hauser und D. Wirth.

Metagenomics: Perspectives, Methods, and Applications provides thorough coverage of the growing field of metagenomics. A diverse range of chapters from international experts offer an introduction to the field and examine methods for metagenomic analysis of microbiota, metagenomic computational tools, and recent metagenomic studies in various environments. The emphasis on application makes this text particularly useful for applied researchers, practitioners, clinicians and students seeking to employ metagenomic approaches to advance knowledge in the biomedical and life sciences. Case-study based application chapters examine topics ranging from viral metagenome profiling, metagenomics in oral disease and health, metagenomic insights into the human gut microbiome and metabolic syndromes, and more. Additionally, perspectives on future potential at the end of each chapter provoke new thought and motivations for continued study in this exciting and fruitful research area.

RNA Modification, Volume 41 examines the powerful ability to regulate the function of RNA molecules or modify the message transmitted by RNA molecules. Chapters in this newly released volume include The Importance of Being Modified: Modifications Shape RNA Function through Chemistry, Structure and Dynamics, The evolution of multi-substrate specificity by RNA modification enzymes, TrmD: a methyl transferase for tRNA methylation with m1G37, Structures and activities of the Elongator complex and its co-factors, RNA pseudouridylation: Mechanism and Function, The activity of 5'3' exonucleases on hypo modified tRNA substrates and other structured RNAs, and the Synthesis, heterogeneity and function of post-transcriptional nucleotide modifications in eukaryotic ribosomal RNAs. This field has recently seen a very rapid progress in the understanding of the mechanism and enzymes involved in RNA modification. This volume presents some of the most recent advances in the identification and function of enzymes involved in modifying RNA molecules.

To harness the high-throughput potential of DNA microarray technology, it is crucial that the analysis stages of the process are decoupled from the requirements of operator assistance. Microarray Image Analysis: An Algorithmic Approach presents an automatic system for microarray image processing to make this decoupling a reality. The proposed system integrates and extends traditional analytical-based methods and custom-designed novel algorithms. The book first explores a new technique that takes advantage of a multiview approach to image analysis and addresses the challenges of applying powerful traditional techniques, such as clustering, to full-scale microarray experiments. It then presents an effective feature identification approach, an innovative technique that renders highly detailed surface models, a new approach to subgrid detection, a novel technique for the background removal process, and a useful technique for removing "noise." The authors also develop an expectation-maximization (EM) algorithm for modeling gene regulatory networks from gene expression time series data. The final chapter describes the overall benefits of these techniques in the biological and computer sciences and reviews future research topics. This book systematically brings together the fields of image processing, data analysis, and molecular biology to advance the state of the art in this important area. Although the text focuses on improving the processes involved in the analysis of microarray image data, the methods discussed can be applied to a broad range of medical and computer vision analysis areas.

In recent years, a number of groundbreaking structural and mechanistic studies deepened our understanding of helicase mechanisms and established new approaches for their analyses. Many fundamental mechanistic questions ranging from the mechanism of force generation, mechanochemical coupling to distinct mechanisms by which the same enzyme translocates on DNA removing obstacles, unwinds DNA and/or remodels nucleoprotein complexes, however, remain to be answered. It is even less understood how the helicase motors are incorporated into a wide range of genome maintenance and repair machines. The field has reached a stage when the studies of molecular mechanisms and basic biology of helicases can and shall be integrated with the studies of development, cancer and longevity. The objective of this book is to provide the first systematic overview of structure, function and regulation of DNA helicases and related molecular motors. By integrating the knowledge obtained through the diverse technical approaches ranging from single-molecule biophysics to cellular and molecular biological studies the editors aim to provide a unified view on how helicases function in the cell, are regulated in response to different cellular stresses and are integrated into large macromolecular assemblies to form a complex and adaptive living system.

The book gives an overview of developments in Quantitative Genetics and variance component analysis in an era of Big Data and Sequenced Genomes. It provides a detailed description of a direct method of estimation that will be a useful means of extracting information from a large set of data that was inconceivable 10 to 20 years ago.The book is a combination of a history of variance component analysis and a forward looking view as to how direct methods of estimation arise from the availability of big data sets and sequenced genomes of each individual in the sample.Many papers and books on quantitative genetics versions of the general linear model from statistics are useful for analyzing the data, using relatively small sets of data. In this book, new methods of direct estimation are introduced and analyzed that are appropriate for an era of big sets of data and sequences genomes. These direct methods of estimation are based on taking conditional expectations rather the methods of least squares that characterize many applications of the general linear model of statistics.

