Genetics (non-medical) Books

Book SynopsisThis book focuses on the previously neglected interface between the conservation of plant genetic resources and their utilization. Only through utilization can the potential value of conserved genetic resources be realised. However, as this book shows, much conserved germplasm has to be subjected to long-term pre-breeding and genetic enhancement before it can be used in plant breeding programmes.The authors explore the rationale and approaches for such pre-breeding efforts as the basis for broadening the genetic bases of crop production. Examples from a range of major food crops are presented and issues analysed by leading authorities from around the world.Table of Contentsa: Foreword, M Duwayri and G Hawtin b: Preface, D Cooper, C Spillane and T Hodgkin PART ONE: GENERAL PRINCIPLES 1: Broadening the genetic base of crops: an overview, D Cooper, T Hodgkin and C Spillane 2: Evolutionary and genetic perspectives on the dynamics of crop genepools, C Spillane and P Gepts 3: Base broadening: introgression and incorporation, B Spoor and N Simmonds 4: The role of local level gene flow in enhancing and maintained genetic diversity, J Berthaud et al. 5: Regulatory aspects of breeding for diversity, N Louwaars 6: Decentralized and participatory plant breeding for marginal environments, S Ceccarelli et al. 7: Empowering farmers and broadening the genetic base: agricultural research and resource management, R Salazar PART TWO: CROP CASE STUDIES 8: The state of millet diversity and its use in West Africa, O Niangado 9: State of the use of maize genetic diversity in the USA and sub-Saharan Africa, S P Tallury and M M Goodman 10: The state of use of potato genetic diversity, R Ortiz 11: The state of use of cassava genetic diversity and a proposal to enhance it, G Second and C Iglesias 12: State of use of Musa diversity, S Sharrock and E Frison PART THREE: POPULATION MANAGEMENT 13: Dynamic management of genetic resources: a 13 year experiment on wheat, I Goldringer et al. 14: Genetic base broadening of barley (Hordeum vulgare L.) in the Nordic countries, M Vetelainen and E A J Nissila 15: Evolutionary changes in Cambridge Composite Cross Five of barley, K M Ibrahim and J A Barrett 16: Genetic base broadening in the West Indies Sugar Cane Breeding Program by the incorporation of wild species, A J Kennedy 17: Potential of genetic resources and breeding strategies for base broadening in Beta, L Frese, B Desprez, and D Ziegler 18: HOPE, a hierarchical, open-ended system for broadening the breeding base of maize, L Kannenberg 19: The germplasm enhancement of maize (GEM) project: Private and public sector collaboration, L Pollak and W Salhuana 20: A French cooperative program for management and utilization of maize genetic resources, A Gallais, J P Monod, and others PART FOUR: OTHER APPROACHES TO BROADENING THE GENETIC BASE OF CROPS 21: Broadening the genetic base of lentil in South Asia, W Erskine et al. 22: Genetic diversity of barley: use of locally adapted germplasm to enhance yield and yield stability of barley in dry areas, S Grando, R Von Bothmer, S Ceccarelli 23: Breeding Phaseolus for intercrop combinations in the Andean highlands, J P Baudoin, F Camarena and M Lobo 24: Improving potato resistance to disease under the Global Initiative on Late Blight, T Bodo, R Trognitz, M Bonierbale, J A Landeo, G Forbes, J E Bradshaw, G R Mackay, R Waugh, M A Huarte, and L Colon 25: A Mexican bean breeding program for comprehensive horizontal resistance to all locally important pests and diseases, R G Espinosa, R A Robinson, P R Vallejo, F C Gonzalez and F R Rosales 26: The impact of decentralized and participatory plant breeding on the genetic base of crops, J Witcombe 27: Base broadening for client-oriented impact, L Sperling et al.

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Book SynopsisPlant genotyping, or DNA fingerprinting of plants, is a technology that has matured and is poised for widespread practical application in the fields of breeding, commerce and research. This book examines the technologies available and their application in the analysis of:Wild plant populationsGermplasm collections Plant breedingContributors include leading research workers in this field from North America, Europe and Australasia.Table of Contents1: Molecular markers available for use in plant genotyping 2: Plant genotyping by analysis of single nucleotide polymorphisms, K J Edwards and R Mogg, University of Bristol, UK 3: Plant genotyping by analysis of microsatellites T A Holton, Southern Cross University, Australia 4: Plant genotyping using arbitrarily amplified DNA, G Caetano-Anollés, University of Oslo, Norway 5: Plant genotyping based upon analysis of single nucleotide polymorphisms using microarrays, B Lemieux, University ofDelaware, USAGenotyping plant genetic resource collections 6: Genotyping in plant genetic resources, B V Ford-Lloyd, University of Birmingham, UK 7: Applications of molecular marker techniques to the use of international germplasm collections, M Warburton and D Hoisington, Applied Biotechnology Center, CIMMYT, México Genotyping cultivated and wild germplasm 8: Molecular analysis of wild plant germplasm: the case of tea tree (Melaleuca alternifolia), L S Lee, M Rossetto, L Homer, R J Henry, Southern Cross University, Australia 9: Genotyping Pacific Island Taro (Colocasia esculenta (L.) Schott) germplasm, I D Godwin, E S Mace and Nurzuhairawaty,The University of Queensland, Australia 10: Molecular marker systems for sugarcane germplasm analysis, G M Cordeiro, Southern Cross University, Australia 11: Microsatellite analysis in cultivated hexaploid wheat and wild wheat relatives, A McLauchlan, R J Henry, Southern Cross University, Australia, P G Isaac, Agrogene, France and K J Edwards, University of Bristol, UK 12: Comparison of RFLP & AFLP marker systems for assessing genetic diversity in Australian barley varieties & breeding, K Chalmers, University of Adelaide, South Australia Development of molecular markers for use in plant genotyping 13: Discovery and application of single nucleotide polymorphism markers in plants, D Bhattramakki and A Rafalski, DuPont Agricultural Products, USA 14: Producing and exploiting enriched microsatellite libraries, T L Maguire, University of Queensland, Australia 15: Sourcing of SSR markers from related plant species, M Rossetto, Southern Cross University, Australia 16: Microsatellites derived from ESTs, and their comparison with those derived by other methods, K D Scott, Southern Cross University, AustraliaTechnical developments and issues in plant genotyping 17: Plant DNA Extraction, R J Henry, Southern Cross University, Australia 18: Collection, reporting and storage of microsatellite genotype data, N Harker, Southern Cross University, Australia 19: Commercial applications of plant genotyping, L S Lee and R J Henry, Southern Cross University, Australia 20: Non-gel based techniques for plant genotyping, R Kota, Southern Cross University, Australia 21: Using molecular information for decision support in wheat breeding, H Eagles, CRC for Molecular Plant Breeding, M Cooper, The University of Queensland, R Shorter, CSIRO Tropical Agriculture, P Fox, CIMMYT, 22: Application of DNA profiling to an outbreeding forage species, J Forster, E Jones, R Kölliker, M Drayton, M Dupal, K Guthridge, La Trobe University, Australia & K Smith, Pastoral & Veterinary Institute, Australia

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Book SynopsisThis book has been developed from the keynote addresses delivered at the third IOBC International Symposium (co-organized with CILBA) that was held in Montpellier in October 2002, to address recent developments in genetics and evolutionary biology as applied to biological control. Chapters are organized around the following themes: Genetic structure of pest and natural enemy populations Molecular diagnostic tools in biological control Tracing the origin of pests and natural enemies Predicting evolutionary change in pests and natural enemies Compatibility of transgenic crops and natural enemies Genetic manipulation of natural enemies. The authors identify new issues for each of the major approaches in applied biological control. These include the (1) use of molecular genetics to trace the origin of target pests in classical biological control, (2) potential of mass-reared, transgenic agents in augmentative biological control, and (3) compatibility of transgenic crops and natural eneTable of Contents1: Genetic structure of natural plant and pathogen populations, J J Burdon and P H Thrall, CSIRO, Canberra, Australia 2: Measuring genetic variation in natural enemies used for biological control: why and how? E Wajnberg, INRA, France 3: Molecular systematics, Chalcidoidea and biological control, J Heraty, University of California, USA 4: Genetic markers in rust fungi and their application to weed biocontrol, K J Evans, Tasmanian Institute of Agricultural Research, Australia and D R Gomez, University of Adelaide, Australia 5: Tracing the origin of pests and natural enemies: genetic and statistical approaches, G K Roderick, University of California, USA 6: Tracing the origin of cryptic insect pests and vectors, and their natural enemies, J K Brown, University of Arizona, USA 7: Predicting evolutionary change in invasive, exotic plants and its consequences for plant-herbivore interactions, H Müller-Schärer and T Steinger, Université de Fribourg, Swizterland 8: Experimental evolution in host-parasitoid interactions, A R Kraaijeveld, Imperial College at Silwood Park, Ascot, UK 9: Interactions between natural enemies and transgenic insecticidal crops, J J Obrycki, Iowa State University, USA, J R Ruberson, University of Georgia, USA and J E Losey, Cornell University, USA 10: The GMO guidelines project: development of international scientific environmental biosafety testing guidelines for transgenic plants, A Hilbeck, Swiss Federal Institute of Technology, (ETH), Switzerland and Steering Comittee of the GMO Guildlines Project 11: Genetic manipulation of natural enemies: can we improve biological control by manipulating the parasitoid and/or the plant? G M Poppy, University of Southampton, UK and W Powell, Rothamsted Research, Harpenden, UK 12: Sex-ratio distorters and other selfish genetic elements: implications for biological control, R Stouthamer, University of California, USA

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Book SynopsisThis volume explores the latest methods used by researchers to study the detection, characterization, and various aspects of viroids. The chapters in this book are organized into seven parts and cover topics such as detection methods based on the biology of viroids; detection techniques based on electrophoresis and hybridization techniques; PCR-based techniques that provide high degrees of sensitivity; emerging area of nucleic acid sequence-based technology; and emerging techniques in viroid research such as RNA silencing, splicing, and viroid structure. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and comprehensive, Viroids: Methods and Protocols is a valuable resource for researchers and graduaTable of ContentsPreface…Table of Contents…Contributing Authors…Part I Biological Techniques1. Study and Detection of Citrus Viroids in Woody HostsRobert R. Krueger and Georgios Vidalakis2. Detection and Characterization of Viroids via Biological Assays on Herbaceous HostsRosemarie W. Hammond3. Analysis on RNA Motif-Based RNA Trafficking in PlantsHeather N. Smith, Junfei Ma, and Ying Wang4. Isolation and Transfection of Citrus Protoplasts with Citrus Exocortis ViroidSubhas Hajeri, James Ng, Jude Grosser, and Georgios VidalakisPart II Electrophoresis and Hybridization Techniques5. High-Throughput RNA Extraction from Citrus Tissues for the Detection of ViroidsTyler Dang, Fatima Osman, Jinbo Wang, Tavia Rucker, Sohrab Bodaghi, Shih-hua Tan, Deborah Pagliaccia, Irene Lavagi-Craddock, and Georgios Vidalakis6. Extraction and Purification of Viroids from Herbaceous HostsRosemarie W. Hammond7. Detection of Viroids by sPAGE Gel ElectrophoresisNúria Duran-Vila8. Two-Dimensional Polyacrylamide-Gel Electrophoresis Analysis of Viroid RNAsJosé-Antonio Daròs9. A Simplified Dot-Blot Hybridization Protocol for Potato spindle tuber viroid Detection in SolanaceaeOxana Kekstidou, Christina Varveri, and Nikon Vassilakos10. Gel Blot Hybridization for ViroidsPedro Serra11. Tissue Print Hybridization for Detection and Characterization of ViroidsMaria S. Kaponi, Teruo Sano, and Panayota E. Kyriakopoulou12. Fluorescein-Based Electrophoretic Mobility Shift AssayShachinthaka D. Dissanayaka Mudiyanselage and Ying WangPart III PCR Techniques13. Detection of Viroids by RT-PCRNerida J. Donovan, Grant A. Chambers, and Mengji Cao 14. Detection of Viroids using RT-qPCRSubhas Hajeri, Georgios Vidalakis, and Raymond Yokomi15. Multiplex RT-PCR Francesco Faggioli and Marta Luigi16. Real-Time Detection of Viroids using Singleplex and Multiplex Quantitative Polymerase Chain ReactionFatima Osman and Georgios Vidalakis17. Reverse Transcription-Loop Mediated Isothermal AMPlification (RT-LAMP) at the Service of Viroid DetectionIraklis N. Boubourakas and Panayota E. Kyriakopoulou18. SYBR ® Green RT-qPCR for the Universal Detection of Citrus ViroidsGeorgios Vidalakis, Jinbo Wang, Tyler Dang, Tavia Rucker, Sohrab Bodaghi, Shi-hua Tan, Irene Lavagi-Craddock, Alexandra Syed, Gerardo Uribe, Yi Hsieh, and Joana Carbajal-Moreno19. Detection of Avocado sunblotch and Other Viroids using RNA Filter Paper Capture and RT-PCRDeborah M. Mathews, Sohrab Bodaghi, James A. Heick, and J. Allan DoddsPart IV Cloning and Sequencing Techniques20. Cloning and Sequencing of ViroidsRosemarie W. Hammond21. QuantiGene Plex Assay: A Method for High-Throughput Multiplex Citrus Viroid Detection and IdentificationTyler Dang, Jinbo Wang, Tavia Rucker, Sohrab Bodaghi, Irene Lavagi-Craddock, and Georgios Vidalakis22. Culture-Independent Discovery of Viroids by Deep Sequencing and Computational AlgorithmsAli Raza, Shou-Wei Ding, and Qingfa Wu 23. An In Silico Detection of a Citrus Viroid from Raw High Throughput Sequencing DataTyler Dang, Andres Espindola, Georgios Vidalakis, and Kitty CardwellPart V RNA Silencing Techniques24. Detection of Viroid RNA and vd-siRNA in N. benthamiana Plants: Northern Blot Analyses for Viroid and vd-siRNAsKonstantina Katsarou, Nikoleta Kryovrysanaki, and Kriton KalantidisPart VI Splicing Techniques25. Production of Recombinant RNA in Escherichia coli Using Eggplant Latent Viroid as a ScaffoldBeltrán Ortolá and José-Antonio DaròsPart VII Structural Analysis26. Predicting the Structure of a ViroidGerhard StegerSubject Index List…

