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DNA Replication Control in Microbial Cell Factories
by Monika Glinkowska Lidia Boss Grzegorz WegrzynThis 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.
DNA Replication - Damage from Environmental Carcinogens
by Huidong ZhangThis book reviews the main concepts concerning DNA damage due to environmental carcinogens, the effects of DNA damage on DNA replication using a single DNA polymerase or DNA replisome, and the effects of carcinogens on various cell activities. It also introduces the detailed protocols for bypassing DNA damage. As we know, various environmental carcinogens are produced as a result of industry, agriculture, chemical engineering and vehicle exhaust in our daily life. It has been reported that the environmental carcinogens can be connected to tumors and cancer, directly threatening human health. In this regard, DNA replication is highly susceptible to damage. This book provides graduate students and researchers with an overview of the effects of environmental carcinogens on DNA replication and biological activities in cells. It offers important information for research in the areas of biochemistry, cell biology, medicine, toxicology and public health.
DNA Replication, Recombination, and Repair
by Fumio Hanaoka Kaoru SugasawaThis book is a comprehensive review of the detailed molecular mechanisms of and functional crosstalk among the replication, recombination, and repair of DNA (collectively called the "3Rs") and the related processes, with special consciousness of their biological and clinical consequences. The 3Rs are fundamental molecular mechanisms for organisms to maintain and sometimes intentionally alter genetic information. DNA replication, recombination, and repair, individually, have been important subjects of molecular biology since its emergence, but we have recently become aware that the 3Rs are actually much more intimately related to one another than we used to realize. Furthermore, the 3R research fields have been growing even more interdisciplinary, with better understanding of molecular mechanisms underlying other important processes, such as chromosome structures and functions, cell cycle and checkpoints, transcriptional and epigenetic regulation, and so on. This book comprises 7 parts and 21 chapters: Part 1 (Chapters 1-3), DNA Replication; Part 2 (Chapters 4-6), DNA Recombination; Part 3 (Chapters 7-9), DNA Repair; Part 4 (Chapters 10-13), Genome Instability and Mutagenesis; Part 5 (Chapters 14-15), Chromosome Dynamics and Functions; Part 6 (Chapters 16-18), Cell Cycle and Checkpoints; Part 7 (Chapters 19-21), Interplay with Transcription and Epigenetic Regulation. This volume should attract the great interest of graduate students, postdoctoral fellows, and senior scientists in broad research fields of basic molecular biology, not only the core 3Rs, but also the various related fields (chromosome, cell cycle, transcription, epigenetics, and similar areas). Additionally, researchers in neurological sciences, developmental biology, immunology, evolutionary biology, and many other fields will find this book valuable.
DNS of Wall-Bounded Turbulent Flows: A First Principle Approach
by Tapan K. Sengupta Swagata BhaumikThis book highlights by careful documentation of developments what led to tracking the growth of deterministic disturbances inside the shear layer from receptivity to fully developed turbulent flow stages. Associated theoretical and numerical developments are addressed from basic level so that an uninitiated reader can also follow the materials which lead to the solution of a long-standing problem. Solving Navier-Stokes equation by direct numerical simulation (DNS) from the first principle has been considered as one of the most challenging problems of understanding what causes transition to turbulence. Therefore, this book is a very useful addition to advanced CFD and advanced fluid mechanics courses.
DNA Sequencing
by Dr Luke AlpheyThe technique of DNA Sequencing lies at the heart of modern molecular biology. Since current methods were first introduced, sequence databases have grown exponentially, and are now an indispensable research tool. This up-to-date, practical guide is unique in covering all aspects of the methodology of DNA sequencing, as well as sequence analysis. It describes the basic methods (both manual and automated) and the more advanced techniques (for example, those based on PCR) before moving on to key applications. The final section focuses on the analysis of sequence data; it details the software available, and explains how the Internet can be used for accessing software and major databases.By explaining the options available and their merits, DNA Sequencing allows newcomers to the field to decide which method is the most suitable for their application. For experienced sequencers the book is a useful reference source for details of the less common techniques and as a means of updating knowledge.
DNA Sequencing Protocols
by Alison J.M. Hill Colin A GrahamColin Graham and a team of leading investigators and expert clinical scientists update the acclaimed first edition with a collection of powerful, up-to-date PCR-based methods for DNA sequencing, many suitable for human genome sequencing and mutation detection in human disease. This second edition offers new material on automated DNA sequencers, capillary DNA sequencers, heterozygote mutation detection, web-based sequencing databases and genome sequencing sites, and the human genome project. State-of-the-art and highly practical, DNA Sequencing Protocols, 2nd Edn. constitutes an essential laboratory handbook for geneticists and molecular biologists, offering concise, easy-to-follow methods that will work and impact today's genome sequencing projects.
