Genetics (non-medical) Books

Book SynopsisHuman Population Genetics will provide an introduction to mathematical population genetics, along with relevant examples from human (and some non-human primate) populations, and will also present concepts and methods of population genetics that are specific to the study of human populations.Trade Review“Relethford’s Human Population Geneticsis a superb attempt at facing the challenges of explaining the basics of population genetics to those with a limited background in evolutionary theory and a fear of the quantitative.” (The Quarterly Review of Biology, 1 September 2014) “For many students, and likely some instructors, who have found the mathematical underpinnings of evolutionary genetics daunting, this new volume will be a welcome addition to the bookshelf. It is an easy book to recommend either as a primary text in anthropological genetics courses, or as a recommended or adjunct text in upper division/beginning graduate courses in human biology, human genetics, or human evolution.” (American Journal of Physical Anthropology, 19 September 2013) Table of ContentsForeword vii Preface ix 1 Genetic, Mathematical, and Anthropological Background 1 I. The Scope of Population Genetics 2 II. Genetics Background 5 III. Principles of Probability 14 IV. The Anthropological Connection 17 V. A Closing Thought 21 2 Hardy–Weinberg Equilibrium 23 I. Genotype and Allele Frequencies 24 II. What is Hardy–Weinberg Equilibrium? 30 III. The Mathematics of Hardy–Weinberg Equilibrium 31 IV. Using Hardy–Weinberg Equilibrium 37 V. Extensions of Hardy–Weinberg Equilibrium 40 VI. Hardy–Weinberg Equilibrium and Evolution 44 VII. Summary 45 3 Inbreeding 49 I. Quantifying Inbreeding 51 II. Population Genetics and Inbreeding 62 III. Inbreeding in Human Populations 65 IV. Summary 75 4 Mutation 77 I. The Nature of Mutations 77 II. Models of Mutation 81 III. Mutational History and Anthropological Questions 88 IV. Summary 96 5 Genetic Drift 101 I. What is Genetic Drift? 102 II. Genetic Drift and Population Size 112 III. Effects on Genetic Variation 120 IV. Mutation and Genetic Drift 121 V. Coalescent Theory 125 VI. Summary 131 6 Models of Natural Selection 139 I. How Does Natural Selection Work? 140 II. A General Model of Natural Selection 145 III. Types of Natural Selection 147 IV. Other Aspects of Selection 160 V. Summary 167 7 Natural Selection in Human Populations 181 I. Case Studies of Natural Selection in Human Populations 182 II. Are Humans Still EvolVIng? 198 III. Summary 203 8 Gene Flow 205 I. The Evolutionary Impact of Gene Flow 206 II. Models of Gene Flow 208 III. Gene Flow and Genetic Drift 213 IV. Estimating Admixture in Human Populations 226 V. Summary 230 9 Human Population Structure and History 237 I. Case Studies of Human Population Structure 238 II. The Origin of Modern Humans 242 III. Case Studies of Population Origins 247 IV. Summary 255 Glossary 257 References 267 Index 279

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Book SynopsisThe only book available in the area of forward-time population genetics simulationsapplicable to both biomedical and evolutionary studies The rapid increase of the power of personal computers has led to the use of serious forward-time simulation programs in genetic studies. Forward-Time Population Genetics Simulations presents both new and commonly used methods, and introduces simuPOP, a powerful and flexible new program that can be used to simulate arbitrary evolutionary processes with unique features like customized chromosome types, arbitrary nonrandom mating schemes, virtual subpopulations, information fields, and Python operators. The book begins with an overview of important concepts and models, then goes on to show how simuPOP can simulate a number of standard population genetics modelswith the goal of demonstrating the impact of genetic factors such as mutation, selection, and recombination on standard Wright-Fisher models. The rest of the book is devoted to aTable of ContentsPreface ix Acknowledgments xiii List of examples xxiii 1. Basic concepts and models 1 1.1 Biological and genetic concepts 2 1.2 Population and evolutionary genetics 6 1.3 Statistical genetics and genetic epidemiology 17 2. Simulation of population genetics models 25 2.1 Random genetic drift 25 2.2 Demographic models 29 2.3 Mutation 31 2.4 Migration 34 2.5 Recombination and linkage disequilibrium 36 2.6 Natural selection 37 2.7 Genealogy of forward-time simulations 41 3. Ascertainment bias in population genetics 47 3.1 Introduction 47 3.2 Methods 49 3.3 Results 54 3.4 Discussion and Conclusions 58 4. Observing properties of evolving populations 63 4.1 Introduction 64 4.2 Simulation of the evolution of allele spectra 66 4.3 Extensions to the basic model 78 5. Simulating populations with complex human diseases 89 5.1 Introduction 89 5.2 Controlling disease allele frequencies at the present generation 91 5.3 Forward-time simulation of realistic samples 102 5.4 Discussion 119 6. Nonrandom mating and its applications 125 6.1 Assortative mating 126 6.2 More complex non-random mating schemes 132 6.3 Hetergeneous mating schemes 140 6.4 Simulation of age structured populations 145 Appendix: Forward-time simulations using stimulPOP 157 A.1 Introduction 157 A.2 Population 160 A.3 Operators 172 A.4 Evolve on or more populations 181 A.5 A complete stimuPOP script 185

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Book SynopsisThe latest edition of this highly successful textbook introduces the key techniques and concepts involved in cloning genes and in studying their expression and variation. The new edition features: Increased coverage of whole-genome sequencing technologies and enhanced treatment of bioinformatics. Clear, two-colour diagrams throughout. A dedicated website including all figures. 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.Trade Review“This third edition is absolutely necessary to incorporate the recent advances, such as genome sequencing, polymerase chain reaction, and microarray technology, in this field.” (Doody’s, 19 October 2012)Table of ContentsPreface xiii 1 From Genes to Genomes 1 1.1 Introduction 1 1.2 Basic molecular biology 4 1.2.1 The DNA backbone 4 1.2.2 The base pairs 6 1.2.3 RNA structure 10 1.2.4 Nucleic acid synthesis 11 1.2.5 Coiling and supercoilin 11 1.3 What is a gene? 13 1.4 Information flow: gene expression 15 1.4.1 Transcription 16 1.4.2 Translation 19 1.5 Gene structure and organisation 20 1.5.1 Operons 20 1.5.2 Exons and introns 21 1.6 Refinements of the model 22 2 How to Clone a Gene 25 2.1 What is cloning? 25 2.2 Overview of the procedures 26 2.3 Extraction and purification of nucleic acids 29 2.3.1 Breaking up cells and tissues 29 2.3.2 Alkaline denaturation 31 2.3.3 Column purification 31 2.4 Detection and quantitation of nucleic acids 32 2.5 Gel electrophoresis 33 2.5.1 Analytical gel electrophoresis 33 2.5.2 Preparative gel electrophoresis 36 2.6 Restriction endonucleases 36 2.6.1 Specificity 37 2.6.2 Sticky and blunt ends 40 2.7 Ligation 42 2.7.1 Optimising ligation conditions 44 2.7.2 Preventing unwanted ligation: alkaline phosphatase and double digests 46 2.7.3 Other ways of joining DNA fragments 48 2.8 Modification of restriction fragment ends 49 2.8.1 Linkers and adaptors 50 2.8.2 Homopolymer tailing 52 2.9 Plasmid vectors 53 2.9.1 Plasmid replication 54 2.9.2 Cloning sites 55 2.9.3 Selectable markers 57 2.9.4 Insertional inactivation 58 2.9.5 Transformation 59 2.10 Vectors based on the lambda bacteriophage 61 2.10.1 Lambda biology 61 2.10.2 In vitro packaging 65 2.10.3 Insertion vectors 66 2.10.4 Replacement vectors 68 2.11 Cosmids 71 2.12 Supervectors: YACs and BACs 72 2.13 Summary 73 3 Genomic and cDNA Libraries 75 3.1 Genomic libraries 77 3.1.1 Partial digests 77 3.1.2 Choice of vectors 80 3.1.3 Construction and evaluation of a genomic library 83 3.2 Growing and storing libraries 86 3.3 cDNA libraries 87 3.3.1 Isolation of mRNA 88 3.3.2 cDNA synthesis 89 3.3.3 Bacterial cDNA 93 3.4 Screening libraries with gene probes 94 3.4.1 Hybridization 94 3.4.2 Labelling probes 98 3.4.3 Steps in a hybridization experiment 99 3.4.4 Screening procedure 100 3.4.5 Probe selection and generation 101 3.5 Screening expression libraries with antibodies 103 3.6 Characterization of plasmid clones 106 3.6.1 Southern blots 107 3.6.2 PCR and sequence analysis 108 4 Polymerase Chain Reaction (PCR) 109 4.1 The PCR reaction 110 4.2 PCR in practice 114 4.2.1 Optimisation of the PCR reaction 114 4.2.2 Primer design 115 4.2.3 Analysis of PCR products 117 4.2.4 Contamination 118 4.3 Cloning PCR products 119 4.4 Long-range PCR 121 4.5 Reverse-transcription PCR 123 4.6 Quantitative and real-time PCR 123 4.6.1 SYBR Green 123 4.6.2 TaqMan 125 4.6.3 Molecular beacons 125 4.7 Applications of PCR 127 4.7.1 Probes and other modified products 127 4.7.2 PCR cloning strategies 128 4.7.3 Analysis of recombinant clones and rare events 129 4.7.4 Diagnostic applications 130 5 Sequencing a Cloned Gene 131 5.1 DNA sequencing 131 5.1.1 Principles of DNA sequencing 131 5.1.2 Automated sequencing 136 5.1.3 Extending the sequence 137 5.1.4 Shotgun sequencing; contig assembly 138 5.2 Databank entries and annotation 140 5.3 Sequence analysis 146 5.3.1 Identification of coding region 146 5.3.2 Expression signals 147 5.4 Sequence comparisons 148 5.4.1 DNA sequences 148 5.4.2 Protein sequence comparisons 151 5.4.3 Sequence alignments: Clustal 157 5.5 Protein structure 160 5.5.1 Structure predictions 160 5.5.2 Protein motifs and domains 162 5.6 Confirming gene function 165 5.6.1 Allelic replacement and gene knockouts 166 5.6.2 Complementation 168 6 Analysis of Gene Expression 169 6.1 Analysing transcription 169 6.1.1 Northern blots 170 6.1.2 Reverse transcription-PCR 171 6.1.3 In situ hybridization 174 6.2 Methods for studying the promoter 174 6.2.1 Locating the promoter 175 6.2.2 Reporter genes 177 6.3 Regulatory elements and DNA-binding proteins 179 6.3.1 Yeast one-hybrid assays 179 6.3.2 DNase I footprinting 181 6.3.3 Gel retardation assays 181 6.3.4 Chromatin immunoprecipitation (ChIP) 183 6.4 Translational analysis 185 6.4.1 Western blots 185 6.4.2 Immunocytochemistry and immunohistochemistry 187 7 Products from Native and Manipulated Cloned Genes 189 7.1 Factors affecting expression of cloned genes 190 7.1.1 Transcription 190 7.1.2 Translation initiation 192 7.1.3 Codon usage 193 7.1.4 Nature of the protein product 194 7.2 Expression of cloned genes in bacteria 195 7.2.1 Transcriptional fusions 195 7.2.2 Stability: conditional expression 198 7.2.3 Expression of lethal genes 201 7.2.4 Translational fusions 201 7.3 Yeast systems 204 7.3.1 Cloning vectors for yeasts 204 7.3.2 Yeast expression systems 206 7.4 Expression in insect cells: baculovirus systems 208 7.5 Mammalian cells 209 7.5.1 Cloning vectors for mammalian cells 210 7.5.2 Expression in mammalian cells 213 7.6 Adding tags and signals 215 7.6.1 Tagged proteins 215 7.6.2 Secretion signals 217 7.7 In vitro mutagenesis 218 7.7.1 Site-directed mutagenesis 218 7.7.2 Synthetic genes 223 7.7.3 Assembly PCR 223 7.7.4 Synthetic genomes 224 7.7.5 Protein engineering 224 7.8 Vaccines 225 7.8.1 Subunit vaccines 225 7.8.2 DNA vaccines 226 8 Genomic Analysis 229 8.1 Overview of genome sequencing 229 8.1.1 Strategies 230 8.2 Next generation sequencing (NGS) 231 8.2.1 Pyrosequencing (454) 232 8.2.2 SOLiD sequencing (Applied Biosystems) 235 8.2.3 Bridge amplification sequencing (Solexa/Ilumina) 237 8.2.4 Other technologies 239 8.3 De novo sequence assembly 239 8.3.1 Repetitive elements and gaps 240 8.4 Analysis and annotation 242 8.4.1 Identification of ORFs 243 8.4.2 Identification of the function of genes and their products 250 8.4.3 Other features of nucleic acid sequences 251 8.5 Comparing genomes 256 8.5.1 BLAST 256 8.5.2 Synteny 257 8.6 Genome browsers 258 8.7 Relating genes and functions: genetic and physical maps 260 8.7.1 Linkage analysis 261 8.7.2 Ordered libraries and chromosome walking 262 8.8 Transposon mutagenesis and other screening techniques 263 8.8.1 Transposition in bacteria 263 8.8.2 Transposition in Drosophila 266 8.8.3 Transposition in other organisms 268 8.8.4 Signature-tagged mutagenesis 269 8.9 Gene knockouts, gene knockdowns and gene silencing 271 8.10 Metagenomics 273 8.11 Conclusion 274 9 Analysis of Genetic Variation 275 9.1 Single nucleotide polymorphisms 276 9.1.1 Direct sequencing 278 9.1.2 SNP arrays 279 9.2 Larger scale variations 280 9.2.1 Microarrays and indels 281 9.3 Other methods for studying variation 282 9.3.1 Genomic Southern blot analysis: restriction fragment length polymorphisms (RFLPs) 282 9.3.2 VNTR and microsatellites 285 9.3.3 Pulsed-field gel electrophoresis 287 9.4 Human genetic variation: relating phenotype to genotype 289 9.4.1 Linkage analysis 289 9.4.2 Genome-wide association studies (GWAS) 292 9.4.3 Database resources 294 9.4.4 Genetic diagnosis 294 9.5 Molecular phylogeny 295 9.5.1 Methods for constructing trees 298 10 Post-Genomic Analysis 305 10.1 Analysing transcription: transcriptomes 305 10.1.1 Differential screening 306 10.1.2 Other methods: transposons and reporters 308 10.2 Array-based methods 308 10.2.1 Expressed sequence tag (EST) arrays 309 10.2.2 PCR product arrays 310 10.2.3 Synthetic oligonucleotide arrays 312 10.2.4 Important factors in array hybridization 313 10.3 Transcriptome sequencing 315 10.4 Translational analysis: proteomics 316 10.4.1 Two-dimensional electrophoresis 317 10.4.2 Mass spectrometry 318 10.5 Post-translational analysis: protein interactions 320 10.5.1 Two-hybrid screening 320 10.5.2 Phage display libraries 321 10.6 Epigenetics 323 10.7 Integrative studies: systems biology 324 10.7.1 Metabolomic analysis 324 10.7.2 Pathway analysis and systems biology 325 11 Modifying Organisms: Transgenics 327 11.1 Transgenesis and cloning 327 11.1.1 Common species used for transgenesis 328 11.1.2 Control of transgene expression 330 11.2 Animal transgenesis 333 11.2.1 Basic methods 333 11.2.2 Direct injection 333 11.2.3 Retroviral vectors 335 11.2.4 Embryonic stem cell technology 336 11.2.5 Gene knockouts 339 11.2.6 Gene knock-down technology: RNA interference 340 11.2.7 Gene knock-in technology 341 11.3 Applications of transgenic animals 342 11.4 Disease prevention and treatment 343 11.4.1 Live vaccine production: modification of bacteria and viruses 343 11.4.2 Gene therapy 346 11.4.3 Viral vectors for gene therapy 347 11.5 Transgenic plants and their applications 349 11.5.1 Introducing foreign genes 349 11.5.2 Gene subtraction 351 11.5.3 Applications 352 11.6 Transgenics: a coda 353 Glossary 355 Bibliography 375 Index 379