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Book SynopsisThis volume details generation of gene-edited cell lines and organisms as models for human diseases, pest control, and large animal welfare and production outcomes. Chapters guide readers through gene regulation, editing, screening of cell lines, genome editing, and an overview of the tools for efficient genome editing including; ZFNs, TALENs, and CRISPR. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step- by-step, readily reproducible protocols. Authoritative and cutting-edge, Applications of Genome Modulation and Editing aims to be a useful and practical guide for researchers to commence or advance their study in this field. Table of ContentsPart I: Gene Editing Approaches 1. Historical DNA manipulation Overview LLuis Montoliu 2. Tools for efficient genome editing; ZFN, TALEN, and CRISPR Yasaman Shamshirgaran,,Jun Liu, Huseyin Sumer, Paul J. Verma and Amir Taheri-Ghahfarokhi Part II: Genetic Manipulation Methods 3. Efficient generation of stable cell lines with inducible neuronal transgene expression using the piggyBac transposon system Jinchao Gu, Huseyin Sumer and Brett Cromer 4. Modifying Bacterial Artificial Chromosomes for Extended Genome Modification Hannah Auch, Nikolai Klymiuk and Petra Runa-Vochozkova 5. Site specific editing of the genome in Pluripotent cells Luis Ortega and Joseph Rosenbluh 6. Targeting the AAVS1 site with transgene cassette by CRISPR/Cas9 with an inducible transgene cassette for the to neuronal differentiation of human pluripotent stem cells Jinchao Gu, Ben Rollo, Huseyin Sumer and Brett Cromer 7. Microinjection of zygotes for CRISPR/Cas9 mediated insertion of transgenes into the murine Rosa26 safe harbour Fabien Delerue and Lars M. Ittner 8. CRISPR-on for endogenous activation of SMARCA4 expression in bovine embryos Virgilia Alberio, Virginia Savy and Daniel F. Salamone Part III: Applications of Genome Manipulation 9. CRISPR/Cas mutagenesis to generate novel traits in Bactrocera tryoni for Sterile Insect Technique Amanda Choo, Elisabeth Fung, Thu N.M. Nguyen, Anzu Okada and Peter Crisp 10. CRISPR/Cas9 Genome Editing in the New World Screwworm and Australian Sheep Blowfly Daniel F. Paulo, Megan E. Williamson and Maxwell J. Scott 11. Generation of gene drive mice for invasive pest population suppression Mark Bunting, Chandran Pfitzner, Luke Gierus, Melissa White, Sandra Piltz and Paul Thomas Part IV: Large animal models of human disease 12. Generation of a human deafness sheep model using the CRISPR/Cas system Martina Crispo, Vanessa Chenouard, Pedro dos Santos-Neto, Laurent Tesson, Marcela Souza, JeanMarie Heslan, Federico Cuadro, Ignacio Anegón and Alejo Menchaca 13. Targeted Gene Editing in Porcine Germ Cells Taylor Goldsmith, Alla Bondareva, Dennis Webster, Anna Laura Voigt, Lin Su, Daniel F. Carlson and Ina Dobrinski 14. Generating a Heat Tolerance Mouse Model Jun Liu and Paul J. Verma Part V: Large Animal Welfare and Production Outcomes 15. Generation of pigs that produce single sex progeny Björn Petersen and Stefanie Kurtz 16. Generation of Double-muscled Sheep and Goats by CRISPR/Cas9-mediated Knockout of the Myostatin Gene Peter Kalds, Martina Crispo, Chao Li, Laurent Tesson, Ignacio Anegon, Yulin Chen, Xiaolong Wang and Alejo Menchaca Part VI: Concluding Remarks 17. Regulatory and policy considerations around applications of genome editing in agriculture Steffi Friedrichs, Karinne Ludlowand Peter Kearns

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Book SynopsisThis second edition provides new and updated protocols that can be used for generation of knockout animals. Chapters guide the reader through basic protocols for three genome editing technologies, target design tools, and specific protocols for each animal. Written in the successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Genome Editing in Animals: Methods and Protocols, Second Edition aims to be a useful practical guide to researches to help further their study in this field. Table of Contents1. Construction and Evaluation of Zinc Finger Nucleases Hiroshi Ochiai and Takashi Yamamoto 2. Updated overview of TALEN construction systems Tetsushi Sakuma and Takashi Yamamoto 3. CRISPR/Cas9 Izuho Hatada, Sumiyo Morita, and Takuro Horii 4 SNPD-CRISPR: Single Nucleotide Polymorphism-Distinguishable Repression or Enhancement of a Target Gene Expression by CRISPR System Shohei Maruyama, Takashi Kusakabe, Xinyi Zou, Yoshiaki Kobayashi, Yoshimasa Asano, Qingbo S. Wang, and Kumiko Ui-Tei 5. Utilizing large functional and population genomics resources for CRISPR/Cas perturbation experiment design Qingbo S. Wang, Kumiko Ui-Tei 6. Generation of genome-edited mice by cytoplasmic injection of CRISPR-Cas9 RNA Takuro Horii and Izuho Hatada 7. Gene targeting in mouse embryonic stem cells via CRISPR/Cas9 ribonucleoprotein (RNP) mediated genome editing. Manabu Ozawa, Chihiro Emori, and Masahito Ikawa 8. Generation of Knock-in Mouse by Genome Editing Wataru Fujii 9. Introduction of genetic mutations into mice by Base Editor and Target-AID Hiroki Sasaguri 10. Genome editing in mouse and rat by electroporation Takehito Kaneko 11. Generation of floxed mice by sequential electroporation Takuro Horii, Ryosuke Kobayashi, and Izuho Hatada 12. Efficient detection of flox mice using in vitro Cre recombination Ryosuke Kobayashi, Takuro Horii, and Izuho Hatada 13. VCre/VloxP and SCre/SloxP as reliable site-specific recombination systems for genome engineering Manabu Nakayama 14. Efficient CRISPR/Cas9-Assisted Knockin of Large DNA Donors by Pronuclear Microinjection During S-phase in Mouse Zygotes Takaya Abe, Ken-ichi Inoue, and Hiroshi Kiyonari 15. Genome editing of murine liver hepatocytes by AAV vector-mediated expression of Cas9 in vivo Yuji Kashiwakura and Tsukasa Ohmori 16. Non-Viral Ex Vivo Genome-Editing in Mouse Bona Fide Hematopoietic Stem Cells with CRISPR/Cas9 Hiromasa Hara1, Natsagdorj Munkh-Erdene, Suvd Byambaa, and Yutaka Hanazono 17. Genome editing of rat Takehito Kaneko 18. A simple and efficient method for generating KO rats using in vitro fertilized oocytes Kohtaro Morita, Arata Honda, and Masahide Asano 19. Editing the Genome of the Golden Hamster (Mesocricetus auratus) Michiko Hirose, Toshiko Tomishima, and Atsuo Ogura 20. Gene targeting in rabbits: single-step generation of knockout rabbits by microinjection of CRISPR/Cas9 plasmids Arata Honda 21. Genome Editing of Pig Masahito Watanabe and Hiroshi Nagashima 22. GEEP method: an optimized electroporation-mediated gene-editing approach for establishment of knockout pig lines Fuminori Tanihara, Maki Hirata, and Takeshige Otoi 23. Genome editing mediated by primordial germ cell in chicken Jae Yong Han and Hong Jo Lee 24. CRISPR–Cas9-mediated genome modifications in zebrafish Yusuke Kamachi and Atsuo Kawahara 25. Genome Editing of Medaka Rie Hara, Satoshi Ansai, and Masato Kinoshita 26. CRISPR-Cas9 based functional analysis in amphibians; Xenopus laevis, Xenopus tropicalis, and Pleurodeles waltl Miyuki Suzuki, Midori Iida, Toshinori Hayashi, and Ken-ichi T Suzuki 27. Genome Editing of Silkworms Takuya Tsubota, Hiroki Sakai, and Hideki Sezutsu 28. Improved genome editing in the ascidian Ciona with CRISPR/Cas9 and TALEN Yasunori Sasakura and Takeo Horie 29. Genome editing of C. elegans Takuma Sugi

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Book SynopsisRNA Isolation from Human Stem Cell Derived Retinal Organoids.- Next generation Sequencing Application a Systematic Approach for High quality RNA Isolation from Skeletal Muscles.- Ultrasound induced Enrichment of Ultra trace miRNA Biosensing in Nanoliter Samples.- Direct Detection of SARS CoV 2 RNA in Saliva with Colorimetric RT LAMP.- NASBA Coupled to Paper Microfluidics for RNA Detection.- Single cell Imaging of mRNA by Target RNA initiated RCA.- Detection of Foodborne RNA Viruses by Reverse Transcriptase Droplet Digital PCR.- Single molecule RNA Imaging in Live Cells with an Avidity based Fluorescent Light up Aptamer biRhoBAST.- Assessing MicroRNA Profiles from Low Concentration Extracellular Vesicle RNA Utilizing NanoString nCounter Technology.- Liquid and Solid Hybridization Methods to Detect RNAs.- Visualization of Individual RNA Molecules by Proximity Ligation based Chromogenic In Situ Hybridization Assay.- Quantum Dots Based Protocols for the Detection of RNAs.- RNA Analysis Using Immunoassay Detection Format.- Fluorescent Techniques for RNA Detection in Nanoparticles.- Sequencing 10X Genomics 3' HT assay for Gene Expression.- Single Cell Sequencing of 3' RNA Transcripts.- Short Read RNA Seq.- RNA Seq Data Analysis.- Bi clustering for Epi transcriptomic Co functional Analysis.- RNA Folding, Mutation and Detection.- Epitranscriptomic Mass Spectrometry.- Polyvinylamine and Its Derivative as Effective Carrier for Targeted Delivery of Small RNAs.- Delivery of mRNA with histidine-lysine peptides.- Plant Virus Like Particles for RNA Delivery.- Lipid-based Nanoparticles for RNA Delivery.- In vitro Amplification and Selection of Engineered RNase P ribozyme for Gene Targeting Applications.- Rapid Ribonuclease P Kinetics Measured by Stopped-Flow Fluorescence and Fluorescence Anisotropy.- Computational Design of Allosteric Ribozymes via Genetic Algorithms.

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Book SynopsisModified Alkaline Comet Assay to Detect Oxidative DNA Damage.- Radiation-Induced DNA Strand Break Detection by Gel Electrophoresis.- Quantitative Measurement of 8-Hydroxy-2′-Deoxyguanosine in Serum/Plasma and Urine Using an Enzyme-Linked Immunosorbent Assay.- Radiation-Induced Gamma-H2AX Foci Staining and Analysis.- Non-Radiolabeled Radioresistant DNA Synthesis and S-Phase Checkpoint Analysis.- Constant Field Gel Electrophoresis Analysis for DNA Double-Strand Break and Its Repair.- Detection of Chromatid Break and Micronucleus Formation Induced by Low- and High-LET Irradiation.- Measurement of DNA Polymerase and Microhomology-Mediated End-Joining Activities by Gel Electrophoresis and smFRET Techniques.- UV-Induced DNA Damage Detection by ELISA Analysis.- G2 Premature Chromosome Condensation (G2-PCC) by Calyculin A to Analyze DNA Double-Strand Breaks and Their Repair.- Mitotic Shake-Off and Cell Cycle Synchronization.- DCFDA Assay for Oxidative Stress Measurement in Fluorometer.- HPRT Mutation Assay for Chinese Hamster Ovary Cells.- Detection of De Novo Mutations by Sequencing Reduced Representation Libraries.- Chemical-Induced DNA Damage Identification by High-Throughput Detection of DNA Double-Strand Break.- Assessing DNA Damage Through the Cell Cycle Using Flow Cytometry.- A Mass Spectrometry-Based Proteomics Workflow for Concurrent Profiling of Protein Thiol Oxidation and Phosphorylation.- Analyzing Homologous Recombination Using Antibiotic Marker Substrates in Mammalian Cells.