DNA Sequencing Protocols
by Annette M. Griffin Hugh G. GriffinDNA Sequencing Protocols provides you with the knowledge to become a sequencing expert. An all-star cast of investigators covers virtually all aspects, including developments in cycle sequencing, sequencing PCR products, sequencing lambda and cosmids, multiplex sequencing, direct blotting electrophoresis, sequencing of chemiluminescence, and automated sequencing.
DNA Systems Under Internal and External Forcing: An Exploration Using Coarse-Grained Modelling (Springer Theses)
by Megan Clare EngelThe interactions of DNA with force are central to manifold fields of inquiry, including the de novo design of DNA nanostructures, the use of DNA to probe the principles of biological self-assembly, and the operation of cellular nanomachines. This work presents a survey of three distinct ways coarse-grained simulations can help characterize these interactions. A non-equilibrium energy landscape reconstruction technique is validated for use with the oxDNA model and a practical framework to guide future applications is established. A novel method for calculating entropic forces in DNA molecules is outlined and contrasted with existing, flawed approaches. Finally, a joint experimental-simulation study of large DNA origami nanostructures under force sheds light on design principles and, through vivid illustrations, their unfolding process. This text provides an accessible and exciting launching point for any student interested in the computational study of DNA mechanics and force interactions.
DNA Technology in Forensic Science
by Committee on DNA Technology in Forensic ScienceMatching DNA samples from crime scenes and suspects is rapidly becoming a key source of evidence for use in our justice system. DNA Technology in Forensic Science offers recommendations for resolving crucial questions that are emerging as DNA typing becomes more widespread. The volume addreses key issues: Quality and reliability in DNA typing, including the introduction of new technologies, problems of standardization, and approaches to certification. DNA typing in the courtroom, including issues of population genetics, levels of understanding among judges and juries, and admissibility. Societal issues, such as privacy of DNA data, storage of samples and data, and the rights of defendants to quality testing technology. Combining this original volume with the new update--The Evaluation of Forensic DNA Evidence--provides the complete, up-to-date picture of this highly important and visible topic. This volume offers important guidance to anyone working with this emerging law enforcement tool: policymakers, specialists in criminal law, forensic scientists, geneticists, researchers, faculty, and students.
DNA Topoisomerase Protocols, Volume I: DNA Topology and Enzymes (Methods in Molecular Biology #94)
by Mary-Ann Bjornsti Neil OsheroffDNA Topoisomerase Protocols, I: DNA Topology and Enzymes brings together an unprecedented collection of cutting-edge experimental protocols for investigating DNA structure, topology, and DNA topoisomerase function. Described by expert experimentalists who have perfected the techniques, these unfailingly reproducible methods utilize new approaches to study changes in DNA topology (linking number, knotting, catenation, and relaxation) and DNA structure (bending), as well as to assess chromosome structure through FLP-mediated recombination and to analyze bacterial nucleoid structure. State-of-the-art protocols also detail the expression and purification of bacterial, viral, and eukaryotic DNA topoisomerases from a variety of sources, including baculovirus, and bacterial, yeast and mammalian expression systems. A companion volume, DNA Topoisomerase Protocols, v. 2: Enzymology and Drugs, provides detailed protocols to study the catalytic activities of DNA topoisomerases, as well as their specific interactions with topoisomerase-targeted antitumor and antibacterial drugs.<P><P> DNA Topoisomerase Protocols, I: DNA Topology and Enzymes will be of immense value to the many basic scientists and clinicians who want better to understand and to exploit proficiently the wealth of recent discoveries about chromatin structure and its relation to gene expression, about DNA topoisomerases as the targets of antitumor and antibacterial agents, and about DNA repair.