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Book SynopsisThis book takes the novel approach to cover both the sequence and structure analysis of proteins in one volume and from an algorithmic perspective. Key features of the book include:* Provides a comprehensive introduction to the analysis of protein sequence and structure analysis.Table of ContentsPreface. Acknowledgements. Part I: SEQUENCE ANALYSIS. 1. Pairwise Global Alignment of Sequences. 1.1 Alignment and Evolution. 1.2 What is an Alignment? 1.3 A Scoring Scheme for the Model. 1.4 Finding Highest-Scoring Alignments with Dynamic Programming. 1.4.1 Determine Hi,j. 1.4.2 Use of matrices. 1.4.3 Finding the alignments that give the highest score. 1.4.4 Gaps. 1.5 Scoring Matrices. 1.6 Scoring Gaps: Gap Penalties. 1.7 Dynamic Programming for General Gap Penalty. 1.8 Dynamic Programming for Affine Gap Penalty. 1.9 Alignment Score and Sequence Distance. 1.10 Exercises. 1.11 Bibliographic notes. 2 Pairwise Local Alignment and Database Search. 2.1 The Basic Operation: Comparing Two Sequences. 2.2 Dot Matrices. 2.2.1 Filtering. 2.2.2 Repeating segments. 2.3 Dynamic Programming. 2.3.1 Initialization. 2.3.2 Finding the best local alignments. 2.3.3 Algorithms. 2.3.4 Scoring matrices and gap penalties. 2.4 Database Search: BLAST. 2.4.1 The procedure. 2.4.2 Preprocess the query: make the word list. 2.4.3 Scanning the database sequences. 2.4.4 Extending to HSP. 2.4.5 Introducing gaps. 2.4.6 Algorithm. 2.5 Exercises. 2.6 Bibliographic notes. 3. Statistical Analysis. 3.1 Hypothesis Testing for Sequence Homology. 3.1.1 Random generation of sequences. 3.1.2 Use of Z values for estimating the statistical significance. 3.2 Statistical Distributions. 3.2.1 Poisson probability distribution. 3.2.2 Extreme value distributions. 3.3 Theoretical Analysis of Statistical Significance. 3.3.1 The P value has an extreme value distribution. 3.3.2 Theoretical analysis for database search. 3.4 Probability Distributions for Gapped Alignments. 3.5 Assessing and Comparing Programs for Database Search. 3.5.1 Sensitivity and specificity. 3.5.2 Discrimination power. 3.5.3 Using more sequences as queries. 3.6 Exercises. 3.7 Bibliographic notes. 4 .Multiple Global Alignment and Phylogenetic Trees. 4.1 Dynamic Programming. 4.1.1 SP score of multiple alignments. 4.1.2 A pruning algorithm for the DP solution. 4.2 Multiple Alignments and Phylogenetic Trees. 4.3 Phylogeny. 4.3.1 The number of different tree topologies. 4.3.2 Molecular clock theory. 4.3.3 Additive and ultrametric trees. 4.3.4 Different approaches for reconstructing phylogenetic trees. 4.3.5 Distance-based construction. 4.3.6 Rooting of trees. 4.3.7 Statistical test: bootstrapping. 4.4 Progressive Alignment. 4.4.1 Aligning two subset alignments. 4.4.2 Clustering. 4.4.3 Sequence weights. 4.4.4 CLUSTAL. 4.5 Other Approaches. 4.6 Exercises. 4.7 Bibliographic notes. 5. Scoring Matrices. 5.1 Scoring Matrices Based on Physio-Chemical Properties. 5.2 PAM Scoring Matrices. 5.2.1 The evolutionary model. 5.2.2 Calculate substitution matrix. 5.2.3 Matrices for general evolutionary time. 5.2.4 Measuring sequence similarity by use of Mτ. 5.2.5 Odds matrices. 5.2.6 Scoring matrices (log-odds matrices). 5.2.7 Estimating the evolutionary distance. 5.3 BLOSUM Scoring Matrices. 5.3.1 Log-odds matrix. 5.3.2 Developing scoring matrices for different evolutionary distances. 5.4 Comparing BLOSUM and PAM Matrices. 5.5 Optimal Scoring Matrices. 5.5.1 Analysis for one sequence. 5.6 Exercises. 5.7 Bibliographic notes. 6. Profiles. 6.1 Constructing a Profile. 6.1.1 Notation. 6.1.2 Removing rows and columns. 6.1.3 Position weights. 6.1.4 Sequence weights. 6.1.5 Treating gaps. 6.2 Searching Databases with Profiles. 6.3 Iterated BLAST: PSI-BLAST. 6.3.1 Making the multiple alignment. 6.3.2 Constructing the profile. 6.4 HMM Profile. 6.4.1 Definitions for an HMM. 6.4.2 Constructing a profile HMM for a protein family. 6.4.3 Comparing a sequence with an HMM. 6.4.4 Protein family databases. 6.5 Exercises. 6.6 Bibliographic notes. 7. Sequence Patterns. 7.1 The PROSITE Language. 7.2 Exact/Approximate Matching. 7.3 Defining Pattern Classes by Imposing Constraints. 7.4 Pattern Scoring: Information Theory. 7.4.1 Information theory. 7.4.2 Scoring patterns. 7.5 Generalization and Specialization. 7.6 Pattern Discovery: Introduction. 7.7 Comparison-Based Methods. 7.7.1 Pivot-based methods. 7.7.2 Tree progressive methods. 7.8 Pattern-Driven Methods: Pratt. 7.8.1 The main procedure. 7.8.2 Preprocessing. 7.8.3 The pattern space. 7.8.4 Searching. 7.8.5 Ambiguous components. 7.8.6 Specialization. 7.8.7 Pattern scoring. 7.9 Exercises. 7.10 Bibliographic notes. Part II: STRUCTURE ANALYSIS 8. Structures and Structure Descriptions. 8.1 Units of Structure Descriptions. 8.2 Coordinates. 8.3 Distance Matrices. 8.4 Torsion Angles. 8.5 Coarse Level Description. 8.5.1 Line segments (sticks). 8.5.2 Ellipsoid. 8.5.3 Helices. 8.5.4 Strands and sheets. 8.5.5 Topology of Protein Structure (TOPS). 8.6 Identifying the SSEs. 8.6.1 Use of distance matrices. 8.6.2 Define Secondary Structure of Proteins (DSSP). 8.7 Structure Comparison. 8.7.1 Structure descriptions for comparison. 8.7.2 Structure representation. 8.8 Framework for Pairwise Structure Comparison. 8.9 Exercises. 8.10 Bibliographic notes. 9. Superposition and Dynamic Programming. 9.1 Superposition. 9.1.1 Coordinate RMSD. 9.1.2 Distance RMSD. 9.1.3 Using RMSD as scoring of structure similarities. 9.2 Alternating Superposition and Alignment. 9.3 Double Dynamic Programming. 9.3.1 Low-level scoring matrices. 9.3.2 High-level scoring matrix. 9.3.3 Iterated double dynamic programming. 9.4 Similarity of the Methods. 9.5 Exercises. 9.6 Bibliographic notes. 10. Geometric Techniques. 10.1 Geometric Hashing. 10.1.1 Two-dimensional geometric hashing. 10.1.2 Geometric hashing for structure comparison. 10.1.3 Geometric hashing for SSE representation. 10.1.4 Clustering. 10.2 Distance Matrices. 10.2.1 Measuring the similarity of distance (sub)matrices. 10.3 Exercises. 10.4 Bibliographic notes. 11. Clustering: Combining Local Similarities. 11.1 Compatibility and Consistency. 11.2 Searching for Seed Matches. 11.3 Consistency. 11.3.1 Test for consistency. 11.3.2 Overlapping clusters. 11.4 Clustering Algorithms. 11.4.1 Linear clustering. 11.4.2 Hierarchical clustering. 11.5 Clustering by Use of Transformations. 11.5.1 Comparing transformations. 11.5.2 Calculating the new transformation. 11.5.3 Algorithm. 11.6 Clustering by Use of Relations. 11.6.1 How many relations to compare? 11.6.2 Geometric relation. 11.6.3 Distance relation. 11.6.4 Use of graph theory. 11.7 Refinement. 11.8 Exercises. 11.9 Bibliographic notes. 12. Significance and Assessment of Structure Comparisons. 12.1 Constructing Random Structure Models. 12.1.1 Use of distance geometry. 12.2 Use of Structure Databases. 12.2.1 Constructing nonredundant subsets. 12.2.2 Demarcation line for similarity. 12.3 Reversing the Protein Chain. 12.4 Randomized Alignment Models. 12.5 Assessing Comparison and Scoring Methods. 12.6 Is RMSD Suitable for Scoring? 12.7 Scoring and Biological Significance. 12.8 Exercises. 12.9 Bibliographic notes. 13. Multiple Structure Comparison. 13.1 Multiple Superposition. 13.2 Progressive Structure Alignment. 13.2.1 Scoring. 13.2.2 Construction of consensus. 13.3 Finding a Common Core from a Multiple Alignment. 13.4 Discovering Common Cores. 13.4.1 Finding the multiple seed matches. 13.4.2 Pairwise clustering. 13.4.3 Determining common cores. 13.4.4 Scoring clusters. 13.5 Local Structure Patterns. 13.5.1 Local packing patterns. 13.5.2 Discovering packing patterns. 13.5.3 The approach. 13.5.4 Scoring the packing motifs. 13.6 Exercises. 13.7 Bibliographic notes. 14. Protein Structure Classification. 14.1 Protein Domains. 14.2 An Ising Model for Domain Identification. 14.3 Domain Classes. 14.3.1 Mainly-? domains. 14.3.2 Mainly-? domains. 14.3.3 ?–? domains. 14.4 Folds. 14.5 Automatic Approaches to Classification. 14.6 Databases for Structure Classification. 14.7 FSSP-Dali Domain Dictionary. 14.8 CATH. 14.8.1 Domains. 14.8.2 Class. 14.8.3 Architecture. 14.8.4 Topology (fold family). 14.8.5 Homologous superfamily. 14.8.6 Sequence families. 14.8.7 The CATH classification procedure. 14.9 Classification Based on Sticks. 14.10 Exercises. 14.11 Bibliographic notes. Part III: SEQUENCE-STRUCTUREANALYSIS. 15. Structure Prediction: Threading. 15.1 Protein Secondary Structure Prediction. 15.1.1 Artificial neural networks. 15.1.2 The PHD program. 15.1.3 Accuracy in secondary structure prediction. 15.2 Threading. 15.3 Methods Based on Sequence Alignment. 15.3.1 The 3D–1D matching method. 15.3.2 The FUGUE method. 15.4 Methods Using 3D Interactions. 15.4.1 Potentials of mean force. 15.4.2 Towards modelling methods. 15.5 Alignment Methods. 15.5.1 Frozen approximation. 15.5.2 Double Dynamic Programming. 15.6 Multiple Sequence/Structure Threading. 15.6.1 Simple multiple sequence threading. 15.7 Combined Sequence/Threading Methods. 15.8 Assessment of Threading Methods. 15.8.1 Fold recognition. 15.8.2 Alignment accuracy. 15.8.3 CASP and CAFASP. 15.9 Bibliographic notes. Appendix A: Basics in Mathematics, Probability and Algorithms. A.1 Mathematical Formulae and Notation. A.2 Boolean Algebra. A.3 Set Theory. A.4 Probability. A.4.1 Permutation and combination. A.4.2 Probability distributions. A.4.3 Expected value. A.5 Tables, Vectors and Matrices. A.6 Algorithmic Language. A.6.1 Alternatives. A.6.2 Loops. A.7 Complexity. Appendix B: Introduction to Molecular Biology. B.1 The Cell and the Molecules of Life: DNA–RNA Proteins. B.2 Chromosomes and Genes. B.3 The Central Dogma of Molecular Biology. B.4 The Genetic Code. B.5 Protein Function. B.5.1 The gene ontology. B.6 Protein Structure. B.7 Evolution. B.8 Insulin Example. B.9 Bibliographic notes. References. Index.

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Book SynopsisThis 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.Table of ContentsContributors xi Introduction 1 Philip W. Becraft Chapter 1 Large-Scale Mutant Analysis of Seed Development in Arabidopsis 5 David W. Meinke Introduction 5 Historical Perspective 5 Arabidopsis Embryo Mutant System 7 Large-Scale Forward Genetic Screens for Seed Mutants 7 Approaches to Mutant Analysis 8 Strategies for Approaching Saturation 10 SeedGenes Database of Essential Genes in Arabidopsis 11 Embryo Mutants with Gametophyte Defects 13 General Features of EMB Genes in Arabidopsis 14 Value of Large Datasets of Essential Genes 15 Directions for Future Research 16 Acknowledgments 17 References 17 Chapter 2 Embryogenesis in Arabidopsis: Signaling, Genes, and the Control of Identity 21 D. L. C. Kumari Fonseka, Xiyan Yang, Anna Mudge, Jennifer F. Topping, and Keith Lindsey Introduction 21 Cellular Events 21 Genes and Signaling – the Global Picture 23 Coordination of Genes and Cellular Processes: a Role for Hormones 25 Genes and Pattern 30 Conclusion and Future Directions 36 References 36 Chapter 3 Endosperm Development 43 Odd-Arne Olsen and Philip W. Becraft Introduction 43 Overview of Endosperm Structure and Development 43 Endosperm Cell Fate Specification and Differentiation 48 Genomic Resources 53 Transcriptional Profiling of Endosperm Development 54 Gene Imprinting in Cereal Endosperm 56 Conclusion 57 Acknowledgments 58 References 58 Chapter 4 Epigenetic Control of Seed Gene Imprinting 63 Christian A. Ibarra, Jennifer M. Frost, Juhyun Shin, Tzung-Fu Hsieh, and Robert L. Fischer Introduction 63 Genomic Imprinting and Parental Conflict Theory 63 Epigenetic Regulators of Arabidopsis Imprinting 65 Mechanisms Establishing Arabidopsis Gene Imprinting 69 Imprinting in the Embryo 74 Imprinting in Monocots 75 Evolution of Plant Imprinting 77 Conclusion 78 Acknowledgments 78 References 78 Chapter 5 Apomixis 83 Anna M. G. Koltunow, Peggy Ozias-Akins, and Imran Siddiqi Introduction 83 Biology of Apomixis in Natural Systems 84 Phylogenetic and Geographical Distribution of Apomixis 89 Inheritance of Apomixis 90 Genetic Diversity in Natural Apomictic Populations 93 Molecular Relationships between Sexual and Apomictic Pathways 94 Features of Chromosomes Carrying Apomixis Loci and Implications for Regulation of Apomixis 95 Genes Associated with Apomixis 96 Transferring Apomixis to Sexual Plants: Clues from Apomicts 97 Synthetic Approach to Building Apomixis 98 Synthetic Clonal Seed Formation 102 Conclusion and Future Prospects 103 References 103 Chapter 6 High-Throughput Genetic Dissection of Seed Dormancy 111 Jose M. Barrero, Colin Cavanagh, and Frank Gubler Introduction 111 Profiling of Transcriptomic Changes 113 Use of New Sequencing Platforms and Associated Techniques to Study Seed Dormancy 114 Visualization Tools 116 Coexpression Studies and Systems Biology Approaches 116 Mapping Populations for Gene Discovery 117 Perspective 118 Acknowledgments 119 References 119 Chapter 7 Genomic Specification of Starch Biosynthesis in Maize Endosperm 123 Tracie A. Hennen-Bierwagen and Alan M. Myers Introduction 123 Overview of Starch Biosynthetic Pathway 124 Genomic Specification of Endosperm Starch Biosynthesis in Maize 126 Conclusion 134 References 134 Chapter 8 Evolution, Structure, and Function of Prolamin Storage Proteins 139 David Holding and Joachim Messing Introduction 139 Prolamin Multigene Families 139 Endosperm Texture and Storage of Prolamins 143 Conclusion 154 References 154 Chapter 9 Improving Grain Quality: Wheat 159 Peter R. Shewry Introduction 159 Grain Structure and Composition 159 End Use Quality 161 Redesigning the Grain 163 Manipulation of Grain Protein Content and Quality 163 Manipulation of Grain Texture 167 Development of Wheat with Resistant Starch 168 Improving Content and Composition of Dietary Fiber 169 Wheat Grain Cell Walls 169 Conclusion 173 Acknowledgments 173 References 173 Chapter 10 Legume Seed Genomics: How to Respond to the Challenges and Potential of a Key Plant Family? 179 Mélanie Noguero, Karine Gallardo, Jérôme Verdier, Christine Le Signor, Judith Burstin, and Richard Thompson Introduction 179 Development of Genomics Tools 180 Applications of Genomics Tools to Legume Seed Biology 185 Future Challenges 192 References 193 Chapter 11 Cotton Fiber Genomics 203 Xueying Guan and Z. Jeffrey Chen Introduction 203 Cotton Fiber Development 204 Roles for Transcription Factors in Development of Arabidopsis Leaf Trichomes, Seed Hairs, and Cotton Fibers 204 Fiber Cell Expansion through Cell Wall Biosynthesis 208 Regulation of Phytohormones during Cotton Fiber Development 209 Cotton Fiber Genes in Diploid and Tetraploid Cotton 210 Roles for Small RNAs in Cotton Fiber Development 211 Conclusion 212 References 213 Chapter 12 Genomic Changes in Response to 110 Cycles of Selection for Seed Protein and Oil Concentration in Maize 217 Christine J. Lucas, Han Zhao, Martha Schneerman, and Stephen P. Moose Introduction 217 Background on the Illinois Long-Term Selection Experiment 217 Phenotypic Responses to Selection 219 Additional Traits Affected by Selection 220 Unlimited Genetic Variation? 221 Genetic Response to Selection: QTL Mapping in the Crosses of IHP x ILP and IHO x ILO 222 New Mapping Population: Illinois Protein Strain Recombinant Inbreds 223 Characterization of Zein Genes and Their Expression in Illinois Protein Strains 225 Contribution of Zein Regulatory Factor Opaque2 to Observed Responses to Selection in Illinois Protein Strains 227 Major Effect QTL May Explain IRHP Phenotype 228 Zein Promoter-Reporter Lines to Investigate Regulation of 22-kDa α-Zein Gene Expression in Illinois Protein Strains 229 Regulatory Changes in FL2-mRFP Expression When Crossed to Illinois Protein Strains 230 Regulation of FL2-mRFP 232 Acknowledgments 233 References 234 Chapter 13 Machine Vision for Seed Phenomics 237 Jeffery L. Gustin and A. Mark Settles Introduction 237 High-Energy Imaging: X-ray Tomography and Fluorescence 238 Optical Imaging: Visible Spectrum 240 Resonance Absorption: Infrared Spectrum 242 Resonance Emission: Nuclear Magnetic Resonance 245 Conclusion 246 Acknowledgments 246 References 246 Color plate section found between pages 42 and 43. Index 253

