In DNA Cloning and Assembly Methods, expert researchers in the field detail many of the methods which are now commonly used for DNA cloning and make cloning procedures faster, more reliable and also suitable for high-throughput handling. These include methods and protocols that are based on several mechanisms including type II and IIS restriction enzymes, single stranded annealing, sequence overlap, and recombination. With additional chapters on software programs that are suitable for primer design, a feature crucial for the functionality of the described methods. 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 key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, DNA Cloning and Assembly Methods seeks to provide scientist with a valuable and useful resource for wet lab researchers within life sciences.

Since the independent invention of DNA sequencing by Sanger and by Gilbert 30 years ago, it has grown from a small scale technique capable of reading several kilobase-pair of sequence per day into today's multibillion dollar industry. This growth has spurred the development of new sequencing technologies that do not involve either electrophoresis or Sanger sequencing chemistries. Sequencing by Synthesis (SBS) involves multiple parallel micro-sequencing addition events occurring on a surface, where data from each round is detected by imaging.
New High Throughput Technologies for DNA Sequencing and Genomics is the second volume in the Perspectives in Bioanalysis series, which looks at the electroanalytical chemistry of nucleic acids and proteins, development of electrochemical sensors and their application in biomedicine and in the new fields of genomics and proteomics. The authors have expertly formatted the information for a wide variety of readers, including new developments that will inspire students and young scientists to create new tools for science and medicine in the 21st century.
Reviews of complementary developments in Sanger and SBS sequencing chemistries, capillary electrophoresis and microdevice integration, MS sequencing and applications set the framework for the book.
* 'Hot Topic' with DNA sequencing continuing as a major research activity in many areas of life science and medicine.
* Bringing together new developments in DNA sequencing technology
* Reviewing issues relevant to the new applications used

DNA Repair and Human Disease highlights the molecular complexities of a few well-known human hereditary disorders that arise due to perturbations in the fidelity of diverse DNA repair machineries.

This volume includes, in an integrated way, modern computational studies of nucleic acids, ranging from advanced electronic structure quantum chemical calculations through explicit solvent molecular dynamics (MD) simulations up to mesoscopic modelling, with the main focus given to the MD field.It gives an equal emphasis to the leading methods and applications while successes as well as pitfalls of the computational techniques are discussed. The systems and problems studied include: Accurate calculations of base pairing energies; Electronic properties of nucleic acids and electron transfer, through various types of nucleic acid; and, Calculating DNA elasticity. This book is ideally suited to academics and researchers in organic and computational chemistry as well as biochemistry and particularly those interested in the molecular modelling of nucleic acids.Besides the state-of-the art science, the book also provides introductory information to non-specialists to enter this field.

For several decades, Arabidopsis thaliana has been the organism of choice in the laboratories of many plant geneticists, physiologists, developmental biologists, and biochemists around the world. During this time, a huge amount of knowledge has been acquired on the biology of this plant species, which has resulted in the development of molecular tools that account for much more efficient research. The significance that Arabidopsis would attain in biological research may have been difficult to foresee in the 1980s, when its use in the laboratory started. In the meantime, it has become the model plant organism, much the same way as Drosophila, Caenorhabditis, or mouse have for animal systems. Today, it is difficult to envision research at the cutting edge of plant biology without the use of Arabidopsis. Since the first edition of Arabidopsis Protocols appeared, new developments have fostered an impressive advance in plant biology that prompted us to prepare Arabidopsis Protocols, Second Edition. Completion of the Arabidopsis genome sequence offered for the first time the opportunity to have in hand all of the genetic information required for studying plant function. In addition, the development of whole systems approaches that allow global analysis of gene expression and protein and metabolite dynamics has encouraged scientists to explore new scenarios that are extending the limits of our knowledge.