DNA Topoisomerase Protocols, Volume II: Enzymology and Drugs
by Mary-Ann Bjornsti Neil OsheroffDNA Topoisomerase Protocols, II: Enzymology and Drugs brings together an unprecedented collection of cutting-edge experimental protocols for investigating the catalytic activities of DNA topoisomerases, as well as their specific interactions with topoisomerase-targeted antitumor and antibacterial drugs. Described by expert experimentalists who have perfected the techniques, these unfailingly reproducible methods include assays for enzyme-catalyzed DNA relaxation/supercoiling, DNA cleavage, DNA nicking, DNA decatenation, and ATP hydrolysis. Several modified DNA substrates, used to dissect enzyme mechanisms by trapping intermediates, are also described. Methodologies to determine the action of topoisomerase-targeted drugs include biochemical assays of drug-induced enzyme-DNA complexes, methods for assaying drug uptake, and cell-based assays for determining drug specificity and mechanisms of resistance. A companion volume, DNA Topoisomerase Protocols, I: DNA Topology and Enzymes, provides state-of-the-art experimental protocols for investigating DNA structure, topology, and DNA topoisomerase function.<P><P> DNA Topoisomerase Protocols, II: Enzymology and Drugs provides, for the first time, a comprehensive description of the methods and experimental systems needed to investigate fully the catalytic mechanisms of DNA topoisomerases from bacterial, viral, and eukaryotic sources. For the many basic scientists and clinicians who want better to understand and to exploit the action of topoisomerase-targeted drugs in a variety of in vitro and in vivo systems, it will immediately develop immense value as the new standard reference in the field.
DNA Topoisomerases
by Duncan J. ClarkeDue to their importance to cell biology, DNA topology-altering enzymes, collectively DNA topoisomerases and gyrases, have been studied thoroughly from a biochemical perspective, yet the expansion of research at the molecular and cellular levels continues to show a great deal of promise. In DNA Topoisomerases: Methods and Protocols, experts in the field present a compendium of protocols that extends into the new areas of research that have been recently uncovered in order to elucidate the methodology needed to study topoisomerases in the molecular and cellular context. The volume examines subjects such as the analysis of DNA topologies and the interaction of topoisomerases with DNA as tools to measure topoisomerase functions, the binding of topoisomerases to specific sites in the genomes of eukaryotes, including origins of DNA replication, as well as exploration of perturbed topoisomerase function. As a volume in the highly successful Methods in Molecular BiologyTM series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, laboratory protocols, and notes on trouble-shooting and avoiding known pitfalls. Cutting-edge and easy-to-use, DNA Topoisomerases: Methods and Protocols provides key content which reflects an expanded understanding of the functions of these essential enzymes in the hope of inspiring researchers to further important discoveries in this dynamic field.
DNA Traffic in the Environment
by Hiromi Nishida Taku OshimaThis book comprehensively discusses our current understanding of the role and biological mechanisms of horizontal transfer of genetic elements in the environment, which has been important in the evolution of prokaryotes (archaea and bacteria). Horizontal transfer of genetic elements generates variations of prokaryotes and their genomes. Comparative studies of genomes revealed that it frequently occurred during archaeal and bacterial evolution. The book introduces a variety of studies related to horizontal gene transfer, gene silencing, plasmids, phages, transposons, and the emergence of microbes that degrade man-made xenobiotics and have antimicrobial resistance. Written by leading researchers in DNA traffic, the book is a valuable guide to horizontal transfer for both young scientists and experts in the field.
DNA Tumor Viruses
by James Pipas Blossom DamaniaThis unique book focuses on the DNA viruses in the human population that are associated with cancers. It covers most of the viruses that are thought to contribute to human malignancy. This book represents a comprehensive review of the field of DNA tumor virology. Right now, while there are books out there that cover individual viruses that are also covered in this book, there is no single book that covers this topic comprehensively. This book is the first current, comprehensive review of its kind in the market.
DNA USA: A Genetic Portrait of America
by Bryan SykesCrisscrossing the continent, a renowned geneticist provides a groundbreaking examination of America through its DNA. The best-selling author of The Seven Daughters of Eve now turns his sights on the United States, one of the most genetically variegated countries in the world. From the blue-blooded pockets of old-WASP New England to the vast tribal lands of the Navajo, Bryan Sykes takes us on a historical genetic tour, interviewing genealogists, geneticists, anthropologists, and everyday Americans with compelling ancestral stories. His findings suggest: * Of Americans whose ancestors came as slaves, virtually all have some European DNA. * Racial intermixing appears least common among descendants of early New England colonists. * There is clear evidence of Jewish genes among descendants of southwestern Spanish Catholics. * Among white Americans, evidence of African DNA is most common in the South. * European genes appeared among Native Americans as early as ten thousand years ago. An unprecedented look into America's genetic mosaic and how we perceive race, DNA USA challenges the very notion of what we think it means to be American.