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Book SynopsisFully integrated and comprehensive in its coverage, Root Genomics and Soil Interactions examines the use of genome-based technologies to understand root development and adaptability to biotic and abiotic stresses and changes in the soil environment.Table of ContentsContributors ix Preface xv Chapter 1 Genomics of Root Development 3Boris Parizot and Tom Beeckman Introduction 3 Genomics of LRI 7 Rise of New Technologies to Understand Lateral Root Development 19 ComparativOmics, the Future 20 Acknowledgments 21 References 21 Chapter 2 The Complex Eukaryotic Transcriptome: Nonprotein-Coding RNAs and Root Development 29F. Ariel, A.B. Moreno, F. Bardou, and M. Crespi Genomic Approaches Reveal Novel Aspects of the Eukaryotic Transcriptome 29 The Role of RNA-Binding Proteins in npcRNA Metabolism and Activity 34 Nonprotein-Coding RNAs in Root Development 38 Future Perspectives 42 Acknowledgments 42 References 42 Chapter 3 Genomics of Auxin Action in Roots 49Elisabeth L. Williams and Ive De Smet Introduction 49 The Basis of Auxin Biology 49 Auxin Genomics in Root Development 55 Auxin and Root Hair Development 56 Auxin in Gravitropism 57 Auxin in LR Initiation 57 Conclusion 58 Acknowledgments 58 References 58 Chapter 4 Cell-Type Resolution Analysis of Root Development and Environmental Responses 63Jose R. Dinneny Introduction 63 Tools for Cell-Type Resolution Analysis 64 Analysis of Spatiotemporal Expression Patterns in the Arabidopsis Root 69 Analysis of Cell-Type-Specific Expression Patterns in the Rice Root 70 Cell-Type-Specific Analysis of Auxin 71 Cell-Type-Specific Analyses of Chromatin 71 Cell-Type-Specific Analyses of Responses to Environmental Change 72 Future Prospects 76 Acknowledgments 76 References 77 Chapter 5 Toward a Virtual Root: Interaction of Genomics and Modeling to Develop Predictive Biology Approaches 79Julien Lavenus, Leah Band, Alistair Middleton, Michael Wilson, Mikael Lucas, Laurent Laplaze, and Malcolm Bennett Assembling Root Gene Regulatory Pathways Using Genomics 79 Modeling Well-Characterized Small Root Gene Regulatory Networks 81 Building New Large-Scale Root Gene Regulatory Network 84 Multi-Scale Modeling Approaches to Study Root Growth and Development 88 Conclusions and Future Challenges 89 References 91 Chapter 6 Genomics of Root Hairs 93Hyung-Taeg Cho Genomics with Single Cells 93 Root Hair Development 94 High-Throughput Approaches for the Characterization of Root Hairs 95 Functions of Root Hair-Specific Genes 103 The Regulatory Pathway for Root Hair-Specific Genes 110 Perspective 111 Acknowledgments 111 References 112 Chapter 7 The Effects of Moisture Extremes on Plant Roots and Their Connections with Other Abiotic Stresses 117Laura M. Vaughn and Henry T. Nguyen Introduction 117 Low Water Availability—Drought 118 Excess Water—Soil Waterlogging, Flooding, and Submergence 128 Common Plant Root Responses to Abiotic Stressors 135 Continuing Challenges in Breeding for Plant Root Systems Tolerant to Abiotic Stress 137 Acknowledgments 138 References 138 Chapter 8 Legume Roots and Nitrogen-Fixing Symbiotic Interactions 145Philippe Laporte, Andreas Niebel, and Florian Frugier Genetic Dissection of the Legume Root System 145 Functional Genomic Analyses of Legume Nodules and Roots 155 Concluding Remarks 161 Acknowledgments 162 References 162 Chapter 9 What the Genomics of Arbuscular Mycorrhizal Symbiosis Teaches Us about Root Development 171Damien Formey, Cyril Jourda, Christophe Roux, and Pierre-Marc Delaux Forward and Reverse Genetics for Identifying Myc Mutants 172 Comparative Transcriptomics of AM Symbiosis: Toward Identification of Genes Involved in Root Development 175 Small RNAs in AM Symbiosis 181 Acknowledgments 183 References 183 Chapter 10 How Pathogens Affect Root Structure 189Michael Quentin, Tarek Hewezi, Isabelle Damiani, Pierre Abad, Thomas Baum, and Bruno Favery Introduction 189 Root Infection and Feeding Cell Ontogenesis 190 Genome-Wide Analysis of the Plant Response to Infection 192 The Plant Cytoskeleton Is Targeted by Root Pathogens 193 Root Pathogens Hijack Cell Cycle Regulators 194 Severe Cell Wall Remodeling Is Associated with Feeding Site Formation 195 Phytohormones Regulating Development and Defense May Control Feeding Site Formation 196 Role of miRNAs in Feeding Site Formation and Function 198 Nematode Effectors That Alter Root Cell Development during Parasitism 200 Conclusion 203 Acknowledgments 204 References 204 Chapter 11 Genomics of the Root—Actinorhizal Symbiosis 211Valerie Hocher, Nicole Alloisio, Laurent Laplaze, Didier Bogusz, and Philippe Normand Introduction 211 Actinorhizal Symbiosis 212 Development of Actinorhizal Nodules 214 Genomic Resources for Studying Actinorhizal Symbiosis 217 What Did We Learn from Actinorhizal Genomics? 220 Conclusion and Future Directions 222 Acknowledgments 222 References 223 Chapter 12 Plant Growth Promoting Rhizobacteria and Root Architecture 227Thais L.G. Carvalho, Paulo C.G. Ferreira, and Adriana S. Hemerly Introduction 227 Different Root Niches for PGPR Colonization 228 PGPR Recognition by Plants 229 Modulation of Root Growth and Architecture by PGPRs 232 Mechanisms of Plant Growth Promotion by PGPRs 234 Plant Genetic Programs Controlling Modulation of Root Growth and Architecture by PGPRs 240 Conclusions 241 Acknowledgments 242 References 242 Chapter 13 Translational Root Genomics for Crop Improvement 249Reyazul Rouf Mir, Mahendar Thudi, Siva K. Chamarthi, L. Krishnamurthy, Pooran M. Gaur, and Rajeev K. Varshney Introduction 249 Molecular Dissection of Root Trait 258 Molecular Breeding for Root Traits 259 Summary and Outlook 260 Acknowledgments 260 References 260 Index 265

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Book SynopsisThis edited volume spans the latest developments and applications in a new and exciting field of spectroscopy - Fourier Transform Infra-Red (FTIR) spectroscopy.Table of ContentsTheoretical Analyses of the Amide I Infrared Bands of GlobularProteins (H. Torii & M. Tasumi). Fourier Transform Infrared Spectroscopy of Enzyme Systems (J.Alben). Light-Induced Fourier Transform Infrared Difference Spectroscopy ofthe Primary Electron Donor in Photosynthetic Reaction Centers (E.Nabedryk). Equipment: Slow and Fast Infrared Kinetic Studies (F.Siebert). Ultrafast Infrared Spectroscopy of Biomolecules (B. Cohen & R.Hochstrasser). Infrared Spectroscopy of Nucleic Acids (J. Liquier & E.Taillandier). Fourier Transform Infrared Spectroscopy in the Study of HydratedLipids and Lipid Bilayer Membranes (R. Lewis & R.McElhaney). Fourier Transform Infrared Spectroscopic Studies of Cell SurfacePolysaccharides (K. Brandenburg & U. Seydel). Fourier Transform Infrared Spectroscopy of Biomembrane Systems (P.Haris & D. Chapman). What Can Infrared Spectroscopy Tell Us About the Structure andComposition of Intact Bacterial Cells? (D. Naumann, et al.). Biomedical Infrared Spectroscopy (M. Jackson & H.Mantsch). New Trends in Isotope-Edited Infrared Spectroscopy (H. Fabian, etal.). Index.

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Book SynopsisThe field of molecular biology has revolutionized the study of biology. The applications to medicine are enormous, ranging from diagnostic techniques for disease and genetic disorders, to drugs, to gene therapy. Focusing on the fundamentals of molecular biology and encompassing all aspects of the expression of genetic information, the Encyclopedia of Molecular Biology will become the first point of reference for both newcomers and established professionals in molecular biology needing to learn about any particular aspect of the field.

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Book SynopsisThis book describes comprehensive step-by-step protocols for the delineation of genetic amplification and histological detection techniques. Each procedure has been tested and validated for its sensitivity, precision, and reproducibility, and the authors give advice on the design of primers for PCR applications and on optimizing these protocols for use with plant, insect, and prokaryotic cells.Table of ContentsOverview; Review of the PCR Technique; Preliminary Solution-Based Reactions; Preparation of Glass Slides and Tissues; In Situ PCR: DNA and RNA Targets; Special Applications of In Situ Amplification; Hybridization Reactions; Validation and Controls; Materials and Methods; Select Biography; Appendices; Index; About the Authors.

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Book SynopsisThis text aims to address the need for investigators to understand the basic concepts, as well as the practical concerns, associated with the use of antisense oligonucleotides in modifying gene expression.Trade Review"This book will be most useful to workers in the field and advanced graduate students." --The Quarterly Review of Biology, June 1999Table of ContentsCHEMISTRY, OLD AND NEW. Oligonucleoside Methylphosphonates: Synthesis and Properties (P. Miller). Oligo(Nucleoside Phosphorothioate)s (P. Guga, et al.). Modified Oligodeoxynucleotides as Antisense Therapeutics (P. Seeberger & M. Caruthers). Novel Chemistry (K. Altmann, et al.). OLIGONUCLEOTIDE INTERNALIZATION, MECHANISM OF ACTION, AND NON-SEQUENCE SPECIFICITY. Cellular Uptake and Biodistribution of Oligodeoxynucleotides (B. Hanss, et al.). Use of Cationic Lipid Complexes for Antisense Oligonucleotide Delivery (C. Bennett). Nonantisense Effects of Antisense Oligonucleotides (L. Neckers & K. Iyer). Ribonuclease H-Mediated Antisense Effects of Oligonucleotides and Controls for Antisense Experiments (D. Tidd). SEQUENCE-SPECIFIC INHIBITION OF GENE EXPRESSION. The Development of C-5 Propyne Oligonucleotides as Inhibitors of Gene Function (W. Flanagan & R. Wagner). The Use of Antisense Oligonucleotides to Inhibit Expression of Isozymes of Protein Kinase C (N. Dean, et al.). BCR-ABL as a Target for Antisense Intervention (S. O'Brien & T. Smetsers). The NF-kB Transcription Factor (R. Narayanan). Disruption of the Map Kinase Signaling Pathway Using Antisense Oligonucleotide Inhibitors Targeted to RAS and RAF Kinase (B. Monia). Protein Kinase A-Directed Antisense Blockade of Cancer Growth: Single Gene-Based Therapeutic Approach (Y. Cho-Chung). Use of Antisense Oligonucleotides in the Central Nervous System: Why Such Success? (M. McCarthy). APPLIED ANTISENSE OLIGONUCLEOTIDE THERAPEUTICS. Perturbing Hematopoietic Cell Gene Expression with Oligodeoxynucleotides: Research and Clinical Applications (A. Gewirtz & M. Ratajczak). BCL2 (B. Jansen & B. Brown). Biological Activity of Guanosine Quartet-Forming Oligonucleotides (R. Rando & M. Hogan). OLIGONUCLEOTIDES AS ANTI-HIV AGENTS. Perspectives on Antisense Technology Against HIV (J. Gee, et al.). In Vivo Pharmacokinetics of Oligonucleotides (S. Agrawal). Early Clinical Trails with Gem 91, A Systemic Oligodeoxynucleotide (R. Martin). THERAPEUTIC OLIGONUCLEOTIDE DATA BASE: PHARMACOKINETICS, IMMUNE STIMULATION, AND USE AS ANTIRESTENOTIC AGENTS. Antisense Therapy to Inhibit Angioplasty Restenosis (L. Rabbani & W. Wang). Pharmacokinetics of Oligonucleotides: A Review of Current Knowledge and Issues for the Future (T. Wallace & P. Cossum). Leukocyte Stimulation by Oligodeoxynucleotides (A. Krieg). SELECTED OLIGODEOXYNUCLEOTIDE DEVELOPMENTAL TOPICS: SPLICING AND TRIPLEXES. Modification of Alternative Splicing of Pre-mRNA by Antisense Oligonucleotides (R. Kole). Gene-Targeted Triple-Helix-Forming Oligonucleotides (F. Svinarchuk & C. Malvy). Triplex-Forming Oligonucleotides for Genetic Manipulation: An Alternative View (A. Faruqi & P. Glazer). A REVIEW OF RIBOZYME TECHNOLOGY. Therapeutic Ribozymes: Principles, Applications, and Problems (J. Rossi). Index.

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Book SynopsisPlant Breeding Reviews is an ongoing series presenting state-of-the art review articles on research in plant genetics, especially the breeding of commercially important crops. Articles perform the valuable function of collecting, comparing, and contrasting the primary journal literature in order to form an overview of the topic. This detailed analysis bridges the gap between the specialized researcher and the broader community of plant scientists.Table of ContentsDedication: Arnel R. Hallauer, Scientist, Maize Breeder,Quantitative Geneticist (K. Lamkey). Molecules Involved in Self-Incompatibility in Flowering Plants (P.Dodds, et al.). Genetic Mosaics and Plant Improvement (M. Marcotrigiano & T.Gradziel). Quantitative Trait Loci: Separating, Pyramiding, and Cloning (Y.Xu). Doubled Haploid Breeding in Cereals (S. Raina). Spelt: Agronomy, Genetics, and Breeding (K. Campbell). Cowpea Breeding (A. Hall, et al.). Recurrent Selection in Soybean (K. Lewers & R. Palmer). Gene Action and Plant Breeding (D. Fasoula & V. Fasoula). Indexes.

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Book SynopsisIn Monte Carlo Methods in Chemical Physics: An Introduction to the Monte Carlo Method for Particle Simulations J. Ilja Siepmann Random Number Generators for Parallel Applications Ashok Srinivasan, David M. Ceperley and Michael Mascagni Between Classical and Quantum Monte Carlo Methods: Variational QMC Dario Bressanini and Peter J. Reynolds Monte Carlo Eigenvalue Methods in Quantum Mechanics and Statistical Mechanics M. P. Nightingale and C.J. Umrigar Adaptive Path-Integral Monte Carlo Methods for Accurate Computation of Molecular Thermodynamic Properties Robert Q. Topper Monte Carlo Sampling for Classical Trajectory Simulations Gilles H. Peslherbe Haobin Wang and William L. Hase Monte Carlo Approaches to the Protein Folding Problem Jeffrey Skolnick and Andrzej Kolinski Entropy Sampling Monte Carlo for Polypeptides and Proteins Harold A. Scheraga and Minh-Hong Hao Macrostate Dissection of Thermodynamic Monte Carlo Integrals Bruce W. Church, Alex Ulitsky, and David Shalloway Simulated AnTable of ContentsAn Introduction to the Monte Carlo Method for Particle Simulations (J. Siepmann). Random Number Generators for Parallel Applications (A. Srinivasan, et al.). Between Classical and Quantum Monte Carlo Methods: "Variational" QMC (D. Bressanini & P. Reynolds). Monte Carlo Eigenvalue Methods in Quantum Mechanics and Statistical Methods (M. Nightingale & C. Umrigar). Adaptive Path-Integral Monte Carlo Methods for Accurate Computation of Molecular Thermodynamic Properties (R. Topper). Monte Carlo Sampling for Classical Trajectory Simulations (G. Peslherbe, et al.). Monte Carlo Approaches to the Protein Folding Problem (J. Skolnick & A. Kolinski). Entropy Sampling Monte Carlo for Polypeptides and Proteins (H. Scheraga & M. Hao). Macrostate Dissection of Thermodynamic Monte Carlo Integrals (B. Church, et al.). Simulated Annealing-Optimal Histogram Methods (D. Ferguson & D. Garrett). Monte Carlo Methods for Polymeric Systems (J. de Pablo & F. Escobedo). Thermodynamic-Scaling Methods in Monte Carlo and Their Application to Phase Equilibria (J. Valleau). Semigrand Canonical Monte Carlo Simulation: Integration Along Coexistence Lines (D. Kofke). Monte Carlo Methods for Simulating Phase Equilibria of Complex Fluids (J. Siepmann). Reactive Canonical Monte Carlo (J. Johnson). New Monte Carlo Algorithms for Classical Spin Systems (G. Barkema & M. Newman). Indexes.

