Conrad Bessant, Darren Oakley, and Ian Shadforth
- Published in print:
- 2014
- Published Online:
- April 2014
- ISBN:
- 9780199658558
- eISBN:
- 9780191779466
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199658558.001.0001
- Subject:
- Biology, Biomathematics / Statistics and Data Analysis / Complexity Studies, Biochemistry / Molecular Biology
This book provides an introduction to three of the main tools used in the development of bioinformatics software — Perl, R, and MySQL — and explains how these can be used together to tackle the ...
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This book provides an introduction to three of the main tools used in the development of bioinformatics software — Perl, R, and MySQL — and explains how these can be used together to tackle the complex data-driven challenges that typify modern biology. The book is intended to provide the reader with the knowledge and confidence needed to create databases, to write programs to analyse and visualise data, and to develop interactive web-based applications. Platform-independent examples are provided throughout, making the book suitable for users of Windows, Mac OS or Linux.Less
This book provides an introduction to three of the main tools used in the development of bioinformatics software — Perl, R, and MySQL — and explains how these can be used together to tackle the complex data-driven challenges that typify modern biology. The book is intended to provide the reader with the knowledge and confidence needed to create databases, to write programs to analyse and visualise data, and to develop interactive web-based applications. Platform-independent examples are provided throughout, making the book suitable for users of Windows, Mac OS or Linux.
Bruce Walsh and Michael Lynch
- Published in print:
- 2018
- Published Online:
- September 2018
- ISBN:
- 9780198830870
- eISBN:
- 9780191868986
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/oso/9780198830870.001.0001
- Subject:
- Biology, Evolutionary Biology / Genetics, Biochemistry / Molecular Biology
Quantitative traits—be they morphological or physiological characters, aspects of behavior, or genome-level features such as the amount of RNA or protein expression for a specific gene—usually show ...
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Quantitative traits—be they morphological or physiological characters, aspects of behavior, or genome-level features such as the amount of RNA or protein expression for a specific gene—usually show considerable variation within and among populations. Quantitative genetics, also referred to as the genetics of complex traits, is the study of such characters and is based on mathematical models of evolution in which many genes influence the trait and in which non-genetic factors may also be important. Evolution and Selection of Quantitative Traits presents a holistic treatment of the subject, showing the interplay between theory and data with extensive discussions on statistical issues relating to the estimation of the biologically relevant parameters for these models. Quantitative genetics is viewed as the bridge between complex mathematical models of trait evolution and real-world data, and the authors have clearly framed their treatment as such. This is the second volume in a planned trilogy that summarizes the modern field of quantitative genetics, informed by empirical observations from wide-ranging fields (agriculture, evolution, ecology, and human biology) as well as population genetics, statistical theory, mathematical modeling, genetics, and genomics. Whilst volume 1 (1998) dealt with the genetics of such traits, the main focus of volume 2 is on their evolution, with a special emphasis on detecting selection (ranging from the use of genomic and historical data through to ecological field data) and examining its consequences. This extensive work of reference is suitable for graduate level students as well as professional researchers (both empiricists and theoreticians) in the fields of evolutionary biology, genetics, and genomics. It will also be of particular relevance and use to plant and animal breeders, human geneticists, and statisticians.Less
Quantitative traits—be they morphological or physiological characters, aspects of behavior, or genome-level features such as the amount of RNA or protein expression for a specific gene—usually show considerable variation within and among populations. Quantitative genetics, also referred to as the genetics of complex traits, is the study of such characters and is based on mathematical models of evolution in which many genes influence the trait and in which non-genetic factors may also be important. Evolution and Selection of Quantitative Traits presents a holistic treatment of the subject, showing the interplay between theory and data with extensive discussions on statistical issues relating to the estimation of the biologically relevant parameters for these models. Quantitative genetics is viewed as the bridge between complex mathematical models of trait evolution and real-world data, and the authors have clearly framed their treatment as such. This is the second volume in a planned trilogy that summarizes the modern field of quantitative genetics, informed by empirical observations from wide-ranging fields (agriculture, evolution, ecology, and human biology) as well as population genetics, statistical theory, mathematical modeling, genetics, and genomics. Whilst volume 1 (1998) dealt with the genetics of such traits, the main focus of volume 2 is on their evolution, with a special emphasis on detecting selection (ranging from the use of genomic and historical data through to ecological field data) and examining its consequences. This extensive work of reference is suitable for graduate level students as well as professional researchers (both empiricists and theoreticians) in the fields of evolutionary biology, genetics, and genomics. It will also be of particular relevance and use to plant and animal breeders, human geneticists, and statisticians.
