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This work describes the current knowledge of biochemical mechanisms regulating initiation of DNA replication in Escherichia coli, which focuses on the control of activity of the DnaA protein. Examples of direct linkages between DNA replication and other cellular processes are provided. In addition, similarities of the mechanisms of regulation of DNA replication operating in prokaryotic and eukaryotic cells are identified, and implications for understanding more complex processes, like carcinogenesis are suggested.Studies of recent years provided evidence that regulation of DNA replication in bacteria is more complex than previously anticipated. Multiple layers of control seem to ensure coordination of this process with the increase of cellular mass and the division cycle. Metabolic processes and membrane composition may serve as points where integration of genome replication with growth conditions occurs. It is also likely that coupling of DNA synthesis with cellular metabolism may involve interactions of replication proteins with other macromolecular complexes, responsible for various cellular processes. Thus, the exact set of factors participating in triggering the replication initiation may differ depending on growth conditions. Therefore, understanding the regulation of DNA duplication requires placing this process in the context of the current knowledge on bacterial metabolism, as well as cellular and chromosomal structure. Moreover, in both Escherichia coli and eukaryotic cells, replication initiator proteins were shown to play other roles in addition to driving the assembly of replication complexes, which constitutes another, yet not sufficiently understood, layer of coordinating DNA replication with the cell cycle.
Around 200,000 years ago, a man--identical to us in all important respects--lived in Africa. Every person alive today is descended from him. How did this real-life Adam wind up father of us all? What happened to the descendants of other men who lived at the same time? And why, if modern humans share a single prehistoric ancestor, do we come in so many sizes, shapes, and races? Showing how the secrets about our ancestors are hidden in our genetic code, Spencer Wells reveals how developments in the cutting-edge science of population genetics have made it possible to create a family tree for the whole of humanity. We now know not only where our ancestors lived but who they fought, loved, and influenced. Informed by this new science, The Journey of Man is replete with astonishing information. Wells tells us that we can trace our origins back to a single Adam and Eve, but that Eve came first by some 80,000 years. We hear how the male Y-chromosome has been used to trace the spread of humanity from Africa into Eurasia, why differing racial types emerged when mountain ranges split population groups, and that the San Bushmen of the Kalahari have some of the oldest genetic markers in the world. We learn, finally with absolute certainty, that Neanderthals are not our ancestors and that the entire genetic diversity of Native Americans can be accounted for by just ten individuals. It is an enthralling, epic tour through the history and development of early humankind--as well as an accessible look at the analysis of human genetics that is giving us definitive answers to questions we have asked for centuries, questions now more compelling than ever.
Innate DNA and RNA Recognition: Method and Protocols presents validated experimental strategies to dissect nucleic acid sensing in-vitro and in-vivo sources. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Innate DNA and RNA Recognition: Method and Protocols provides a resource for immunologists, molecular biologists, virologists, microbiologists, and researchers studying how the innate immune system handles nucleic acids from endogenous or foreign sources.
In its short but active history, the use of DNA typing has revolutionized criminal investigations. It is almost inconceivable to bring a case to trial without positive identification through what is now our most accurate means. Proficiency with the methodology, principles, and interpretation of DNA evidence is crucial for today's criminalist. An introductory text, Forensic DNA Analysis: A Laboratory Manual presents a contextual history and overview of the science and use of DNA typing. Logically organized, with clear, concise language, this manual provides a fundamental understanding of forensic DNA analysis and a thorough background in the molecular techniques used to determine an individual's identity. Students are provided with a sound working knowledge of the investigative methodology, scientific principles, and the analysis and interpretation of the resulting data. After laying a foundation on the rules of the laboratory, the basic scientific principles, and the types of biological materials, such as hair, blood, and bone, this practical, hands-on manual provides 12 exercises outlining techniques commonly used in DNA typing. Designed to be performed in a common laboratory, the experiments cover DNA extraction, concentration, and assessment; DNA analysis using restriction fragment length polymorphisms; polymerase chain reaction and PCR-based typing tests; short tandem repeat analysis; and mitochondrial DNA analysis. Many of the procedures described have been adapted from methods used in federal, state, and private forensic laboratories and are suitable to a wide range of applications. There is also an extensive glossary for DNA typing terminology and basic terms used in molecular biology. Instilling confidence, analytical clarity, and a sense of curiosity, this comprehensive introduction is the perfect tool for grasping the techniques and applications of forensic DNA analysis and exploring the questions and issues involved in forensic science investigations.