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Book SynopsisThis volume describes the complete process of analyzing protein sequences by mass spectrometry including sample preparation, analysis, and data interpretation at a practical level. It provides sufficient experimental detail to carry out the experiments and consistently achieve good results.Trade Review"[the authors] present their own laboratory-tested protocols for the analysis of a wide variety of samples, providing sufficient detail for duplication of their methods..." (SciTech Book News Vol. 25, No. 2 June 2001) "...an informative, well-written and well-illustrated book with a large number of useful references.... It should prove invaluable to anyone working in the field of protein sequencing." (Spectroscopyeurope.com)Table of ContentsAn Introduction to Protein Sequencing Using Tandem Mass Spectrometry. The Primary Structure of Proteins and a Historical Overview of Protein Sequencing. Fundamental Mass Spectrometry. Collisionally Induced Dissociation of Protonated Peptide Ions and the Interpretation of Product Ion Spectra. Basic Polyacrylamide Gel Electrophoresis. The Preparation of Protein Digests for Mass Spectrometric Sequencing Experiments. Mass Spectrometric Analysis of Tryptic Digests. Protein Identification by Database Searching. Sequence Analysis of Novel Proteins. The Characterization of Post-Translationally Modified Proteins Using Tandem Mass Spectrometry. Index.

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Book SynopsisA unique exploration of the principles and methods underlying the Human Genome Project and modern molecular genetics and biotechnology-from two top researchers In Genomics, Charles R. Cantor, former director of the Human Genome Project, and Cassandra L. Smith give the first integral overview of the strategies and technologies behind the Human Genome Project and the field of molecular genetics and biotechnology. Written with a range of readers in mind-from chemists and biologists to computer scientists and engineers-the book begins with a review of the basic properties of DNA and the chromosomes that package it in cells. The authors describe the three main techniques used in DNA analysis-hybridization, polymerase chain reaction, and electrophoresis-and present a complete exploration of DNA mapping in its many different forms. By explaining both the theoretical principles and practical foundations of modern molecular genetics to a wide audience, the book brings the scientific communiTrade Review"this book is to be highly recommended..."(Human Genetics, May 2000)Table of ContentsDNA Chemistry and Biology. A Genome Overview at the Level of Chromosomes. Analysis of DNA Sequences by Hybridization. Polymerase Chain Reaction and Other Methods for In Vitro DNA Amplification. Principles of DNA Electrophoresis. Genetic Analysis. Cytogenetics and Pseudogenetics. Physical Mapping. Enhanced Methods for Physical Mapping. DNA Sequencing: Current Tactics. Strategies for Large-Scale DNA Sequencing. Future DNA Sequencing Without Length Fractionation. Finding Genes and Mutations. Sequence-Specific Manipulation of DNA. Results and Implications of Large-Scale DNA Sequencing. Appendix. Index.

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Book SynopsisAs with all biotechnologies in the midst of rapid growth, nutrigenomics faces ethical, legal, and social implications that are likely to affect the public and the medical community. This title identifies and examines the anticipated risks and expected benefits of nutrigenomics from an ethical perspective.Trade Review"…a worthy acquisition for any medical library…along with students and instructors in nutrition and health care." (CHOICE, June 2007) "This concise overview of nutritional genomics covers a variety of topics surrounding this controversial topic." (Doody's Health Services)Table of ContentsPreface. Acknowledgments. 1 NUTRITIONAL GENOMICS: OPPORTUNITIES AND CHALLENGES. 1.1 Introduction. 1.2 What is Nutritional Genomics? 1.3 Methodology and Approach of this Book. 1.4 Opportunities and Challenges for Nutrigenomics. 1.4.1 Improved health. 1.4.2 Personalized dietary advice. 1.4.3 Improved diet. 1.4.4 More development of health-enhancing food products. 1.4.5 Consumer empowerment. 1.4.6 Reducing health disparities. 1.4.7 Health care savings. 1.5 Challenges and a Road Map of This Book. References. 2 THE SCIENCE OF NUTRIGENOMICS AND NUTRIGENETICS. 2.1 Introduction. 2.2 The Scientific Context. 2.2.1 Nutrigenomics. 2.2.2 Nutrigenetics. 2.3 The Case of MTHFR. 2.4 Room for Improvement. 2.4.1 Study design. 2.4.2 Epigenetics. 2.4.3 SNPs and haplotypes. 2.4.4 Dietary intake assessment. 2.4.5 Biomarkers. 2.4.6 Susceptibility and predictions. 2.4.7 Analytical and clinical validity. 2.4.8 Clinical utility. 2.5 Science and Technology Assessment. 2.6 Conclusion. References. 3 THE ETHICS OF NUTRIGENOMIC TESTS AND INFORMATION. 3.1 Introduction. 3.2 Ethical Principles. 3.3 Nutrigenomics Testing in the Clinical Setting. 3.3.1 Informed consent. 3.3.2 Confidentiality. 3.3.3 Secondary information. 3.3.4 Families. 3.3.5 Genetic testing of children and adolescents. 3.4 Use of Nutrigenomics Information for Research. 3.5 Use of Nutrigenomics Information by Private Third Parties. 3.5.1 Insurance. 3.5.2 Employment. 3.5.3 Legal and social responses to fears of discrimination. 3.6 Conclusion. References. 4 ALTERNATIVES FOR NUTRIGENOMIC SERVICE DELIVERY. 4.1 Introduction. 4.2 Considerations for Nutrigenomic Service Delivery. 4.2.1 Strength of the science. 4.2.2 Regulatory environment. 4.2.3 Human resource capacity and professional competence. 4.2.4 Funding policy. 4.2.5 Professional politics and culture. 4.2.6 Consumers and patients. 4.3 Four Alternative Models. 4.3.1 Consumer model. 4.3.2 Health practitioner model. 4.3.3 Blended models. 4.3.4 Public health model. 4.4 Conclusion. References. 5 NUTRIGENOMICS AND THE REGULATION OF HEALTH CLAIMS FOR FOODS AND DRUGS. 5.1 Introduction. 5.1.1 Genetic tests, service delivery, and genetic antidiscrimination. 5.2 Food Categories: Functional Foods, Nutraceuticals, Medicinal Foods, and Dietary Supplements. 5.2.1 Functional foods. 5.2.2 Nutraceuticals. 5.2.3 Medical or medicinal foods. 5.2.4 Dietary supplements. 5.3 Health-Related Claims Associated with Foods Compared to Drugs. 5.3.1 Structure–function claims. 5.3.2 Health claims. 5.3.3 Medical food claims. 5.3.4 Disease risk reduction claims. 5.4 Nutrigenomic Information and the Regulation of Foods Compared to Drugs. 5.4.1 The regulation of foods. 5.4.2 The regulation of drugs. 5.5 Food and Drug Regulations in Japan, the United States, and Canada. 5.5.1 Japan. 5.5.2 United States. 5.5.3 Canada. 5.6 Conclusion. References. 6 NUTRIGENOMICS: JUSTICE, EQUITY, AND ACCESS. 6.1 Introduction. 6.2 Industrialized Country Context. 6.2.1 Individualized nutrigenomic testing. 6.2.2 Population-based nutrigenomics. 6.3 Developing Country Context. 6.3.1 Individualized nutrigenomic testing. 6.4 Nutrigenomics and Intellectual Property. 6.4.1 An issue of access to scientific information. 6.5 Conclusion. References. 7 CONCLUSIONS AND RECOMMENDATIONS. 7.1 Introduction. 7.1.1 Nutrigenomic science. 7.1.2 Nutrigenomics and health information management. 7.1.3 Nutrigenomic service delivery. 7.1.4 Regulation of nutrigenomics. 7.1.5 Access and equity. 7.2 A Final Word. Index.

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Book SynopsisThis advanced textbook teaches the theory and practice of molecular genetic analysis to senior undergraduates and graduates studying genetics, molecular biology and cell biology. It uses a case study approach, with the yeast Saccharomyces as the model genetic organism, to explain the theory and practice of molecular genetic analysis.Trade Review"...Students new to yeast genetics and those of us keeping abreast of fusing disciplines should add this publication to our reading list..." (The Biochemist, 4 October 2002) "... useful addition to the literature..." (Biologist, Vol.50. No.2, 2003) "...a valuable addition to the reference library of any research laboratory at universities, research institutes and the industry." (Acta Biotechnologica, Vol.23, No.2-3, 2003) "...The aim of every teacher is to inspire students to move down from the stands, step up to the plate, and start hitting on their own. This book is a wonderful tool to help in that quest." (Cell Biology Education, 16 June 2003)Table of ContentsIntroduction. SECTION I: SACCHAROMYCES CEREVISIAE AS A GENETIC RESEARCH ORGANISM. Saccharomyces cerevisiae As a Genetic Model Organism Techniques in Cell and Molecular Biology Saccharomyces Cell Structure. SECTION II: TECHNIQUES OF GENETIC ANALYSIS. Mutant Hunts - To Select or to Screen (perhaps even by brute force). Complementation Analysis: How many Genes are Involved? Epistasis Analysis. Gene Isolation and Analysis of Multiple Mutant Alleles. Suppression Analysis. Enhancement and Synthetic Phenotypes Two-hybrid Analysis Advanced Concepts in Molecular Genetic Analysis Genomic Analysis SECTION III: CASE STUDIES FROM THE SACCHAROMYCES GENETIC LITERATURE. Case Study I: Glucose Sensing and signaling Mechanisms in Saccharomyces. Case Study II: Secretion, Exocytosis and Vesicle Trafficking in Saccharomyces. Case Study III: The Cell Division Cycle of Saccharomyces. Case Study IV: Mating-type Pheromone Response Pathway of Saccharomyces. Index.

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Book SynopsisGene Therapy Technologies, Applications and Regulations From Laboratory to Clinic Edited by Anthony Meager Division of Immunobiology, The National Institute for Biological Standards and Control, South Mimms, UK The development of gene-based technologies has been rapid over the past decade and has consequently resulted in a surge of interest in human gene therapy, the deliberate transfer of genes to somatic cells to cure or alleviate disease symptoms. Hundreds of clinical protocols involving variously designed vectors for efficient gene transfer have been developed. However, the use of such complex ''gene medicines'' containing potentially heritable genes has raised numerous concerns regarding quality, efficacy and safety. Encompassing recent developments in the field and addressing current concerns this book: * surveys many of the current technologies for preparing vectors for use in gene therapy protocols * reviews the application of gene-mediated therapies to a range of medicTrade Review"It succeeds in putting together, possibly for the first time, gene therapy vectors, clinical applications, and regulatory production issues." --Human Genetics, April 2000Table of ContentsCationic Liposomes for Gene Therapy Applications (J. Clancy & E. Sorscher). DNA Condensation and Receptor-mediated Gene Transfer (A. Ziady & T. Ferkol). Retroviral Vectors (W. Günzburg & B. Salmons). Lentiviral Vectors (A. Lever). Adenoviral Vectors (S. Connelly). Adeno-associated Viral Vectors (T. Flotte & B. Carter). Advances in Engineering HSV Vectors for Gene Transfer to the Nervous System (M. Soares, et al.). Mammalian Artificial Chromosomes: Prospects for Gene Therapy (T. Ebersole & C. Farr). Gene Therapy for Severe Combined Immunodeficiency (A. Thrasher, et al.). Gene Therapy for Haemophilia (R. Hoeben, et al.). Cystic Fibrosis: Gene Therapy Approaches (N. Caplen). Therapeutic Approaches to Haemoglobinopathies (Y. Beuzard). Gene Therapy Approaches to Duchenne Muscular Dystrophy (S. Murphy & G. Dickson). Lysosomal Storage Diseases (L. Lashford, et al.). Prospects for Gene Therapy of HIV Infections and AIDS (C. Lee, et al.). The Developemnt of the Regulatory Process in Europe for Biological Medicines: How it Affects Gene Therapy Products (A. Meager, et al.). Developement and Regulation of Gene Therapy Drugs in Germany (K. Cichutek). The Transfer of Technology from the Laboratory to the Clinic: In Process Controls and Final Product Testing (F. Borellini & J. Ostrove). Good Laboratory Practice in the Research and Development Laboratory (A. Shepherd). Facilities for Large-scale Production of Vectors Under GMP Conditions (J. Boyd). Addendum. Index.

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Book SynopsisCoumarins: Biology, Applications and Mode of Action predominantly focuses on the parent compound, coumarin, and its main metabolite in humans, 7-hydroxycoumarin. It describes in detail every facet of these compounds including history, toxicology, chemistry, metabolism, analysis, clinical, veterinary and other applications, their roles as immunomodulatory agents and speculates on their mode of action.Table of ContentsPartial table of contents: History of the Development and Applications of Coumarin and Coumarin-related Compounds (I. Weinmann). The Chemistry and Occurrence of Coumarins (G. Keating & R. O'Kennedy). Coumarin as an Immunomodulator (G. Zlabinger). Mode of Action of Coumarin in the Treatment of Thermal Injuries (N. Piller). The Potential Role of Coumarins in the Therapy of Prostate Cancer (J. Mohler, et al.). Clinical and Biological Observations Associated with Coumarins (R. Thornes). Analysis of Coumarins (D. Bogan, et al.). Suggested Modes of Action of Coumarins and Some Comments on their Significance (R. O'Kennedy & R. Thornes). Index.

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Book SynopsisPopulation Genetics of Multiple Loci F.B. Christiansen University of Aarhus, Denmark "This is a very beautiful and powerful study of an area that Christiansen has dominated for many years. " - Marcus Feldman, Stanford University, USA Population genetics thrives on the constant interaction between theoretical and empirical knowledge.Trade Review"...a significant contribution to mathematical population genetics...recommended" --Monatshefte fur Mathematik, Vol 131/2, 2000 "This book makes an excellent contribution." --Genetical Research, Vol 75, 2000Table of ContentsInteractions among Genes. RECOMBINATION AND SEGREGATION. Random Mating: Sexes Equal. Random Mating: Sex Difference. Inbreeding: Partial Selfing. Migration and Mixing. Phenotypic Variation. SELECTION. Viability Selection. Symmetric Viability Selection. Fertility Selection. Mutation and Selection. Migration and Selection. Evolution of Recombination. Glossary. References. Index.