The book gives an overview of developments in Quantitative Genetics and variance component analysis in an era of Big Data and Sequenced Genomes. It provides a detailed description of a direct method of estimation that will be a useful means of extracting information from a large set of data that was inconceivable 10 to 20 years ago.The book is a combination of a history of variance component analysis and a forward looking view as to how direct methods of estimation arise from the availability of big data sets and sequenced genomes of each individual in the sample.Many papers and books on quantitative genetics versions of the general linear model from statistics are useful for analyzing the data, using relatively small sets of data. In this book, new methods of direct estimation are introduced and analyzed that are appropriate for an era of big sets of data and sequences genomes. These direct methods of estimation are based on taking conditional expectations rather the methods of least squares that characterize many applications of the general linear model of statistics.

This volume provides techniques on recent developments that use RNA scaffolds as molecular tools. RNA Scaffolds: Methods and Protocols guides readers through methods on various domains as molecular biology, nanotechnologies, and structural biology. Written for the Methods in Molecular Biology series, 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.Practical and authoritative, RNA Scaffolds: Methods and Protocols will serve as an invaluable reference for those interested in further study into this fascinating field.

Cutting edge reviews by leading researchers illuminate key aspects of DNA repair in mammalian systems and its relationship to human genetic disease and cancer. Major topics include UV and X-Ray repair, repair of chemical damage, recombinational repair, mismatch repair, transcription-repair coupling, and the role of DNA repair in disease prevention. Extensive up-to-date references and rigorous peer-review of each chapter make this volume definitive and bring it to the active frontiers of research.

This second part in the two-volume work Microarrays details applications and data analysis. It includes insight into non-mammalian vertebrate systems, processes and protocols for high quality glass-based microarrays. Coverage includes applications in DNA, peptide, antibody and carbohydrate microarraying, oligonucleotide microarrays generated from hydrolysis PCR probe sequences, microarray platforms in clinical practice, and screening of cDNA libraries on glass slide microarrays. Authors in this volume also discuss protocols for predicting DNA duplex stability on oligonucleotide arrays and integrated analysis of microarray results.

Epigenomics in Health and Disease discusses the next generation sequencing technologies shaping our current knowledge with regards to the role of epigenetics in normal development, aging, and disease. It includes the consequences for diagnostics, prognostics, and disease-based therapies made possible by the study of the complete set of epigenetic modifications to the genetic material of human cells. With coverage pertinent to both basic biology and translational research, the book will be of particular interest for medical and bioscience researchers and students seeking current translational knowledge in epigenesis and epigenomics. Coverage includes the latest findings on epigenome-wide research in disease-based profiling, epidemiological implications, epigenome-wide epigenetic studies, the cancer epigenome, and other pervasive disease categories.

Genomics and Society; Ethical, Legal-Cultural, and Socioeconomic Implications is the first book to address the vast and thorny web of ELSI topics identified as core priorities of the NHGRI in 2011. The work addresses fundamental issues of biosociety and bioeconomy as the revolution in biology moves from research lab to healthcare system. Of particular interest to healthcare practitioners, bioethicists, and health economists, and of tangential interest to the gamut of applied social scientists investigating the societal impact of new medical paradigms, the work describes a myriad of issues around consent, confidentiality, rights, patenting, regulation, and legality in the new era of genomic medicine.

The nitrogen (N) cycle is one of the most important nutrient cycles on the planet, and many of its steps are performed by microbial organisms. During the cycling process, greenhouse gases are formed, including nitrous oxide and methane. In addition, the use of nitrogen fertilizers increases freshwater nitrate levels, causing pollution and human health problems. A greater knowledge of the microbial communities involved in nitrogen transformations is necessary to understand and counteract nitrogen pollution. This book - written by renowned researchers who are specialized in the most relevant and emerging topics in the field - provides comprehensive information on the new theoretical, methodological, and applied aspects of metagenomics and other 'omics' approaches used to study the microbial N cycle. The book provides a thorough account of the contributions of metagenomics to microbial N cycle background theory. It also reviews state-of-the-art investigative methods and explores new applications in water treatment, agricultural practices, climate change, among others. The book is recommended for microbiologists, environmental scientists, and anyone interested in microbial communities, metagenomics, metatranscriptomics, and metaproteomics of the microbial N cycle.