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Book SynopsisMicroRNAs in Medicine provides an access point into the current literature on microRNA for both scientists and clinicians, with an up-to-date look at what is happening in the emerging field of microRNAs and their relevance to medicine.Table of ContentsForeword ix Sir David Baulcombe Preface xi Contributors xiii 1 MICRORNAS: A BRIEF INTRODUCTION 1 Charles H. Lawrie PART I: MICRORNAS AS PHYSIOLOGICAL REGULATORS 25 2 MICRORNA REGULATION OF STEM CELL FATE AND REPROGRAMMING 27 Erika Lorenzo Vivas, Gustavo Tiscornia, and Juan Carlos Izpisua Belmonte 3 MICRORNAS AS REGULATORS OF IMMUNITY 41 Donald T. Gracias and Peter D. Katsikis 4 REGULATION OF SENESCENCE BY MICRORNAS 59 Ioannis Grammatikakis and Myriam Gorospe 5 THE EMERGENCE OF GEROMIRS: A GROUP OF MICRORNAS IMPLICATED IN AGING 77 Alejandro P. Ugalde, Agnieszka Kwarciak, Xurde M. Caravia, Carlos López-Otín, and Andrew J. Ramsay 6 MICRORNAS AND HEMATOPOIESIS 91 Sukhinder K. Sandhu and Ramiro Garzon 7 MICRORNAS IN PLATELET PRODUCTION AND ACTIVATION 101 Leonard C. Edelstein, Srikanth Nagalla, and Paul F. Bray PART II: MICRORNAS IN INFECTIOUS DISEASE: HOST–PATHOGEN INTERACTIONS 117 8 MICRORNAS AS KEY PLAYERS IN HOST-VIRUS INTERACTIONS 119 Aurélie Fender and Sébastien Pfeffer 9 MICRORNA EXPRESSION IN AVIAN HERPESVIRUSES 137 Yongxiu Yao and Venugopal Nair 10 FUNCTION OF HUMAN CYTOMEGALOVIRUS MICRORNAS AND POTENTIAL ROLES IN LATENCY 153 Natalie L. Reynolds, Jon A. Pavelin, and Finn E. Grey 11 INVOLVEMENT OF SMALL NON-CODING RNA IN HIV-1 INFECTION 165 Guihua Sun, John J. Rossi, and Daniela Castanotto 12 MICRORNA IN MALARIA 183 Panote Prapansilp and Gareth D.H. Turner PART III: CANCER 199 13 THE MICRORNA DECALOGUE OF CANCER INVOLVEMENT 201 Tanja Kunej, Irena Godnic, Minja Zorc, Simon Horvat, and George A. Calin 14 MICRORNAS AS ONCOGENES AND TUMOR SUPPRESSORS 223 Eva E. Rufi no-Palomares, Fernando J. Reyes-Zurita, Jose Antonio Lupiáñez, and Pedro P. Medina 15 LONG NON-CODING RNAS AND THEIR ROLES IN CANCER 245 Yolanda Sánchez and Maite Huarte 16 REGULATION OF HYPOXIA RESPONSES BY MICRORNA EXPRESSION 267 Carme Camps, Adrian L. Harris, and Jiannis Ragoussis 17 CONTROL OF RECEPTOR FUNCTION BY MICRORNAS IN BREAST CANCER 287 Claudia Piovan and Marilena V. Iorio 18 MICRORNAS IN HUMAN PROSTATE CANCER: FROM PATHOGENESIS TO THERAPEUTIC IMPLICATIONS 311 Mustafa Ozen and Omer Faruk Karatas 19 MICRORNA SIGNATURES AS BIOMARKERS OF COLORECTAL CANCER 329 Katrin Pfütze, Xiaoya Luo, and Barbara Burwinkel 20 GENETIC VARIATIONS IN MICRORNA-ENCODING SEQUENCES AND MICRORNA TARGET SITES ALTER LUNG CANCER SUSCEPTIBILITY AND SURVIVAL 343 Ming Yang and Dongxin Lin 21 MICRORNA IN MYELOPOIESIS AND MYELOID DISORDERS 353 Sara E. Meyer and H. Leighton Grimes 22 MICRORNA DEREGULATION BY ABERRANT DNA METHYLATION IN ACUTE LYMPHOBLASTIC LEUKEMIA 371 Xabier Agirre and Felipe Prósper 23 ROLE OF MIRNAS IN THE PATHOGENESIS OF CHRONIC LYMPHOCYTIC LEUKEMIA 383 Veronica Balatti, Yuri Pekarsky, Lara Rizzotto, and Carlo M. Croce 24 MICRORNA IN B-CELL NON-HODGKIN’S LYMPHOMA: DIAGNOSTIC MARKERS AND THERAPEUTIC TARGETS 403 Nerea Martínez, Lorena Di Lisio, and Miguel Angel Piris 25 MICRORNAS IN DIFFUSE LARGE B-CELL LYMPHOMA 419 Izidore S. Lossos and Alvaro J. Alencar 26 THE ROLE OF MICRORNAS IN HODGKIN’S LYMPHOMA 435 Wouter Plattel, Joost Kluiver, Arjan Diepstra, Lydia Visser, and Anke van den Berg 27 MICRORNA EXPRESSION IN CUTANEOUS T-CELL LYMPHOMAS 449 Cornelis P. Tensen PART IV: HEREDITARY AND OTHER NON-INFECTIOUS DISEASES 463 28 MICRORNAS AND HEREDITARY DISORDERS 465 Matías Morín and Miguel A. Moreno-Pelayo 29 MICRORNAS AND CARDIOVASCULAR DISEASES 477 Koh Ono 30 MICRORNAS AND DIABETES 495 Romano Regazzi 31 MICRORNAS IN LIVER DISEASES 509 Patricia Munoz-Garrido, Marco Marzioni, Elizabeth Hijona, Luis Bujanda, and Jesus M. Banales 32 MICRORNA REGULATION IN MULTIPLE SCLEROSIS 523 Andreas Junker 33 THE ROLE OF MICRORNAS IN ALZHEIMER’S DISEASE 539 Shahar Barbash and Hermona Soreq 34 CURRENT VIEWS ON THE ROLE OF MICRORNAS IN PSYCHOSIS 553 Aoife Kearney, Javier A. Bravo, and Timothy G. Dinan PART V: CIRCULATING MICRORNAS AS CELLULAR MESSENGERS AND NOVEL BIOMARKERS 567 35 CIRCULATING MICRORNAS AS NON-INVASIVE BIOMARKERS 569 Heidi Schwarzenbach and Klaus Pantel 36 CIRCULATING MICRORNAS AS CELLULAR MESSENGERS 589 Kasey C. Vickers 37 RELEASE OF MICRORNA-CONTAINING VESICLES CAN STIMULATE ANGIOGENESIS AND METASTASIS IN RENAL CARCINOMA 607 Federica Collino, Cristina Grange, and Giovanni Camussi PART VI: THERAPEUTIC USES OF MICRORNAS: CURRENT PERSPECTIVES AND FUTURE DIRECTIONS 623 38 MICRORNA REGULATION OF CANCER STEM CELLS AND MICRORNAS AS POTENTIAL CANCER STEM CELL THERAPEUTICS 625 Can Liu and Dean G. Tang 39 THERAPEUTIC MODULATION OF MICRORNAS 639 Achim Aigner and Hannelore Dassow 40 LOCKED NUCLEIC ACIDS AS MICRORNA THERAPEUTICS 663 Henrik Ørum Index 673

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Book SynopsisLANDSCAPE GENETICS: CONCEPTS, METHODS, APPLICATIONS LANDSCAPE GENETICS: CONCEPTS, METHODS, APPLICATIONS Edited by Niko Balkenhol, Samuel A. Cushman, Andrew T. Storfer, Lisette P. Waits Landscape genetics is an exciting and rapidly growing field, melding methods and theory from landscape ecology and population genetics to address some of the most challenging and urgent ecological and evolutionary topics of our time. Landscape genetic approaches now enable researchers to study in detail how environmental complexity in space and time affect gene flow, genetic drift, and local adaptation. However, learning about the concepts and methods underlying the field remains challenging due to the highly interdisciplinary nature of the field, which relies on topics that have traditionally been treated separately in classes and textbooks. In this edited volume, some of the leading experts in landscape genetics provide the first comprehensive introduction to underlyinTable of ContentsList of Contributors ix Website xi Acknowledgments xiii Glossary xv 1 Introduction to Landscape Genetics – Concepts Methods Applications 1 Niko Balkenhol Samuel A. Cushman Andrew Storfer and Lisette P. Waits 1.1 Introduction 1 1.2 Defining landscape genetics 2 1.3 The three analytical steps of landscape genetics 3 1.4 The interdisciplinary challenge of landscape genetics 3 1.5 Structure of this book – concepts methods applications 5 References 6 Part 1: Concepts 2 Basics of Landscape Ecology: An Introduction to Landscapes and Population Processes for Landscape Geneticists 11 Samuel A. Cushman Brad H. McRae and Kevin McGarigal 2.1 Introduction 11 2.2 How landscapes affect population genetic processes 12 2.3 Defining the landscape for landscape genetic research 16 2.4 Defining populations and characterizing dispersal processes 21 2.5 Putting it together: combinations of landscape and population models 24 2.6 Frameworks for delineating landscapes and populations for landscape genetics 26 2.7 Current challenges and future opportunities 30 References 30 3 Basics of Population Genetics: Quantifying Neutral and Adaptive Genetic Variation for Landscape Genetic Studies 35 Lisette P. Waits and Andrew Storfer 3.1 Introduction 35 3.2 Overview of landscape influences on genetic variation 36 3.3 Overview of DNA types and molecular methods 38 3.4 Important population genetic models 41 3.5 Measuring genetic diversity 45 3.6 Evaluating genetic structure and detecting barriers 46 3.7 Estimating gene flow using indirect and direct methods 50 3.8 Conclusion and future directions 52 References 53 4 Basics of Study Design: Sampling Landscape Heterogeneity and Genetic Variation for Landscape Genetic Studies 58 Niko Balkenhol and Marie-Josée Fortin 4.1 Introduction 58 4.2 Study design terminology used in this Chapter 59 4.3 General study design considerations 60 4.4 Considerations for landscape genetic study design 61 4.5 Current knowledge about study design effects in landscape genetics 66 4.6 Recommendations for optimal sampling strategies in landscape genetics 71 4.7 Conclusions and future directions 73 References 74 5 Basics of Spatial Data Analysis: Linking Landscape and Genetic Data for Landscape Genetic Studies 77 Helene H. Wagner and Marie-Josée Fortin 5.1 Introduction 77 5.2 How to model landscape effects on genetic variation 84 5.3 How to model isolation-by-distance 93 5.4 Future directions 95 Acknowledgments 96 References 96 Part 2: Methods 6 Simulation Modeling in Landscape Genetics 101 Erin Landguth Samuel A. Cushman and Niko Balkenhol 6.1 Introduction 101 6.2 A brief overview of models and simulations 101 6.3 General benefits of simulation modeling 102 6.4 Landscape genetic simulation modeling 103 6.5 Examples of simulation modeling in landscape genetics 104 6.6 Designing and choosing landscape genetic simulation models 108 6.7 The future of landscape genetic simulation modeling 111 References 111 7 Clustering and Assignment Methods In Landscape Genetics 114 Olivier François and Lisette P. Waits 7.1 Introduction 114 7.2 Exploratory data analysis and model-based clustering for population structure analysis 115 7.3 Spatially explicit methods in landscape genetics 119 7.4 Spatial EDA methods: spatial PCA and spatial factor analysis 119 7.5 Spatial MBC methods 120 7.6 Habitat and environmental heterogeneity models 121 7.7 Discussion 123 References 125 8 Resistance Surface Modeling in Landscape Genetics 129 Stephen F. Spear Samuel A. Cushman and Brad H. McRae 8.1 Introduction 129 8.2 Techniques for parameterizing resistance surfaces 133 8.3 Estimating connectivity from resistance surfaces 137 8.4 Statistical validation of resistance surfaces 139 8.5 The future of the resistance surface in landscape genetics 142 8.6 Conclusions 144 References 144 9 Genomic Approaches in Landscape Genetics 149 Andrew Storfer Michael F. Antolin Stéphanie Manel Bryan K. Epperson and Kim T. Scribner 9.1 Introduction 149 9.2 Current landscape genomics methods 150 9.3 General challenges in landscape genomics 157 9.4 Spatial autocorrelation 157 9.5 Applications of landscape genomics to climate change 159 References 160 10 Graph Theory and Network Models In Landscape Genetics 165 Melanie Murphy Rodney Dyer and Samuel A. Cushman 10.1 Introduction 165 10.2 Background on graph theory 167 10.3 Landscape genetic applications 170 10.4 Recommendations for using graph approaches in landscape genetics 175 10.5 Current research needs 176 10.6 Conclusion – potential for application of graphs for conservation 176 References 177 Part 3: Applications 11 Landscapes and Plant Population Genetics 183 Rodney J. Dyer 11.1 Introduction 183 11.2 Contemporary population genetic processes 186 11.3 Historical population genetic processes 190 11.4 Future research 192 References 194 12 Applications of Landscape Genetics to Connectivity Research In Terrestrial Animals 199 Lisette P. Waits Samuel A. Cushman and Steve F. Spear 12.1 Introduction 199 12.2 General overview of terrestrial animal study systems and research challenges 199 12.3 Detecting barriers and defining corridors 202 12.4 Evaluating population dynamics 205 12.5 Detecting and predicting the response to landscape change 206 12.6 Common limitations of landscape genetic studies involving terrestrial animals 208 12.7 Testing ecological hypotheses about gene flow in heterogeneous landscapes 208 12.8 Knowledge gaps and future directions 213 References 214 13 Waterscape Genetics – Applications of Landscape Genetics To Rivers Lakes and Seas 220 Kimberly A. Selkoe Kim T. Scribner and Heather M. Galindo 13.1 Introduction 220 13.2 Understanding marine and freshwater environments 223 13.3 Typical research questions and approaches 229 13.4 Applications of landscape genetic approaches 234 13.5 Future directions: knowledge gaps research challenges and limitations 237 Acknowledgments 238 References 238 14 Current Status Future Opportunities and Remaining Challenges in Landscape Genetics 247 Niko Balkenhol Samuel A. Cushman Lisette P. Waits and Andrew Storfer 14.1 Introduction 247 14.2 Conclusion 1: issues of scale need to be considered 248 14.3 Conclusion 2: sampling needs to specifically target landscape genetic questions 248 14.4 Conclusion 3: choice of appropriate statistical methods remains challenging 249 14.5 Conclusion 4: simulations play a key role in landscape genetics 249 14.6 Conclusion 5: measures of genetic variation are rarely developed specifically for landscape genetics 249 14.7 Conclusion 6: landscape resistance is just one of the possible landscape–genetic relationships 250 14.8 Conclusion 7: genomics provides novel opportunities but also creates new challenges 250 14.9 Conclusion 8: the scope of landscape genetics needs to expand 251 14.10 Conclusion 9: specific hypotheses are rarely stated in current landscape genetic studies 251 14.11 Conclusion 10: a comprehensive theory for landscape genetics is currently missing 252 14.12 The future of landscape genetics 252 References 253 Index 257

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Book SynopsisThe simplicity and lack of redundancy in their regulatory genes have made ascidians one of the most useful species in studying developmental genomics. In Developmental Genomics of Ascidians, Dr.Trade Review"In his preface, the author describes Developmental Genomics of Ascidians as his “last and largest contribution to ascidian developmental biology” (p. xi). This book is indeed a major accomplishment and a great resource for the community" (The Quarterly Review of Biology 2016)Table of ContentsPREFACE ix CHAPTER 1 A BRIEF INTRODUCTION TO ASCIDIANS 1 CHAPTER 2 THE DEVELOPMENT OF TADPOLE LARVAE AND SESSILE JUVENILES 9 CHAPTER 3 GENOMICS, TRANSCRIPTOMICS, AND PROTEOMICS 19 CHAPTER 4 RESEARCH TOOLS 31 CHAPTER 5 THE FUNCTION AND REGULATION OF MATERNAL TRANSCRIPTS 41 CHAPTER 6 LARVAL TAIL MUSCLE 53 CHAPTER 7 ENDODERM 63 CHAPTER 8 EPIDERMIS 69 CHAPTER 9 NOTOCHORD 77 CHAPTER 10 THE LARVAL AND ADULT NERVOUS SYSTEMS 89 CHAPTER 11 MESENCHYME 107 CHAPTER 12 MAKING BLUEPRINT OF CHORDATE BODY: DYNAMIC ACTIVITIES OF REGULATORY GENES 113 CHAPTER 13 DEVELOPMENT OF THE JUVENILE HEART 137 CHAPTER 14 GERM-CELL LINE, GAMETES, FERTILIZATION, AND METAMORPHOSIS 145 CHAPTER 15 INNATE IMMUNE SYSTEM AND BLOOD CELLS 159 CHAPTER 16 COLONIAL ASCIDIANS: ASEXUAL REPRODUCTION AND COLONY SPECIFICITY 167 CHAPTER 17 EVOLUTIONARY DEVELOPMENTAL GENOMICS 175 INDEX 193