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'.
Structural Genomics and Drug Discovery: Methods and Protocols focuses on high throughput structure determination methods and how they can be applied to lay the groundwork for structure aided drug discovery. The methods and protocols that are described can be applied in any laboratory interested in using detailed structural information to advance the initial stages of drug discovery. 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, Structural Genomics and Drug Discovery: Methods and Protocols seeks to aid scientists in the further study into structural genomics approach as an efficient initial step toward drug discovery and the methods described will be useful to anyone interested in moving in this direction.
DNA Microarrays: Methods Express covers the very latest in DNA microarray technology, with a clear focus on how these techniques can be used in the lab to gain the very best results. The authors are from some of the leading laboratories in the field and write with real authority on the latest methodology and its applications. Every chapter provides detailed step-by-step protocols with valuable hints and tips for success, as well as giving typical experimental results and selected literature citations. This book is must have manual for researchers in all fields of biology, medicine and agriculture.
The simplicity and lack of redundancy in their regulatory genes have made ascidians one of the most useful species in studying developmental genomics. In Developmental Genomics of Ascidians, Dr. Noriyuki Satoh explains the developmental genomics of ascidians, stresses the simplicity of Ciona developmental system, and emphasizes single-cell level analyses. This book actively accentuates the advantages of using ascidians as model organisms in an up-and-coming field of developmental genomics.
With humor, depth, and philosophical and historical insight, "DNA" reaches out to a wide range of readers with its graphic portrayal of a complicated science. Suitable for use in and out of the classroom, this volume covers DNA's many marvels, from its original discovery in 1869 to early-twentieth-century debates on the mechanisms of inheritance and the deeper nature of life's evolution and variety.
Even readers who lack a background in science and philosophy will learn a tremendous amount from this engaging narrative. The book elucidates DNA's relationship to health and the cause and cure of disease. It also covers the creation of new life forms, nanomachines, and perspectives on crime detection, and considers the philosophical sources of classical Darwinian theory and recent, radical changes in the understanding of evolution itself. Already these developments have profoundly affected our notions about living things. Borin Van Loon's humorous illustrations recount the contributions of Gregor Mendel, Frederick Griffith, James Watson, and Francis Crick, among other biologists, scientists, and researchers, and vividly depict the modern controversies surrounding the Human Genome Project and cloning.
Inferring the precise locations and splicing patterns of genes in DNA is a difficult but important task, with broad applications to biomedicine. The mathematical and statistical techniques that have been applied to this problem are surveyed and organized into a logical framework based on the theory of parsing. Both established approaches and methods at the forefront of current research are discussed. Numerous case studies of existing software systems are provided, in addition to detailed examples that work through the actual implementation of effective gene-predictors using hidden Markov models and other machine-learning techniques. Background material on probability theory, discrete mathematics, computer science, and molecular biology is provided, making the book accessible to students and researchers from across the life and computational sciences. This book is ideal for use in a first course in bioinformatics at graduate or advanced undergraduate level, and for anyone wanting to keep pace with this rapidly-advancing field.
Sociogenomics has rapidly become one of the trendiest sciences of the new millennium. Practitioners view human nature and life outcomes as the result of genetic and social factors. In Social by Nature, Catherine Bliss recognizes the promise of this interdisciplinary young science, but also questions its implications for the future. As she points out, the claim that genetic similarities cause groups of people to behave in similar ways is not new-and a dark history of eugenics warns us of its dangers. Over the last decade, sociogenomics has enjoyed a largely uncritical rise to prominence and acceptance in popular culture. Researchers have published studies showing that things like educational attainment, gang membership, and life satisfaction are encoded in our DNA long before we say our first word. Strangely, unlike the racial debates over IQ scores in the '70s and '90s, sociogenomics has not received any major backlash. By exposing the shocking parallels between sociogenomics and older, long-discredited, sciences, Bliss persuasively argues for a more thoughtful public reception of any study that reduces human nature to a mere sequence of genes. This book is a powerful call for researchers to approach their work in more socially responsible ways, and a must-read for anyone who wants to better understand the scholarship that impacts how we see ourselves and our society.