DNA Vaccines
by Monica Rinaldi Daniela Fioretti Sandra IuresciaDNA Vaccines: Methods and Protocols, Third Edition explores innovative approaches and technologies used to design, deliver, and enhance the efficacy of DNA vaccines. Featuring applications which should be of great value in moving vaccines from research to clinic, this detailed volume includes sections on DNA vaccine design and enhancement, delivery systems, production, purification, and quality, as well as chapters on new vaccine applications. Written in the highly successful Methods in Molecular Biology series format, chapters contain introductions 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, DNA Vaccines: Methods and Protocols, Third Edition serves the important role of further documenting the potential of the DNA vaccination as a platform technology for treatment and prevention of human disease.
Do Animals Think?
by Clive D. WynneDoes your dog know when you've had a bad day? Can your cat tell that the coffee pot you left on might start a fire? Could a chimpanzee be trained to program your computer? In this provocative book, noted animal expert Clive Wynne debunks some commonly held notions about our furry friends. It may be romantic to ascribe human qualities to critters, he argues, but it's not very realistic. While animals are by no means dumb, they don't think the same way we do. Contrary to what many popular television shows would have us believe, animals have neither the "theory-of-mind" capabilities that humans have (that is, they are not conscious of what others are thinking) nor the capacity for higher-level reasoning. So, in Wynne's view, when Fido greets your arrival by nudging your leg, he's more apt to be asking for dinner than commiserating with your job stress. That's not to say that animals don't possess remarkable abilities--and Do Animals Think? explores countless examples: there's the honeybee, which not only remembers where it found food but communicates this information to its hivemates through an elaborate dance. And how about the sonar-guided bat, which locates flying insects in the dark of night and devours lunch on the wing? Engagingly written, Do Animals Think? takes aim at the work of such renowned animal rights advocates as Peter Singer and Jane Goodall for falsely humanizing animals. Far from impoverishing our view of the animal kingdom, however, it underscores how the world is richer for having such a diversity of minds--be they of the animal or human variety.
Do Bees Poop?: Learning About Living And Nonliving Things With The Garbage Gang (The\garbage Gang's Super Science Questions Ser.)
by Thomas Kingsley TroupeThe Garbage Gang discovers a beehive in a stinky situation and they wonder, Do Bees Poop? With the help of a little bee friend, they get an answer to their burning question. By the end, they’ll be knee deep in knowledge about living and nonliving things.
Do Chocolate Lovers Have Sweeter Babies?: The Surprising Science of Pregnancy
by Jena PincottBrain Candy for expectant parents! Pregnancy is an adventure. Lots of books tell you the basics—“the baby is the size of [insert fruit here].” But pregnant science writer Jena Pincott began to wonder just how a baby might tinker with her body—and vice versa—and chased down answers to the questions she wouldn’t ask her doctor, such as: • Does stress sharpen your baby’s mind—or dull it? • Can you predict your baby’s temperament? • Why are babies born in the darker months of the year more likely to grow up to be novelty-loving risk takers? • Are bossy, dominant women more likely to have boys? • How can the cells left behind by your baby affect you years later? This is a different kind of pregnancy book—thoughtful, fun, and filled with information you won’t find anywhere else.
Do Dice Play God?: The Mathematics of Uncertainty
by Ian StewartA celebrated mathematician explores how math helps us make sense of the unpredictableWe would like to believe we can know things for certain. We want to be able to figure out who will win an election, if the stock market will crash, or if a suspect definitely committed a crime. But the odds are not in our favor. Life is full of uncertainty --- indeed, scientific advances indicate that the universe might be fundamentally inexact --- and humans are terrible at guessing. When asked to predict the outcome of a chance event, we are almost always wrong. Thankfully, there is hope. As award-winning mathematician Ian Stewart reveals, over the course of history, mathematics has given us some of the tools we need to better manage the uncertainty that pervades our lives. From forecasting, to medical research, to figuring out how to win Let's Make a Deal, Do Dice Play God? is a surprising and satisfying tour of what we can know, and what we never will.
Do Gentlemen Really Prefer Blondes? Why He Fancies You and Why He Doesn't
by Jena PincottQ: Do Gentlemen Really Prefer Blondes? A: Marilyn Monroe, Scarlet Johansson and Gwyneth Paltrow would be happy to know that they do. During the Ice Age, when even cavemen were in short supply, the blonde woman really did get her man - simply because her light coloured hair made her stand out. Plus scientists have recently discovered that natural blondes have higher oestrogen levels. In short, golden (preferably long) hair shouts : 'I am young, sexy - and fertile' to every member of the male species within a few miles. Q: When's the best time to seduce my man? A: Your other half will definitely get more possessive and more attracted to you when you're ovulating and at your most fertile. You'll spend time on your make-up and choose next day's outfit before you go to bed. Your lips will be fuller, and your skin will be radiant because of the high levels of oestrogen being pumped through your blood. But don't get carried away by how sexy you feel. You are also more likely to be unfaithful during this period and your boyfriend is also likely to run away with another equally fertile member of the female species. Q: How do I get him to change his wild lifestyle? A: Get pregnant. Shocking but true. Fathers have lower testosterone levels than single men which means that they are more easy-going and less confrontational, they take fewer life threatening risks, and they are far less likely to have an affair with the leggier, skinnier blonde from the office.