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Book SynopsisComputational and high-throughput methods, such as genomics, proteomics, and transcriptomics, known collectively as -omics, have been used to study plant biology for well over a decade now. This book provides an introduction to key omicsbased methods and their application in plant breeding.Trade Review“Accessible to advanced students, researchers, and professionals, Omics in Plant Breeding will be an essential entry point into this innovative and exciting field.” (Biotechnology, Agronomy, Society and Environment, 1 October 2014) Table of ContentsList of Contributors ix Foreword xiii 1 Omics: Opening up the "Black Box" of the Phenotype 1Roberto Fritsche-Neto and Aluizio Borem The Post-Genomics Era 3 The Omics in Plant Breeding 4 Genomics, Precision Genomics, and RNA Interference 5 Transcriptomics and Proteomics 8 Metabolomics and Physiognomics 8 Phenomics 9 Bioinformatics 10 Prospects 10 References 10 2 Genomics 13Antonio Costa de Oliveira, Luciano Carlos da Maia, Daniel da Rosa Farias, and Naciele Marini The Rise of Genomics 13 DNA Sequencing 13 Development of Sequence-based Markers 18 Genome Wide Selection (GWS) 25 Structural and Comparative Genomics 27 References 28 3 Transcriptomics 33Carolina Munari Rodrigues, Valeria S. Mafra, and Marcos Antonio Machado Methods of Studying the Transcriptome 34 Applications of Transcriptomics Approaches for Crop Breeding 46 Conclusions and Future Prospects 51 Acknowledgements 51 References 51 4 Proteomics 59Ilara Gabriela F. Budzinski, Thais Regiani, Monica T. Veneziano Labate, Simone Guidetti-Gonzalez, Danielle Izilda R. da Silva, Maria Juliana Calderan Rodrigues, Janaina de Santana Borges, Ivan Miletovic Mozol, and Carlos Alberto Labate History 59 Different Methods for the Extraction of Total Proteins 60 Subcellular Proteomics 64 Post-Translational Modifications 66 Quantitative Proteomics 69 Perspectives 72 References 73 5 Metabolomics 81Valdir Diola (in memoriam), Danilo de Menezes Daloso, and Werner Camargos Antunes Introduction 81 Metabolomic and Biochemical Molecules 83 Technologies for Metabolomics 83 Metabolomic Database Analysis 86 Metabolomics Applications 89 Metabolomics-assisted Plant Breeding 91 Associative Genome Mapping and mQTL Profiles 95 Large-scale Phenotyping Using Metabolomics 97 Conclusion and Outlook 98 References 99 6 Physionomics 103Frederico Almeida de Jesus, Agustin Zsogon, and Lazaro Eustaquio Pereira Peres Introduction 103 Early Studies on Plant Physiology and the Discovery of Photosynthesis 104 Biochemical Approaches to Plant Physiology and the Discovery of Plant Hormones 104 Genetic Approaches to Plant Physiology and the Discovery of Hormone Signal Transduction Pathways 106 Alternative Genetic Models for Omics Approaches in Plant Physiology 112 "Physionomics" as an Integrator of Various Omics for Functional Studies and Plant Breeding 117 Acknowledgements 121 References 121 7 Phenomics 127Roberto Fritsche-Neto, Aluizio Borem, and Joshua N. Cobb Introduction 127 Examples of Large-scale Phenotyping 128 Important Aspects for Phenomics Implementation 134 Main Breeding Applications 141 Final Considerations 144 References 144 8 Electrophoresis, Chromatography, and Mass Spectrometry 147Thais Regiani, Ilara Gabriela F. Budzinski, Simone Guidetti-Gonzalez, Monica T. Veneziano Labate, Fernando Cotinguiba, Felipe G. Marques, Fabricio E. Moraes, and Carlos Alberto Labate Introduction 147 Two-dimensional Electrophoresis (2DE) 148 Chromatography 150 Mass Spectrometry 155 Data Analysis 161 References 164 9 Bioinformatics 167J. Miguel Ortega and Fabricio R. Santos Introduction 167 The "Omics" Megadata and Bioinformatics 167 Hardware for Modern Bioinformatics 169 Software for Genomic Sequencing 170 Software for Contig Assembling 172 Assembly Using the Graph Theory 173 New Approaches in Bioinformatics for DNA and RNA Sequencing 174 Databases, Identification of Homologous Sequences and Functional Annotation 175 Annotation of a Complete Genome 179 Computational System with Chained Tasks Manager (Workflow) 181 Applications for Studies in Plants 182 Final Considerations 183 References 184 10 Precision Genetic Engineering 187Thiago J. Nakayama, Aluizio Borem, Lucimara Chiari, Hugo Bruno Correa Molinari, and Alexandre Lima Nepomuceno Introduction 187 Zinc Finger Nucleases (ZFNs) 190 Transcription Activator-like Effector Nucleases (TALENs) 193 Meganucleases (LHEs: LAGLIDADG Homing Endonucleases) 194 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) 195 Implications and Perspectives of the use of PGE in Plant Breeding 197 References 202 11 RNA Interference 207Francisco J.L. Aragao, Abdulrazak B. Ibrahim, and Maria Laine P. Tinoco Introduction 207 Discovery of RNAi 208 Mechanism of RNA Interference 209 Applications in Plant Breeding: Naturally Occurring Gene Silencing and Modification by Genetic Engineering 211 Resistance to Viruses 215 Host-induced Gene Silencing 218 Insect and Disease Control 218 Improving Nutritional Values 219 Secondary Metabolites 220 Perspectives 220 References 222 Index 229