This book reflects more than three decades of research on Cellular Automata (CA), and nearly a decade of work on the application of CA to model biological strings, which forms the foundation of 'A New Kind of Computational Biology' pioneered by the start-up, CARLBio. After a brief introduction on Cellular Automata (CA) theory and functional biology, it reports on the modeling of basic biological strings with CA, starting with the basic nucleotides leading to codon and anti-codon CA models. It derives a more involved CA model of DNA, RNA, the entire translation process for amino acid formation and the evolution of protein to its unique structure and function. In subsequent chapters the interaction of Proteins with other bio-molecules is also modeled. The only prior knowledge assumed necessary is an undergraduate knowledge of computer programming and biology. The book adopts a hands-on, "do-it-yourself" approach to enable readers to apply the method provided to derive the CA rules and comprehend how these are related to the physical 'rules' observed in biology. In a single framework, the authors have presented two branches of science - Computation and Biology. Instead of rigorous molecular dynamics modeling, which the authors describe as a Bottoms-Up model, or relying on the Top-Down new age Artificial Intelligence (AI) and Machine Language (ML) that depends on extensive availability of quality data, this book takes the best from both the Top-Down and Bottoms-up approaches and establishes how the behavior of complex molecules is represented in CA. The CA rules are derived from the basic knowledge of molecular interaction and construction observed in biological world but mapped to a few subset of known results to derive and predict results. This book is useful for students, researchers and industry practitioners who want to explore modeling and simulation of the physical world complex systems from a different perspective. It raises the inevitable the question - 'Are life and the universe nothing but a collection of continuous systems processing information'.

Population genomics is a recently emerged discipline, which aims at understanding how evolutionary processes influence genetic variation across genomes. Today, in the era of cheaper next-generation sequencing, it is no longer as daunting to obtain whole genome data for any species of interest and population genomics is now conceivable in a wide range of fields, from medicine and pharmacology to ecology and evolutionary biology. However, because of the lack of reference genome and of enough "a priori" data on the polymorphism, population genomics analyses of populations will still involve higher constraints for researchers working on non-model organisms, as regards the choice of the genotyping/sequencing technique or that of the analysis methods. Therefore, "Data Production and Analysis in Population Genomics" purposely puts emphasis on protocols and methods that are applicable to species where genomic resources are still scarce. It is divided into three convenient sections, each one tackling one of the main challenges facing scientists setting up a population genomics study. The first section helps devising a sampling and/or experimental design suitable to address the biological question of interest. The second section addresses how to implement the best genotyping or sequencing method to obtain the required data given the time and cost constraints as well as the other genetic resources already available, Finally, the last section is about making the most of the (generally huge) dataset produced by using appropriate analysis methods in order to reach a biologically relevant conclusion. Written in the 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 protocols, advice on methodology and implementation, and notes on troubleshooting and avoiding known pitfalls.

Authoritative and easily accessible, "Data Production and Analysis in Population Genomics" serves a wide readership by providing guidelines to help choose and implement the best experimental or analytical strategy for a given purpose.

Modern DNA microarray technologies have evolved over the past 25 years to the point where it is now possible to take many million measurements from a single experiment. These two volumes, Parts A & B in the Methods in Enzymology series provide methods that will shepard any molecular biologist through the process of planning, performing, and publishing microarray results.
Part A starts with an overview of a number of microarray platforms, both commercial and academically produced and includes wet bench protocols for performing traditional expression analysis and derivative techniques such as detection of transcription factor occupancy and chromatin status. Wet-bench protocols and troubleshooting techniques continue into Part B. These techniques are well rooted in traditional molecular biology and while they require traditional care, a researcher that can reproducibly generate beautiful Northern or Southern blots should have no difficulty generating beautiful array hybridizations.
Data management is a more recent problem for most biologists. The bulk of Part B provides a range of techniques for data handling. This includes critical issues, from normalization within and between arrays, to uploading your results to the public repositories for array data, and how to integrate data from multiple sources. There are chapters in Part B for both the debutant and the expert bioinformatician.
- Provides an overview of platforms
- Includes experimental design and wet bench protocols
- Presents statistical and data analysis methods, array databases, data visualization and meta analysis

