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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.
A Practical Guide to the Highly Dynamic Area of Massively Parallel Sequencing The development of genome and transcriptome sequencing technologies has led to a paradigm shift in life science research and disease diagnosis and prevention. Scientists are now able to see how human diseases and phenotypic changes are connected to DNA mutation, polymorphism, genome structure, and epigenomic abnormality. Next-Generation Sequencing Data Analysis shows how next-generation sequencing (NGS) technologies are applied to transform nearly all aspects of biological research. The book walks readers through the multiple stages of NGS data generation and analysis in an easy-to-follow fashion. It covers every step in each stage, from the planning stage of experimental design, sample processing, sequencing strategy formulation, the early stage of base calling, reads quality check and data preprocessing to the intermediate stage of mapping reads to a reference genome and normalization to more advanced stages specific to each application. All major applications of NGS are covered, including: RNA-seq: mRNA-seq and small RNA-seq Genotyping and variant discovery through genome re-sequencing De novo genome assembly ChIP-seq to study DNA-protein interaction Methylated DNA sequencing on epigenetic regulation Metagenome analysis through community genome shotgun sequencing Before detailing the analytic steps for each of these applications, the book presents the ins and outs of the most widely used NGS platforms, with side-by-side comparisons of key technical aspects. This helps practitioners decide which platform to use for a particular project. The book also offers a perspective on the development of DNA sequencing technologies, from Sanger to future-generation sequencing technologies. The book discusses concepts and principles that underlie each analytic step, along with software tools for implementation. It highlights key features of the tools while omitting tedious details to provide an easy-to-follow guide for practitioners in life sciences, bioinformatics, and biostatistics. In addition, references to detailed descriptions of the tools are given for further reading if needed. The accompanying website for the book provides step-by-step, real-world examples of how to apply the tools covered in the text to research projects. All the tools are freely available to academic users.
Due to the potential benefits of biotechnology, interest in the interaction between DNA and surfactants and polymers has become increasingly significant. Now, "DNA Interactions with Polymers and Surfactants" provides an extensive, up-to-date overview of the subject, giving readers a basis for understanding the factors leading to complexation between DNA and different cosolutes, including metal ions, polyelectrolytes, spermine, spermidine, surfactants and lipids, and proteins.
As a major defence against environmental damage to cells DNA repair is present in all organisms including bacteria, yeast, drosophila, fish, amphibians, rodents and humans. DNA repair is involved in processes that minimise cell killing, mutations, replication errors, persistence of DNA damage and genomic instability. Abnormalities in these processes have been implicated in cancer and ageing. This book presents leading-edge research from around the world in this frontal field.
The advancement of DNA sequencing technologies has resulted in a movement away from the single gene, and towards a whole genome focus. Previously DNA sequencing was expensive, slow and tedious, but new technologies have been developed that facilitate the relatively cheap and rapid generation of raw sequence from whole bacterial genomes. The sequencing of the human genome was also accelerated in the final phases as a result of new sequencing methods. However, generating the raw sequence is just the start, and tools are required to convert it into useful biological knowledge. This book highlights the new advances in DNA sequencing, and summarises the process of genome and protein annotation. The book also describes the tools required to achieve this, and provides examples within the context of specific genomes.
This book examines the application of soybean genome sequences to comparative, structural, and functional genomics. Since the availability of the soybean genome sequence has revolutionized molecular research on this important crop species, the book also describes how the genome sequence has shaped research on transposon biology and applications for gene identification, tilling and positional gene cloning. Further, the book shows how the genome sequence influences research in the areas of genetic mapping, marker development, and genome-wide association mapping for identifying important trait genes and soybean breeding. In closing, the economic and botanical aspects of the soybean are also addressed.
Assembling the work of an international panel of researchers, Mass Spectrometry of Nucleosides and Nucleic Acids summarizes and reviews the latest developments in the field and provides a window on the next generation of analysis. Beginning with an overview of recent developments, the book highlights the most popular ionization methods and illustrates the diversity of strategies employed in the characterization and sequencing of DNA and RNA oligomers, nucleosides, nucleotides, and adducts. It describes studies performed on deoxyinosine and its analogues and provides an introduction to tandem mass spectrometry (MS/MS).
Next, the contributors examine mass spectrometric application in the study of cyclic nucleotides in biochemical signal transduction. They analyze urinary modified nucleosides and explore DNA adducts. They discuss isotope labeling of DNA-mass spectrometry (ILD-MS) and examine various uses of electrospray ionization mass spectrometry (ESI-MS). The book reviews recent progress in the direct MS characterization of noncovalent nucleic acid-protein complexes, explores the interaction and ionization of guanidine-derived compounds with highly acidic biomolecules, and examines quantitative identification of nucleic acids via signature digestion products detected using mass spectrometry.