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Book SynopsisBacteria in various habitats are subject to continuously changing environmental conditions, such as nutrient deprivation, heat and cold stress, UV radiation, oxidative stress, dessication, acid stress, nitrosative stress, cell envelope stress, heavy metal exposure, osmotic stress, and others. In order to survive, they have to respond to these conditions by adapting their physiology through sometimes drastic changes in gene expression. In addition they may adapt by changing their morphology, forming biofilms, fruiting bodies or spores, filaments, Viable But Not Culturable (VBNC) cells or moving away from stress compounds via chemotaxis. Changes in gene expression constitute the main component of the bacterial response to stress and environmental changes, and involve a myriad of different mechanisms, including (alternative) sigma factors, bi- or tri-component regulatory systems, small non-coding RNA's, chaperones, CHRIS-Cas systems, DNA repair, toxin-antitoxin systems, the stringent rTable of ContentsVOLUME 1 Preface, xiii Acknowledgements, xiv List of contributors, xv 1 Introduction, 1Frans J. de Bruijn Section 2: Key overview chapters, 3 2.1 Stress-induced changes in transcript stability, 5Dvora Biran and Eliora Z. Ron 2.2 StressChip for monitoring microbial stress response in the environment, 9Joy D. Van Nostrand, Aifen Zhou and Jizhong Zhou 2.3 A revolutionary paradigm of bacterial genome regulation, 23Akira Ishihama 2.4 Role of changes in σ70-driven transcription in adaptation of E. coli to conditions of stress or starvation, 37Umender K. Sharma 2.5 The distribution and spatial organization of RNA polymerase in Escherichia coli: growth rate regulation and stress responses, 48Ding Jun Jin, Cedric Cagliero, Jerome Izard, Carmen Mata Martin, and Yan Ning Zhou 2.6 The ECF classification: a phylogenetic reflection of the regulatory diversity in the extracytoplasmic function σ factor protein family, 64Daniela Pinto andThorsten Mascher 2.7 Toxin–antitoxin systems in bacteria and archaea, 97Yoshihiro Yamaguchi and Masayori Inouye 2.8 Bacterial sRNAs: regulation in stress, 108Marimuthu Citartan, Carsten A. Raabe, Chee-Hock Hoe, Timofey S. Rozhdestvensky, andThean-Hock Tang 2.9 Bacterial stress responses as determinants of antimicrobial resistance, 115Michael Fruci and Keith Poole 2.10 Transposable elements: a toolkit for stress and environmental adaptation in bacteria, 137Anna Ullastres, Miriam Merenciano, Lain Guio, and Josefa González 2.11 CRISPR–Cas system: a new paradigm for bacterial stress response through genome rearrangement, 146Joseph A. Hakim, Hyunmin Koo, Jan D. van Elsas, Jack T. Trevors, and Asim K. Bej 2.12 The copper metallome in prokaryotic cells, 161Christopher Rensing, Hend A. Alwathnani, and Sylvia F. McDevitt 2.13 Ribonucleases as modulators of bacterial stress response, 174Cátia Bárria, Vánia Pobre, Afonso M. Bravo, and Cecília M. Arraiano 2.14 Double-strand-break repair, mutagenesis, and stress, 185Elizabeth Rogers, Raul Correa, Brittany Barreto, María Angélica Bravo Núñez, P.J. Minnick, Diana Vera Cruz, Jun Xia, P.J. Hastings, and Susan M. Rosenberg 2.15 Sigma factor competition in Escherichia coli: kinetic and thermodynamic perspectives, 196Kuldeepkumar Ramnaresh Gupta and Dipankar Chatterji 2.16 Iron homeostasis and iron–sulfur cluster assembly in Escherichia coli, 203Huangen Ding 2.17 Mechanisms underlying the antimicrobial capacity of metals, 215Joe A. Lemire and Raymond J. Turner 2.18 Acyl-homoserine lactone-based quorum sensing in members of the marine bacterial Roseobacter clade: complex cell-to-cell communication controls multiple physiologies, 225Alison Buchan, April Mitchell,W. Nathan Cude, and Shawn Campagna 2.19 Native and synthetic gene regulation to nitrogen limitation stress, 234J örg Schumacher Section 3: One-, two-, and three-component regulatory systems and stress responses, 247 3.1 Two-component systems that control the expression of aromatic hydrocarbon degradation pathways, 249\Tino Krell 3.2 Cross-talk of global regulators in Streptomyces, 257Juan F. Martín, Fernando Santos-Beneit, Alberto Sola-Landa, and Paloma Liras 3.3 NO–H-NOX-regulated two-component signaling, 268Dhruv P. Arora, Sandhya Muralidharan, and Elizabeth M. Boon 3.4 The two-component CheY system in the chemotaxis of Sinorhizobium meliloti, 277Martin Haslbeck 3.5 Stimulus perception by histidine kinases, 282Hannah Schramke, Yang Wang, Ralf Heermann, and Kirsten Jung Section 4: Sigma factors and stress responses, 301 4.1 The extracytoplasmic function sigma factor EcfO protects Bacteroides fragilis against oxidative stress, 303Ivan C. Ndamukong, Samantha Palethorpe, Michael Betteken, and C. Jeffrey Smith 4.2 Regulation of energy metabolism by the extracytoplasmic function (ECF) σ factors of Arcobacter butzleri, 311Irati Martinez-Malaxetxebarria, Rudy Muts, Linda van Dijk, Craig T. Parker, William G. Miller, Steven Huynh,Wim Gaastra, Jos P.M. van Putten, Aurora Fernandez-Astorga, and Marc M.S.M Wösten 4.3 Extracytoplasmic function sigma factors and stress responses in Corynebacterium pseudotuberculosis, 321Thiago L.P. Castro, Nubia Seyffert, Anne C. Pinto, Artur Silva, Vasco Azevedo, and Luis G.C. Pacheco 4.4 The complex roles and regulation of stress response σ factors in Streptomyces coelicolor, 328Jan Kormanec, Beatrica Sevcikova, Renata Novakova, Dagmar Homerova, Bronislava Rezuchova, and Erik Mingyar 4.5 Proteolytic activation of extra cytoplasmic function (ECF) σ factors, 344JessicaL. Hastie and Craig D. Ellermeier 4.6 The ECF family sigma factor σH in Corynebacterium glutamicum controls the thiol-oxidative stress response, 352Tobias Busche and Jörn Kalinowski 4.7 Posttranslational regulation of antisigma factors of RpoE: a comparison between the Escherichia coli and Pseudomonas aeruginosa systems, 361Sundar Pandey, Kyle L. Martins, and Kalai Mathee Section 5: Small noncoding RNAs and stress responses, 369 5.1 Bacterial small RNAs in mixed regulatory circuits, 371Jonathan Jagodnik, DenisThieffry, and Maude Guillier 5.2 Role of small RNAs in Pseudomonas aeruginosa virulence and adaptation, 383Hansi Kumari, Deepak Balasubramanian, and Kalai Mathee 5.3 Physiological effects of posttranscriptional regulation by the small RNA SgrS during metabolic stress inEscherichia coli, 393Gregory R. Richards 5.4 Three rpoS-activating small RNAs in pathways contributing to acid resistance of Escherichia coli, 402Geunu Bak, Kook Han, Daun Kim, Kwang-sun Kim, and Younghoon Lee 5.5 Thermal stress noncoding RNAs in prokaryotes and eukaryotes: a comparative approach, 412Mercedes de la Fuente and José Luis Martínez-Guitarte Section 6: Toxin-antitoxin systems and stress responses, 423 6.1 Epigenetics mediated by restriction modification systems, 425Iwona Mruk and Ichizo Kobayashi 6.2 Toxin–antitoxin systems as regulators of bacterial fitness and virulence, 437Brittany A. Fleming and Matthew A. Mulvey 6.3 Mechanisms of stress-activated persister formation in Escherichia coli, 446Stephanie M. Amato and Mark P. Brynildsen 6.4 Identification and characterization of type II toxin–antitoxin systems in the opportunistic pathogenAcinetobacter baumannii, 454Edita Sûziedéliené, Milda Jurénaité, and Julija Armalyté 6.5 Transcriptional control of toxin–antitoxin expression: keeping toxins under wraps until the time is right, 463Barbara Kℷedzierska and Finbarr Hayes 6.6 Opposite effects of GraT toxin on stress tolerance of Pseudomonas putida, 473Rita Hõrak and Hedvig Tamman Section 7: Stringent response to stress, 479 7.1 Preferential cellular accumulation of ppGpp or pppGpp in Escherichia coli, 481K. Potrykus and M. Cashel 7.2 Global Rsh-dependent transcription profile of Brucella suis during stringent response unravels adaptation to nutrient starvation and cross-talk with other stress responses, 489Stephan Köhler, Nabil Hanna, Safia Ouahrani-Bettache, Kenneth L. Drake, L. Garry Adams, and Alessandra Occhialini 7.3 The stringent response and antioxidant defences in Pseudomonas aeruginosa, 500Gowthami Sampathkumar, Malika Khakimova, Tevy Chan, and Dao Nguyen 7.4 Molecular basis of the stringent response in Vibrio cholerae, 507Shreya Dasgupta, Bhabatosh Das, Pallabi Basu, and Rupak K. Bhadra Section 8: Responses to UV irradiation, 517 8.1 UV stress-responsive genes associated with ICE SXT/R391 group, 519Patricia Armshaw and J. Tony Pembroke 8.2 Altered outer membrane proteins in response to UVC radiation in Vibrio parahaemolyticus and Vibrio alginolyticus, 528Fethi Ben Abdallah 8.3 Ultraviolet-B radiation effects on the community, physiology, and mineralization of magnetotactic bacteria, 532Yingzhao Wang and Yongxin Pan 8.4 Nucleotide excision repair system and gene expression in Mycobacterium smegmatis, 545Angelina Cordone Section 9: SOS and double stranded repair systems and stress, 551 9.1 The SOS response modulates bacterial pathogenesis, 553Darja ¢§Zgur Bertok 9.2 RNAP secondary-channel interactors in Escherichia coli: makers and breakers of genome stability, 561Priya Sivaramakrishnan and Christophe Herman 9.3 How a large gene network couples mutagenic DNA break repair to stress in Escherichia coli, 570Elizabeth Rogers, P.J. Hastings, María Angélica Bravo Núñez, and Susan M. Rosenberg 9.4 Double-strand DNA break repair in mycobacteria, 577Richa Gupta and Michael S. Glickman Section 10: Adaptation to oxidative stress, 587 10.1 Peroxide-sensing transcriptional regulators in bacteria, 58James M. Dubbs and Skorn Mongkolsuk 10.2 Regulation of oxidative stress–related genes implicated in the establishment of opportunistic infections by Bacteroides fragilis, 603Felipe Lopes Teixeira, Regina Maria Cavalcanti Pilotto Domingues, and Leandro Araujo Lobo 10.3 Investigation into oxidative stress response of Shewanella oneidensis reveals a distinct mechanism, 609Jie Yuan, Fen Wan, and Haichun Gao 10.4 An omics view on the response to singlet oxygen, 619Bork A. Berghoff and Gabriele Klug 10.5 Regulators of oxidative stress response genes in Escherichia coli and their conservation in bacteria, 632Herb E. Schellhorn, Mohammad Mohiuddin, Sarah M. Hammond, and Steven Botts 10.6 Hydrogen peroxide resistance in Bifidobacterium animalis subsp. lactis and Bifidobacterium longum, 638Taylor S. Oberg and Jeff R. Broadbent Section 11: Adaptation to osmotic stress, 647 11.1 Interstrain variation in the physiological and transcriptional responses of Pseudomonas syringae to osmotic stress, 649Gwyn A. Beattie, Chiliang Chen, Lindsey Nielsen, and Brian C. Freeman 11.2 Management of osmotic stress by Bacillus subtilis: genetics and physiology, 657Tamara Hoffmann and Erhard Bremer 11.3 Hyperosmotic response of Streptococcus mutans: from microscopic physiology to transcriptomic profile, 677Lu Wang and Xin Xu 11.4 Defective ribosome maturation or function makes Escherichia coli cells salt-resistant, 687Hyouta Himeno, Takefusa Tarusawa, Shion Ito, and Simon Goto Section 12: Dessication tolerance and drought stress, 693 12.1 Consequences of elevated salt concentrations on expression profiles in the rhizobium S. meliloti 1021 likely involved in heat and desiccation stress, 695Jan A.C. Vriezen, Caroline M. Finn, and Klaus Nüsslein 12.2 Genes involved in the formation of desiccationresistant cysts in Azotobacter vinelandii, 709Guadalupe Espín 12.3 Osmotic and desiccation tolerance in Escherichia coli O157:H7 and Salmonella enterica requires rpoS (σ38), 716Zach Pratt, Megan Shiroda, Andrew J. Stasic, Josh Lensmire, and C.W. Kaspar 12.4 Desiccation of Salmonella enterica induces cross-tolerance to other stresses, 725Shlomo Sela (Saldinger) and Chellaiah Edward Raja Index, i1 VOLUME 2 Preface, xiii Acknowledgements, xiv List of contributors, xv Section 13: Heat shock responses, 737 13.1 Heat shock response in bacteria with large genomes: lessons from rhizobia, 739Ana Alexandre and Solange Oliveira 13.2 Small heat shock proteins in bacteria, 747Martin Haslbeck 13.3 Transcriptome analysis of bacterial response to heat shock using next-generation sequencing, 754Kok-Gan Chan 13.4 Comparative analyses of bacterial transcriptome reorganisation in response to temperature increase, 757Bei-Wen Ying and Tetsuya Yomo 13.5 Participation of Ser–Thr protein kinases in regulation of heat stress responses in Synechocystis, 766Anna A. Zorina, Galina V. Novikova, and Dmitry A. Los Section 14: Chaperonins and stress, 781 14.1 GroEL/ES chaperonin: unfolding and refolding reactions, 783Victor V. Marchenkov, Nataliya A. Ryabova, Olga M. Selivanova, and Gennady V. Semisotnov 14.2 Functional comparison between the DnaK chaperone systems of Streptococcus intermedius and Escherichia coli, 791Toshifumi Tomoyasu and Hideaki Nagamune 14.3 Coevolution analysis illuminates the evolutionary plasticity of the chaperonin system GroES/L, 796Mario A. Fares 14.4 ClpL ATPase: a novel chaperone in bacterial stress responses, 812Pratick Khara and Indranil Biswas 14.5 Duplicated groEL genes inMyxococcus xanthus DK1622, 820Yan Wang, Xiao-jing Chen, and Yue-zhong Li Section 15: Cold shock responses, 827 15.1 Gene regulation by cold shock proteins via transcription antitermination, 829Sangita Phadtare and Konstantin Severinov 15.2 Metagenomic analysis of microbial cold stress proteins in polar lacustrine ecosystems, 837Hyunmin Koo, Joseph A. Hakim, and Asim K. Bej 15.3 Role of two-component systems in cold tolerance of Clostridium botulinum, 845Yâgmur Derman, Elias Dahlsten, and Hannu Korkeala 15.4 Cold shock CspA protein production during periodic temperature cycling in Escherichia coli, 854David Stopar and Tina Ivancic 15.5 Cold shock response in Escherichia coli: a model system to study posttranscriptional regulation, 859Anna Maria Giuliodori 15.6 New insight into cold shock proteins: RNA-binding proteins involved in stress response and virulence, 873Charlotte Michaux and Jean-Christophe Giard 15.7 Light regulation of cold stress responses in Synechocystis, 881Kirill S. Mironov and Dmitry A. Los 15.8 Escherichia coli cold shock gene profiles in response to overexpression or deletion of CsdA, RNase R, andPNPase and relevance to low-temperature RNA metabolism, 890Sangita Phadtare Section 16: Adaptation to acid stress, 897 16.1 Acid-adaptive responses of Streptococcus mutans, and mechanisms of integration with oxidative stress, 899Robert G. Quivey Jr., Roberta C. Faustoferri, Brendaliz Santiago, Jonathon Baker, Benjamin Cross, and Jin Xiao 16.2 Acid survival mechanisms in neutralophilic bacteria, 911Eugenia Pennacchietti, Fabio Giovannercole, and Daniela De Biase 16.3 Two-component systems in sensing and adapting to acid stress in Escherichia coli, 927Yoko Eguchi and Ryutaro Utsumi 16.4 Slr1909, a novel two-component response regulator involved in acid tolerance in Synechocystis sp. PCC 6803, 935Lei Chen, Qiang Ren, Jiangxin Wang, and Weiwen Zhang 16.5 Comparative mass spectrometry–based proteomics to elucidate the acid stress response in Lactobacillusplantarum, 944Tiaan Heunis, Shelly Deane, and Leon M.T. Dicks Section 17: Adaptation to nitrosative stress, 95317.1 Transcriptional regulation by thiol-based sensors of oxidative and nitrosative stress, 955Timothy Tapscott, Matthew A. Crawford, and Andr´es Vázquez-Torres 17.2 Haemoglobins of Mycobacterium tuberculosis and their involvement in management of environmental stress, 967Kanak L. Dikshit 17.3 What is it about NO that you don’t understand? The role of heme and HcpR in Porphyromonas gingivalis’s response to nitrate (NO3), nitrite (NO2), and nitric oxide (NO), 976Janina P. Lewis and Benjamin R. Belvin 17.4 Di-iron RICs: players in nitrosative-oxidative stress defences, 989Lígia S. Nobre and Lí©¥gia M. Saraiva 17.5 The Vibrio cholerae stress response: an elaborate system geared toward overcoming host defenses during infection, 997Karl-Gustav Rueggeberg and Jun Zhu 17.6 Ensemble modeling enables quantitative exploration of bacterial nitric oxide stress networks, 1009Jonathan L. Robinson and Mark P. Brynildsen Section 18: Adaptation to cell envelope stress, 1015 18.1 The Cpx inner membrane stress response, 1017Randi L. Guest and Tracy L. Raivio 18.2 New insights into stimulus detection and signal propagation by the Cpx-envelope stress system, 1025Patrick Hoernschemeyer and Sabine Hunke 18.3 Promiscuous functions of cell envelope stress-sensing systems in Klebsiella pneumoniae and Acinetobacterbaumannii, 1031Vijaya Bharathi Srinivasan and Govindan Rajamohan 18.4 Influence of BrpA and Psr on cell envelope homeostasis and virulence of Streptococcus mutans, 1043Zezhang T.Wen, Jacob P. Bitoun, Sumei Liao, and Jacqueline Abranches 18.5 Modulators of the bacterial two-component systems involved in envelope stress, transport, and virulence, 1055Rajeev Misra Section 19: Iron homeostasis, 1065 19.1 Iron homeostasis and environmental responses in cyanobacteria: regulatory networks involving Fur, 1067María Luisa Peleato, María Teresa Bes, and María F. Fillat 19.2 Interplay between O2 and iron in gene expression: environmental sensing by FNR, ArcA, and Fur in bacteria, 1079Bryan Troxell and Hosni M. Hassan 19.3 The iron–sulfur cluster biosynthesis regulator IscR contributes to iron homeostasis and resistance tooxidants in Pseudomonas aeruginosa, 1090Adisak Romsang, James M. Dubbs, and Skorn Mongkolsuk 19.4 Transcriptional analysis of iron-responsive regulatory networks in Caulobacter crescentus, 1103José F. da Silva Neto 19.5 Protein–protein interactions regulate the release of iron stored in bacterioferritin, 1109Huili Yao, YanWang, and Mario Rivera 19.6 Protein dynamics and ion traffic in bacterioferritin function: a molecular dynamics simulation study onwild-type and mutant Pseudomonas aeruginosa BfrB, 1118Huan Rui, Mario Rivera, and Wonpil Im Section 20: Metal resistance, 1131 20.1 Nickel toxicity, regulation, and resistance in bacteria, 1133Lee Macomber and Robert P. Hausinger 20.2 Metabolic networks to counter Al toxicity in Pseudomonas fluorescens: a holistic view, 1145Christopher Auger, Nishma D. Appanna, and Vasu D. Appanna 20.3 Genomics of the resistance to metal and oxidative stresses in cyanobacteria, 1154Corinne Cassier-Chauvat and Franck Chauvat 20.4 Cross-species transcriptional network analysis reveals conservation and variation in response to metal stress in cyanobacteria, 1165Jiangxin Wang, Gang Wu, Lei Chen, and Weiwen Zhang 20.5 The extracytoplasmic function sigma factor–mediated response to heavy metal stress in Caulobacter crescentus, 1171Rogério F. Lourenco and Suely L. Gomes 20.6 Metal ion toxicity and oxidative stress in Streptococcus pneumoniae, 1184Christopher A. McDevitt, Stephanie L. Begg, and James C. Paton Section 21: Quorum sensing, 1195 21.1 Quorum sensing and bacterial social interactions in biofilms: bacterial cooperation and competition, 1197Yung-Hua Li and Xiao-Lin Tian 21.2 Recent advances in bacterial quorum quenching, 1206Kok-Gan Chan, Wai-Fong Yin, and Kar-Wai Hong 21.3 LuxR-type quorum-sensing regulators that are antagonized by cognate pheromones, 1221Stephen C. Winans, Ching-Sung Tsai, Gina T. Ryan, Ana Lidia Flores-Mireles, Esther Costa, Kevin Y. Shih, Thomas C.Winans, Youngchang Kim, Robert Jedrzejczak, and Gekleng Chhor 21.4 Adaptation to environmental stresses in Streptococcus mutans through the production of its quorum-sensing peptide pheromone, 1232Delphine Dufour, Vincent Leung, and Céline M. Lévesque 21.5 Quorum sensing in Bacillus cereus in relation to cysteine metabolism and the oxidative stress response, 1242Eugénie Huillet and Michel Gohar Section 22: Chemotaxis and biofilm formation, 1253 22.1 The flagellum as a sensor, 1255Rasika M. Harshey 22.2 Flagellar motility and fitness in xanthomonads, 1265Marie-Agnès Jacques, Jean-Françis Guimbaud, Martial Briand, Arnaud Indiana, and Armelle Darrasse 22.3 Understanding Listeriamonocytogenes biofilms: perspectives into mechanisms of adaptation and regulation under stress conditions, 1274Lizziane Kretli Winkelströter, Fernanda Barbosa dos Reis-Teixeira, Gabriela Satti Lameu, and Elaine Cristina Pereira De Martinis 22.4 Biofilm formation and environmental signals in Bordetella, 1279Tomoko Hanawa 22.5 Biofilm formation by rhizobacteria in response to water-limiting conditions, 1287Pablo Bogino, Fiorela Nievas, and Walter Giordano 22.6 Stress conditions triggering mucoid-to-nonmucoid morphotype variation in Burkholderia, and effects onvirulence and biofilm formation, 1295Leonilde M. Moreira, Inês N. Silva, Ana S. Ferreira, and Mário R. Santos 22.7 Effect of environmental conditions present in the fishery industry on the biofilm-forming ability of Staphylococcus aureus, 1304Daniel Vázquez-Sánchez 22.8 Biofilm development and stress response in the cholera bacterium, 1310Anisia J. Silva and Jorge A. Benitez 22.9 Outer membrane vesicle secretion: from envelope stress to biofilm formation, 1322Thomas Baumgarten and Hermann J. Heipieper Section 23: Viable but nonculturable (VBNC) cells, 1329 23.1 Resuscitation of Vibrios fromthe viable but nonculturable state is induced by quorum-sensing molecules, 1331Mesrop Ayrapetyan, Tiffany C. Williams, and James D. Oliver 23.2 Differential resuscitative effects of pyruvate and its analogs on VBNC (viable but nonculturable)Salmonella, 1338Fumio Amano 23.3 Environmental persistence of Shiga toxin–producing E. coli, 1346Philipp Aurass and Antje Flieger 23.4 Of a tenacious and versatile relic: the role of inorganic polyphosphate (poly-P) metabolism in the survival, adaptation, and virulence of Campylobacter jejuni, 1354Issmat I. Kassem and Gireesh Rajashekara Index, i1

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Book SynopsisPerform genome analysis and sequencing of data with Amazon Web Services Genomics in the AWS Cloud: Analyzing Genetic Code Using Amazon Web Services enables a person who has moderate familiarity with AWS Cloud to perform full genome analysis and research. Using the information in this book, you''ll be able to take a FASTQ file containing raw data from a lab or a BAM file from a service provider and perform genome analysis on it. You''ll also be able to identify potentially pathogenic gene sequences. Get an introduction to Whole Genome Sequencing (WGS) Make sense of WGS on AWS Master AWS services for genome analysis Some key advantages of using AWS for genomic analysis is to help researchers utilize a wide choice of compute services that can process diverse datasets in analysis pipelines. Genomic sequencers that generate raw data files are located in labs on premises and AWS provides solutions to make it easy for customTable of ContentsIntroduction xix Chapter 1 Why Do Genome Analysis Yourself When Commercial Offerings Exist? 1 Chapter 2 A Crash Course in Molecular Biology 9 Chapter 3 Obtaining Your Genome 25 Chapter 4 The Bioinformatics Workflow 39 Chapter 5 AWS Services for Genome Analysis 59 Chapter 6 Building Your Environment in the AWS Cloud 77 Chapter 7 Linux and AWS Command-Line Basics for Genomics 115 Chapter 8 Processing the Sequencing Data 143 Chapter 9 Visualizing the Genome 211 Chapter 10 Containerizing Your Workflow on the Desktop 235 Chapter 11 Variants and Applications 249 Chapter 12 Cancer Genomics 267 Index 291