Microarray Technology, Volumes 1 and 2, present information in designing and fabricating arrays and binding studies with biological analytes. This is done while providing the reader with a broad description of microarray technology tools and their potential applications. The first volume deals with methods and protocols for the preparation of microarrays. The second volume details applications and data analysis, which is important in analyzing the enormous data coming out of microarray experiments. Microarray Technology, Volumes 1 and 2, provide ample information to all levels of scientists from novice to those intimately familiar with array technology.

This book puts the ethics, policy and politics of stem cells into context in a way that helps readers understand why past and current issues have developed the way they have and what the implications are for their work going forward. It also addresses emerging issues as the field progresses towards clinical and industrial uses. While there is a superabundance of material on the ethics of embryo use and questions of embryonic "personhood," there is little that covers what practicing scientists and managers need to know in order to plan and execute responsible research. Furthermore, researchers funded by the NIH are required to have ethics training as a condition of the grant. As such, this book is an essential resource to all of these pre-professional students whether they plan to move into industry, government or academia.

In the last few years, significant advances have been made in understanding how a yeast cell responds to the stress of producing a recombinant protein, and how this information can be used to engineer improved host strains. The molecular biology of the expression vector, through the choice of promoter, tag and codon optimization of the target gene, is also a key determinant of a high-yielding protein production experiment. Recombinant Protein Production in Yeast: Methods and Protocols examines the process of preparation of expression vectors, transformation to generate high-yielding clones, optimization of experimental conditions to maximize yields, scale-up to bioreactor formats and disruption of yeast cells to enable the isolation of the recombinant protein prior to purification. 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 practical, Recombinant Protein Production in Yeast: Methods and Protocols, seeks to aid scientists in adopting yeast as a protein production host.

Gene regulatory networks are the most complex, extensive control systems found in nature. The interaction between biology and evolution has been the subject of great interest in recent years. The author, Eric Davidson, has been instrumental in elucidating this relationship. He is a world renowned scientist and a major contributor to the field of developmental biology.
The Regulatory Genome beautifully explains the control of animal development in terms of structure/function relations of inherited regulatory DNA sequence, and the emergent properties of the gene regulatory networks composed of these sequences. New insights into the mechanisms of body plan evolution are derived from considerations of the consequences of change in developmental gene regulatory networks. Examples of crucial evidence underscore each major concept. The clear writing style explains regulatory causality without requiring a sophisticated background in descriptive developmental biology. This unique text supersedes anything currently available in the market.
* The only book in the market that is solely devoted to the genomic regulatory code for animal development
* Written at a conceptual level, including many novel synthetic concepts that ultimately simplify understanding
* Presents a comprehensive treatment of molecular control elements that determine the function of genes
* Provides a comparative treatment of development, based on principles rather than description of developmental processes
* Considers the evolutionary processes in terms of the structural properties of gene regulatory networks
* Includes 42 full-color descriptive figures and diagrams

Blood has long been viewed as a conduit for therapy, stemming from the ancient days of phlebotomy to remove evil humors to the development of successful blood transfusions to replace missing blood components. The identification and characterization of hematopoietic stem cells by Drs. Till and McCulloch revolutionized the field and soon after, non-hematopoietic stem and progenitor cells were characterized from the blood and bone marrow. Some of these cell types and various blood-derived cell lineages are involved in the repair of various types of tissue damage that span the spectrum of medical disorders. The goal of this book is to provide an up-to-date review of the various types of blood-derived cells with regenerative capacity, identify opportunities for intervention by examining specific clinical applications, and recognize the regulatory environment that will encompass future therapies in regenerative medicine.

