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How genes are not the only basis of heredity--and what this means for evolution, human life, and disease For much of the twentieth century it was assumed that genes alone mediate the transmission of biological information across generations and provide the raw material for natural selection. In Extended Heredity, leading evolutionary biologists Russell Bonduriansky and Troy Day challenge this premise. Drawing on the latest research, they demonstrate that what happens during our lifetimes--and even our grandparents' and great-grandparents' lifetimes--can influence the features of our descendants. On the basis of these discoveries, Bonduriansky and Day develop an extended concept of heredity that upends ideas about how traits can and cannot be transmitted across generations. By examining the history of the gene-centered view in modern biology and reassessing fundamental tenets of evolutionary theory, Bonduriansky and Day show that nongenetic inheritance--involving epigenetic, environmental, behavioral, and cultural factors--could play an important role in evolution. The discovery of nongenetic inheritance therefore has major implications for key questions in evolutionary biology, as well as human health. Extended Heredity reappraises long-held ideas and opens the door to a new understanding of inheritance and evolution.
Advances in sequencing technology have allowed scientists to study the human genome in greater depth and on a larger scale than ever before - as many as hundreds of millions of short reads in the course of a few days. But what are the best ways to deal with this flood of data? Algorithms for Next-Generation Sequencing is an invaluable tool for students and researchers in bioinformatics and computational biology, biologists seeking to process and manage the data generated by next-generation sequencing, and as a textbook or a self-study resource. In addition to offering an in-depth description of the algorithms for processing sequencing data, it also presents useful case studies describing the applications of this technology.
DNA microarray technology has become a useful technique in gene expression analysis for the development of new diagnostic tools and for the identification of disease genes and therapeutic targets for human cancers. Appropriate control for DNA microarray experiment and reliable analysis of the array data are key to performing the assay and utilizing the data correctly. The most difficult challenge has been the lack of a powerful method to analyze the data for all genes (more than 30,000 genes) simultaneously and to use the microarray data in a decision-making process. In this book, the authors describe DNA microarray technology and data analysis by pointing out current advantages and disadvantages of the technique and available analytical methods. Crucially, new ideas and analytical methods based on the authors' own experience in DNA microarray study and analysis are introduced. It is believed that this new way of interpreting and analyzing microarray data will bring us closer to success in decision-making using the information obtained through the DNA microarray technology.
This textbook provides a fresh, comprehensive and accessible introduction to the rapidly expanding field of molecular pharmacology. Adopting a drug target-based, rather than the traditional organ/system based, approach this innovative guide reflects the current advances and research trend towards molecular based drug design, derived from a detailed understanding of chemical responses in the body. Drugs are then tailored to fit a treatment profile, rather than the traditional method of 'trial and error' drug discovery which focuses on testing chemicals on animals or cell cultures and matching their effects to treatments.
Providing an invaluable resource for advanced under-graduate and MSc/PhD students, new researchers to the field and practitioners for continuing professional development, "Molecular Pharmacology "explores; recent advances and developments in the four major human drug target families (G-protein coupled receptors, ion channels, nuclear receptors and transporters), cloning of drug targets, transgenic animal technology, gene therapy, pharmacogenomics and looks at the role of calcium in the cell. Current - focuses on cutting edge techniques and approaches, including new methods to quantify biological activities in different systems and ways to interpret and understand pharmacological data.Cutting Edge - highlights advances in pharmacogenomics and explores how an individual's genetic makeup influences their response to therapeutic drugs and the potential for harmful side effects.Applied - includes numerous, real-world examples and a detailed case-study based chapter which looks at current and possible future treatment strategies for cystic fibrosis. This case study considers the relative merits of both drug therapy for specific classes of mutation and gene therapy to correct the underlying defect.Accessible - contains a comprehensive glossary, suggestions for further reading at the end of each chapter and an associated website that provides a complete set of figures from within the book.