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Book SynopsisTalk of genetically engineered organisms (GEOs) has moved from the hushed corridors of life science corporations to the front pages of major newspapers. This book examines these issues from the diverse perspectives of sociology, geography, law, environmental studies and political science.Table of ContentsList of Illustrations Acknowledgments Introduction. Biotechnology in the New Millennium: Technological Change, Institutional Change, and Political Struggle Rachel A. Schurman 1. Wonderful Potencies? Deep Structure and the Problem of Monopoly in Agricultural Biotechnology William Boyd 2. Building a Better Tree: Genetic Engineering and Fiber Farming in Oregon and Washington W. Scott Prudham 3. The Migration of Salmon from Nature to Biotechnology Dennis Doyle Takahashi Kelso 4. Making Biotech History: Social Resistance to Agricultural Biotechnology and the Future of the Biotechnology Industry Rachel A. Schurman and William A. Munro 5. Eating Risk: The Politics of Labeling Genetically Engineered Foods Julie Guthman 6. The Global Politics of GEOs: The Achilles' Heel of the Globalization Regime? Frederick H. Buttel 7. Biotech Battles: Plants, Power, and Intellectual Property in the New Global Governance Regimes Kathleen McAfee 8. From Molecules to Medicines: The Use of Genetic Resources in Pharmaceutical Research Astrid J. Scholz 9. The Brave New Worlds of Agricultural Technoscience: Changing Perspectives, Recurrent Themes, and New Research Directions in Agro-Food Studies David Goodman Conclusion. Recreating Democracy Dennis Doyle Takahashi Kelso Glossary Contributors Bibliography Index

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Book SynopsisEpigenetics, the study of heritable changes in gene expression, has been heralded as one of the most promising new fields of scientific inquiry. Current large-scale studies selectively draw on epigenetics to connect behavioral choices made by pregnant people, such as diet and exercise, to health risks for future generations. As the first ethnography of its kind, Weighing the Future examines the sociopolitical implications of ongoing pregnancy trials in the United States and the United Kingdom, illuminating how processes of scientific knowledge production are linked to capitalism, surveillance, and environmental reproduction. Natali Valdez argues that a focus on individual behavior rather than social environments ignores the vital impacts of systemic racism. The environments we imagine to shape our genes, bodies, and future health are intimately tied to race, gender, and structures of inequality. This groundbreaking book makes the case that science, and how we translate it, is a reproductive project that requires feminist vigilance. Instead of fixating on a future at risk, this book brings attention to the present at stake.Trade Review"A ground-breaking book, both subtle and razor-sharp in its analysis. It provides an immensely valuable critique of the workings of epigenetic foreclosure in pregnancy trials." * Medical Anthropology Quarterly *Table of ContentsContents List of Illustrations Acknowledgments Introduction: Weighing the Future Part I 1. Epistemic Environments: Reproducing Solutions to Past, Present, and Future Maternal Health 2. Un/Altered: The Durability of Individualized Interventions for Multidimensional Illness Part II 3. Politics of Recruitment: How Fatness, Race, and Risk Shape Contemporary Pregnancy Trials 4. Pregnant Narratives: Experiencing Lifestyle Interventions Part III 5. Environmental Animations: What Counts as the Maternal Environment? 6. Prospecting Pregnancies: Data, Time, and Speculative Value Conclusion: The Afterbirth of Foreclosure Epilogue: [The Future] Is Composed of Nows Notes References Index

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Book SynopsisEpigenetics, the study of heritable changes in gene expression, has been heralded as one of the most promising new fields of scientific inquiry. Current large-scale studies selectively draw on epigenetics to connect behavioral choices made by pregnant people, such as diet and exercise, to health risks for future generations. As the first ethnography of its kind, Weighing the Future examines the sociopolitical implications of ongoing pregnancy trials in the United States and the United Kingdom, illuminating how processes of scientific knowledge production are linked to capitalism, surveillance, and environmental reproduction. Natali Valdez argues that a focus on individual behavior rather than social environments ignores the vital impacts of systemic racism. The environments we imagine to shape our genes, bodies, and future health are intimately tied to race, gender, and structures of inequality. This groundbreaking book makes the case that science, and how we translate it, is a reproduTrade Review"A ground-breaking book, both subtle and razor-sharp in its analysis. It provides an immensely valuable critique of the workings of epigenetic foreclosure in pregnancy trials." * Medical Anthropology Quarterly *Table of ContentsContents List of Illustrations Acknowledgments Introduction: Weighing the Future Part I 1. Epistemic Environments: Reproducing Solutions to Past, Present, and Future Maternal Health 2. Un/Altered: The Durability of Individualized Interventions for Multidimensional Illness Part II 3. Politics of Recruitment: How Fatness, Race, and Risk Shape Contemporary Pregnancy Trials 4. Pregnant Narratives: Experiencing Lifestyle Interventions Part III 5. Environmental Animations: What Counts as the Maternal Environment? 6. Prospecting Pregnancies: Data, Time, and Speculative Value Conclusion: The Afterbirth of Foreclosure Epilogue: [The Future] Is Composed of Nows Notes References Index

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Book SynopsisThe 11th Hour Series is designed to be used when a textbook doesn''t make sense, when the course content is tough, or when you just want a better grade in the course. The authors cut through the fluff, get to what you need to know, and then help you understand it. Clinical correlations or everyday applications include examples from the real world to help students understand key concepts more readily. Dedicated web page, there 24 hours a day, will give extra help, tips, warnings of trouble spots, extra visuals and more. A quick check on what background students will need to apply helps equip them to conquer a topic. The most important information is highlighted and explained, showing the big picture and eliminating the guesswork. After every topic and every chapter, lots of opportunity for drill is provided in every format, multiple choice, true/false, short answer, essay. An easy trouble spot identifier dTable of Contents11th Hour Guide to Success. Preface. DNA: The Genetic Material. From DNA to RNA: The Process of Transcription. From Messenger RNA to Protein: The Process of Translation. Mutations.. MIDTERM EXAM. Regulation of Gene Expression in Bacteria. Regulation of Gene Expression in Eukaryotes. Recombinant DNA.. FINAL EXAM. Index.

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Book SynopsisIn a book that promises to change the way we think and talk about genes and genetic determinism, Evelyn Fox Keller, one of our most gifted historians and philosophers of science, provides a powerful, profound analysis of the achievements of genetics and molecular biology in the twentieth century, the century of the gene.Trade ReviewSometimes, with great luck, you happen on a book that is wondrous in its ability to take a topic apart and explain it lucidly. Sometimes, the joy is to be found in the way an author is able to put those pieces back together. And sometimes, it is the elegance both of analysis and synthesis that makes a book truly great. The Century of the Gene, by Evelyn Fox Keller, reaches that level and then vaults past it into the category of rare volumes that are unforgettable. This is the sort of book that, once found, can never be relinquished. The breadth of intellect is so strong, the importance of the subject so acute, the language so beautifully wrought, that you find yourself drawn to read it again and again, only to find a new dimension each time… In fact—and this is one of the most intense pleasures of the book—Fox Keller’s explanation of how the thinking about the gene has evolved over the past century is both as simple and as complex as the gene itself. Her topic is also her metaphor. -- Alanna Mitchell * Globe and Mail *[Keller] is at the same time enthusiastic about the light that has been shed on the nature of life and critical of the oversimplifications that she feels have been made… She is well qualified to draw [her conclusions]. She has an admirable grasp of recent research in molecular genetics…and has read widely in the history of genetics… She has also thought hard about both the history and the current state of the subject… We need Keller’s voice. -- John Maynard Smith * New York Review of Books *[Keller writes] with a peculiar, elegant blend of linguistic skill, historical reflection, conceptual analysis and synthetic outlook, and with the generously encompassing gesture of someone who participated in and followed the developments of molecular biology and genetics over several decades… Keller sees her book as a plea for scientific and political realism. Indeed it is. But it is more than just that. It engages historians, philosophers, scientists and the educated lay public alike in a discussion that self-consciously resists the temptation of polemics…about the conceptual and experimental developments in life sciences during the course of the twentieth century. -- Hans-Jorg Rheinberger * American Scientist *[In] a lucid analysis of the mind-boggling advances in genetics and molecular biology in the twentieth century, Keller says it’s time to change the way we think about the gene. * Atlanta Journal-Constitution *The Century of the Gene is unusual among popular histories of science in that it largely avoids both technical minutiae and sociological or historical background. Rather, it is almost exclusively a history of ideas, even a history of just one idea—the concept of the gene. Keller’s aim, one that she achieves admirably, is to give readers just enough information about discoveries in molecular biology so that they can appreciate the consequence of those discoveries for our understanding of what genes are. -- Austin L. Hughes * Commonweal *The very word ‘gene’ symbolizes our self-obsessed culture. All we do, know, learn, and sacrifice is somehow explained away by appealing to this tiny and elusive biological structure. Yet according to at least one scientist, it’s time for us to shift our focus and branch out to other possible, and perhaps more suitable, interpretations of our natures. In The Century of the Gene, Evelyn Fox Keller urges the genomic society to break free of the linguistic (and therefore conceptual) restraints and the historical baggage inherent in the use of the term ‘gene’—a break she sees as imperative and, ultimately, inevitable. * Rain Taxi *The Century of the Gene, by Evelyn Fox Keller, not only provides an insightful overview of the role of a gene in the creation of an organism but also traces the history of our perception of the gene’s role in that creation… Keller provides several concise figures that allow a person with minimal knowledge of molecular biology to understand the basics of what a gene is and how it functions within the body. This book also captures past and present thought from critical scientists and philosophers who have contributed to our current understanding of molecular biology… [The] overall outlook provides a new understanding of the dynamics of gene regulation and predicts that a new era in which we can understand how to control our own evolution is approaching. From a research perspective, we hope to be able to use this knowledge to help correct medical disorders. However, from a moral and religious perspective, many new boundaries are being crossed. Read this book. You will challenge yourself in trying to figure out what the future will be. -- Dr. John J. Nemunaitis * Baylor University Medical Center Proceedings *Evelyn Fox Keller’s The Century of the Gene is a clear, concise and challenging contribution to our understanding of the history of genetics and of modern biology more generally. There can be no doubt that Keller’s analysis of ‘gene talk,’ that is, her analysis of the variety of contexts and ways in which biologists have deployed the word ‘gene’, is more than timely. -- Paolo Palladino * British Journal for the History of Science *The notes…are detailed and useful… Her book is a thought-provoking review of the history and philosophy of genetics and genomics. -- Victor A. McKusick * Bulletin of the History of Medicine *Among the many books on cloning and genetic therapy, The Century of the Gene, an overview of current research and thought by philosopher of science Evelyn Fox Keller, seems especially promising. -- Martin Levin * Globe and Mail *Although brief, this book is packed with good things. The historical analysis is unfailingly interesting, the scientific reportage lucid. Best of all, perhaps, is the sheer excitement the book communicates about the state of genetics and the need to get that state into proper focus, using all the intellectual resources going… I am impressed by the diversity of gene concepts within what Keller sees…as a single concept… Her own contribution to the case for conceptual unity is an important one. -- Gregory Radick * Heredity *[This] book opens up exciting possibilities of new ways of thinking about biological organization, which are not overshadowed by traditional language or by ‘historical baggage’… Evelyn Fox Keller has put down a marker in this important book. The time has come for us to take on a richer understanding of genetics and with it some new language and concepts. -- Sue Weldon * New Genetics and Society *Once again, with the prescience her readers have come to expect from her, Evelyn Fox Keller is ahead of the curve in identifying and illuminating new questions for our attention… [Keller] addresses myths and misunderstandings that surround the concept of a gene… [Her] informed and entertaining volume takes the reader on a quick historical tour through the gestation and birth of molecular genetics and then, with a few helpful illustrations, into current perceptions of gene structure and function in sufficient detail to explain her critical arguments… Her fascinating tale should raise your interest in the biological mysteries that remain. -- Cecily Cannan Selby * Radcliffe Quarterly *For anyone fascinated by biology, the technology used to explore it, and the medical promises implicit in the information contained within our genetic material, Keller’s overview makes for clear, engaging, and exciting reading. -- Tom Bowden * Tech Directions *Keller traces the evolution of genetic science over the course of the twentieth century, during which Gregor Mendel’s theories of inheritance were rediscovered, the structure of DNA revealed, and the human genome mapped—world-changing achievements that have taken our understanding of genetics far beyond the level at which the now too-simple word gene was coined. -- Donna Seaman * Booklist *Top-drawer science reading. -- Ray Olson * Booklist *In this tight, clearly written survey, Keller does a wonderful job of explaining and demonstrating how our knowledge of genetics has accumulated… In her articulate and insightful…history of genetics and molecular biology, she suggests that most of our common assumptions about genes are either too simplistic or simply incorrect. * Publishers Weekly *In The Century of the Gene, Evelyn Keller gathers together her considerable skills as a mathematician, physicist, historian and philosopher and applies them to the central problem of the last 100 years of biology, namely the relation of the genes to the building of an organism. The scholarship is masterly, not only because of her wide reading of the literature, but her deep, penetrating understanding of what she reads. To cap it all she writes clearly and elegantly so that the book is a pleasure to read. This is a conspicuously intelligent book. -- John Bonner, Princeton UniversityEvelyn Keller has the disturbing ability to make you think again from scratch about things you thought you had already understood. It is a long time since I have thought so hard about fundamental problems in genetics as I did when reading The Century of the Gene. -- Richard Lewontin, Harvard UniversityGenes have captured the scientific and popular imagination. But in The Century of the Gene, Evelyn Fox Keller provides us with a powerful analysis of the limits of the gene as an explanatory concept. Indeed, the success of molecular biology and greater understanding of biological development have exposed the wide gap between genetic information and biological meaning, undermining the very concept of the gene. Yet gene talk with all its historical baggage persists in shaping both science and popular perceptions. Keller argues convincingly for a new language, for new concepts that will enable us to deal with the real complexity of biological organization. This is a critically important book to be very widely read. -- Dorothy Nelkin, New York UniversityIn this elegantly written book, Evelyn Fox Keller tells the fascinating story of how the heuristic power of genetic experimentation interacts with the narrative power of the word ‘gene.’ Both are built on and reinforce each other. I never saw an equally convincing and well informed narrative on how language mediates the interaction between experimental research and its social context. -- Günter P. Wagner, Yale UniversityTable of Contents* Introduction: The Life of a Powerful Word *1. Motors of Stasis and Change: The Regulation of Genetic Stability *2. The Meaning of Gene Function: What Does a Gene Do? *3. The Concept of a Genetic Program: How to Make an Organism *4. Limits of Genetic Analysis: What Keeps Development on Track? * Conclusion: What Are Genes For? * Notes * References * Acknowledgments * Index

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Book SynopsisRepresents an original look at the biotechnology research in the wake of the mapping of the human genome. Presenting a series of interviews with various key players in Celera Diagnostics, this title opens a window on the complexity of corporate scientific innovation.Trade Review"The strength of Rabinow's approach is that we hear the voices of scientists at work. Not only do they describe the science itself, but they also provide their perception of its importance. Rabinow is a skillful interviewer who elicits motivation from his subjects. We are given a rare glimpse into the professional lives of the participants and the energy that drives their scientific and personal decisions."--William A. Haseltine, Science "Paul Rabinow is the leading anthropologist of contemporary biotechnology... It would be easy for him to use his authority to apportion praise and blame, or to develop a magisterial contribution to anthropological theory. But [he] resists coming to artificially neat conclusions... This book's compelling insights should be required reading for everyone who pictures themselves a scientific entrepreneur, or who cares about the state of contemporary science."--Christine Hine, New Scientist "A Machine to Make a Future by Paul Rabinow and Talia Dan-Cohen, a book as impressive as the previous two works in Rainbow's biotechnology trilogy ... Is an in-depth and well-constructed anthropological chronicle of this new Californian scientific enterprise. With his student Talia Dan-Cohen, Rabinow has provided a highly readable account of Celera Diagnostics' formative period ... through a series of lengthy but insightful interviews with the original researchers."--Xuefeng Bruce Ling, The Journal of Clinical Investigation "This book is a good choice for even a layperson to get a grip on the current developments in the world of genomics and how these diagnostics can help health and health care."--Rukmini Rajagopalan, Current Science "This book may signal an entirely new way of viewing scientific innovation in a globalized, competitive environment, integrating new technologies and methodological insights."--Biology Digest "[Paul Rabinow's] interviews are expertly conducted and provide a rich resource that can be mined from a variety of perspectives--including scientific, business, legal, ethical, and philosophical."--George Jannas, Quarterly Review of BiologyTable of ContentsOverture: A MACHINE TO MAKE A FUTURE 1 Chapter One: ENDING AND BEGINNING 13 Chapter Two: THE STATE OF THINGS AT CELERA DIAGNOSTICS, EXPLAINED TO INVESTORS AND TO ANTHROPOLOGISTS 38 Chapter Three: THE MACHINERY AND ITS STEWARDS 62 Chapter Four: ETHICAL AND SOCIAL CONSULTANCY 97 Chapter Five: CONFIDENCE AND TRUST 111 Chapter Six: MODELS ORIENT, TECHNOLOGIES PERFORM, SAMPLES SPEAK (OR VICE VERSA) 144 Chapter Seven: SUMMER 2003 169 Illustrations 187 Appendix: A CORPORATE HISTORY 189 Notes 191 Glossary 195

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Book SynopsisJohn Tyler Bonner, one of our most distinguished and insightful biologists, here challenges a central tenet of evolutionary biology. In this concise, elegantly written book, he makes the bold and provocative claim that some biological diversity may be explained by something other than natural selection. With his customary wit and accessible style,Trade Review"[I]ncredibly useful ... refreshingly honest ... witty and engaging."--Tiffany Taylor, Times Higher Education "[F]orthright, informal, and humorous. His reminder that not every trait has a biologically adaptive function is a welcome lesson, as is his self-deprecating description of his ideas as just another 'just-so' story... [A] call to the biologists who take over from him to do more research to confirm or to refute the often surprising ideas here."--Rob Hardy, Commercial Dispatch "[Bonner] provides a well-written, well-documented collection of evidence suggesting randomness as a primary engine behind natural selection... This is an excellent essay, valuable to a wide audience. Evolution is an important, timely topic, making Bonner's work a worthy contribution."--Choice "[T]he book provides a careful analysis of the relationship between randomness and size in evolution and makes a good case for neutral morphologies."--James Bradley, Quarterly Review of Biology "The main strength of this provocative book is that it undoubtedly provides a successful argument against the widespread tendency to give an adaptive explanation for any biological trait, and, above all, it opens the door to a fruitful way to reconsider the traditional view of evolution as mainly driven by natural selection."--Francesca Merlin, Biol TheoryTable of ContentsIllustrations vii Preface ix 1 Life and the Riddle of Randomness 1 2 Time, Size, and Complexity 17 3 Small Organisms and Neutral Morphologies 40 4 The Evolution of the Decrease of Randomness 63 5 An Exception: Where Small Organisms Suppress Randomness 93 6 The Division of Labor: Two Cases of the Return of Randomness in Higher Forms 101 7 Envoi 118 Acknowledgments 121 Bibliography 125 Index 131

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Book SynopsisTrade Review"Co-Winner of the 2018 Best Book Award, Evolution, Biology, and Society Section, American Sociological Association""Winner of the 2018 Otis Dudley Duncan Award, Section on Population of the American Sociological Association"

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Book SynopsisThis third, fully revised edition, brings the reader up to date with recent advances made in the study of disease at the molecular and cellular level, and examines the new possibilities for treatment. Subjects covered include methods used in molecular medicine and the polymerase chain reaction.Table of ContentsMolecular and cell biology in clinical medicine; methods in molecular medicine; the polymerase chain reaction - a tool for molecular medicine; an introduction to cells; stem cells in normal growth and disease; cell reproduction; apoptosis (programmed cell death); cell to cell and cell to matrix adhesion; how do receptors at the cell surface transmit signals to the cell interior?; membrane traffic, from cell to clinic; cytoskeleton and disease; the cell nucleus' gene regulation and transcription factors; genes and cancer; human congenital malformations - insights from molecular genetics; molecular genetics of common diseases; impact of molecular biology on clinical genetics; monoclonal antibodies in medicine; production and use of therapeutic agents; gene therapy.