Do Hard Things: Why We Get Resilience Wrong and the Surprising Science of Real Toughness
by Steve MagnessNational Bestseller"In Do Hard Things, Steve Magness beautifully and persuasively reimagines our understanding of toughness. This is a must-read for parents and coaches and anyone else looking to prepare for life's biggest challenges." -- Malcolm Gladwell, author of Outliers and Talking to Strangers and host of the Revisionist History podcastFrom beloved performance expert, executive coach, and coauthor of Peak Performance Steve Magness comes a radical rethinking of how we perceive toughness and what it means to achieve our high ambitions in the face of hard things.Toughness has long been held as the key to overcoming a challenge and achieving greatness, whether it is on the sports field, at a boardroom, or at the dining room table. Yet, the prevailing model has promoted a mentality based on fear, false bravado, and hiding any sign of weakness. In other words, the old model of toughness has failed us.Steve Magness, a performance scientist who coaches Olympic athletes, rebuilds our broken model of resilience with one grounded in the latest science and psychology. In Do Hard Things, Magness teaches us how we can work with our body – how experiencing discomfort, leaning in, paying attention, and creating space to take thoughtful action can be the true indications of cultivating inner strength. He offers four core pillars to cultivate such resilience: Pillar 1- Ditch the Façade, Embrace RealityPillar 2- Listen to Your BodyPillar 3- Respond, Instead of React Pillar 4- Transcend Discomfort Smart and wise all at once, Magness flips the script on what it means to be resilient. Drawing from mindfulness, military case studies, sports psychology, neuroscience, psychology, and philosophy, he provides a roadmap for navigating life’s challenges and achieving high performance that makes us happier, more successful, and, ultimately, better people.
Do Humankind’s Best Days Lie Ahead?: The Munk Debates (The Munk Debates #2015)
by Steven Pinker Matt Ridley Alain de Botton Malcolm GladwellProgress. It is one of the animating concepts of the modern era. From the Enlightenment onwards, the West has had an enduring belief that through the evolution of institutions, innovations, and ideas, the human condition is improving. This process is supposedly accelerating as new technologies, individual freedoms, and the spread of global norms empower individuals and societies around the world. But is progress inevitable? Its critics argue that human civilization has become different, not better, over the last two and a half centuries. What is seen as a breakthrough or innovation in one period becomes a setback or limitation in another. In short, progress is an ideology not a fact; a way of thinking about the world as opposed to a description of reality.In the seventeenth semi-annual Munk Debates, which was held in Toronto on November 6, 2015, pioneering cognitive scientist Steven Pinker and bestselling author Matt Ridley squared off against noted philosopher Alain de Botton and bestselling author Malcolm Gladwell to debate whether humankind’s best days lie ahead.
Do I Know You?: A Faceblind Reporter's Journey into the Science of Sight, Memory, and Imagination
by Sadie DingfelderAn award-winning science writer discovers she&’s faceblind and investigates the neuroscience of sight, memory, and imagination—while solving some long-running mysteries about her own life. Science writer Sadie Dingfelder has always known that she&’s a little quirky. But while she&’s made some strange mistakes over the years, it&’s not until she accosts a stranger in a grocery store (whom she thinks is her husband) that she realizes something is amiss. With a mixture of curiosity and dread, Dingfelder starts contacting neuroscientists and lands herself in scores of studies. In the course of her nerdy midlife crisis, she discovers that she is emphatically not neurotypical. She has prosopagnosia (faceblindness), stereoblindness, aphantasia (an inability to create mental imagery), and a condition called severely deficient autobiographical memory. As Dingfelder begins to see herself more clearly, she discovers a vast well of hidden neurodiversity in the world at large. There are so many different flavors of human consciousness, and most of us just assume that ours is the norm. Can you visualize? Do you have an inner monologue? Are you always 100 percent sure whether you know someone or not? If you can perform any of these mental feats, you may be surprised to learn that many people—including Dingfelder—can&’t. A lively blend of personal narrative and popular science, Do I Know You? is the story of one unusual mind&’s attempt to understand itself—and a fascinating exploration of the remarkable breadth of human experience.