A companion website with additional resources is available at www.wiley.com/go/dickenson/dnamolecular
Recent advances in the study and understanding of human disease have largely been made possible by advances in molecular biology methodology. However, as the number and variety of laboratory techniques increases, so does the requirement for sufficient quantities of genomic DNA. This shortfall in availability of DNA has been addressed by the development of a number of whole genome amplification (WGA) approaches. Using these methods, it is possible to generate microgram quantities of DNA starting with as little as one nanogram of genomic DNA and in some cases even a single eukaryotic or bacterial cell. The implementation of such WGA methods provides an ample supply of DNA for large-scale genetic studies. This book will be welcomed by experienced researchers wishing to take advantage of the latest developments and by newcomers to the field who need to rapidly identify reliable techniques and approaches that will yield success in the laboratory.
Genomes 4 has been completely revised and updated. It is a thoroughly modern textbook about genomes and how they are investigated. As with Genomes 3, techniques come first, then genome anatomies, followed by genome function, and finally genome evolution. The genomes of all types of organism are covered: viruses, bacteria, fungi, plants, and animals including humans and other hominids. Genome sequencing and assembly methods have been thoroughly revised including a survey of four genome projects: human, Neanderthal, giant panda, and barley. Coverage of genome annotation emphasizes genome-wide RNA mapping, with CRISPR-Cas 9 and GWAS methods of determining gene function covered. The knowledge gained from these techniques forms the basis of the three chapters that describe the three main types of genomes: eukaryotic, prokaryotic (including eukaryotic organelles), and viral (including mobile genetic elements). Coverage of genome expression and replication is truly genomic, concentrating on the genome-wide implications of DNA packaging, epigenome modifications, DNA-binding proteins, non-coding RNAs, regulatory genome sequences, and protein-protein interactions. Also included are applications of transcriptome analysis, metabolomics, and systems biology. The final chapter is on genome evolution, focusing on the evolution of the epigenome, using genomics to study human evolution, and using population genomics to advance plant breeding. Established methods of molecular biology are included if they are still relevant today and there is always an explanation as to why the method is still important. Each chapter has a set of short-answer questions, in-depth problems, and annotated further reading. There is also an extensive glossary. Genomes 4 is the ideal text for upper level courses focused on genomes and genomics.
Over the last twenty years, genome-wide association studies (GWAS) have revealed a great deal about the genetic basis of a wide range of complex diseases and they will undoubtedly continue to have a broad impact as we move to an era of personalised medicine. This authoritative text, written by leaders and innovators from both academia and industry, covers the basic science as well as the clinical, biotechnological and pharmaceutical potential of these methods. With special emphasis given to highlighting pharmacogenomics and population genomics studies using next-generation technology approaches, this is the first book devoted to combining association studies with single nucleotide polymorphisms, copy number variants, haplotypes and expressed quantitative trait loci. A reliable guide for newcomers to the field as well as for experienced scientists, this is a unique resource for anyone interested in how the revolutionary power of genomics can be applied to solve problems in complex disease.
Unravelling the Double Helix covers the most colourful period in the history of DNA, from the discovery of 'nuclein' in the late 1860s to the landmark publication of James Watson's The Double Helix in 1968. These hundred years included the advent of the Nobel Prize, antibiotics, X-ray crystallography and the atom bomb as well as two devastating world wars - events which are strung along the narrative thread of DNA like beads on a necklace. The story of DNA is a saga packed with awful mistakes as well as brilliant science, with a wonderful cast of heroes and villains. Surprisingly, much of it is unfamiliar. The elucidation of the double helix was one of the most brilliant gems of twentieth-century science, but some of the scientists who played crucial roles have been airbrushed out of history. Others were plunged into darkness when the spotlight fell on James Watson, Francis Crick, Maurice Wilkins and Rosalind Franklin. Watson and Crick solved a magnificent mystery, but Gareth Williams shows that their contribution was to click into place the last few pieces of a gigantic jigsaw puzzle assembled over several decades.