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Book SynopsisEdited by leaders in the field, written by experts from around the globe, and brimming with full-color illustrations, Genomic Medicine is an indispensable guide to the full potential of the DNA-based transformation of medicine.Trade ReviewAn indispensable guide to the full potential of the DNA-based transformation of medicine. Human Reproduction and Genetic Ethics The editors have assembled a fine set of short, readable and highly authoritative articles by eminent authors. The book is beautifully produced and will give an accessible entry into genetic medicine to its target audience of non-specialist clinicians. Readers of this journal will need no persuading of the fascination and ever growing importance of genetic medicine and these themes are well communicated. -- Andrew P. Read Human Genetics 2004Table of ContentsForewordPrefaceList of Contributors GlossaryChapter 1. Getting Ready for Gene-Based MedicineChapter 2. Genomic Medicine – A PrimerChapter 3. Genetic TestingChapter 4. Population Screening in the Age of Genomic Medicine Chapter 5. Inheritance and Drug Response Chapter 6. Pharmacogenomics – Drug Disposition, Drug Targets, and Side EffectsChapter 7. Pharmacogenetics in the Laboratory and the Clinic Chapter 8. Hereditary Colorectal CancerChapter 9. Alzheimer's Disease and Parkinson's DiseaseChapter 10. Molecular Diagnosis of the Hematologic CancersChapter 11. Breast and Ovarian CancerChapter 12. Cardiovascular DiseaseChapter 13. Ethical, Legal, and Social Implications of Genomic MedicineChapter 14. Genomics as a Probe for Disease Biology Chapter 15. Welcome to the Genomic EraIndex

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Book SynopsisTrade Review"An impressive, timely, and critically important book and the first scholarly work to take stock of what the genomics turn means for the social sciences. With uncommon interpretive clarity and dazzling interdisciplinary range, Bliss takes us behind the scenes of the emergent field of sociogenomics. Social by Nature forcefully reveals how genetic social science may share a genealogy with earlier eugenics research—even if unwittingly—and urgently points us to the dangers that may arise from this twenty-first century attempt to link deeply-complex social concerns to narrow genetic causes." -- Alondra Nelson * Columbia University *"Catherine Bliss's Social by Nature is critical to understanding the social dangers of over-interpreting genomic data." -- J. Craig Venter, Founder, Chairman, and CEO * J. Craig Venter Institute *"Social by Nature is an insightful, in-depth investigation of the scientific, ethical and political stakes in the emerging field of social genomics. As social scientists and policymakers are urged to jump on the sociogenomics band wagon, Catherine Bliss sounds an urgently needed note of caution and call for more meaningful public engagement." -- Dorothy Roberts * Author, Fatal Invention: How Science, Politics, and Big Business Re-create Race in the Twenty-first Century. *"[Social by Nature] is a brilliant book—dense at times, but insightful and filled with illustrative anecdotes and case studies. It's one you should read if you care about what drives academic research, scientific racism or genetic futurism." -- Nathaniel Comfort * Nature *Table of ContentsContents and Abstracts1Genes and Their Environments chapter abstractChapter 1 provides a social history of the "nature-nurture" divide. Starting with protobiological notions at work in early modern thought and moving forward to modern and late modern biology, this chapter reveals the roots of today's gene-environment emphasis. Situating social genomics amid long-standing sciences such as sociobiology and behavior genetics, and more recent fields such as evolutionary psychology and neuropolitics, it examines the features specific to today's sociogenomic paradigm. 2Science without Borders chapter abstractChapter 2 takes us into the world of social genomics, exposing the who, what, when, and where of the emerging science. It shows that social genomics is not a loose network of independent scientists who are working to benefit the greater good of the sciences more broadly and who have been stochastically drawn into genetic research as a result of shared concepts, methods, and expertise. Rather, it is a fast-evolving field with a great deal of unexamined influence due to its irreverence for discipline. 3Toward the "Deeper Descriptions" chapter abstractChapter 3 shines a light on social genomics' foundational theory and methodology, including novel approaches like the multicohort GWAS and multivariate risk analysis, to show the ways the science innovates genetic explanantia and evolutionary theory. Scientists are currently training their attention on broader natural science debates, even in their attempts to usher in their methodology in the social sciences and to interpret the relevance of their findings for policy. Their focus is less on tackling deep social science conundrums or participating in policy analysis, and more on aligning with health and medical science. 4Determining Difference chapter abstractChapter 4 reveals how sociogenomics is remaking societal notions of human difference in terms of the media as well as basic science characterizations of race, gender, and sexuality. This chapter builds on prior analyses of genome science to evince the ways that new avenues in sociogenomics privilege and perpetuate a genetically deterministic lens for human difference. It shows that troubling, biologically reductive definitions of race, gender, and sexuality thrive in a sociogenomic world. 5The Breakthrough chapter abstractChapter 5 uncovers the central "positions and dispositions" of social genomics, including how participating scientists see their mandate vis-à-vis science writ large. It shows the ways researchers have formed a flexible matrix of specialized knowledge in an attempt to produce credible research innovations and conclusions about the genomics of behavior that can have an impact on bioscience and the wider public. As scientists have invested in the notion of moving theory and methods forward for all sciences, they have formed a confrontational style of practice that is characterized by a unique brand of pioneerism and optimism. 6A Bigger, Better Science chapter abstractChapter 6 examines the impact social genomics is having on the wider world of science. It shows how the field is being received and interpreted by its vast array of collaborator fields, and prioritized by the major funding agencies of our time. This chapter similarly discusses key successes and challenges the field faces going forward, pertaining to funding, governmental support, and scientific publication. 7Applied Science chapter abstractChapter 7 explores the uptake of sociogenomic applications by experts working in the public domain. Whereas use of genomic applications has largely been reserved for biomedical settings, sociogenomic applications have enjoyed adoption in criminal justice, education, and other legal arenas. This chapter presents the salience of sociogenomics for these domains, including how experts in the wider public understand and utilize it, and how the organizations, institutions, and fields they work in perceive its value. The chapter further uncovers key policy issues that scientists see as relevant in sociogenomics' expansion to new public arenas. 8The Business of Sociogenomics chapter abstractChapter 8 presents the array of technologies and therapeutics that have arisen in the commercial domain of genes and behavior. From inborn talent tests to genomic matchmaking, a cottage industry in sociogenomic science has arisen to serve the rising Genome Generation. While only some of these tests have been a direct result of sociogenomic efforts, their usage contributes to the popularization of the sociogenomic paradigm in the mass public. This chapter details the ways the bullish strength of broader markets in personal genomic technology is spurring on sociogenomics as a valuable set of personal predictive indicators. Conclusion chapter abstractThe Conclusion draws together analyses from the preceding chapters to consider the meaning of the sociogenomic paradigm in society. Not only is sociogenomics a scientific orientation, a governmental framework, and a tool in the expert's toolkit; it is a popular lens for deciphering the individual, and a game-changer in public notions of human difference. The analysis ends by signaling meaningful ways that we can critically engage with sociogenomics so that socially responsible frameworks may take hold.

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Book SynopsisThe complete mapping of the horse genome sequence makes a significant contribution to understanding equine biology. This book provides a timely comprehensive overview of equine genomic research.Trade Review“Equine Genomicsis an excellent text that compiles historical accomplishments in equine genetics and molecular biology, describes state-of-theart approaches to understanding the equine genome, and provides glimpses of where the field may go in the future . . . It is our responsibility to try to keep up, and I believe this book will help us do that.” (Journal of the American Veterinary Medical Association, 15 June 2014)Table of ContentsContributors ix Preface xi Chapter 1 Defining the equine genome: The nuclear genome and the mitochondrial genome 1Bhanu P. Chowdhary Chapter 2 Genetic linkage maps 11June Swinburne and Gabriella Lindgren Chapter 3 Physical and comparative maps 49Terje Raudsepp and Bhanu P. Chowdhary Chapter 4 The Y-chromosome 73Terje Raudsepp, Nandina Paria, and Bhanu P. Chowdhary Chapter 5 Unexpected structural features of the equine major histocompatibility complex 93Loren C. Skow and Candice L. Brinkmeyer-Langford Chapter 6 Assembly and analysis of the equine genome sequence 103Claire M. Wade Chapter 7 Genomic tools and resources: Development and applications of an equine SNP genotyping array 113Molly McCue and Jim Mickelson Chapter 8 Functional genomics 125Stephen J. Coleman, Michael J. Mienaltowski, and James N. MacLeod Chapter 9 Coat color genomics 143Samantha A. Brooks and Rebecca R. Bellone Chapter 10 Genomics of skin disorders 155Amy E. Young, Stephen D. White, and Danika L. Bannasvch Chapter 11 Genomics of muscle disorders 171James R. Mickelson, Stephanie J. Valberg, Carrie J. Finno, and Molly E. McCue Chapter 12 Genomics of skeletal disorders 187Ottmar Distl Chapter 13 Genomics of reproduction and fertility 199Terje Raudsepp, Pranab J. Das and Bhanu P. Chowdhary Chapter 14 Genetics of equine neurologic disease 217Carrie J. Finno and Monica Aleman Chapter 15 Molecular genetic testing and karyotyping in the horse 241M. C. T. Penedo and Terje Raudsepp Chapter 16 Genomics of laminitis 255Jim K. Belknap Chapter 17 Genomics of performance 265Emmeline W. Hill, Lisa M. Katz, and David E. MacHugh Chapter 18 Genomics of the circadian clock 285Barbara A. Murphy Chapter 19 Mitochondrial genome: Clues about the evolution of extant equids and genomic diversity of horse breeds 311Cynthia C. Steiner, Kateryna D. Makova, and Oliver A. Ryder Index 323

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Book SynopsisThoroughly covers genetic and genomics research in weedy and invasive plants Identifies future areas of research necessary to managing weedy and invasive species Applies advances in genomics to these specific plants Written by an international team of experts in the field.Table of ContentsContributors xi Preface xv Chapter 1 Why Should Weed Scientists Care About Genomics? 3WILLIAM K. VENCILL Genomics To A Weed Scientist 3 Resistance 4 Better Use Of Existing Herbicides 8 Chapter 2 An Introduction To Molecular Genetic And Genomic Techniques 11CHHANDAK BASU AND SAM R. ZWENGER Weeds As A Source Of Genes For Crop Improvement 11 Tools And Approaches For Understanding Weediness At The Molecular Level 12 Chapter 3 Arabidopsis Is Not A Weed, And Mostly Not A Good Model For Weed Genomics; There Is No Good Model For Weed Genomics 25JONATHAN GRESSEL Introduction: Arabidopsis And Weediness 25 Questions About Weeds—Can Arabidopsis Genomics Answer Them? 27 The Misdirected Approach In Using Arabidopsis To Elucidate New Herbicide Targets 28 Arabidopsis Genomics Can Help In Dealing With Transgene Flow—In A Limited Manner 29 Lessons To Be Learned 30 Chapter 4 Model Weeds For Genomics Research 33WUN S. CHAO AND DAVID P. HORVATH What Makes A Good Model Species? 34 Leveraging From Other Models 36 Genomics Tools For Weeds That Are Under Development 44 Chapter 5 21st-Century Weed Science: A Call For Amaranthus Genomics 53PATRICK J. TRANEL AND FEDERICO TRUCCO The Amaranthus Genus 53 Hybridization And Adaptive Evolution 61 Herbicide Resistance 64 Currently Available Genomic Resources 71 Needs And Opportunities 75 Chapter 6 Evolutionary Genomics Of Weedy Rice 83BRIANA L. GROSS AND KENNETH M. OLSEN Phenotypic Diversity Of Weedy Rice 84 Genomic Diversity Of Weedy Rice 85 The Origin(s) And Evolution Of Weedy Rice 89 The Genetic Basis Of Weediness And Use Of Weedy Rice In Crop Breeding 94 Chapter 7 Rhizomatousness: Genes Important For A Weediness Syndrome 99ANDREW H. PATERSON Developmental Context 100 An Exemplary Case: Johnsongrass 101 Dissecting The Genetic Control Of Rhizomatousness 103 Early Insights Into The Sorghum Rhizo-Transcriptome 105 Future Work And Potential Applications 107 Synthesis 109 Chapter 8 Leafy Spurge: An Emerging Model To Study Traits Of Perennial Weeds 113DAVID P. HORVATH AND JAMES V. ANDERSON Regulation Of Shoot Development And Growth 113 Regulation Of Bud Dormancy 116 Case Study: Leafy Spurge 117 Future Work 122 Chapter 9 Herbicide Resistance: Target Site Mutations 127CHRISTOPHER PRESTON Resistance To Photosystem II-Inhibiting Herbicides 128 Resistance To Acetohydroxyacid Synthase-Inhibiting Herbicides 131 Resistance To Acetyl Coenzyme A Carboxylase-Inhibiting Herbicides 136 Resistance To Glyphosate 138 Resistance To Microtubule Assembly Inhibitors 140 Resistance To Phytoene Desaturase Inhibitors 141 Chapter 10 Molecular and Genomic Mechanisms Of Non-Target-Site Herbicide Resistance 149JUN HU, PATRICK J. TRANEL, C. NEAL STEWART JR., AND JOSHUA S. YUAN Herbicide Application And Resistance 149 Herbicide Classification And Resistance 150 Non-Target Herbicide Resistance 150 Signal Transduction 150 Detoxification and Modification 151 Chapter 11 A Herbicide Defense Trait That Is Distinct From Resistance: The Evolutionary Ecology And Genomics Of Herbicide Tolerance 163REGINA S. BAUCOM Resistance Versus Tolerance In Weed Science 163 Tolerance In Evolutionary Ecology 166 Tolerance Traits And The Genomics Of Tolerance 171 Why Again Should We Focus On Tolerance, Tolerance Traits, And The Genomics Of Tolerance? 172 Chapter 12 The Genomics of Plant Invasion: A Case Study In Spotted Knapweed 177AMANDA K. BROZ AND JORGE M. VIVANCO Why Study Invasive Plant Genomics? 177 Spotted Knapweed Life History 178 Allelopathy And The Novel Weapons Hypothesis 180 Genomics Resources And Approaches For Studying Spotted Knapweed 185 Chapter 13 Molecular Ecology Of Plant Competition 197DOMINIK D. SCHMIDT, MERIJN R. KANT, AND IAN T. BALDWIN Competition Signals And Their Perception By Plants 198 Molecular Basis Of Competitively Important Traits 207 Transcriptomic Insights Into Competitive Interactions Of Weedy Plants 211 Chapter 14 Genomics And Weeds: A Synthesis 221STEPHEN O. DUKE, SCOTT R. BAERSON, AND JONATHAN GRESSEL From Fundamental Information To Practical Solutions 222 Where Do We Go From Here? 241 Index 249

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Book SynopsisExplores the debate on the biological significance and cultural meaning of genes in the development of organisms - the molecular paradigmTrade Review“The rich scientific knowledge about the genetic basis of life and it complex involvement in the life of individuals and populations is highly relevant to our worldview. Genes in Development helps to bring understandings of the conceptual and philosophical implications of molecular genetics up to date.”—Werner Arber, Nobel Laureate in Medicine and Emeritus Professor of Molecular Microbiology, University of Basel“Together the essays in Genes in Development give lively voice to many of the current alternatives to genetic reductionism. Well-known figures from the debates of the past two decades are represented alongside a good number of emerging scholars.”—Hans-Jörg Rheinberger, Max Planck Institute for the History of Science, BerlinTable of ContentsIntroduction / Eva M. Neumann-Held and Christoph Rehmann-Sutter 1 I. Empirical Approaches 1. Genome Analysis and Developmental Biology: The Nematode Caenorhabditis elegans as a Model System / Thomas R. Burglin 15 2. Genes and Form: Inherency in the Evolution of Developmental Mechanisms / Stuart A. Newman and Gerd B. Muller 38 II. Looking Back into History 3. From Genes as Determinants to DNA as Resource: Historical Notes on Development and Genetics / Sahotra Sarkar 77 III. Theorizing Genes 4. The Origin of Species: A Structuralist Approach / Gerry Webster and Brian C. Goodwin 99 5. On the Problem of the Molecular versus the Organismic Approach in Biology / Ulrich Wolf 135 6. Genes, Development, and Semiosis / Jesper Hoffmeyer 152 7. The Fearless Vampire Conservator: Philip Kitcher, Genetic Determinism, and the Informational Gene / Paul E. Griffiths 175 8. Genetics from an Evolutionary Process Perspective / James Griesemer 199 9. Genes-Causes-Codes: Deciphering DNA’s Ontological Privilege / Eva M. Newmann-Held 238 10. Boundaries and (Constructive) Interaction / Susan Oyama 272 11. Beyond the Gene but Beneath the Skin / Evelyn Fox Keller 290 12. Poiesis and Praxis: Two Modes of Understanding Development / Christoph Rehmann-Sutter 313 IV. Social and Ethical Implications 13. Developmental Emergence, Genes, and Responsible Science / Brian C. Goodwin 337 14. Nothing Like a Gene / Jackie Leach Scully 349 Contributors 365 Index 369