The book describes a direct-infusion ESI-MS approach that can serve as a screening technique for the presence of modified nucleosides from small RNAs. Lastly, it discusses the LC-MS/MS method for the in vitro replication studies on damage-containing DNA substrates, and concludes with an examination of the influence of metal ions on the structure and reactivity of nucleic acids.
The exciting developments in mass spectrometry technology have fueled incredible advances in our understanding of nucleic acids and their complexes. The contributions presented in this volume capture the range of these advances, helping to inspire new findings and avenues of research.
Deoxyribonucleic acid (DNA) is a chemical found primarily in the nucleus of cells. DNA is a long, spiralling molecule that orchestrates the cell's daily operations and provides the genetic blueprint for the physical characteristics of all living organisms. It is the molecule that encodes genetic information in the nucleus of cells. It determines the structure, function and behaviour of the cell. DNA is made up of two complementary strands, the strands intertwine like a spiral staircase to form a structure called a double helix. Subunits, called bases, are the rungs of the staircase. The four nucleotides in DNA contain the bases: adenine (A), guanine (G), cytosine (C), and thymine (T). This book presents leading-edge research in this dynamic field.
Gene silencing is a general term describing epigenetic processes of gene regulation. The term gene silencing is generally used to describe the 'switching off' of a gene by a mechanism other than genetic mutation. That is, a gene which would be expressed (turned on) under normal circumstances, is switched off by machinery in the cell. Genes are regulated at either the transcriptional or post-transcriptional level. Transcriptional gene silencing is the result of histone modifications, creating an environment of heterochromatin around a gene that makes it inaccessible to transcriptional machinery (RNA polymerase, transcription factors, etc.). Post-transcriptional gene silencing is the result of mRNA of a particular gene being destroyed. The destruction of the mRNA prevents translation to form an active gene product (in most cases, a protein). A common mechanism of post-transcriptional gene silencing is RNAi. Both transcriptional and post-transcriptional gene silencing are used to regulate endogenous genes. This book presents the latest research in this important field.
Functional genomics--the deconstruction of the genome to determine the biological function of genes and gene interactions--is one of the most fruitful new areas of biology. The growing use of DNA microarrays allows researchers to assess the expression of tens of thousands of genes at a time. This quantitative change has led to qualitative progress in our ability to understand regulatory processes at the cellular level.This book provides a systematic introduction to the use of DNA microarrays as an investigative tool for functional genomics. The presentation is appropriate for readers from biology or bioinformatics. After presenting a framework for the design of microarray-driven functional genomics experiments, the book discusses the foundations for analyzing microarray data sets, genomic data-mining, the creation of standardized nomenclature and data models, clinical applications of functional genomics research, and the future of functional genomics.
Epigenetics and Regeneration compiles the first foundational reference on epigenetic mechanisms governing tissue development, repair, homeostasis, and regeneration, as well as pathways to employ these mechanisms in clinical practice and translational science. In this book, life science researchers, clinicians, and students will discover an interdisciplinary resource bringing together common themes in the field, background overviews, research methods, recent advances, and opportunities for drug discovery. Throughout this volume, special attention is paid to pre-clinical and first clinical studies aimed at increasing the regenerative potential of damaged tissues by epigenetic drugs, as well as innovative, discipline spanning strategies to enhance cell reprogramming. As an all-inclusive, evidence-based volume, Epigenetics and Regeneration will stimulate discussion and boost new research in this fascinating and impactful area of translational epigenetics.
The genomic approach of technology development and large-scale generation of community resource data sets has introduced an important new dimension in biological and biomedical research. Interwoven advances in genetics, comparative genomics, high throughput biochemistry and bioinformatics are combining to attack basic understanding of human life and disease and to develop strategies to combat disease. Genomic Research began with The Human Genome Project (HGP), the international research effort that determined the DNA sequence of the entire human genome, completed in April 2003. The HGP also included efforts to characterize and sequence the entire genomes of several other organisms, many of which are used extensively in biological research. Identification of the sequence or function of genes in a model organism is an important approach to finding and elucidating the function of human genes. Integral to the HGP are similar efforts to understand the genomes of various organisms commonly used in biomedical research, such as mice, fruit flies and roundworms. Such organisms are called "model organisms," because they can often serve as research models for how the human organism behaves. This new book brings together leading research from throughout the world in this cutting-edge field.