This book is intended for non-specialists and students, presenting a unique introduction to the field of DNA nanotechnology. The primary focus is on the extraordinary advantages of specificity and sensitivity obtained by integrating DNA nanostructures in bioanalytical devices.DNA Nanotechnology for Bioanalysis provides a concise and rigorous description for the fabrication of various types of functional nanostructures by optimized software-aided high-yield synthesis. Following this is the explanation of methods to decorate these nanostructures with molecules such as proteins, metal nanoparticles or bioorganic moieties covalently bonded onto DNA via self-assemblage processes. Also provided is a concise review on non-canonical DNA structures (such as G-quadruplexes) and their targeting by small molecules for applications in pharmacology. Finally, it describes the exciting applications of DNA nanostructures in life sciences and nanomedicine, including ultraspecific molecular delivery, control of cell behavior, analysis of cell lysate and DNA-based nano-tools for super-resolution sub-cellular imaging.
This fourth edition reflects the most recent technical advances in DNA-protein interaction research. With fully updated chapters that describe techniques proven by their continuous value, the volume also many new chapters have been added that mostly deal with larger-scale experiments, reflecting recent advances in "big biology", combining to offer a very useful compendium of protocols allowing readers to delve into the intricacies of protein-DNA interaction at levels ranging from the very small (as in the case of single-molecule FRET) to the very complex (as with circular chromatin conformation capture or 4C). Written for the highly successful 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 up-to-date, DNA-Protein Interactions: Principles and Protocols, Fourth Edition will aid researchers in continuing the incredible progress made in this vital area of study.
Mapping the genomic landscapes is one of the most exciting frontiers of science. We have the opportunity to reverse engineer the blueprints and the control systems of living organisms. Computational tools are key enablers in the deciphering process. This book provides an in-depth presentation of some of the important computational biology approaches to genomic sequence analysis. The first section of the book discusses methods for discovering patterns in DNA and RNA. This is followed by the second section that reflects on methods in various ways, including performance, usage and paradigms.
Around 250,000 people have had their genomes sequenced and scientists expect that number to rise to one billion by 2025. Steven J. Heine argues that the first thing we will do on receiving our DNA test results is to misinterpret them completely. In DNA Is Not Destiny, Heine shares his research to not only show what your genes can tell you about your health, intelligence, ethnic identity and family but also highlight the psychological biases that make us so vulnerable to the media hype. Heine's fresh, surprising conclusions about the promise, and limits, of genetic engineering and DNA testing upend conventional thinking and reveal a simple, profound truth: your genes create life-but they do not control it.
Written with biologists, biochemists and other molecular scientists
in mind, this volume meets the long-felt need for a textbook
dedicated to the topic and recreates the excitement surrounding the
scientific revolution sparked by the discovery of RNA interference
in 1998. Students and instructors alike will profit from the
author's exclusive first-hand knowledge, drawing on his
breakthrough discoveries at the Tuschl lab at Rockefeller
Epigenetics can potentially revolutionize our understanding of the structure and behavior of biological life on Earth. It explains why mapping an organism's genetic code is not enough to determine how it develops or acts and shows how nurture combines with nature to engineer biological diversity. Surveying the twenty-year history of the field while also highlighting its latest findings and innovations, this volume provides a readily understandable introduction to the foundations of epigenetics. Nessa Carey, a leading epigenetics researcher, connects the field's arguments to such diverse phenomena as how ants and queen bees control their colonies; why tortoiseshell cats are always female; why some plants need cold weather before they can flower; and how our bodies age and develop disease. Reaching beyond biology, epigenetics now informs work on drug addiction, the long-term effects of famine, and the physical and psychological consequences of childhood trauma. Carey concludes with a discussion of the future directions for this research and its ability to improve human health and well-being.