Foods from natural products are a major contributor to contemporary dietary needs. The knowledge of interactions of specific natural products on genes is accumulating due to recent scientific advancements. Natural Products Interactions on Genomes focuses on recent developments in understanding human genome interactions with various natural products. The book first examines selected major natural products and their interactions with selected genes for each chromosome in mammals, then moves on to focused discussions on interactions of natural products with genes that are involved in specific diseases. It includes studies on breast cancer and prostate cancer. The focus then shifts to the effects of natural products on microbial growth and a final chapter that discusses future challenges and prospects in the field. This book also presents a unique real-time approach by providing hyperlinks to websites with updated literature on natural products and interactions with genes involved in metabolic pathways. With a broad range of relevance among disciplines including biology, biomedical science, pharmacy, medicinal chemistry, and naturopathic and herbal medicine, Natural Products Interactions on Genomes provides a valuable reference. It gives you an understanding of the methods of study of natural products and their effects on genomes while pointing toward the future of natural products and the areas they impact in health and science.

In the past half century, filamentous fungi have grown in commercial importance not only in the food industry but also as sources of pharmaceutical agents for the treatment of infectious and metabolic diseases and of specialty proteins and enzymes used to process foods, fortify detergents, and perform biotransformations. The commercial impact of molds is also measured on a negative scale since some of these organisms are significant as pathogens of crop plants, agents of food spoilage, and sources of toxic and carcinogenic compounds. Recent advances in the molecular genetics of filamentous fungi are finding increased application in the pharmaceutical, agricultural, and enzyme industries, and this trend promises to continue as the genomics of fungi is explored and new techniques to speed genetic manipulation become available.

This volume focuses on the filamentous fungi and highlights the advances of the past decade, both in methodology and in the understanding of genomic organization and regulation of gene and pathway expression.

This book is open access under a CC BY 4.0 license This open access book brings together the latest genome base prediction models currently being used by statisticians, breeders and data scientists. It provides an accessible way to understand the theory behind each statistical learning tool, the required pre-processing, the basics of model building, how to train statistical learning methods, the basic R scripts needed to implement each statistical learning tool, and the output of each tool. To do so, for each tool the book provides background theory, some elements of the R statistical software for its implementation, the conceptual underpinnings, and at least two illustrative examples with data from real-world genomic selection experiments. Lastly, worked-out examples help readers check their own comprehension.The book will greatly appeal to readers in plant (and animal) breeding, geneticists and statisticians, as it provides in a very accessible way the necessary theory, the appropriate R code, and illustrative examples for a complete understanding of each statistical learning tool. In addition, it weighs the advantages and disadvantages of each tool.

Small DNA tumour viruses are a group of double-stranded DNA viruses made up of the polyomavirus, the adenovirus, and the papillomavirus families. In this title, scientists from around the globe review current topics in this area, providing an overview of the molecular biology of these viruses and their interactions with the host.

In today's world, we are witnessing simultaneous breakthroughs in reproductive technologies, genomics, and molecular biology. Advances in molecular genetic technology and understanding of the bovine genome have led to the development of tools that can be used to enhance profitability on cow-calf enterprises. Factors Affecting Calf Crop: Biotechnology of Reproduction provides a detailed compilation of current and forthcoming technology for managing reproduction in cattle.

The book discusses topics such as: approved techniques for controlling the estrous cycle in cattle; managing follicular growth with progesterone, estrogens, and prostaglandins; freezing, thawing, and transfer of cattle embryos; application of embryo transfer to the beef cattle industry; embryo transfer in topically adapted cattle; new factors affecting bull fertility; embryo collection and utilization technology, in vitro fertilization, somatic cell cloning, and genetic technologies; uses of real-time ultrasound; and sexed semen.

Over 25 leading animal scientists have combined their expertise to produce the first single-source reference that covers successful reproductive techniques that will, most likely, be the wave of the future. Expansive in scope, the book addresses current biotechnologies as they impact the production of beef cattle. Written at a level to appeal to the researcher, commercial producer, or student, Factors Affecting Calf Crop: Biotechnology of Reproduction presents you with a wealth of technologies applicable to animal agriculture.

In 2010, scientists led by J. Craig Venter became the first to successfully create 'synthetic life' -- putting humankind at the threshold of the most important and exciting phase of biological research, one that will enable us to actually write the genetic code for designing new species to help us adapt and evolve for long-term survival. The science of synthetic genomics will have a profound impact on human existence, including chemical and energy generation, health, clean water and food production, environmental control, and possibly even our evolution. In Life at the Speed of Light, Venter presents a fascinating and authoritative study of this emerging field from the inside -- detailing its origins, current challenges and controversies, and projected effects on our lives. This scientific frontier provides an opportunity to ponder anew the age-old question 'What is life?' and examine what we really mean by 'playing God'. Life at the Speed of Light is a landmark work, written by a visionary at the dawn of a new era of biological engineering.