Barry Halliwell and John M. C. Gutteridge
- Published in print:
- 2015
- Published Online:
- October 2015
- ISBN:
- 9780198717478
- eISBN:
- 9780191802133
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780198717478.001.0001
- Subject:
- Biology, Biochemistry / Molecular Biology, Disease Ecology / Epidemiology
The new edition of this well-established book is thoroughly revised and gives a comprehensive account of the role of free radicals, other reactive species (RS), and antioxidants in life, health, and ...
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The new edition of this well-established book is thoroughly revised and gives a comprehensive account of the role of free radicals, other reactive species (RS), and antioxidants in life, health, and disease. Chapter 1 reviews how oxygen (O2) is used by living organisms, why it can be toxic, and introduces the concept of oxygen radicals and other RS; their chemistry is detailed in Chapter 2, especially for superoxide, hydroxyl radical (including Fenton chemistry), peroxynitrite, nitric oxide, ozone, and singlet O2, with emphasis on their redox properties. Subsequent chapters detail what antioxidants can be made in vivo (e.g. superoxide dismutases, peroxiredoxins) and which can come from diet (e.g. vitamins E and C, carotenoids, and polyphenols such as the flavonoids) and how they work in vivo. The role of RS in cell proliferation, senescence, and death (e.g. by apoptosis, necrosis, or intermediate forms) is presented. Methods for measuring RS are described in detail, including electron paramagnetic resonance and biomarker determination. Useful roles for RS (e.g. cell signalling, phagocyte action), as well as systems in which they cause particular problems (e.g. premature babies, the eye, the ear) are presented. Acute and chronic inflammation are used to illustrate both roles There is a comprehensive description of the role of RS in human diseases, from cancer to heart disease to dementia, in the ageing process, and in the toxicity of many agents, from ethanol to carbon tetrachloride to paraquat. Therapeutic agents active against RS are reviewed in detail, including NADPH oxidase inhibitors, N-acetylcysteine, and Ebselen.Less
The new edition of this well-established book is thoroughly revised and gives a comprehensive account of the role of free radicals, other reactive species (RS), and antioxidants in life, health, and disease. Chapter 1 reviews how oxygen (O2) is used by living organisms, why it can be toxic, and introduces the concept of oxygen radicals and other RS; their chemistry is detailed in Chapter 2, especially for superoxide, hydroxyl radical (including Fenton chemistry), peroxynitrite, nitric oxide, ozone, and singlet O2, with emphasis on their redox properties. Subsequent chapters detail what antioxidants can be made in vivo (e.g. superoxide dismutases, peroxiredoxins) and which can come from diet (e.g. vitamins E and C, carotenoids, and polyphenols such as the flavonoids) and how they work in vivo. The role of RS in cell proliferation, senescence, and death (e.g. by apoptosis, necrosis, or intermediate forms) is presented. Methods for measuring RS are described in detail, including electron paramagnetic resonance and biomarker determination. Useful roles for RS (e.g. cell signalling, phagocyte action), as well as systems in which they cause particular problems (e.g. premature babies, the eye, the ear) are presented. Acute and chronic inflammation are used to illustrate both roles There is a comprehensive description of the role of RS in human diseases, from cancer to heart disease to dementia, in the ageing process, and in the toxicity of many agents, from ethanol to carbon tetrachloride to paraquat. Therapeutic agents active against RS are reviewed in detail, including NADPH oxidase inhibitors, N-acetylcysteine, and Ebselen.