Despite progress in genetic research, knowledge about the exact structure of the chromosome continues to provide a challenge. Much of that challenge lies with the need for improved tools and methods that researchers require to perform novel analyses beyond the DNA level. Fortunately, rapid advances in nanotechnology, are now being employed to examine, analyze, and manipulate biological material at the chromosome level. Chromosome Nanoscience and Technology reviews these advances and their contribution to trends and applications in chromosome research. In addition to offering a guide to current progress, this book serves as the culminating report on a Japanese nanobiology project in the field of chromosome science begun in 2000. The project brought together researchers from disparate backgrounds that included molecular biology, biochemistry, protein science, immunology, genetics, anatomy, semiconductor production, polymer chemistry, material science, microscopy, and informatics, among others. Looking at chromosomes as nanomaterials, their contributions cover: Devices for chromosome handling, which includes the construction and application of nano and micro devices used for dissecting, analyzing, and manipulating chromosomes Visualization of chromosomes at nano and micro levels, which discusses methods for revealing nano-level folding of chromatin fibers Chromosomes as nanomaterials, which presents a new chromosome protein framework based on the cataloging of over 200 chromosomal proteins Informatics of chromosome images, which examines a new chromosome image database system for animals and plants This project, initiated a few years ago, now lays the groundwork for those scientists looking to perform further research in chromosome science. It provides them with starting points, as well as useful applications and methodology to assist in the long quest to gain a deepened understanding of life itself.
With the first draft of the human genome project in the public
domain and full analyses of model genomes now available, the
subject matter of 'Principles of Genome Analysis and Genomics' is
even 'hotter' now than when the first two editions were published
in 1995 and 1998. In the new edition of this very practical guide
to the different techniques and theory behind genomes and genome
analysis, Sandy Primrose and new author Richard Twyman provide a
fresh look at this topic. In the light of recent exciting
advancements in the field, the authors have completely revised and
rewritten many parts of the new edition with the addition of five
new chapters. Aimed at upper level students, it is essential that
in this extremely fast moving topic area the text is up to date and
This book contains eight chapters. The first three focus on three different layered systems, namely, mercurocuprate, BSCCO and RE-123 and present exciting features like their unusual chemistry, vortex physics and novel characteristics of the multilayers formed with some of them. The remaining five chapters of the volume describe studies carried out on recently discovered magnesium diboride, which superconducts at 39K. New and interesting work has been presented which describes, noteworthy advances in their flux pinning and mechanical properties and also bring out their future potential as this films and SQUID devices.
DNA microarrays are the modern, parallel version of classic molecular biology hybridization techniques allowing the exploration of thousands of sequences in a single run. The technique permits the complete analysis of genetic material and the monitoring of expression changes occurring in a biological sample under various conditions. Microarrays have been used successfully in various research areas including: sequencing, single nucleotide polymorphism (SNP) detection, characterization of protein-DNA interactions, DNA computing, mRNA profiling, and many more. Applications of microarrays in the biosciences include: gene expression studies, disease diagnosis, pharmacogenomics, drug screening, pathogen detection, and genotyping. This book focuses on the current successful applications of microarrays in various areas of bioscience. The authors describe the use of microarrays to assist basic research and drug discovery by the generation of gene expression maps, the reconstruction of gene networks and the study of biochemical pathways, the classification of genes and biological samples, and a real case study on the transcriptional effects of vaccine treatment. An entire chapter is dedicated to applications of microarrays that do not involve gene expression.
The field of forensic DNA analysis has grown immensely in the past two decades and genotyping of biological samples is now routinely performed in human identification (HID) laboratories. Application areas include paternity testing, forensic casework, family lineage studies, identification of human remains, and DNA databasing. Forensic DNA Analysis: Current Practices and Emerging Technologies explores the fundamental principles and the application of technologies for each aspect of forensic DNA analysis. The book begins by discussing the value of DNA evidence and how to properly recognize, document, collect, and store it. The remaining chapters examine: The most widely adopted methods and the best practices for DNA isolation from forensic biological samples and human remains Studies carried out on the use of both messenger RNA and small (micro) RNA profiling Real-time polymerase chain reaction (PCR) methods for quantification and assessment of human DNA prior to genotyping Capillary electrophoresis (CE) as a tool for forensic DNA analysis Next-generation short tandem repeat (STR) genotyping kits for forensic applications, the biological nature of STR loci, and Y-chromosome STRs (Y-STRs) Mitochondrial DNA (mtDNA) sequence analysis Single nucleotide polymorphisms (SNPs) and insertion/deletion polymorphisms (indels) in typing highly degraded DNA Deep-sequencing technologies The current state of integrated systems in forensic DNA analysis The book concludes by discussing various aspects of sample-processing training and the entities that provide such training programs. This volume is an essential resource for students, researchers, teaching faculties, and other professionals interested in human identification/forensic DNA analysis.