This volume provides detailed coverage of modern methods for molecular analysis of enzymes and enzyme systems that function in the maintenance of genome integrity. Coverage areas include base excision repair, nucleotide excision repair, translesion DNA polymerases, mismatch repair, genetic recombination, and double strand break repair.
*A laboratory standard for more than 40 years
*Over 400 volumes strong
*Also available on ScienceDirect
*Part A of a 2-part series

This volume emphasizes the intracellular consequences of DNA damage, describing procedures for analysis of checkpoint responses, DNA repair in vivo, replication fork encounter of DNA damage, as well as biological methods for analysis of mutation production and chromosome rearrangements. It also describes molecular methods for analysis of a number of genome maintenance activities including DNA ligases, helicases, and single-strand binding proteins.
*Part B of a 2-part series
*Addresses DNA maintenance enzymes
*Discusses damage signaling
*Presents "In vivo" analysis of DNA repair
*Covers mutation and chromosome rearrangements

The Chlamydomonas Sourcebook: Introduction to Chlamydomonas and Its Laboratory Use, Volume One, Third Edition has been fully revised and updated to include a wealth of new resources for the Chlamydomonas community (new mutant libraries, new omics studies, and potentially more information about different Chlamydomonas species in the environment). In addition to updates on molecular techniques and analysis of the sequenced genome, the book presents the latest in research and best practices for applications in research, including methods for culture, preservation of cultures, preparation of media, and more.

This comprehensive laboratory manual describes the various protocols involved in Actinobacterial research. The content is divided into fifteen major sections, each of which is further divided into sub-sections describing the respective aim, principles, materials & methods, protocol, expected results and diagrams. Readers will find essential protocols for e.g. sample collection, isolation, characterization, analysis, profiling and evaluation of Actinobacteria for various applications. Gathering all relevant protocols concerning Actinobacteria, and written by a team of experienced Actinobacterial researchers, it is the first book of its kind.

This authoritative reference presents the modern concepts of mesenchymal stem cells (MSCs) and biomaterials as they pertain to the dental field. The book is organized around three main topics: MSCs biology, advanced biomaterials, and clinical applications. The chapters present basic information on stem cell biology and physiology, modern biomaterials that improve bone tissue regeneration, the biomatrices like platelet-rich fibrin (PRF) used to functionalize the biomaterials surface, the strategic and safe intraoral seats of harvesting, the new sources for MSCs, as well as the future perspectives and new challenges in these exciting fields. The contributors are top scientists with a great deal of experience in regenerative dentistry and biomedical research. They offer an international perspective and are richly cross-disciplinary, representing academia, research, and industry. MSCs and Innovative Biomaterials in Dentistry is indispensable reading for students, researchers, and clinicians who need to stay up-to-date on the cutting-edge developments of tissue engineering and regenerative medicine applied to dental sciences.

This volume is based on the workshop Modelling in Molecular Biology that tookplacein2002inSingapore. Themaingoaloftheworkshopwastopresent models/methods used in solving some fundamental problems in biosciences. The volume consists of a selection of papers presented at the workshop as well as of some other papers that are included so that the presentation of the theme of the workshop is broader and more balanced. As a matter of fact we feel that the collection of papers comprising this volume represents a wide spectrum of quite diverse ideas and trends. The paper by D. A. Beard et al. explores the common thesis that und- standingthebehaviouroflargeinteractingsystemsofmanyenzymesandre- tants underlies the modelling and simulation of whole-cell systems. Moreover, the models need to represent the basic stoichiometry, with balanced che- cal reactions and the conservation of mass, energy and charge. The authors discuss the stoichiometric and then kinetic details of approaches to modelling and simulation of biochemical systems. P. R. A. Campos et al. are concerned with models of evolution and adaptation (which is essential for precise - derstanding of molecular phylogeny). In particular, their paper is concerned with the rate of adaptation of asexual organisms(which is important because it in?uences the speed of the assumed molecular clock). It is known that for such organisms the rate of adaptation does not steadily increase with the - creasing rate of advantageous mutations, and this paper studies the mutual interference of two advantageous mutants that are each initially present in only a single organism."