Through this book, researchers and students will learn to use R for analysis of large-scale genomic data and how to create routines to automate analytical steps. The philosophy behind the book is to start with real world raw datasets and perform all the analytical steps needed to reach final results. Though theory plays an important role, this is a practical book for graduate and undergraduate courses in bioinformatics and genomic analysis or for use in lab sessions. How to handle and manage high-throughput genomic data, create automated workflows and speed up analyses in R is also taught. A wide range of R packages useful for working with genomic data are illustrated with practical examples. The key topics covered are association studies, genomic prediction, estimation of population genetic parameters and diversity, gene expression analysis, functional annotation of results using publically available databases and how to work efficiently in R with large genomic datasets. Important principles are demonstrated and illustrated through engaging examples which invite the reader to work with the provided datasets. Some methods that are discussed in this volume include: signatures of selection, population parameters (LD, FST, FIS, etc); use of a genomic relationship matrix for population diversity studies; use of SNP data for parentage testing; snpBLUP and gBLUP for genomic prediction. Step-by-step, all the R code required for a genome-wide association study is shown: starting from raw SNP data, how to build databases to handle and manage the data, quality control and filtering measures, association testing and evaluation of results, through to identification and functional annotation of candidate genes. Similarly, gene expression analyses are shown using microarray and RNAseq data. At a time when genomic data is decidedly big, the skills from this book are critical. In recent years R has become the de facto< tool for analysis of gene expression data, in addition to its prominent role in analysis of genomic data. Benefits to using R include the integrated development environment for analysis, flexibility and control of the analytic workflow. Included topics are core components of advanced undergraduate and graduate classes in bioinformatics, genomics and statistical genetics. This book is also designed to be used by students in computer science and statistics who want to learn the practical aspects of genomic analysis without delving into algorithmic details. The datasets used throughout the book may be downloaded from the publisher's website.
This book is the first to focus on the application of mathematical
networks for analyzing microarray data. This method goes well
beyond the standard clustering methods traditionally used.
What is a genetic superhero and could you be one? Is all your DNA important or is a load of it just junk? Can genetics inform your love life, your mental health and your ability to grow a tail? How to Code a Human takes you on a mind-bending journey through the world of the double helix, examining how our DNA encodes our genes and makes us unique. Covering all aspects of modern genetics from the evolution of our species to inherited diseases, "junk" DNA, genetic engineering and the intricacies of the molecular processes inside our cells, this is a beautiful, visual guide to the code of life.
Until recently, bacteria were frequently depicted as "bags of enzymes" in which proteins and DNA were distributed relatively haphazardly compared with animal and plant cells. Research performed over the past decade has revolutionized our understanding of bacterial cells, however, revealing that they are in fact highly organized and contain numerous subcompartments. Written and edited by experts in the field, this volume includes contributions discussing the three dimensional organization of the bacterial cell, various subcellular structures found in bacteria, membrane bounded organelles such as magnetosomes, and the organization of the cell membrane. Other chapters examine the recently identified bacterial cytoskeletal filaments which turn out to be remarkably similar to their eukaryotic counterparts as well as the roles of these filaments in morphogenesis and cytokinesis. Also covered are the extraordinary organization of the bacterial genome and the dynamic mechanisms that couple its replication and partitioning at cell division. In addition, the book reviews the various different multicellular structures bacteria can form, such as biofilms, along with new imaging techniques that promise to reveal even more about their subcellular machinery. It is thus of interest to microscopists and biochemists, as well as all microbiologists and cell biologists interested in how bacteria and other prokaryotes function.
Plant Genes, Genomes and Genetics provides a comprehensive treatment of all aspects of plant gene expression. Unique in explaining the subject from a plant perspective, it highlights the importance of key processes, many first discovered in plants, that impact how plants develop and interact with the environment. This text covers topics ranging from plant genome structure and the key control points in how genes are expressed, to the mechanisms by which proteins are generated and how their activities are controlled and altered by posttranslational modifications. Written by a highly respected team of specialists in plant biology with extensive experience in teaching at undergraduate and graduate level, this textbook will be invaluable for students and instructors alike. Plant Genes, Genomes and Genetics also includes: specific examples that highlight when and how plants operate differently from other organisms; special sections that provide in-depth discussions of particular issues; end-of-chapter problems to help students recapitulate the main concepts; rich, full-colour illustrations and diagrams clearly showing important processes in plant gene expression; a companion website with PowerPoint slides, downloadable figures, and answers to the questions posed in the book. Aimed at upper level undergraduates and graduate students in plant biology, this text is equally suited for advanced agronomy and crop science students inclined to understand molecular aspects of organismal phenomena. It is also an invaluable starting point for professionals entering the field of plant biology.