Jay F. Storz
- Published in print:
- 2018
- Published Online:
- December 2018
- ISBN:
- 9780198810681
- eISBN:
- 9780191847929
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/oso/9780198810681.001.0001
- Subject:
- Biology, Evolutionary Biology / Genetics, Biochemistry / Molecular Biology
The aims of this book are to provide a synthesis of our current understanding of hemoglobin structure, function, and evolution, and to illustrate how research on this paradigmatic protein has ...
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The aims of this book are to provide a synthesis of our current understanding of hemoglobin structure, function, and evolution, and to illustrate how research on this paradigmatic protein has provided general insights into mechanisms of molecular evolution and biochemical adaptation. The book promotes an appreciation of how mechanistic insights into protein function can enrich our understanding of how evolution works and, reciprocally, it highlights how approaches in evolutionary genetics (such as phylogenetic comparative methods and ancestral sequence reconstruction) can be brought to bear on questions about the functional evolution of proteins. This treatise on the functional evolution of hemoglobin illustrates how research on a single, well-chosen model system can enhance our investigative acuity and bring key conceptual questions into sharp focus. Hemoglobin: Insights into Protein Structure, Function, and Evolution is suitable for a wide range of graduate level students taking interdisciplinary courses in biochemical physiology and protein evolution, and will serve as a key reference for researchers in molecular evolution, biochemistry, and comparative physiology.Less
The aims of this book are to provide a synthesis of our current understanding of hemoglobin structure, function, and evolution, and to illustrate how research on this paradigmatic protein has provided general insights into mechanisms of molecular evolution and biochemical adaptation. The book promotes an appreciation of how mechanistic insights into protein function can enrich our understanding of how evolution works and, reciprocally, it highlights how approaches in evolutionary genetics (such as phylogenetic comparative methods and ancestral sequence reconstruction) can be brought to bear on questions about the functional evolution of proteins. This treatise on the functional evolution of hemoglobin illustrates how research on a single, well-chosen model system can enhance our investigative acuity and bring key conceptual questions into sharp focus. Hemoglobin: Insights into Protein Structure, Function, and Evolution is suitable for a wide range of graduate level students taking interdisciplinary courses in biochemical physiology and protein evolution, and will serve as a key reference for researchers in molecular evolution, biochemistry, and comparative physiology.
Mark R. Sanderson and Jane V. Skelly (eds)
- Published in print:
- 2007
- Published Online:
- September 2007
- ISBN:
- 9780198520979
- eISBN:
- 9780191706295
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780198520979.001.0001
- Subject:
- Biology, Biochemistry / Molecular Biology
Macromolecular crystallography is the study of macromolecules (proteins and nucleic acids) using X-ray crystallographic techniques in order to determine their molecular structure. The knowledge of ...
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Macromolecular crystallography is the study of macromolecules (proteins and nucleic acids) using X-ray crystallographic techniques in order to determine their molecular structure. The knowledge of accurate molecular structures is a pre-requisite for rational drug design, and for structure-based function studies to aid the development of effective therapeutic agents and drugs. The successful determination of the complete genome (genetic sequence) of several species (including humans) has recently directed scientific attention towards identifying the structure and function of the complete complement of proteins that make up that species; a new and rapidly growing field of study called ‘structural genomics’. There are now several important and well-funded global initiatives in operation to identify all of the proteins of key model species. One of the main requirements for these initiatives is a high-throughput crystallization facility to speed-up the protein identification process. The extent to which these technologies have advanced calls for an updated review of current crystallographic theory and practice. This book features the latest conventional and high-throughput methods, and includes contributions from a team of internationally recognized leaders and experts.Less
Macromolecular crystallography is the study of macromolecules (proteins and nucleic acids) using X-ray crystallographic techniques in order to determine their molecular structure. The knowledge of accurate molecular structures is a pre-requisite for rational drug design, and for structure-based function studies to aid the development of effective therapeutic agents and drugs. The successful determination of the complete genome (genetic sequence) of several species (including humans) has recently directed scientific attention towards identifying the structure and function of the complete complement of proteins that make up that species; a new and rapidly growing field of study called ‘structural genomics’. There are now several important and well-funded global initiatives in operation to identify all of the proteins of key model species. One of the main requirements for these initiatives is a high-throughput crystallization facility to speed-up the protein identification process. The extent to which these technologies have advanced calls for an updated review of current crystallographic theory and practice. This book features the latest conventional and high-throughput methods, and includes contributions from a team of internationally recognized leaders and experts.