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Book SynopsisEdited and written by leading researchers from around the world, The Ecological Genomics of Fungi covers a broad diversity of fungal systems and provides unique insight into the functions of those fungi in various ecosystems, from soil, to plant, to human.Trade Review“I think the volume may succeed in its ambition to serve as a catalyst for further studies by showing researchers venturing into ecological genomics and those already in genomics the width of the field. This may, in turn, further more integrative studies that will benefit our understanding of fungi.” (The Quarterly Review of Biology, 1 October 2015) Table of ContentsContributors vii Preface xiii Section 1 Sequencing Fungal Genomes 1 1 A Changing Landscape of Fungal Genomics 3 Igor V. Grigoriev 2 Repeated Elements in Filamentous Fungi with a Focus on Wood-Decay Fungi 21 Claude Murat, Thibaut Payen, Denis Petitpierre, and Jessy Labbé Section 2 Saprotrophic Fungi 41 3 Wood Decay 43 Dan Cullen 4 Aspergilli and Biomass-Degrading Fungi 63 Isabelle Benoit, Ronald P. de Vries, Scott E. Baker, and Sue A. Karagiosis 5 Ecological Genomics of Trichoderma 89 Irina S. Druzhinina and Christian P. Kubicek Section 3 Plant-Interacting Fungi 117 6 Dothideomycetes: Plant Pathogens, Saprobes, and Extremophiles 119 Stephen B. Goodwin 7 Biotrophic Fungi (Powdery Mildews, Rusts, and Smuts) 149 Sébastien Duplessis, Pietro D. Spanu, and Jan Schirawski 8 The Mycorrhizal Symbiosis Genomics 169 Francis Martin and Annegret Kohler 9 Lichen Genomics: Prospects and Progress 191 Martin Grube, Gabriele Berg, ólafur S. Andrésson, Oddur Vilhelmsson, Paul S. Dyer, and Vivian P.W. Miao Section 4 Animal-Interacting Fungi 213 10 Ecogenomics of Human and Animal Basidiomycetous Yeast Pathogens 215 Sheng Sun, Ferry Hagen, Jun Xu, Tom Dawson, Joseph Heitman, James Kronstad, Charles Saunders, and Teun Boekhout 11 Genomics of Entomopathogenic Fungi 243 Chengshu Wang and Raymond J. St. Leger 12 Ecological Genomics of the Microsporidia 261 Nicolas Corradi and Patrick J. Keeling Section 5 Metagenomics and Biogeography of Fungi 279 13 Metagenomics for Study of Fungal Ecology 281 Björn D. Lindahl and Cheryl R. Kuske 14 Metatranscriptomics of Soil Eukaryotic Communities 305 Laurence Fraissinet-Tachet, Roland Marmeisse, Lucie Zinger, and Patricia Luis 15 Fungi in Deep-Sea Environments and Metagenomics 325 Stéphane Mahé, Vanessa Rédou, Thomas Le Calvez, Philippe Vandenkoornhuyse, and Gaëtan Burgaud 16 The Biodiversity, Ecology, and Biogeography of Ascomycetous Yeasts 355 Marc-André Lachance Index 371

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Book SynopsisPlant Genes, Genomes and Genetics provides a comprehensive treatment of all aspects of plant gene expression. Unique in explaining the subject from a plant perspective, it highlights the importance of key processes, many first discovered in plants, that impact how plants develop and interact with the environment.Table of ContentsAcknowledgements xi Introduction xiii About the Companion Website xix PART I: PLANT GENOMES AND GENES Chapter 1 Plant genetic material 3 1.1 DNA is the genetic material of all living organisms, including plants 3 1.2 The plant cell contains three independent genomes 8 1.3 A gene is a complete set of instructions for building an RNA molecule 10 1.4 Genes include coding sequences and regulatory sequences 11 1.5 Nuclear genome size in plants is variable but the numbers of protein-coding, non-transposable element genes are roughly the same 12 1.6 Genomic DNA is packaged in chromosomes 15 1.7 Summary 15 1.8 Problems 15 References 16 Chapter 2 The shifting genomic landscape 17 2.1 The genomes of individual plants can differ in many ways 17 2.2 Differences in sequences between plants provide clues about gene function 20 2.3 SNPs and lengthmutations in simple sequence repeats are useful tools for genome mapping and marker assisted selection 22 2.4 Genome size and chromosome number are variable 28 2.5 Segments of DNA are often duplicated and can recombine 30 2.6 Some genes are copied nearby in the genome 31 2.7 Whole genome duplications are common in plants 34 2.8 Whole genome duplication has many effects on the genome and on gene function 37 2.9 Summary 41 2.10 Problems 42 Further reading 42 References 42 Chapter 3 Transposable elements 45 3.1 Transposable elements are common in genomes of all organisms 45 3.2 Retrotransposons are mainly responsible for increases in genome size 46 3.3 DNA transposons create small mutations when they insert and excise 52 3.4 Transposable elements move genes and change their regulation 57 3.5 How are transposable elements controlled? 60 3.6 Summary 60 3.7 Problems 61 References 61 Chapter 4 Chromatin, centromeres and telomeres 63 4.1 Chromosomes are made up of chromatin, a complex of DNA and protein 63 4.2 Telomeres make up the ends of chromosomes 66 4.3 The chromosome middles–centromeres 71 4.4 Summary 77 4.5 Problems 77 Further reading 77 References 77 Chapter 5 Genomes of organelles 79 5.1 Plastids and mitochondria are descendants of free-living bacteria 79 5.2 Organellar genes have been transferred to the nuclear genome 80 5.3 Organellar genes sometimes include introns 82 5.4 Organellar mRNA is often edited 82 5.5 Mitochondrial genomes contain fewer genes than chloroplasts 84 5.6 Plant mitochondrial genomes are large and undergo frequent recombination 87 5.7 All plastid genomes in a cell are identical 91 5.8 Plastid genomes are similar among land plants but contain some structural rearrangements 93 5.9 Summary 95 5.10 Problems 95 Further reading 95 References 95 PART II: TRANSCRIBING PLANT GENES Chapter 6 RNA 99 6.1 RNA links components of the Central Dogma 99 6.2 Structure provides RNA with unique properties 102 6.3 RNA has multiple regulatory activities 105 6.4 Summary 108 6.5 Problems 108 References 109 Chapter 7 The plant RNA polymerases 111 7.1 Transcription makes RNA from DNA 111 7.2 Varying numbers of RNA polymerases in the different kingdoms 112 7.3 RNA polymerase I transcribes rRNAs 114 7.4 RNA polymerase III recruitment to upstream and internal promoters 116 7.5 Plant-specific RNP-IV and RNP-V participate in transcriptional gene silencing 117 7.6 Organelles have their own set of RNA polymerases 117 7.7 Summary 118 7.8 Problems 118 References 118 Chapter 8 Making mRNAs – Control of transcription by RNA polymerase II 121 8.1 RNA polymerase II transcribes protein-coding genes 121 8.2 The structure of RNA polymerase II reveals how it functions 121 8.3 The core promoter 123 8.4 Initiation of transcription 125 8.5 The mediator complex 127 8.6 Transcription elongation: the role of RNP-II phosphorylation 128 8.7 RNP-II pausing and termination 129 8.8 Transcription re-initiation 130 8.9 Summary 130 8.10 Problems 130 References 130 Chapter 9 Transcription factors interpret cis-regulatory information 133 9.1 Information on when, where and how much a gene is expressed is codified by the gene’s regulatory regions 133 9.2 Identifying regulatory regions requires the use of reporter genes 134 9.3 Gene regulatory regions have a modular structure 135 9.4 Enhancers: Cis-regulatory elements or modules that function at a distance 137 9.5 Transcription factors interpret the gene regulatory code 138 9.6 Transcription factors can be classified in families 138 9.7 How transcription factors bind DNA 139 9.8 Modular structure of transcription factors 143 9.9 Organization of transcription factors into gene regulatory grids and networks 146 9.10 Summary 146 9.11 Problems 146 More challenging problems 147 References 147 Chapter 10 Control of transcription factor activity 149 10.1 Transcription factor phosphorylation 149 10.2 Protein–protein interactions 151 10.3 Preventing transcription factors from access to the nucleus 155 10.4 Movement of transcription factors between cells 156 10.5 Summary 158 10.6 Problems 158 References 158 Chapter 11 Small RNAs 161 11.1 The phenomenon of cosuppression or gene silencing 161 11.2 Discovery of small RNAs 162 11.3 Pathways for miRNA formation and function 163 11.4 Plant siRNAs originate from different types of double-stranded RNAs 166 11.5 Intercellular and systemic movement of small RNAs 168 11.6 Role of miRNAs in plant physiology and development 170 11.7 Summary 171 11.8 Problems 171 References 172 Chapter 12 Chromatin and gene expression 173 12.1 Packing long DNA molecules in a small space: the function of chromatin 173 12.2 Heterochromatin and euchromatin 173 12.3 Histone modifications 174 12.4 Histone modifications affect gene expression 175 12.5 Introducing and removing histone marks: writers and erasers 175 12.6 ‘Readers’ recognize histone modifications 177 12.7 Nucleosome positioning 177 12.8 DNA methylation 178 12.9 RNA-directed DNA methylation 179 12.10 Control of flowering by histone modifications 180 12.11 Summary 181 12.12 Problems 181 References 181 PART III: FROM RNA TO PROTEINS Chapter 13 RNA processing and transport 185 13.1 RNA processing can be thought of as steps 185 13.2 RNA capping provides a distinctive 5’ end to mRNAs 185 13.3 Transcription termination consists of mRNA 3’-end formation and polyadenylation 189 13.4 RNA splicing is another major source of genetic variation 192 13.5 Export of mRNA from the nucleus is a gateway for regulating which mRNAs actually get translated 194 13.6 Summary 196 13.7 Problems 196 References 196 Chapter 14 Fate of RNA 199 14.1 Regulation of RNA continues upon export from nucleus 199 14.2 Mechanisms for RNA turnover 199 14.3 RNA surveillance mechanisms 201 14.4 RNA sorting 202 14.5 RNA movement 203 14.6 Summary 204 14.7 Problems 204 Further reading 205 References 205 Chapter 15 Translation of RNA 207 15.1 Translation: a key aspect of gene expression 207 15.2 Initiation 209 15.3 Elongation 209 15.4 Termination 210 15.5 Tools for studying the regulation of translation 211 15.6 Specific translational control mechanisms 211 15.7 Summary 213 15.8 Problems 214 Further reading 214 References 214 Chapter 16 Protein folding and transport 215 16.1 The pathway to a protein’s function is a complicated matter 215 16.2 Protein folding and assembly 215 16.3 Protein targeting 218 16.4 Co-translational targeting 218 16.5 Post-translational targeting 219 16.6 Post-translational modifications regulating function 220 16.7 Summary 222 16.8 Problems 223 Further reading 223 References 224 Chapter 17 Protein degradation 225 17.1 Two sides of gene expression–synthesis and degradation 225 17.2 Autophagy, senescence and programmed cell death 225 17.3 Protein-tagging mechanisms 226 17.4 The ubiquitin proteasome system rivals gene transcription 228 17.5 Summary 231 17.6 Problems 231 Further reading 231 Reference 231 Index 233

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Book SynopsisEcological Genetics addresses the fundamental problems of which of the many molecular markers should be used and how the resulting data should be analysed in clear, accessible language, suitable for upper--level undergraduates through to research--level professionals.Trade ReviewMolecular ecologists finally have a text-book that deals with their discipline. Ecological Genetics fills the market-gap between general accounts of evolutionary biology and specialist texts focusing on individual research topics. The authors have brought together a useful mix of theory, practical approaches, conceptual issues, and individual case studies to provide a balanced and accessible overview of the field. Peter Hollingsworth, Royal Botanic Garden "This book is a pleasure to read: it is clearly written, well organized and leaves no ambiguity." Andre A Dhondt, Cornell University, Trends in Ecology and Evolution, August 2004 "This book is a well-written, comprehensive overview of the essential techniques underlying ecological genetics. I would certainly recommend it to any new student undertaking postgraduate study in the field of molecular ecology." Dr. Jim Provan, Queen's University BelfastTable of ContentsPreface vii Abbreviations x 1 Ecological genetics 1 Summary 1 1.1 What is ecological genetics? 1 1.2 Why study ecological genetics? 3 References 4 2 Markers and sampling in ecological genetics 6 Summary 6 2.1 Introduction 6 2.2 Methods of data generation 7 2.3 Principles of sampling 15 2.4Practice 20 2.5 Within-population sampling 22 2.6 Among-population sampling 34 2.7 Power analysis 34 2.8 Further reading 35 Essential methods information 36 References 45 3 Genetic diversity and differentiation 52 Summary 52 3.1 Introduction 52 3.2 Factors influencing diversity and differentiation 53 3.3 The Hardy–Weinberg equilibrium 58 3.4Genetic diversity 62 3.5 Genetic differentiation 69 3.6 Genetic distance 81 3.7 Statistical approaches 86 3.8 Use of genetic diversity statistics 89 3.9 Concluding remarks 100 3.10 Further reading 100 References 100 4 Gene flow and mating system 106 Summary 106 4.1 Introduction 106 4.2 Factors governing gene flow 107 4.3 Considerations for measuring gene flow 115 4.4 Measuring gene flow – indirect estimates 122 4.5 Measuring gene flow – direct estimates 134 4.6 The importance of biological and environmental factors on gene flow 143 References 145 5 Intraspecific phylogenies and phylogeography 150 Summary 150 5.1 Introduction 150 5.2 Homology, gene trees, and species trees 157 5.3 Tree form and building 159 5.4Tree interpretation 170 5.5 Organelle versus nuclear intraspecific phylogenies 179 5.6 Further reading 180 Essential methods information 181 References 185 6 Speciation and hybridization 189 Summary 189 6.1 Introduction 189 6.2 Species 190 6.3 Speciation 194 6.4 Hybridization 204 6.5 Analysis of speciation and hybridization 206 6.6 Future developments 233 6.7 Further reading 233 References 233 7 Case studies in ecological genetics: Lycaenid butterflies, ragworts, bears, and oaks 243 Summary 243 7.1 Introduction 244 7.2 Lycaenid butterflies 244 7.3 European ragworts 257 7.4Brown bears 265 7.5 European oaks 274 References 292 Appendix A: Data analysis software 300 Appendix B: Which distance algorithm should be used and when? 306 Glossary 313 Index 320