The problem of unraveling two intertwined strands during the duplication of DNA was recognized shortly after the proposal of the DNA double helix structure in 1953. A group of enzymes called DNA topoisomerases solve this problem by breaking and rejoining DNA molecules in a controlled manner, thereby allowing strands to be passed through each other and thus untangled - not just during DNA replication, but also during many other basic cellular processes. Because of their intimate involvement in the workings of the cell, topoisomerases are also the logical targets of many antibiotics (including Cipro) and anticancer agents. This book, written by James Wang, the discoverer of the first topoisomerase and a leader in the field since, presents ten chapters covering the historical backdrop of the DNA entanglement problem and the discovery of the DNA topoisomerases, how DNA topoisomerases perform their magic in DNA replication, transcription, genetic recombination and chromosome condensation, and how they are targets of therapeutic agents. The book should appeal to readers from undergraduates upwards with interests in the biological and clinical aspects of topoisomerase function, or in the mathematics and physics of topology.
An introduction to how genes work, including basic information about cloning and gene therapy.
"Genome Transcriptome and Proteome Analysis" is a concise introduction to the subject, successfully bringing together these three key areas of research. Starting with a revision of molecular genetics the book offers clear explanations of the tools and techniques widely used in genome, transcriptome and proteome analysis. Subsequent chapters offer a broad overview of linkage maps, physical maps and genome sequencing, with a final discussion on the identification of genes responsible for disease. An invaluable introduction to the basic concepts of the subject, this text offers the student an excellent overview of current research methods and applications and is a good starting point for those new to the area. It gives a clear, concise introduction to the subject of modern genomic analysis. It provides a technology-oriented approach including the latest developments in the field. It is invaluable to those students taking courses in Bioinformatics, Human Genetics, Biochemistry and Molecular Biology.
Over a decade ago, as the Human Genome Project completed its mapping of the entire human genome, hopes ran high that we would rapidly be able to use our knowledge of human genes to tackle many inherited diseases, and understand what makes us unique among animals. But things didn't turn out that way. For a start, we turned out to have far fewer genes than originally thought - just over 20,000, the same sort of number as a fruit fly or worm. What's more, the proportion of DNA consisting of genes coding for proteins was a mere 2%. So, was the rest of the genome accumulated 'junk'? Things have changed since those early heady days of the Human Genome Project. But the emerging picture is if anything far more exciting. In this book, John Parrington explains the key features that are coming to light - some, such as the results of the international ENCODE programme, still much debated and controversial in their scope. He gives an outline of the deeper genome, involving layers of regulatory elements controlling and coordinating the switching on and off of genes; the impact of its 3D geometry; the discovery of a variety of new RNAs playing critical roles; the epigenetic changes influenced by the environment and life experiences that can make identical twins different and be passed on to the next generation; and the clues coming out of comparisons with the genomes of Neanderthals as well as that of chimps about the development of our species. We are learning more about ourselves, and about the genetic aspects of many diseases. But in its complexity, flexibility, and ability to respond to environmental cues, the human genome is proving to be far more subtle than we ever imagined.
How has DNA come to be seen as a cosmic truth, representative of
all life, potential for all cures, repository for all identity, and
end to all stories? In "The Poetics of DNA," Judith Roof examines
the rise of this powerful symbol and the implications of its
ascendancy for the ways we think-about ourselves, about one
another, and about the universe.
This up-to-date review of seed genomics, from basic seed biology to practical applications in crop science, provides a thorough background understanding of seed biology from a basic science perspective. A valuable resource for advanced graduate students, post-docs, researchers and professionals in the Plant and Crop Sciences, this book brings together top researchers in the field to cover three general themes: genomic approaches to studying seeds, genomic analysis of basic seed biology, and crop seed genomics.A valuable resource for advanced graduate students, post-docs, researchers and professionals in the Plant and Crop Sciences
Efficient computer programs have made it possible to elucidate and analyze large-scale genomic sequences. Fundamental tasks, such as the assembly of numerous whole-genome shotgun fragments, the alignment of complementary DNA sequences with a long genome, and the design of gene-specific primers or oligomers, require efficient algorithms and state-of-the-art implementation techniques. This textbook emphasizes basic software implementation techniques for processing large-scale genome sequences and provides executable sample programs.