Rowland H. Davis
- Published in print:
- 2003
- Published Online:
- April 2010
- ISBN:
- 9780195154368
- eISBN:
- 9780199893935
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780195154368.001.0001
- Subject:
- Biology, Biochemistry / Molecular Biology
This book explains the role of simple biological model systems in the growth of molecular biology. Essentially, the whole history of molecular biology is presented here, tracing the work in ...
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This book explains the role of simple biological model systems in the growth of molecular biology. Essentially, the whole history of molecular biology is presented here, tracing the work in bacteriophages in E. coli, the role of other prokaryotic systems, and also the protozoan and algal models — Paramecium and Chlamydomonas, primarily — and the move into eukaryotes with the fungal systems Neurospora, Aspergillus, and yeast. Each model was selected for its appropriateness for asking a given class of questions, and each spawned its own community of investigators. Some individuals made the transition to a new model over time, and remnant communities of investigators continue to pursue questions in all these models, as the cutting edge of molecular biological research flows onward from model to model, and onward into higher organisms and, ultimately, mouse and man.Less
This book explains the role of simple biological model systems in the growth of molecular biology. Essentially, the whole history of molecular biology is presented here, tracing the work in bacteriophages in E. coli, the role of other prokaryotic systems, and also the protozoan and algal models — Paramecium and Chlamydomonas, primarily — and the move into eukaryotes with the fungal systems Neurospora, Aspergillus, and yeast. Each model was selected for its appropriateness for asking a given class of questions, and each spawned its own community of investigators. Some individuals made the transition to a new model over time, and remnant communities of investigators continue to pursue questions in all these models, as the cutting edge of molecular biological research flows onward from model to model, and onward into higher organisms and, ultimately, mouse and man.
Richard Firn
- Published in print:
- 2009
- Published Online:
- February 2010
- ISBN:
- 9780199566839
- eISBN:
- 9780191721700
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199566839.001.0001
- Subject:
- Biology, Ecology, Biochemistry / Molecular Biology
Natural Products (NPs) is the term used to describe the hundreds of thousands of chemical compounds or substances that are continually produced by living organisms (plants and microbes). Hundreds of ...
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Natural Products (NPs) is the term used to describe the hundreds of thousands of chemical compounds or substances that are continually produced by living organisms (plants and microbes). Hundreds of millions of tons of these chemicals are generated annually, and the trade in just a few of these has dominated human economic activity for thousands of years. Indeed, the current world geopolitical map has been shaped by attempts to control the supply of a few of these compounds. Every day of our lives each human spends time and money trying to procure the NPs of their choice. However, despite their overwhelming influence on human culture, they remain poorly understood. A knowledge of NPs can help in our search for new drugs, further the debate about GM manipulation, help us address environmental pollution, and enable a better understanding of drug trafficking. This is the first book to describe Natural Products (NPs) in an evolutionary context, distilling the few simple principles that govern the way in which organisms (including humans) have evolved to produce, cope with, or respond to NPs. It neatly synthesizes a widely dispersed literature and provides a general picture of NPs, encompassing evolution, history, ecology, and environmental issues (along with some deeper theory relevant to biochemistry), with the goal of enabling a wider section of the scientific community to fully appreciate the crucial importance of Natural Products to human culture and future survival.Less
Natural Products (NPs) is the term used to describe the hundreds of thousands of chemical compounds or substances that are continually produced by living organisms (plants and microbes). Hundreds of millions of tons of these chemicals are generated annually, and the trade in just a few of these has dominated human economic activity for thousands of years. Indeed, the current world geopolitical map has been shaped by attempts to control the supply of a few of these compounds. Every day of our lives each human spends time and money trying to procure the NPs of their choice. However, despite their overwhelming influence on human culture, they remain poorly understood. A knowledge of NPs can help in our search for new drugs, further the debate about GM manipulation, help us address environmental pollution, and enable a better understanding of drug trafficking. This is the first book to describe Natural Products (NPs) in an evolutionary context, distilling the few simple principles that govern the way in which organisms (including humans) have evolved to produce, cope with, or respond to NPs. It neatly synthesizes a widely dispersed literature and provides a general picture of NPs, encompassing evolution, history, ecology, and environmental issues (along with some deeper theory relevant to biochemistry), with the goal of enabling a wider section of the scientific community to fully appreciate the crucial importance of Natural Products to human culture and future survival.