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Book SynopsisWith the first draft of the human genome project in the public domain and full analyses of model genomes now available, the subject matter of ''Principles of Genome Analysis and Genomics'' is even ''hotter'' now than when the first two editions were published in 1995 and 1998. In the new edition of this very practical guide to the different techniques and theory behind genomes and genome analysis, Sandy Primrose and new author Richard Twyman provide a fresh look at this topic. In the light of recent exciting advancements in the field, the authors have completely revised and rewritten many parts of the new edition with the addition of five new chapters. Aimed at upper level students, it is essential that in this extremely fast moving topic area the text is up to date and relevant. Completely revised new edition of an established textbook. Features new chapters and examples from exciting new research in genomics, including the human genome project. ExcelTrade Review"...an excellent distillation of current knowledge...The book is clearly written, well presented, and feels good. Recommended." Neil Stoker, Royal Veterninary College, London, Microbiology Today, Vol 30, November 2003 "There is no doubt that this book is a very useful source of information, for students and teachers alike. In spite of its dense text, it makes good reading and will help to reduce the general bewilderment induced by the rapid pace of technological and conceptual innovation in biology." Leon Otten, Plant Molecular Biology Institute, Plant Science, 2003. Principles of Genome Analysis and Genomics, 3rd edition, is "very good indeed and deserves to be a widely popular resource for newcomers to genome analysis." J.Armour, University of Nottingham, Heredity, June 2004 Table of ContentsPreface. Abbreviations. 1. Setting The Scene: The New Science Of Genomics. 2. The Organization And Structure Of Genomes. 3. Subdividing The Genome. 4. Assembling A Physical Map Of The Genome. 5. Sequencing Methods And Strategies. 6. Genome Annotation And Bioinformatics. 7. Comparative Genomics. 8. Protein Structural Genomics. 9. Global Expression Profiling. 10. Comprehensive Mutant Libraries. 11. Mapping Protein Interactions. 12. Applications Of Genome Analysis And Genomics. References. Index

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Book SynopsisMechanisms in Transcriptional Regulation provides a concise discussion of the fundamental concepts in transcription and its regulation.Table of ContentsList of boxes. Preface. Acknowledgments. 1 The vocabulary of transcription. 1.1 Introduction 1. 1.2 The vocabulary of transcription. 1.2.1 RNA biogenesis. 1.2.2 The transcriptional machinery. 1.2.3 Cis-elements. 1.3 Evolutionarily conserved mechanisms of transcription. 1.3.1 Conservation across the three domains of life. 1.3.2 Model eukaryotic organisms (and a plug for genetics). 1.4 What’s coming up. Problems. Further reading. 2 RNA polymerases and the transcription cycle. 2.1 Introduction. 2.2 Core RNA polymerases. 2.2.1 Bacterial core polymerases. 2.2.2 Eukaryotic and archaeal core polymerases. 2.3 Transcriptional elongation. 2.3.1 Phosphoester linkage formation. 2.3.2 Features of the ternary elongation complex. 2.3.3 RNA polymerase as a motor. 2.3.4 Elongation factors and backtracking. 2.4 Transcriptional initiation. 2.4.1 Distinct mechanisms for promoter recognition in bacteria and eukaryotes. 2.4.2 Bacterial σ factors and promoter specificity. 2.5 Transcriptional termination. 2.5.1 Why terminate?. 2.5.2 Termination in bacteria. 2.5.3 Termination in eukaryotes. 2.6 Summary. Problems. Further reading. 3 The eukaryotic basal machinery. 3.1 Introduction. 3.2 The class II core promoter. 3.3 The catalog of factors. 3.4 Pathway to the preinitiation complex. 3.5 Promoter recognition and nucleation of the PIC by TFIID. 3.5.1 TATA box recognition by TBP. 3.5.2 TBP-associated factors and their function in TFIID. 3.6 TFIIB: a functional analog of bacterial σ factors. 3.6.1 TFIIB as a bridge between the promoter and polymerase. 3.6.2 BRF, a TFIIB paralog in the class III machinery,and promoter melting. 3.6.3 Functional similarity between TFIIB family proteins and σ. 3.7 TFIIH in promoter opening and promoter clearance. 3.7.1 A unique DNA helicase requirement for class II promoter opening. 3.7.2 A connection between DNA repair and transcription. 3.7.3 TFIIH and RNA polymerase II phosphorylation. 3.8 Summary. Problems. Further reading. 4 Mechanisms of transcriptional activation. 4.1 Introduction. 4.2 Paradigms from E. coli. 4.2.1 CRP: a sensor of the nutritional environment. 4.2.2 λcI: regulator of the lysis/lysogeny switch. 4.2.3 Sequence-specific DNA recognition: the helix-turn-helix motif. 4.2.4 Dimerization. 4.2.5 Multiple targets for activators in the transcriptional machinery. 4.2.6 How do activator–RNA polymerase contacts activate promoters?. 4.3 Eukaryotic activators and their targets. 4.3.1 The modular nature of eukaryotic activators. 4.3.2 The Mediator: a special activator target in the eukaryotic transcriptional machinery. 4.3.3 Release of Pol II from a paused state as a mechanism of activation. 4.4 Summary. Problems. Further reading. 5 Transcriptional control through the modification of chromatin structure. 5.1 Introduction. 5.2 Chromatin structure. 5.2.1 The nucleosome. 5.2.2 Higher order chromatin structure. 5.2.3 Euchromatin and heterochromatin. 5.3 Histone modification. 5.3.1 Lysine acetylation: diverse roles in gene activation. 5.3.2 Lysine methylation: a chemically stable histone mark. 5.3.3 Cross talk between histone marks. 5.4 ATP-dependent chromatin remodeling enzymes. 5.4.1 A diverse family of chromatin remodeling complexes. 5.4.2 ATP-fueled motors for increasing DNA accessibility. 5.4.3 Targeting of chromatin remodeling complexes. 5.5 Protein motifs that recognize modified histones. 5.5.1 Chromodomains. 5.5.2 Bromodomains. 5.6 Coordination of activator–coactivator interactions. 5.7 Summary. Problems. Further reading. 6 Epigenetic control of transcription. 6.1 Introduction. 6.1.1 Common themes in epigenetics: a central role for histone methylation. 6.2 Heterochromatic silencing. 6.2.1 Chromosomal inheritance of the silent state. 6.2.2 Histone methylation and maintenance of the silent state. 6.2.3 Initiation of heterochromatic silencing. 6.2.4 Evolutionary conservation of mechanisms for heterochromatic silencing. 6.2.5 DNA methylation and heterochromatin. 6.2.6 A distinct mechanism for heterochromatic silencing in budding yeast. 6.3 Epigenetic control by Polycomb and Trithorax group proteins. 6.3.1 Combinatorial control of segment identity. 6.3.2 Establishment and maintenance phases of homeotic gene expression. 6.3.3 Parallels between heterochromatic and PcG silencing. 6.3.4 Maintenance of the active state by TrxG. 6.3.5 A model for the epigenetic regulation of homeoticgene activity. 6.4 X chromosome inactivation: parallels to heterochromatic and Polycomb group silencing. 6.4.1 Random inactivation of the X chromosome. 6.4.2 Cis-acting RNA in X inactivation. 6.4.3 Histone modifications characteristic of both heterochromatic and PcG silencing on Xi. 6.5 Summary. Problems. Further reading. 7 Combinatorial control in development and signal transduction. 7.1 Introduction. 7.2 Synergy and antagonism. 7.2.1 Integration of regulatory inputs by cis-regulatory modules. 7.2.2 The “AND” and “NOT” operators. 7.3 Synergy and the enhanceosome. 7.3.1 Enhanceosome assembly and architectural factors. 7.3.2 Cooperative recruitment of coactivators by enhanceosomes. 7.3.3 Sequential coactivator recruitment. 7.4 Antagonism and stripe formation. 7.4.1 Developmental regulatory networks. 7.4.2 Short-range repression and stripe formation. 7.5 Antagonism and the signal-mediated switch. 7.5.1 Nuclear receptors: antagonism between coregulators. 7.5.2 Receptor tyrosine kinase pathways: competition for a common DNA element. 7.6 Summary. Problems. Further reading. Answers to problems. Glossary. Index. Color plate section

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Book SynopsisThis guide covers aspects of designing microarray experiments and analysing the data generated, including information on some of the tools that are available from non-commercial sources. Concepts and principles underpinning gene expression analysis are emphasised and wherever possible, the mathematics has been simplified. The guide is intended for use by graduates and researchers in bioinformatics and the life sciences and is also suitable for statisticians who are interested in the approaches currently used to study gene expression. Microarrays are an automated way of carrying out thousands of experiments at once, and allows scientists to obtain huge amounts of information very quickly Short, concise text on this difficult topic area Clear illustrations throughout Written by well-known teachers in the subject Provides insight into how to analyse the data produced from microarrays Trade Review"Quite a few recently published books discuss analysis of microarray gene expression data for beginners. Microarray Gene Expression Data Analysis ... is arguably the best of its kind in this regard." Terry Speed, The Walter & Eliza Hall Institute of Medical Research, Nature Cell Biology, December 2003 "Overall this is an excellent book, it is well referenced and, to my mind, covers the vast majority of issues an experimenter needs to consider when venturing into the world of microarray data analysis. The book fills a clear gap in the field, providing a rigorous overview of the often confusing .... data analysis issues that most books on microarrays avoid or treat in a cursory way. I would say it is essential reading for any laboratory or researcher active in this rapidly evolving field and is recommended for the mathematician or statisitican who is interested in the field or who has been persuaded by their biologist colleague to help them with their analysis." Steven Russell, University of Cambridge, Genetical Research, February 2003 "Anyone wishing to gain a basic understanding of microarray gene expression studies will come away enriched ... A good and accessible entry point for any biologist who is interested in getting an overview about how to perform microarray gene expression studies." D.C.Jamison, George Mason University, Heredity, June 2004Table of ContentsPreface. Acknowledgements. Part I: Introduction:. 1. What Are Microarrays?. 2. Use Of Icroarrays To Monitor Gene Expression. 3. Other Uses For Microarrays. 4. Challenges Associated With The Generation Of Large Amounts Of Complex Data. 5. Future Directions. Part II: Aspects Of Experimental Design:. 6. Features Of Microarray Data. 7. Designing The Best Experiment. 8. Preparation of Target. 9. Design of Spotted Arrays. 10. Hybridisation. 11. Long Term Considerations. 12. Verification of Results. Part III: Data Analysis:. 13. Preliminary Processing of Data. 14. Methods for Data Analysis. 15. Graph Models. 16. Software In The Public Domain. 17. Visualisation of Data. Part IV: Glossary:. Index. Colour plates fall between pp. 84 and 85.

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Book SynopsisA study of the multifaceted dimensions of the genetic revolution and its philosophical, ethical, social and political significance. It includes 33 essays, written by prominent figures in the field.Trade Review“The editors are to be congratulated on compiling such a stimulating and provocative volume. This is for those who wish to examine the basis of human bioethics thoroughly, whether they be novice or expert. Those who think they have clear attitudes to many of the ethical and social issues raised by developments in human genetics are likely to be forced to rethink at least some of their positions by the challenging and well-presented arguments that have been gathered together here." Angus Clarke, University of Wales "This timely book makes clear that genetic research will transform healthcare, choices about children, and standards of property. The contributors here stake out key questions facing health professionals and social policy makers, and they have insightful things to say about how we should go about answering those questions." Timothy F. Murphy, University of IllinoisCollege of Medicine at Chicago " ... Genethics makes some important contributions, offering a primer on key aspects of contemporary genetics before focusing on some of the most important ethical, legal, economic, political issues facing researchers, politicians, and, to some extent, the general population ... The book's strengths are its multidisciplinary approach, the overall quality of its contributions, and the refusal of most contributors to oversimplify and risk the microdeterminism of many popular essays." ChoiceTable of ContentsList of Contributors. Acknowledgements. Introduction : Justine Burley (University of Manchester and Exeter College, Oxford) and John Harris (University of Manchester). 1. Stem cells: C.N. Svendsen (University of Cambridge). 2. Gene therapy for neurological disorders: P.R. Lowenstein (Gene Therapeutics Institute). 3. Cloning in biology and medicine: Ian Wilmut (Roslin Institute)Genetics of old age: Thomas B.L. Kirkwood (University of Newcastle). 4. The ethical legacy of Nazi medical war crimes: Paul Weindling (Oxford Bookes University). 5. Biotechnology and animals: Bernard E. Rollin (Colorado State University). 6. The role of informed consent in genetic experimentation: SørenHolm (University of Oslo). 7. Testing children and adolescents: Dorothy Wertz (University of Massachusetts). 8. Genetic testing of children: Lainie Friedman Ross (University of Chicago). 9. Mapping the human genome and "Monster Mythology": George J. Annas (Boston University). 10. The moral status of the gene: Mary Anne Warren (San Francisco State University). 11. The ethical use of human embryonic stem cells in research and therapy: John Harris (University of Manchester). 12. Preimplantation genetic diagnosis and embryo selection: Bonnie Steinbock (State University of New York at Albany). 13. Individual autonomy and genetic choice: Matthew Clayton (Brunel University). 14. Cloning and public policy: Ruth Macklin (Albert Einstein College of Medicine). 15. Sex-selection: The feminist response: Diemut Bubeck (London School of Economics). 16. Creating perfect people: Philip Kitcher (Columbia University). 17. Genetics and personal identity: Carol Rovane (Columbia University). 18. Genetic determinism and gene selection: Richard Dawkins (University of Oxford and New College). 19. The "Darwin Wars" and the human self image: Janet Radcliffe Richards (University College London. 20. Religion and Gene Therapy: Gerald McKenny (Rice University). 21. ‘Race', genetics and human difference: Hussein Kassim (University of London). 22. Self-ownership, begetting and germ-line information: Hillel Steiner (University of Manchester). 23. Justice, genetics and lifestyles: Inez de Beaufort (Erasmus University). 24. Commercial exploitation of the human genome: Ruth Chadwick (Lancaster University) and Adam Hedgecoe (University College London). 25. Forensic DNA typing: David Wasserman (University of Maryland). 26. Privacy and genetics: Madison Powers (Georgetown University). 27. DNA banking: Bartha Maria Knoppers (University of Montreal). 28. Genetic difference in the workplace: Michael Yesley (Los Alamos National Laboratory). 29. The insurance market and discriminatory practices: Tom Sorell (University of Ethics). 30. Legal and ethical issues in biotechnology patenting: Pilar Ossorio (American Medical Association. 31. Patented genes: Mark Sagoff (University of Maryland, College Park). 32. Property, patents, and genetic material: Stephen Munzer (University of California, Los Angeles). 33. Genetic screening from a public health perspective: Scott Burris (Temple University) and Lawrence Gostin (Georgetown University). Afterword: Sir David Weatherall (University of Oxford). Index