In situ gene amplification techniques offer tremendous potential as
aids to clinical diagnosis through their ability to detect a single
copy of a specific microbial, neoplastic, messenger, or mutated
nucleic acid sequence in a cell smear, cell suspension, tissue
section, or chromosome. In situ hybridization, applied in
combination with the polymerase chain reaction (PCR), can be
expected to fuel accelerated developments in the understanding of
embryogenesis, organogenesis, and cell differentiation, as well as
the pathogenesis of numerous disease processes. But the procedures
are cumbersome and fraught with potential variables, and
experimental results are difficult to reproduce.
This book is an excellent introductory text describing the use of bioinformatics to analyze genomic and post-genomic data. It has been translated from the original popular French edition, which was based on a course taught at the well-respected Ecole Polytechnique in Palaiseau. This edition has been fully revised and updated by the authors.
After a brief introduction to gene structure and sequence determination, it describes the techniques used to identify genes, their protein-coding sequences and regulatory regions. The book discusses the methodology of comparative genomics, using information from different organisms to deduce information about unknown sequences. There is a comprehensive chapter on structure prediction, covering both RNA and protein. Finally, the book describes the complex networks of RNA and protein that exist within the cell and their interactions, ending with a discussion of the simulation approaches that can be used to model these networks.
Praise from the reviews:
""In context of the new developments the genomic era has brought, Bioinformatics: Genomics and Post-Genomics becomes a fundamental and indispensable resource for undergraduate and early graduate students...insightfully authored...will immensely help students...in establishing important foundations while shaping their careers."" NEWSLETTER, BRITISH SOCIETY OF CELL BIOLOGY
Researchers from industry and academia review recent pharmaceutical, therapeutic, and biotechnological applications of ribozymes, including the latest principles on application of ribozyme technology to the inhibition of gene expression in living cells. Topics include protocols for the following: mo
Understanding gene expression and how it changes under normal and pathological conditions is essential to our understanding of the fundamentals of cell biology through to the targeted treatment of disease. In Gene Expression Profiling: Methods and Protocols, Second Edition, experts in their particular fields compile detailed protocols for a broad range of techniques, currently available and being further developed, for the analysis of gene expression at the DNA, RNA, and protein levels. 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 tips on troubleshooting and avoiding known pitfalls. Practical and easy-to-use, Gene Expression Profiling: Methods and Protocols, Second Edition presents a collection of clearly described and illustrated chapters, certain to be helpful to researchers in academia, in hospitals, and in industry who are interested in applying techniques, whether basic or advanced, for the analysis of gene expression.
The field of whole genome selection has quickly developed into the breeding methodology of the future. As efforts to map a wide variety of animal genomes have matured and full animal genomes are now available for many animal scientists and breeders are looking to apply these techniques to livestock production. Providing a comprehensive, forward-looking review of animal genomics, Genomic Selection in Animals provides coverage of genomic selection in a variety of economically important species including cattle, swine, and poultry. The historical foundations of genomic selection are followed by chapters that review and assess current techniques. The final chapter looks toward the future and what lies ahead for field as application of genomic selection becomes more widespread. A concise, useful summary of the field by one of the world s leading researchers, Genomic Selection in Animals fills an important gap in the literature of animal breeding and genomics.
"We are sure that DNA: Forensic and Legal Applications will play
its part in promoting this most powerful tool in the forensic
Because it consists of a number of complex steps and procedures subject to both scientific and legal standards, the collection, analysis, presentation, and interpretation of DNA evidence remains a complex process. Any procedural or documentary misstep can potentially render key evidence or testimony useless. To avoid such costly errors, scientists, law enforcement personnel, attorneys, and judges all must possess a detailed knowledge of how forensic DNA works, from the crime scene to the laboratory to the courtroom and beyond.
DNA: Forensic and Legal Applications provides the most comprehensive and up-to-date guide to this important and increasingly prevalent legal tool. Designed to reach readers in both legal and scientific fields, this text gives a global view of the practical issues involved in the forensic use of DNA. In clear, nontechnical language, the text covers:
In a unique combination of legal practice and scientific analysis, DNA: Forensic and Legal Applications provides forensic scientists, potential expert witnesses, and professionals in the criminal justice system with the definitive resource on the methods of DNA analysis as well as the handling, potential, and limitations of DNA evidence.
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