Karl A. Wyant, Jessica R. Corman, and James J. Elser (eds)
- Published in print:
- 2013
- Published Online:
- May 2015
- ISBN:
- 9780199916832
- eISBN:
- 9780190267926
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:osobl/9780199916832.001.0001
- Subject:
- Biology, Biochemistry / Molecular Biology
Phosphorus is essential to all life. A critical component of fertilizers, Phosphorus currently has no known substitute in agriculture. Without it, crops cannot grow. With too much of it, waterways ...
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Phosphorus is essential to all life. A critical component of fertilizers, Phosphorus currently has no known substitute in agriculture. Without it, crops cannot grow. With too much of it, waterways are polluted. Across the globe, social, political, and economic pressures are influencing the biogeochemical cycle of phosphorus. A better understanding of this non-renewable resource and its impacts on the environment is critical to conserving our global supply and increasing agricultural productivity. Most of the phosphorus-focused discussion within the academic community is highly fragmented. This book brings together the necessary multi-disciplinary perspectives to build a cohesive knowledge base of phosphorus sustainability. The book is a direct continuation of processes associated with the first international conference on sustainable phosphorus held in the United States, the Frontiers in Life Sciences: Sustainable Phosphorus Summit, though it is not a book of conference proceedings; rather, the book is part of an integrated, coordinated process that builds on the momentum of the Summit. The first chapter introduces the biological and chemical necessity of phosphorus. The subsequent ten chapters explore different facets of phosphorus sustainability and the role of policy on future global phosphorus supplies. The final chapter synthesizes all of the emerging views contained in the book, drawing out the leading dilemmas and opportunities for phosphorus sustainability.Less
Phosphorus is essential to all life. A critical component of fertilizers, Phosphorus currently has no known substitute in agriculture. Without it, crops cannot grow. With too much of it, waterways are polluted. Across the globe, social, political, and economic pressures are influencing the biogeochemical cycle of phosphorus. A better understanding of this non-renewable resource and its impacts on the environment is critical to conserving our global supply and increasing agricultural productivity. Most of the phosphorus-focused discussion within the academic community is highly fragmented. This book brings together the necessary multi-disciplinary perspectives to build a cohesive knowledge base of phosphorus sustainability. The book is a direct continuation of processes associated with the first international conference on sustainable phosphorus held in the United States, the Frontiers in Life Sciences: Sustainable Phosphorus Summit, though it is not a book of conference proceedings; rather, the book is part of an integrated, coordinated process that builds on the momentum of the Summit. The first chapter introduces the biological and chemical necessity of phosphorus. The subsequent ten chapters explore different facets of phosphorus sustainability and the role of policy on future global phosphorus supplies. The final chapter synthesizes all of the emerging views contained in the book, drawing out the leading dilemmas and opportunities for phosphorus sustainability.