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Book SynopsisA case study of the development and reception of genomics in the Netherlands.Trade Review“Taussig’s monograph provides a counter-weight not only to the bold universal truths declared in the field of science, but also to representations of ‘the west’ as a monolith, because the forces that shape genetic science and biomedicine are, in all their complexity, distinctly Dutch. . . . I encourage a reading of Ordinary Genomes because of its analysis, and also as an exercise in analytical departure, and unstructured flight.” - Abigail Baim-Lance, Somatosphere“. . . [A]n interesting case study of the interplay between science, culture and society. The book will be of particular relevance to scholars in medical anthropology, science and technology studies and health studies. This book will be of use to anyone seeking to explore the dynamics of history, religion, culture and their impact on the making of knowledge in natural science.” - Masae Kato, Genomics, Society and Policy“This well-written book provides an interesting and insightful analysis of genetic knowledge and biosocial practices. The cultural and social connection she uncovers between genetics and the nation is particularly useful.” - Casmir Macgregor, Society and Culture“Ordinary Genomes is a thoughtful, nuanced book. Among its many virtues are the clarity of Karen-Sue Taussig’s prose and her admirably fair and sympathetic presentation and analysis of the geneticists. With her close and careful readings of geneticists at work in the multiple spaces of the laboratory, the field, and the clinic, we get an all too rare ethnographic look at genetics-in-practice. Here we have fleshed out, complex figures who negotiate diagnoses, reflect on their own practices and knowledge, and allow us to enter a professional life that is probably far different from what we might have imagined. I cannot stress enough what an important achievement this is.”—Michael Fortun, editor of the journal Cultural Anthropology“Ordinary Genomes is a timely, provocative, compelling account of how research in the genome sciences at once challenges the norms of national culture and is made meaningful through those norms.”—Priscilla Wald, author of Contagious: Cultures, Carriers, and the Outbreak Narrative“What might suspicions of religious inbreeding; Herman the Bull; anxiety about continued influence of Nazi eugenics; and the quest to be normal all have in common? These themes are skilfully woven together in Karen-Sue Taussig's thoughtful and provocative Ordinary Genomes which makes a very important case for the specificity of Dutch genetic perceptions and practices. Her account convinces us to rethink the meaning of ‘Western’ in light of Taussig's excellent ethnographic account of Dutch praxis—in and out of genetic medicine—as we imagine the many ways it teaches us to think about normality. This is an important book. It provides a classic anthropological argument for the importance of thinking comparatively, as we approach 21st century genomic medicine.”—Rayna Rapp, author of Testing Women, Testing the Fetus: The Social Impact of Amniocentesis in America"An interesting case study of the interplay between science, culture and society. The book will be of particular relevance to scholars in medical anthropology, science and technology studies and health studies. This book will be of use to anyone seeking to explore the dynamics of history, religion, culture and their impact on the making of knowledge in natural science.” -- Masae Kato * Genomics, Society and Policy *“Taussig’s monograph provides a counter-weight not only to the bold universal truths declared in the field of science, but also to representations of ‘the west’ as a monolith, because the forces that shape genetic science and biomedicine are, in all their complexity, distinctly Dutch. . . . I encourage a reading of Ordinary Genomes because of its analysis, and also as an exercise in analytical departure, and unstructured flight.” -- Abigail Baim-Lance * Somatosphere *“This well-written book provides an interesting and insightful analysis of genetic knowledge and biosocial practices. The cultural and social connection she uncovers between genetics and the nation is particularly useful.” -- Casmir Macgregor * Society and Culture *Table of ContentsAcknowledgments ix Introduction. Science, Subjectivity, and Citizenship 1 1. "God Made the World and the Dutch Made Holland" 17 2. Genetics and the Organization of Genetic Practice in the Netherlands 57 3. The Social and Clinical Production of Ordinariness 85 4. Backward and Beautiful: Calvinism, Chromosomes, and the Production of Genetic Knowledge 135 5. Bovine Abominations: Contesting Genetic Technologies 159 Epilogue. Ordinary Genomes in a Globalizing World 189 Notes 201 Bibliography 217 Index 235

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Book SynopsisBased on ethnographic research in Brazil, Colombia, and Mexico, this title explores how the concepts of race, ethnicity, nation, and gender enter into and are affected by genomic research. It involves relations between European men and indigenous or African women, gender is a key factor in Latin American genomics and the analyses in this book.Trade Review“[T]he virtues of the book are many: it opens the geographical scope of studies of genomic research and productively engages with contemporary reconfigurations of race and nation. Last, but not least, it demonstrates the enormous value of collaborative transnational research for science and technology studies.” -- Edna Suárez-Díaz * Journal of Latin American Geography *"Mestizo Genomics makes an important contribution to the study of biology and the human sciences in Latin America.... This book will be useful to any scholar interested in science, race, and nation in Latin America as well as those considering how to formulate large-scale interdisciplinary projects." -- Sarah Walsh * The Latin Americanist *"...this collection is vibrant and exciting, throwing up (without closing down) a finessed repertoire of compelling debates that tantalize with irresistible conceptual nuggets primed for future inquiry.... This kind of heuristic analysis looks set to enhance and extend discussions of mestizaje in the twenty-first century, in the academy and beyond." -- Victoria Carroll * History *"All in all, the clarity of the project, the skill of the researchers, and the fine editing of the book as a whole allow for a study of great breadth and significance.... Mestizo Genomics will be of great interest to science studies scholars interested in racial science, biology, and genomics. Latin Americanists will find a compelling description of the historic and recent developments in scientific theories of diversity, unity, and homogenous identity in the area, and Latin America’s variety and specific taxonomies should be instructive to scholars of U.S. and European genomics." -- Julia Rodriguez * ISIS *"This book... clearly contributes to current international debates on race, genomics and biomedicine. This work is not only of interest to biological anthropologists and historians of science, but also to a wider audience that should include evolutionary biologists and social scientists.” -- Ana Barahona * Metascience *Table of ContentsPreface Acknowledgments Introduction: Genomics, Race Mixture, and Nation in Latin America / Peter Wade, Carlos López Beltrán, Eduardo Restrepo, and Ricardo Ventura Santos Part I. History and Context 1. From Degeneration to Meeting Point: Historical Views on Race, Mixture, and the Biological Diversity of the Brazilian Population / Ricardo Ventura Santos, Michael Kent, and Verlan Valle Gaspar Neto 2. Nation and Difference in the Genetic Imagination of Colombia / Eduardo Restrepo, Ernesto Schwartz-Marín, and Roosbelinda Cádenas 3. Negotiating the Mexican Mestizo: On the Possibility of a National Genomics / Carlos López Beltrán, Vivette García Deister, and Mariana Rios Sandoval Part II. Laboratory Case Studies 4. "The Charrua Are Alive": The Genetic Resurrection of an Extinct Indigenous Population in Southern Brazil / Michael Kent and Ricardo Ventura Santos 5. The Travels of Humans, Categories, and Other Genetic Products: A Case Study of the Practice of Population Genetics in Colombia / María Fernanda Olarte Sierra and Adriana Díaz del Castillo H. 6. Laboratory Life of the Mexican Mestizo / Vivette García Deister 7. Social Categories and Laboratory Practices in Brazil, Colombia, and Mexico: A Comparative Overview / Peter Wade, Vivette García Deister, Michael Kent, and María Fernanda Olarte Sierra Conclusion: Race, Multiculturalism, and Genomics in Latin America / Peter Wade Appendix; Methods and Contexts References Contributors Index

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Book SynopsisBased on ethnographic research in Brazil, Colombia, and Mexico, this title helps you explore how the concepts of race, ethnicity, nation, and gender enter into and are affected by genomic research.Trade Review“[T]he virtues of the book are many: it opens the geographical scope of studies of genomic research and productively engages with contemporary reconfigurations of race and nation. Last, but not least, it demonstrates the enormous value of collaborative transnational research for science and technology studies.” -- Edna Suárez-Díaz * Journal of Latin American Geography *"Mestizo Genomics makes an important contribution to the study of biology and the human sciences in Latin America.... This book will be useful to any scholar interested in science, race, and nation in Latin America as well as those considering how to formulate large-scale interdisciplinary projects." -- Sarah Walsh * The Latin Americanist *"...this collection is vibrant and exciting, throwing up (without closing down) a finessed repertoire of compelling debates that tantalize with irresistible conceptual nuggets primed for future inquiry.... This kind of heuristic analysis looks set to enhance and extend discussions of mestizaje in the twenty-first century, in the academy and beyond." -- Victoria Carroll * History *"All in all, the clarity of the project, the skill of the researchers, and the fine editing of the book as a whole allow for a study of great breadth and significance.... Mestizo Genomics will be of great interest to science studies scholars interested in racial science, biology, and genomics. Latin Americanists will find a compelling description of the historic and recent developments in scientific theories of diversity, unity, and homogenous identity in the area, and Latin America’s variety and specific taxonomies should be instructive to scholars of U.S. and European genomics." -- Julia Rodriguez * ISIS *"This book... clearly contributes to current international debates on race, genomics and biomedicine. This work is not only of interest to biological anthropologists and historians of science, but also to a wider audience that should include evolutionary biologists and social scientists.” -- Ana Barahona * Metascience *Table of ContentsPreface Acknowledgments Introduction: Genomics, Race Mixture, and Nation in Latin America / Peter Wade, Carlos López Beltrán, Eduardo Restrepo, and Ricardo Ventura Santos Part I. History and Context 1. From Degeneration to Meeting Point: Historical Views on Race, Mixture, and the Biological Diversity of the Brazilian Population / Ricardo Ventura Santos, Michael Kent, and Verlan Valle Gaspar Neto 2. Nation and Difference in the Genetic Imagination of Colombia / Eduardo Restrepo, Ernesto Schwartz-Marín, and Roosbelinda Cádenas 3. Negotiating the Mexican Mestizo: On the Possibility of a National Genomics / Carlos López Beltrán, Vivette García Deister, and Mariana Rios Sandoval Part II. Laboratory Case Studies 4. "The Charrua Are Alive": The Genetic Resurrection of an Extinct Indigenous Population in Southern Brazil / Michael Kent and Ricardo Ventura Santos 5. The Travels of Humans, Categories, and Other Genetic Products: A Case Study of the Practice of Population Genetics in Colombia / María Fernanda Olarte Sierra and Adriana Díaz del Castillo H. 6. Laboratory Life of the Mexican Mestizo / Vivette García Deister 7. Social Categories and Laboratory Practices in Brazil, Colombia, and Mexico: A Comparative Overview / Peter Wade, Vivette García Deister, Michael Kent, and María Fernanda Olarte Sierra Conclusion: Race, Multiculturalism, and Genomics in Latin America / Peter Wade Appendix; Methods and Contexts References Contributors Index

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Book SynopsisThe contributors to Postgenomics assess the changes to the life sciences the Human Genome Project's completion brought, develop new frameworks for studying the human genome in the postgenomic era, and show how the environment, technology, race, and gender influence the genome and how we think about it.Trade Review"The volume is an accessible and insightful collection of critical and informed perspectives on how technological and theoretical developments influence science and society, and how they shape the ways we think about biological systems like ourselves." -- Sara Green * Metascience *"Postgenomics suggests just how many questions we may productively ask, and marks some highly fruitful lines of inquiry, as we seek to understand this new chapter in the ongoing interaction among genes, society, and ourselves." -- Robin Wolfe Scheffler * Bulletin of the History of Medicine *"The authors convey exceptionally well the character of postgenomic science and how genomics has changed since the 1990s. . . . essential and very interesting reading for anyone interested in genomics and its recent trajectory." -- Peter Wade * Technology and Culture *"This book not only analyzes the impact of numerous [genome-wide association studies] but also examines emerging research areas such as epigenetics in political, social, and philosophical contexts, in so doing redefining the information ecology of the genome. Highly recommended." -- S. H. Jeong * Choice *"I recommend this book to all biologists and philosophers interested in an accessible overview of the effect of the genomic revolution on the biosciences. It capably discusses both the new discoveries and the technical improvements that have been made since the advent of genomics, as well as the attendant philosophical and sociological implications." -- P. William Hughes * Science *"This book . . . should be widely read by all who are interested in the current state and future of the genomic revolution." -- Michael Yudell * Social History of Medicine *"[Postgenomics] offers readers an imaginative and frequently playful way to approach the increasingly complicated question about how scientific innovation impacts society and vice versa." -- Adrianna Link * Journal of the History of Biology *Table of ContentsForeward. Biology's Love Affair with the Genome / Russ Altman vii 1. Beyond the Genome / Hallam Stevens and Sarah S. Richardson 1 2. The Postgenomic Genome / Evelyn Fox Keller 9 3. What Toll Pursuit: Affective Assemblages in Genomics and Postgenomics / Mike Fortun 32 4. The Polygenomic Organism / John Dupré 56 5. Machine Learning and Genomic Dimensionality: From Features to Landscapes / Adrian Mackenzie 73 6. Networks: Representations and Tools in Postgenomics / Hallam Stevens 103 7. Valuing Data in Postgenomic Biology: How Data Donation and Curation Practices Challenge the Scientific Publication System / Rachel A. Ankeny and Sabina Leonelli 126 8. From Behavior Genetics to Postgenomics / Aaron Panofsky 150 9. Defining Health Justice in the Postgenomic Era / Catherine Bliss 174 10. The Missing Piece of the Puzzle? Measuring the Environment in the Postgenomic Moment / Sara Shostak and Margot Moinester 192 11. Maternal Bodies in the Postgenomic Order: Gender and the Explanatory Landscape of Epigenetics / Sarah S. Richardson 210 12. Approaching Postgenomics / Hallam Stevens and Sarah S. Richardson 232 Bibliography 243 Contributors 281 Index 287

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Book SynopsisThe contributors to Postgenomics assess the changes to the life sciences the Human Genome Project's completion brought, develop new frameworks for studying the human genome in the postgenomic era, and show how the environment, technology, race, and gender influence the genome and how we think about it.Trade Review"The volume is an accessible and insightful collection of critical and informed perspectives on how technological and theoretical developments influence science and society, and how they shape the ways we think about biological systems like ourselves." -- Sara Green * Metascience *"Postgenomics suggests just how many questions we may productively ask, and marks some highly fruitful lines of inquiry, as we seek to understand this new chapter in the ongoing interaction among genes, society, and ourselves." -- Robin Wolfe Scheffler * Bulletin of the History of Medicine *"The authors convey exceptionally well the character of postgenomic science and how genomics has changed since the 1990s. . . . essential and very interesting reading for anyone interested in genomics and its recent trajectory." -- Peter Wade * Technology and Culture *"This book not only analyzes the impact of numerous [genome-wide association studies] but also examines emerging research areas such as epigenetics in political, social, and philosophical contexts, in so doing redefining the information ecology of the genome. Highly recommended." -- S. H. Jeong * Choice *"I recommend this book to all biologists and philosophers interested in an accessible overview of the effect of the genomic revolution on the biosciences. It capably discusses both the new discoveries and the technical improvements that have been made since the advent of genomics, as well as the attendant philosophical and sociological implications." -- P. William Hughes * Science *"This book . . . should be widely read by all who are interested in the current state and future of the genomic revolution." -- Michael Yudell * Social History of Medicine *"[Postgenomics] offers readers an imaginative and frequently playful way to approach the increasingly complicated question about how scientific innovation impacts society and vice versa." -- Adrianna Link * Journal of the History of Biology *Table of ContentsForeward. Biology's Love Affair with the Genome / Russ Altman vii 1. Beyond the Genome / Hallam Stevens and Sarah S. Richardson 1 2. The Postgenomic Genome / Evelyn Fox Keller 9 3. What Toll Pursuit: Affective Assemblages in Genomics and Postgenomics / Mike Fortun 32 4. The Polygenomic Organism / John Dupré 56 5. Machine Learning and Genomic Dimensionality: From Features to Landscapes / Adrian Mackenzie 73 6. Networks: Representations and Tools in Postgenomics / Hallam Stevens 103 7. Valuing Data in Postgenomic Biology: How Data Donation and Curation Practices Challenge the Scientific Publication System / Rachel A. Ankeny and Sabina Leonelli 126 8. From Behavior Genetics to Postgenomics / Aaron Panofsky 150 9. Defining Health Justice in the Postgenomic Era / Catherine Bliss 174 10. The Missing Piece of the Puzzle? Measuring the Environment in the Postgenomic Moment / Sara Shostak and Margot Moinester 192 11. Maternal Bodies in the Postgenomic Order: Gender and the Explanatory Landscape of Epigenetics / Sarah S. Richardson 210 12. Approaching Postgenomics / Hallam Stevens and Sarah S. Richardson 232 Bibliography 243 Contributors 281 Index 287