The latest edition of this highly successful textbook introduces
the key techniques and concepts involved in cloning genes and in
studying their expression and variation.
Noted for its outstanding balance between clarity of coverage
and level of detail, this book provides an excellent introduction
to the fast moving world of molecular genetics.
Genomics has transformed the biological sciences. From epidemiology and medicine to evolution and forensics, the ability to determine an organism's complete genetic makeup has changed the way science is done and the questions that can be asked of it. Its most celebrated achievement was the Human Genome Project, a technologically challenging endeavor that took thousands of scientists around the world 13 years and over 3 billion US dollars to complete. In this Very Short Introduction John Archibald explores the science of genomics and its rapidly expanding toolbox. Sequencing a human genome now takes only a few days and costs as little as $1,000. The genomes of simple bacteria and viruses can be sequenced in a matter of hours on a device that fits in the palm of your hand. The resulting sequences can be used to better understand our biology in health and disease and to 'personalize' medicine. Archibald shows how the field of genomics is on the cusp of another quantum leap; the implications for science and society are profound. ABOUT THE SERIES: The Very Short Introductions series from Oxford University Press contains hundreds of titles in almost every subject area. These pocket-sized books are the perfect way to get ahead in a new subject quickly. Our expert authors combine facts, analysis, perspective, new ideas, and enthusiasm to make interesting and challenging topics highly readable.
The State of the Art in Transcriptome Analysis RNA sequencing (RNA-seq) data offers unprecedented information about the transcriptome, but harnessing this information with bioinformatics tools is typically a bottleneck. RNA-seq Data Analysis: A Practical Approach enables researchers to examine differential expression at gene, exon, and transcript levels and to discover novel genes, transcripts, and whole transcriptomes. Balanced Coverage of Theory and Practice Each chapter starts with theoretical background, followed by descriptions of relevant analysis tools and practical examples. Accessible to both bioinformaticians and nonprogramming wet lab scientists, the examples illustrate the use of command-line tools, R, and other open source tools, such as the graphical Chipster software. The Tools and Methods to Get Started in Your Lab Taking readers through the whole data analysis workflow, this self-contained guide provides a detailed overview of the main RNA-seq data analysis methods and explains how to use them in practice. It is suitable for researchers from a wide variety of backgrounds, including biology, medicine, genetics, and computer science. The book can also be used in a graduate or advanced undergraduate course.
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.
How unassuming government researcher Marshall Nirenberg beat James Watson, Francis Crick, and other world-famous scientists in the race to discover the genetic code. The genetic code is the Rosetta Stone by which we interpret the 3.3 billion letters of human DNA, the alphabet of life, and the discovery of the code has had an immeasurable impact on science and society. In 1968, Marshall Nirenberg, an unassuming government scientist working at the National Institutes of Health, shared the Nobel Prize for cracking the genetic code. He was the least likely man to make such an earth-shaking discovery, and yet he had gotten there before such members of the scientific elite as James Watson and Francis Crick. How did Nirenberg do it, and why is he so little known? In The Least Likely Man, Franklin Portugal tells the fascinating life story of a famous scientist that most of us have never heard of. Nirenberg did not have a particularly brilliant undergraduate or graduate career. After being hired as a researcher at the NIH, he quietly explored how cells make proteins. Meanwhile, Watson, Crick, and eighteen other leading scientists had formed the "RNA Tie Club" (named after the distinctive ties they wore, each decorated with one of twenty amino acid designs), intending to claim credit for the discovery of the genetic code before they had even worked out the details. They were surprised, and displeased, when Nirenberg announced his preliminary findings of a genetic code at an international meeting in Moscow in 1961. Drawing on Nirenberg's "lab diaries," Portugal offers an engaging and accessible account of Nirenberg's experimental approach, describes counterclaims by Crick, Watson, and Sidney Brenner, and traces Nirenberg's later switch to an entirely new, even more challenging field. Having won the Nobel for his work on the genetic code, Nirenberg moved on to the next frontier of biological research: how the brain works.
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