Bioinformatics has ignited the imagination of scientists, entrepreneurs and the general public. At the meeting place of two fast growth disciplines, biology and computer science Bioinformatics is one of the cornerstones of the new biology. It is clearly pivotal to the translation of high throughput projects such the human genome project into useful knowledge. Yet despite all this attention, there is no consensus on what exactly is Bioinformatics. There are several canonical topics, such as gene structure prediction, protein functional classification or structure prediction. The present book explores new frontiers in bioinformatics, such as Glycomics or the computational modeling of genetic processes. We also discuss confounding factors that we find crucial to the development of the field, such as the ability to protect and restrict intellectual property in the field, or the challenges involved in educating bioinformatics users. Finally, we touch upon some fundamental questions, such as what information is and how it is captured in biological systems. By bringing to the readers such a broad spectrum of reviews, we hope to capture the vibrant spirit of this young science and to truly represent the fast pace with which it is still developing.

While there has been an increasing number of books on various aspects of epigenetics, there has been a gap over the years in books that provide a comprehensive understanding of the fundamentals of chromatin. Chromatin is the combination of DNA and proteins that make up the genetic material of chromosomes. Its primary function is to package DNA to fit into the cell, to strengthen the DNA to prevent damage, to allow mitosis and meiosis, and to control the expression of genes and DNA replication. The audience for this book is mainly newly established scientists and graduate students. Rather than going into the more specific areas of recent research on chromatin the chapters in this book give a strong, updated groundwork about the topic. Some the fundamentals that this book will cover include the structure of chromatin and biochemistry and the enzyme complexes that manage it.

This volume presents an overview of recent developments in systems biology and their applications in cancer-related research. The ongoing advances in our understanding of genomics and proteomics, coupled with the development of new and more robust tools, have led to an emphasis on analyzing biological systems at multiple levels. Thus, there is a need to integrate different types of data into a comprehensive "systems" view.

Written by active researchers in the emerging areas, this book gives senior undergraduate students, graduate students and new researchers an idea of where the frontiers of systems biology are and an opportunity to learn high-throughput techniques in use. One of the particular emphases of the book is to elucidate the molecular mechanisms in cancer. The discovery of biomarkers and anti-cancer drugs using systems biology approach is also extensively discussed.

This manual is an indispensable tool for introducing advanced undergraduates and beginning graduate students to the techniques of recombinant DNA technology, or gene cloning and expression. The techniques used in basic research and biotechnology laboratories are covered in detail. Students gain hands-on experience from start to finish in subcloning a gene into an expression vector, through purification of the recombinant protein.
The second edition has been completely re-written, with new laboratory exercises and all new illustrations and text, designed for a typical 15-week semester, rather than a 4-week intensive course. The project approach to experiments was maintained: students still follow a cloning project through to completion, culminating in the purification of recombinant protein. It takes advantage of the enhanced green fluorescent protein-students can actually visualize positive clones following IPTG induction.
*Cover basic concepts and techniques used in molecular biology research labs
*Student-tested labs proven successful in a real classroom laboratories
*Exercises simulate a cloning project that would be performed in a real research lab
*"Project" approach to experiments gives students an overview of the entire process
*Prep-list appendix contains necessary recipes and catalog numbers, providing staff with detailed instructions"

The discovery of the spatial structure of the double-stranded DNA molecule is one of the greatest achievements of science. It would not be an exaggeration to say that the DNA double helix is a distinguished symbol of modern biology.
Divided into three parts, DNA Liquid-Crystalline Dispersions and Nanoconstructions covers the information presently available on the condensation of various forms of DNA and describes practical applications of the peculiar properties of the liquid-crystalline particles.

• Part 1 describes the main methods used for condensation of linear high- and low-molecular mass DNA, including their complexes with polycations and circular DNA
• Part 2 compares the state and reactivity of double-stranded nucleic acid molecules fixed spatially in the liquid-crystalline as well as the same molecules under intracellular conditions
• Part 3 explains how the discovery of the fundamental principles underlying the formation of nucleic acid liquid-crystalline dispersion particles opens a gate for the operational use of these principles in the area of nanotechnology and biosensorics

With detailed coverage of DNA liquid crystals, this book provides an understanding of the information presently available on the condensation of various forms of DNA. Double-stranded nucleic acids, spatially organized in a liquid-crystalline structure, represent an important polyfunctional tool for molecular biology and nanobiotechnology. The possibility of programmed and controlled variations in the properties of these molecules and in the characteristics of their liquid-crystalline dispersions, provides wide options for the formation of biologically active three-dimensional structures with unique, widely applicable properties.