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Book SynopsisGenetics has transformed plant pathology on two occasions: first when Mendelian genetics enabled the discovery that disease resistance was a heritable trait in plants, and secondly when Flor proposed the gene-for-gene hypothesis to explain his observations of plant-parasite interactions, based on his work on flax rust in North Dakota starting in the 1930s. Our knowledge of the genetics of disease resistance and host-pathogen coevolution is now entering a new phase as a result of the cloning of the first resistance genes. This book provides a broad review of recent developments in this important and expanding subject. Both agricultural and natural host-pathogen situations are addressed. While most of the book focuses on plant pathology, in the usual sense of the term embracing fungal, bacterial and viral pathogens, there is also consideration of parasitic plants and a chapter demonstrating lessons to be learnt from the mammalian immune system. Three overall themes are addressed: geneticTable of Contents1: Contributors 2: Preface Part One: Genetic Analyses and Utilization of Resistance 3: Organization of Resistance Genes in Arabidopsis, 4: Genetic Fine Structure of Resistance Loci, 5: Mutation Analysis for the Dissection of Resistance, 6: Cultivar Mixtures in Intensive Agriculture, 7: Crop Resistance to Parasitic Plants, Part Two: Population Genetics 8: The UK Cereal Pathogen Virulence Survey, 9: Adaptation of Powdery Mildew Populations to Cereal Varieties in Relation to Durable and Non-durable Resistance 10: Virulence Dynamics and Genetics of Cereal Rust Populations in North America, 11: Interpreting Population Genetic Data with the Help of Genetic Linkage Maps U E Brändle, 12: Modelling Virulence Dynamics of Airborne Plant Pathogens in Relation to Selection by Host Resistance in Agricultural Crops, 13: An Epidemiological Approach to Modelling the Dynamics of Gene-for-gene Interactions, 14: Modelling Gene Frequency Dynamics, 15: The Genetic Structure of Natural Pathosystems, 16: The Evolution of Gene-for-Gene Interactions in Natural Pathosystems, Part Three: Cell Biology and Molecular Genetics 17: Structural and Biochemical Characterization of Gene-for-Gene Interactions, 18: The Molecular Genetics of Specificity Determinants in Plant Pathogenic Bacteria, 19: Molecular Characterization of Fungal Avirulence, 20: The Molecular Genetics of Plant-Virus Interactions, 21: Molecular Genetics of Disease Resistance: An End to the “Gene-for-Gene” Concept?, 22: Elicitor Generation and Receipt - The Mail Gets Through, But How?, 23: Learning from the Mammalian Immune System in the Wake of The R-Gene Flood, 24: Genetic Disease Control in Plants - Where Now?, 25: Index

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Book SynopsisThis book describes the methodology for predicting the genetic merit of animals in the context of genetic improvement in an animal breeding programme. Information on an animal and its relatives, on either the characteristic to be improved or from other traits, can be used to predict the animal's genetic merit, taking account of the relationships between measurements and the economic values of traits. The methodology is developed from first principles, without unnecessary detail or complexity, and all the required statistical and mathematical concepts are fully described in the book. The text discusses the methods for combining different sources of information and illustrates their use with examples of breeding programmes in cattle, sheep, pigs and poultry. A series of questions with detailed answers is included in the book, to help reinforce the ideas and provide some practical experience in the prediction of genetic merit. The text is aimed at final year undergraduate and first year pTable of Contents1: Introduction to variance 2: ANOVA in a quantitative genetics framework 3: Regression and correlation 4: Identification of animals of high genetic merit 5: Information from relatives 6: Selection index methodology 7: Examples of selection objectives and criteria 8: Factors affecting the rate of genetic improvement 9: Performance testing, progeny testing and MOET 10: Simultaneous prediction of breeding values for several animals 11: Prediction of breeding values and environmental effects 12: Multivariate breeding value prediction 13: Breeding values with a gene of large effect 14: Breeding values for binary traits I: :Appendix: Matrix algebra II: Questions III: Answers IV: References V: Index

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Book SynopsisDuring the last two decades major advances have been made in mammalian genetics. New methods in molecular and cytogenetics, and in biotechnology have been developed. Many of these have been applied to investigating the genetics of sheep and to improving the production of wool, meat and milk. This book is a comprehensive reference work on sheep genetics. All relevant topics have been included, from fundamental genetic structure to the genetics of various production and other traits, to transgenic sheep and genetic conservation. Chapters have been specially commissioned for the volume and written by internationally recognized experts from Europe, USA, Australia and New Zealand. The book will be invaluable to advanced students and research workers in animal genetics, breeding and biotechnology.Table of Contents1: Systematics and Phylogeny of the Sheep I R Franklin, CSIRO, Blacktown, Australia 2: Genetic Aspects of Domestication, Common Breeds and their Origin K Maijala, Helsinki, Finland 3: Genetics of Colour and Hair Texture D P Sponenberg, Virginia-Maryland Regional College of Veterinary Medicine, Blacksburg, USA 4: Genetics of Morphological Traits and Inherited Disorders F W Nicholas, University of Sydney, Australia 5: Biochemical Genetics L Di Stasio, Department of Animal Science, Torino, Italy 6: Molecular Genetics of Sheep B C Powell, University of Adelaide, Glen Osmond, South Australia 7: Molecular Genetics of Immune Molecules W R Hein, Basle Institute for Immunology, Basle, Switzerland 8: Genetics of Disease Resistance and Vaccine Response H W Raadsma, University of Sydney, Australia, G D Gray, University of New England, Armidale, Australia and R R Woolaston, CSIRO Division of Animal Production, Armidale, Australia 9: Molecular Biology and Genetics of Scrapie in Sheep N Hunter, Institute for Animal Health, Edinburgh, UK 10: Cytogenetics: Physical Chromosome Maps T E Broad, AgResearch Invermay Agricultural Centre, New Zealand, H Hayes, Laboratoire de Genetique Biochimique et de Cytogenetique, France and S E Long, University of Bristol, Langford, Bristol, UK 11: The Sheep Linkage Map G W Montgomery and A M Crawford, University of Otago, Dunedin, New Zealand 12: Genetics of Behaviour G N Hinch, University of New England, Armidale, Australia 13: Biology and Genetics of Reproduction I W Purvis and M Hillard, CSIRO Division of Animal Production, Armidale, Australia 14: Modern Reproduction Technologies and Transgenics I Wilmut, K H S Campbell and L Young, Roslin Institute (Edinburgh), Midlothian, UK 15: Development Genetics N E Cockett, Utah State University, Logan, USA 16: Genetic Resources and Conservation R W Ponzoni, South Australian Research and Development Institute, Adelaide, Australia 17: Genetic Improvement of Wool Production K D Atkins, Agricultural Research and Research Centre, Orange, Australia 18: Genetics of Lamb and Meat Production R G Banks, University of New England, Armidale, Australia 19: Genetics of Meat Quality J M Thompson and A J Ball, University of New England, Armidale, Australia 20: Genetics of Milk Production F Barillet, INRA, Castanet-Tolosan Cedex, France 21: Genetic Improvement of Sheep B P Kinghorn, University of New England, Armidale, Australia 22: Standardized Genetic Nomenclature for Sheep C H S Dolling, President of COGNOSAG, South Australia

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Book SynopsisGenetics has transformed plant pathology on two occasions: first when Mendelian genetics enabled the discovery that disease resistance was a heritable trait in plants, and secondly when Flor proposed the gene-for-gene hypothesis to explain his observations of plant-parasite interactions, based on his work on flax rust in North Dakota starting in the 1930s. Our knowledge of the genetics of disease resistance and host-pathogen coevolution is now entering a new phase as a result of the cloning of the first resistance genes. This book provides a broad review of recent developments in this important and expanding subject. Both agricultural and natural host-pathogen situations are addressed. While most of the book focuses on plant pathology, in the usual sense of the term embracing fungal, bacterial and viral pathogens, there is also consideration of parasitic plants and a chapter demonstrating lessons to be learnt from the mammalian immune system. Three overall themes are addressed: geneticTable of Contents1: Genetic Approaches to Manipulation of Fruit Development and Quality in Tomato, J J Giovannoni et al., Texas A & M University, USA 2: Improving Tomato Fruit Quality by Cultivation, L C Ho, Horticulture Research International, UK 3: Applications of Molecular Biology and Genetic Manipulation to Understand and Improve Quality of Fruits and Vegetables, D Grierson, University of Nottingham, UK 4: Gene Expression in Ripening Bananas, R Drury, Horticulture Research International, UK, C R Bird, Zeneca Plant Science, UK and G B Seymour, Horticulture Research International, UK 5: Genes for Fruit Quality in Strawberry, K Manning, Horticulture Research International, UK 6: The Tomato Ethylene Receptor Gene Family: It’s Not Easy Being a Plant, D Tieman and H Klee, University of Florida, USA 7: Environmental Requirements as Determined by Rooting Potential in Leafy Cuttings, 8: R S Harrison-Murray and B H Howard, Horticulture Research International, UK 9: The Use of Mutants and Molecular Biology to Understand Competence for Root Formation, W P Hackett et al., University of Minnesota, USA 10: Physiological Analysis of the Floral Transition, G Bernier et al., Universite de Liege, Belgium 11: Genetic and Environmental Control of Flowering in Strawberry, N H Battey et al., University of Reading, UK 12: Manipulating the Photoperiodic Control of Plant Reproduction, S D Jackson and B Thomas, Horticulture Research International, UK 13: Regulation of Abscisic Acid and Water Stress Response Genes, P K Busk et al., CID, Barcelona, Spain 14: Manipulation of Growth of Horticultural Crops under Environmental Stress, W J Davies and D S Thompson, Lancaster University, UK and J E Taylor, University of Reading, UK 15: Engineering Phytochrome Genes to Improve Crop Performance, H Smith, University of Leicester, UK 16: Regulation of Stem Extension by Temperature, F Allen Langton, Horticulture Research International, UK 17: Modification of Plant Morphology by Genetic Manipulation of Gibberellin Biosynthesis, P Hedden et al., University of Bristol, UK

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Book SynopsisInternational concern over the threat to species and ecosystems caused by human activities is at an all time high, which may result in high costs to present and future generations. The economic costs and benefits associated with the conservation and sustainable use of genetic resources of actual or potential value for food and agriculture is largely unknown. Economic instruments that can encourage implementation of socially optimal genetic resource conservation strategies as well as the sharing of the real benefits and costs are a useful measurement tool. This book is an edited compilation of papers from the Symposium on the Economics of Valuation and Conservation of Genetic Resources for Agriculture held in Rome in May 1996. It addresses some of the key issues involved in the estimation of the economic value of conserving genetic resources for agriculture. It covers the modelling of the value of Plant Genetic Resources (PGRs), empirical studies of PGRs (including field diversity and yTable of ContentsPart I: Modelling the Role of Genetic Resources in Plant Breeding 1.1: Plant Breeding: A Case of Induced Innovation, R E Evenson 1.2: Search Modelling for Traits, D Gollin and M Smale 1.3: The Value of Genetic Resources for Use in Agricultural Improvement, R D Simpson and R A Sedjo 1.4: Development, Agriculture and Diversity: Externalities in the Diffusion of Agriculture, T Swanson Part II: Empirical Studies: Plant Breeding and Field Diversity 2.1: Indicators to Genetic Diversity in Bread Wheats: Selected Evidence on Cultivars Grown in Developing Countries, M Smale 2.2: Farmers’ Valuation and Conservation of Crop Genetic Resources, S B Brush and E Meng Part III: Empirical Studies: Breeding Values 3.1: Maize Breeding and Genetic Resources, W Salhuana and S Smith 3.2: Role of International Germplasm Collections in Italian Durum Wheat Breeding Programs, D Bagnara and V Santiello 3.3: An Application of Hedonic Pricing Methods to Value Rice Genetic Resources in India, D Gollin and R E Evenson 3.4: Varietal Trait Values for Rice in India, K P C Rao and R E Evenson 3.5: Modern Varieties, Traits, Commodity Supply and Factor Demand in Indian Agriculture, R E Evenson 3.6: Crop-Loss Data and Trait Value Estimates for Rice in Indonesia, R E Evenson 3.7: Breeding Values of Rice Genetic Resources, D Gollin and R E Evenson Part IV: Property Rights 4.1: Incentives for Genetic Resource Preservation, A Artuso 4.2: Farmers’ Rights, J Esquinas-Alcázar 4.3: Intellectual Property and Farmers’ Rights, B D Wright 4.4: Valuing Farmers’ Rights, D Gollin Part V: The Implication of Development in Biotechnology 5.1: Impact of Biotechnology on the Demand for Rice Biodiversity, C E Pray 5.2: Biotechnology and Genetic Resources, R E Evenson

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Book SynopsisWinner of a 2009 Outstanding Academic Title (OAT) award!Trees continue to maintain a unique significance in the social, ecological and economic systems of the world - as large, long-lived perennials covering 30% of land on Earth; their very nature dictates their importance. An understanding of forest genetics is essential for providing insight into the evolution, conservation, management and sustainability of both natural and managed forests. Providing a comprehensive introduction to the principles of genetics as important to forest trees, this text integrates the varied sub-disciplines of genetics and their applications in gene conservation, tree improvement and biotechnology. Topics discussed include genetic variation in natural forest trees, the application of genetics in tree improvement and breeding programs, and genomic sciences and molecular technologies.Table of Contents1: Forest Genetics - Concepts, Scope, History and Importance SECTION I: BASIC PRINCIPLES 2: Molecular Basis of Inheritance - Genome Organization, Gene Structure and Regulation 3: Transmission Genetics - Chromosomes, Recombination and Linkage Mendelian Genetics 4: Genetic Markers - Morphological, Biochemical and Molecular Markers 5: Population Genetics - Gene Frequencies, Inbreeding and Forces of Evolution 6: Quantitative Genetics - Polygenic Traits, Heritabilities and Genetic Correlations SECTION II: GENETIC VARIATION IN NATURAL POPULATIONS 7: Within-population Variation - Genetic Diversity, Mating Systems and Stand Structure 8: Geographic Variation - Races, Clines and Ecotypes 9: Evolutionary Genetics - Divergence, Speciation and Hybridization 10: Gene Conservation - In Situ, Ex Situ and Sampling Strategies SECTION III: TREE IMPROVEMENT 11: Tree Improvement Programs - Structure, Concepts and Importance 12: Base Populations - Species, Hybrids, Seed Sources and Breeding Zones 13: Phenotypic Mass Selection - Genetic Gain, Choice of Traits and Indirect Response 14: Genetic Testing - Mating Designs, Field Tests and Test Implementation 15: Data Analysis - Mixed Models, Variance Components and Breeding Values 16: Deployment - Open-pollinated Varieties, Full-sib Families and Clones 17: Advanced-generation Breeding Strategies - Breeding Population Size, Structure and Management SECTION IV: BIOTECHNOLOGY 18: Genomics - Discovery and Functional Analysis of Genes 19: Marker-assisted Selection and Breeding - Indirect Selection, Direct Selection and Breeding Applications 20: Genetic Engineering - Target Traits, Transformation and Regeneration 1: Forest Genetics - Concepts, Scope, History and Importance SECTION I: BASIC PRINCIPLES 2: Molecular Basis of Inheritance - Genome Organization, Gene Structure and Regulation 3: Transmission Genetics - Chromosomes, Recombination and Linkage Mendelian Genetics 4: Genetic Markers - Morphological, Biochemical and Molecular Markers 5: Population Genetics - Gene Frequencies, Inbreeding and Forces of Evolution 6: Quantitative Genetics - Polygenic Traits, Heritabilities and Genetic Correlations SECTION II: GENETIC VARIATION IN NATURAL POPULATIONS 7: Within-population Variation - Genetic Diversity, Mating Systems and Stand Structure 8: Geographic Variation - Races, Clines and Ecotypes 9: Evolutionary Genetics - Divergence, Speciation and Hybridization 10: Gene Conservation - In Situ, Ex Situ and Sampling Strategies SECTION III: TREE IMPROVEMENT 11: Tree Improvement Programs - Structure, Concepts and Importance 12: Base Populations - Species, Hybrids, Seed Sources and Breeding Zones 13: Phenotypic Mass Selection - Genetic Gain, Choice of Traits and Indirect Response 14: Genetic Testing - Mating Designs, Field Tests and Test Implementation 15: Data Analysis - Mixed Models, Variance Components and Breeding Values 16: Deployment - Open-pollinated Varieties, Full-sib Families and Clones 17: Advanced-generation Breeding Strategies - Breeding Population Size, Structure and Management SECTION IV: BIOTECHNOLOGY 18: Genomics - Discovery and Functional Analysis of Genes 19: Marker-assisted Selection and Breeding - Indirect Selection, Direct Selection and Breeding Applications 20: Genetic Engineering - Target Traits, Transformation and Regeneration

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