The study of Hox genes is crucial not only in exploring the enigma of homeosis but also in understanding normal development at the fundamental molecular level. Hox Gene Expression starts with the amazing discovery of the homeobox twenty-three years ago and follows the exciting path thereafter of a series of breakthroughs in Genetics, Development and Evolution. It deals with homeotic genes- their evolution, structure, normal and abnormal function. Researchers and graduate students in Biology and Medicine will benefit from this integrated overview of Hox gene activities.

In this state-of-the-art exploration of a hugely dynamic and fast-evolving field of research, leading researchers share their collective wisdom on the role that stem cells could play in the context of physiological stress and lung injury. The text focuses on reviewing the most relevant-and recent-ideas on using local, endogenous, and exogenous progenitor/stem cells in preventing and treating injury to the lung. The lungs are one of the most complex organs in the human body, with a mature adult lung boasting at least 40 morphologically differentiated cell lineages. Our entire blood supply passes through the lung's alveolar units during oxygenation. This interaction with the outside world, along with the intricacies of its structure, makes the lung a highly susceptible organ that is vulnerable to numerous types of injury and infection. This means that the mechanisms of lung repair are in themselves correspondingly complex. Because of their multipotentiality, as well as the fact of the lung's relatively rapid cell turnover, stem cells are thought to be an important alternative cell-base therapy in lung injury. Despite the controversial nature of stem cell research, there has been growing interest in both local and endogenous stem cells in the lung. This highly topical book with chapters on everything from using mesenchymal stem cells in lung repair to the effect of physical activity on the mobilization of stem and progenitor cells, represents an exciting body of work by outstanding investigators and will be required reading for those with an interest in the subject.

Goringer 's brilliant new work dedicates a chapter to each of the main types of RNA editing the very first volume to do so. All of the sections here have been written by experts in the various research areas and a specific focus is put on the correlation between RNA structure and function, as well as on the complex cellular machineries that catalyze the different editing reactions. This leads to a "state of the art" compendium of our current knowledge on RNA editing.

Naturally occurring RNA always contains numerous biochemically altered nucleotides. They are formed by enzymatic modification of the primary transcripts during the complex RNA maturation process designated RNA modification. A large number of enzymes catalyzing the formation of these modified nucleosides or converting one canonical base into another at the posttranscriptional level have been studied for many years, but only recently have systematic and comparative studies begun. The functions of individual enzymes and/or the modified/edited nucleosides in RNA, however, have remained largely ignored.

This book provides advance information on RNA modification, including the associated editing machinery, while offering the reader some perspective on the significance of such modifications in fine-tuning the structure and functions of mature RNA molecules and hence the ability to influence the efficiency and accuracy of genetic expression. Outstanding scientists who are actively working on RNA modification/editing processes have provided up-to-date information on these intriguing cellular processes that have been generated over the course of millions of years in all living organisms. Each review has been written and illustrated for a large audience of readers, not only specialists in the field, but also for advanced students or researchers who want to learn more about recent progress in RNA modification and editing.

This two-volume work surveys the entire range of general aspects of chromosome research on plants. This first volume is divided into two sections. Section A consists of 11 chapters covering the entire range of general aspects of chromosome research in plants (including a chapter on genetic engineering in crop improvement). Section B is devoted to cytogenetics of cereals and millets (wheat, rye, barley, triticale, oats, maize, rice, pearl millet, and minor millets). More than one chapter is devoted to the same crop to give a detailed treatment of chromosome research (including molecular biology) in these crops.

The second volume deals with cytogenetics of plant materials including legumes, vegetable and oil crops, sugar crops, forage crops, fibre crops, medicinal crops and ornamentals. This work will be useful both as a reference work and a teaching aid to satisfy a wide range of workers. Every chapter has been written by an expert who has been involved in chromosome research on a particular plant material for many years.

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.