This volume is divided in four sections; covering genome wide approaches, techniques for characterize of paRNA structural features are described, selecting pa-RNA, and paRNA therapeutic potential. Chapters describe how siRNAsdirected against paRNAs can be applied in vivo to modulate transcription of important genes controlled by paRNAs. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Promoter Associated RNA: Methods and Protocols aims to demonstrate paRNAs as new class of regulatory molecules, to further investigate and value as tools for fine transcriptional tuning.
The past few years have witnessed intense research in this
fascinating field as well as many controversial discussions. Now
the time is ripe for a comprehensive book covering not only
theoretical aspects, but also such mechanistic topics as principles
and mechanisms of photoinduced charge injection, transport and
trapping in DNA, sequence-dependent DNA dynamics, spectroscopic
investigations of hole transport and much more.
Molecular biologist Elizabeth Blackburn--one of Time magazine's 100 "Most Influential People in the World" in 2007--made headlines in 2004 when she was dismissed from the President's Council on Bioethics after objecting to the council's call for a moratorium on stem cell research and protesting the suppression of relevant scientific evidence in its final report. But it is Blackburn's groundbreaking work on telomeric DNA, which launched the field of telomere research, that will have the more profound and long-lasting effect on science and society. In this compelling biography, Catherine Brady tells the story of Elizabeth Blackburn's life and work and the emergence of a new field of scientific research on the specialized ends of chromosomes and the enzyme, telomerase, that extends them. In the early stages of telomere research, telomerase, heralded as a potential cure for cancer and diseases related to aging, attracted the voracious interest of biotech companies. The surrounding hype succeeded in confusing the role of telemorase in extending the life of a cell with a mechanism that might extend the lifespan of an entire organism. In Brady's hands, Blackburn's story reveals much about the tension between pure and applied science, the politicking that makes research science such a competitive field, and the resourceful opportunism that characterizes the best scientific thinking. Brady describes the science accessibly and compellingly. She explores Blackburn's struggle to break down barriers in an elite, male-dominated profession, her role as a mentor to other women scientists (many of whom have made their mark in telomere research), and the collaborative nature of scientific work. This book gives us a vivid portrait of an exceptional woman and a new understanding of the combination of curiosity, imaginative speculation, and aesthetic delight that powers scientific discovery.Catherine Brady is Assistant Professor in the MFA in Writing Program at the University of San Francisco. She is the author of two collections of short stories, The End of the Class War and Curled in the Bed of Love (a winner of the 2002 Flannery O'Connor Award for Short Fiction).
Explains the structure and function of DNA.
Epigenetics is the study of heritable changes in gene function that do not involve changes in the DNA sequence. These changes, consisting principally of DNA methylation, histone modifications, and non-coding RNAs, maintain or modulate the initial impact of regulatory factors that recognize and associate with particular genomic sequences. Epigenetic modifications are manifest in all aspects of normal cellular differentiation and function, but they can also have damaging effects that result in pathologies such as cancer. Research is continuously uncovering the role of epigenetics in a variety of human disorders, providing new avenues for therapeutic interventions and advances in regenerative medicine. This book's primary goal is to establish a framework that can be used to understand the basis of epigenetic regulation and to appreciate both its derivation from genetics and interdependence with genetic mechanisms. A further aim is to highlight the role played by the three-dimensional organization of the genetic material itself (the complex of DNA, histones and non-histone proteins referred to as chromatin), and its distribution within a functionally compartmentalized nucleus. This architectural organization of the genome plays a major role in the subsequent retrieval, interpretation, and execution of both genetic and epigenetic information.
This volume covers the latest protocols designed to identify and characterize TEs in genomes, ancient or recently inserted. Additionally, this book includes a series of protocols designed to understand how host genomes act to regulate the activity of TEs, from elegant genetic mobilization assays to key biochemical methods. Finally, this book also includes chapters that describe how TEs can be used for biotechnological applications. 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. Authoritative and practical, Transposons and Retrotransposons: Methods and Protocols aims to ensure successful results in the further study of this vital field.
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