David L. Kirchman
- Published in print:
- 2011
- Published Online:
- December 2013
- ISBN:
- 9780199586936
- eISBN:
- 9780191774645
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199586936.001.0001
- Subject:
- Biology, Ecology, Biochemistry / Molecular Biology
This book, which discusses the major processes carried out by viruses, bacteria, fungi, protozoa, and other protists – the microbes – in freshwater, marine, and terrestrial ecosystems, focuses on ...
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This book, which discusses the major processes carried out by viruses, bacteria, fungi, protozoa, and other protists – the microbes – in freshwater, marine, and terrestrial ecosystems, focuses on biogeochemical processes, starting with primary production and the initial fixation of carbon into cellular biomass. It then discusses how that carbon is degraded in both oxygen-rich (oxic) and oxygen-deficient (anoxic) environments. These biogeochemical processes are affected by ecological interactions, including competition for limiting nutrients, viral lysis, and predation by various protists in soils and aquatic habitats. The book links up processes occurring at the micron scale to events happening at the global scale, including the carbon cycle and its connection to climate change issues, and ends with a chapter devoted to symbiosis and other relationships between microbes and large organisms. Microbes have large impacts not only on biogeochemical cycles, but also on the ecology and evolution of large organisms, including Homo sapiens.Less
This book, which discusses the major processes carried out by viruses, bacteria, fungi, protozoa, and other protists – the microbes – in freshwater, marine, and terrestrial ecosystems, focuses on biogeochemical processes, starting with primary production and the initial fixation of carbon into cellular biomass. It then discusses how that carbon is degraded in both oxygen-rich (oxic) and oxygen-deficient (anoxic) environments. These biogeochemical processes are affected by ecological interactions, including competition for limiting nutrients, viral lysis, and predation by various protists in soils and aquatic habitats. The book links up processes occurring at the micron scale to events happening at the global scale, including the carbon cycle and its connection to climate change issues, and ends with a chapter devoted to symbiosis and other relationships between microbes and large organisms. Microbes have large impacts not only on biogeochemical cycles, but also on the ecology and evolution of large organisms, including Homo sapiens.
John E. Till and Helen Grogan (eds)
- Published in print:
- 2008
- Published Online:
- September 2008
- ISBN:
- 9780195127270
- eISBN:
- 9780199869121
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780195127270.001.0001
- Subject:
- Biology, Ecology, Biochemistry / Molecular Biology
This book is an update and major revision to Radiological Assessment: A Textbook on Environmental Dose Analysis published by the U.S. Nuclear Regulatory Commission in 1983. It focuses on risk to the ...
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This book is an update and major revision to Radiological Assessment: A Textbook on Environmental Dose Analysis published by the U.S. Nuclear Regulatory Commission in 1983. It focuses on risk to the public because decision makers typically use that endpoint to allocate resources and resolve issues. Chapters in the book explain the fundamental steps of radiological assessment, and they are organized in a sequence that would typically be used when undertaking an analysis of risk. The key components of radiological risk assessment discussed include source terms, atmospheric transport, surface water transport, groundwater transport, terrestrial and aquatic food chain pathways, estimating exposures, conversion of intakes and exposures to dose and risk, uncertainty analysis, environmental epidemiology, and model validation. A chapter on regulations related to environmental exposure is also included. Contributors to the book are well known experts from the various disciplines addressed.Less
This book is an update and major revision to Radiological Assessment: A Textbook on Environmental Dose Analysis published by the U.S. Nuclear Regulatory Commission in 1983. It focuses on risk to the public because decision makers typically use that endpoint to allocate resources and resolve issues. Chapters in the book explain the fundamental steps of radiological assessment, and they are organized in a sequence that would typically be used when undertaking an analysis of risk. The key components of radiological risk assessment discussed include source terms, atmospheric transport, surface water transport, groundwater transport, terrestrial and aquatic food chain pathways, estimating exposures, conversion of intakes and exposures to dose and risk, uncertainty analysis, environmental epidemiology, and model validation. A chapter on regulations related to environmental exposure is also included. Contributors to the book are well known experts from the various disciplines addressed.