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Book SynopsisThe Handbook of Developmental Science, Behavior, and Genetics brings together the cutting-edge theory, research and methodology that contribute to our current scientific understanding of the role of genetics in the developmental system.Table of ContentsFOREWORD. Gilbert Gottlieb and the Developmental Point of View (Evelyn Fox Keller, Massachusetts Institute of Technology). I. INTRODUCTION. 1. Developmental Systems, Nature-Nurture, and the Role of Genes in Behavior and Development: On the Legacy of Gilbert Gottlieb (Kathryn E. Hood, The Pennsylvania State University, Carolyn Tucker Halpern, University of North Carolina at Chapel Hill, Gary Greenberg, Wichita State University, Richard M. Lerner, Tufts University). 2. Normally Occurring Environmental and Behavioral Influences on Gene Activity: From Central Dogma to Probabilistic Epigenesis (Gilbert Gottlieb). II. THEORETICAL FOUNDATIONS FOR THE DEVELOPMENTAL STUDY OF BEHAVIOR AND GENETICS. 3. Historical and Philosophical Perspectives on Behavioral Genetics and Developmental Science (James Tabery, University of Utah, Paul E. Griffiths, University of Sydney). 4. Development and Evolution Revisited (Mae Wan Ho, Institute of Science in Society). 5. Probabilistic Epigenesis and Modern Behavioral and Neural Genetics (Douglas Wahlsten, University of North Carolina at Greensboro). 6. The Roles of Environment, Experience, and Learning in Behavioral Development (George F. Michel, University of North Carolina at Greensboro). 7. Contemporary Ideas in Physics and Biology in Gottlieb’s Psychology (Ty Partridge, Wayne State University, Gary Greenberg, Wichita State University). III. EMPIRICAL STUDIES OF BEHAVIORAL DEVELOPMENT AND GENETICS. 8. Behavioral Development during the Mother-Young Interaction in Placental Mammals: The Development of Behavior in the Relationship with the Mother (Jay S. Rosenblatt, Institute of Animal Behavior, Rutgers). 9. Amniotic Fluid as an Extended Milieu Interieur (Scott R. Robinson, University of Iowa, Valerie Méndez-Gallardo, University of Iowa). 10. Developmental Effects of Selective Breeding for an Infant Trait (Susan A. Brunelli, Columbia University Medical Center, Betty Zimmerberg, Williams College, Myron A. Hofer, Columbia University Medical Center). 11. Emergence and Constraint in Novel Behavioral Adaptations (Kathryn E. Hood, The Pennsylvania State University). 12. Nonhuman Primate Research Contributions to Understanding Genetic and Environmental Influences on Phenotypic Outcomes across Development (Allyson Bennett and Peter J. Pierre, Wake Forest University). 13. Interactive Contributions of Genes and Early Experience to Behavioural Development: Sensitive Periods and Lateralized Brain and Behaviour (Lesley J. Rogers, University of New England, Armidale). 14. Trans-Generational Epigenetic Inheritance (Lawrence V. Harper, University of California, Davis). 15. The Significance of Non-Replication of Gene-Phenotype Associations (Carolyn Tucker Halpern, University of North Carolina at Chapel Hill). 16. Canalization and Malleability Reconsidered: The Developmental Basis of Phenotypic Stability and Variability (Robert Lickliter and Christopher Harshaw, Florida International University). IV. APPLICATIONS TO DEVELOPMENT. 17. Gene-Parenting Interplay in the Development of Infant Emotionality (Cathi B. Propper, The University of North Carolina at Chapel Hill, Ginger A. Moore, The Pennsylvania State University, W. Roger Mills-Koonce, The University of North Carolina at Chapel Hill). 18. Genetic Research in Psychiatry and Psychology: A Critical Overview (Jay Joseph, Licensed Psychologist). 19. On the Limits of Standard Quantitative Genetic Modeling of Inter-Individual Variation: Extensions, Ergodic Conditions and a New Genetic Factor Model of Intra-Individual Variation (Peter C. M. Molenaar, The Pennsylvania State University). 20. Songs My Mother Taught Me: Gene-Environment Interactions, Brain Development and the Auditory System: Thoughts on Non-Kin Rejection, Part II (Elaine L. Bearer, University of New Mexico). 21. Applications of Developmental Systems Theory to Benefit Human Development: On the Contributions of Gilbert Gottlieb to Individuals, Families, and Communities (Richard M. Lerner, Michelle J. Boyd, Megan K. Kiely, Christopher M. Napolitano, and Kristina L. Schmid, Tufts University). Name Index. Subject Index.

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Book SynopsisPlant biotechnology applies to three major areas of plants and their uses: (1) control of plant growth and development;Table of ContentsPreface.- Section I Plant Biotechnology From Inception to the Present: Overview of Plant Biotechnology from its Early Roots to the Present. The Use of Plant Cell Biotechnology for the Production of Phytochemicals. Molecular Farming of Antibodies in Plants. Use of Cyanobacterial Proteins to Engineer New Crops. Molecular Biology of Secondary Metabolism: Case Study for Glycyrrhiza Plants.- Section II Applications of Plant Biotechnology in Agriculture and Industry: New Developments in Agricultural and Industrial Biotechnology. Phytoremediation: The Wave of the Future. Biotechnology of the Rhizosphere. Plants as Sources of Energy.- Section III Use of Plant Secondary Metabolites in Medicine and Nutrition: Interactions of Bioactive Plant Metabolites: Synergism, Antagonism, and Additivity. The Use of Selected Medicinal Herbs for Chemoprevention and Treatment of Cancer, Parkinson's Disease, Heart Disease, and Depression. Regulating Phytonutrient Levels in Plants -- Towards Modification of Plant Metabolism for Human Health.- Section IV Risks and Benefits Associated with Plant Biotechnology: Risks and Benefits Associated with Genetically Modified (GM) Plants. Risks Involved in the Use of Herbal Products. Risks Associated with Over-collecting Medicinal Plants in Natural Habitats. The Potential of Biofumigants as Alternatives to Methyl Bromide for the Control of Pest Infestation in Grain and Dry Food Products.- Index.

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Book SynopsisHow scientific advances in genetic modification will fundamentally change the natural worldThe process of manipulating the genetic material of one animal to include the DNA of another creates a new transgenic organism. Several animals, notably goats, mice, sheep, and cattle are now genetically modified in this way. In Our Transgenic Future, Lisa Jean Moore wonders what such scientific advances portend. Will the natural world become so modified that it ceases to exist? After turning species into hybrids, can we ever get back to the original, or are they forever lost? Does genetic manipulation make better lives possible, and if so, for whom?Moore centers the story on goats that have been engineered by the US military and civilian scientists using the DNA of spiders. The goat's milk contains a spider-silk protein fiber; it can be spun into ultra-strong fabric that can be used to manufacture lightweight military body armor. Researchers also hope the transgenically produced spider silk willTrade Review"Lisa Jean Moore contributes a very needed conversation regarding the ways technology is built, maintained, and destroyed, and the tensions that evolve in its creation between funding entities, scientific knowledge production, and the general public. Moore walks a narrow line between a fear of dystopian consequences and a realization of the sheer possibilities associated with their human-driven existence. Her voice is nicely interwoven with interspecies relationships, the commodification of nonhuman-nonanimal animals (at least in the natural sense), scientific facts, economic drivers, and the oft-unrealized presence of transgenic technologies in our daily lives." * Andrea Laurent-Simpson, author of Just Like Family: How Companion Animals Joined the Household *"A fascinating and fun read. Lisa Jean Moore deftly analyzes a biologically and ethically complex topic, using reflexive analyses to guide the reader along, and contributing to emergent knowledge about genetically modified animals. Moore’s reflexivity invites the reader to witness her thinking about difficult issues, and thus the book also provides a path for us as readers to think alongside her. She doesn’t tell readers what to think on the topic, or even how to think about it, but by modeling her thinking through the topic, we are able to fully grasp the issue at hand and come to our own (messy) conclusions." * Elizabeth Cherry, author of For the Birds: Protecting Wildlife through the Naturalist Gaze *"For a reader interested in the details and daily routine of this kind of scientific interaction with large animals, there is much in this book to enjoy. One may also learn something about spiders, which are undoubtedly fascinating creatures." -- John Dupré * Los Angeles Review of Books *"Moore's narration is delicate, respectful, and wonder-filled... genuinely fun and eminently accessible. Lisa Jean Moore’s Our Transgenic Future is an entertaining, thoughtful inquiry into genetic engineering in general and all of the many ethical questions that it raises." -- Rebecca Coffey * Forbes *

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Book SynopsisHistory of Clinical Cytogenetics.- DNA, Chromosomes, and Cell Division.- Human Chromosome Nomenclature: An Overview and Definition of Terms.- Basic Cytogenetics Laboratory Procedures.- The Essentials of Light Microscopy.- Quality Control & Quality Assurance.- Instrumentation in the Cytogenetics Laboratory.- Autosomal Aneuploidy.- Structural Chromosome Rearrangements.- Sex Chromosomes, Sex Chromosome Disorders, and Disorders of Sex Development.- The Cytogenetics of Infertility.- Prenatal Cytogenetics.- The Cytogenetics of Spontaneous Abortion.- Chromosome Instability.- The Cytogenetics of Hematologic Neoplasms.- The Cytogenetics of Solid Tumors.- Fluorescence in situ Hybridization (FISH).- Microarray-Based Cytogenetics.- Fragile X: A Family of Disorders: Changing Phenotype and Molecular Genetics.- Genomic Imprinting and Uniparental Disomy.- Genetic Counseling.Trade ReviewFrom the reviews of the third edition:“The audience includes those performing clinical cytogenetic testing or using results for genetic counseling or clinical care. It also would be of interest to anyone interested in cytogenetic analysis and application, from healthcare providers … to the educated lay public. … This is truly a remarkable and comprehensive book on clinical cytogenetics. … You would also want this book as a handy reference for which genetic abnormality is associated with what disease, and the best test method to use to identify the suspected abnormality.” (Valerie Ng, Doody’s Book Reviews, July, 2013)Table of ContentsSECTION 1 - Basic Concepts and Background1. History of Clinical CytogeneticsSteven L. Gersen2. DNA, Chromosomes, and Cell Division Martha B. Keagle3. Human Chromosome Nomenclature: An Overview and Definition of TermsMarilyn L. Slovak, Aaron Theisen, and Lisa G. ShafferSECTION II - Examining and Analyzing Chromosomes4. Basic Cytogenetics Laboratory ProceduresMartha B. Keagle and Steven L. Gersen5. The Essentials of Light MicroscopyNathan Claxton and Stephen Ross6. Quality Control & Quality AssuranceMartha B. Keagle7. Instrumentation in the Cytogenetics LaboratorySteven L. GersenSECTION III – Clinical Cytogenetics8. Autosomal AneuploidyJin-Chen C. Wang9. Structural Chromosome RearrangementsKathleen Kaiser-Rogers and Kathleen Rao10. Sex Chromosomes, Sex Chromosome Disorders, and Disorders of Sex DevelopmentCynthia M. Powell11. The Cytogenetics of InfertilityLinda Marie Randolph12. Prenatal CytogeneticsLinda Marie Randolph13. The Cytogenetics of Spontaneous AbortionSolveig M. V. Pflueger14. Chromosome InstabilityXiao-Xiang ZhangSECTION IV – Cancer Cytogenetics15. The Cytogenetics of Hematologic NeoplasmsAurelia Meloni-Ehrig16. The Cytogenetics of Solid Tumors Linda D. Cooley and Kathleen S. WilsonSECTION V - Adjunct Technologies17. Fluorescence in situ Hybridization (FISH)Daynna J. Wolff18. Microarray-Based CytogeneticsLisa G. ShafferSECTION VI – Beyond Chromosomes19. Fragile X: A Family of Disorders: Changing Phenotype and Molecular GeneticsElaine B. Spector 20. Genomic Imprinting and Uniparental DisomyJin-Chen C. Wang21. Genetic CounselingSarah Hutchings Clark

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Book Synopsis

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Book Synopsis

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Book SynopsisThe potential for the development of therapeutic oligonucleotides into clinical medicines and their use as basic research tools are explored in this volume, which is the proceedings of the 7th NIH Symposium on Therapeutic Oligonucleotides. The focus is on antisense, RNAi, triple-helix, gene repair, DNA chips, and CpG immune modulatory oligonucleotides. Specific chapters address designing better siRNAs, splice switching oligonucleotides, selective delivery of oligonucleotides, and medicinal drugs by receptor-mediated endocytosis, development of a function overriding siRNA silencing in mammalian cells, transcription factor decoys, and modified oligonucleotide hybridization and genetic insertion. NOTE: Annals volumes are available for sale as individual books or as a journal. For information on institutional journal subscriptions, please visit www.blackwellpublishing.com/nyas. ACADEMY MEMBERS: Please contact the New York Academy of Sciences directly to place your order (www.nyas.org). Members of the New York Academy of Science receive full-text access to the Annals online and discounts on print volumes. Please visit http://www.nyas.org/MemberCenter/Join.aspx for more information about becoming a member.Table of ContentsIntroduction: Y S Cho-Chung, Alan M. Gewirtz, and Cy A. Stein. Part I: Kill the Messenger: Gene Silencing by Nucleic Acid Molecules. 1. Knock-down of the Cytoprotective Gene, Clusterin, to Enhance Hormone and Chemosensitivity in Prostate and Other Cancers: Martin Gleave and Kim N. Chi. 2. Recognition of Chromosomal DNA in Human Cells by Peptide Nucleic Acids and Small Duplex RNAs: David R. Corey. Part II: Antisense and siRNA: Chemistry, Sequence Specificity, and Target Validation. 3. Design and Development of Thermolytic DNA Oligonucleotide Prodrugs: Andrzej Grajkowski, Joao Pedras-Vasconcelos, Cristina Ausín, Daniela Verthelyi, and Serge L. Beaucage. 4. Rationally Targeted, Conformationally Constrained, Oxetane-Modified Oligonucleotides Demonstrate Efficient Gene-Silencing Activity in a Cellular System: J B Opalinska and A M Gewirtz. Part III: Delivery Cellular and Phenotype Effect of Silencing Agents:. 5. In Vivo Potentialities Andrei Maksimenko, Valerie Polard, Marie Villemeur, Hind Elhamess, Patrick Couvreur, Jean-Remi Bertrand, Malam Aboubakar, Marina Gottikh, and Claude Malvy of EWS-Fli-1 Targeted Antisense Oligonucleotides-Nanospheres Complexes:. 6. Endo-Porter: A Novel Reagent for Safe, Effective Delivery of Substances into Cells: James E. Summerton. 7. Tumor Reversion: Protein Kinase A Isozyme Switching: Yoon S. Cho-Chung and Maria V. Nesterova. Part IV: Immune Modulation of and Resistance to Silencing Agents. 8. Therapeutic Potential of Oligonucleotides Expressing Immunosuppressive TTAGGG Motifs: Dennis M. Klinman, Ihsan Gursel, Sven Klaschik, Li Dong, Debbie Currie, and Hidekazu Shirota. 9. Breaking Tolerance to Tumors with Dendritic Cell-Based Immunotherapy: Ines Mende and Edgar G. Engleman. 10. Development of Resistance to RNAi in Mammalian Cells: Zhi-Ming Zheng, Shuang Tang, and Mingfang Tao. Part V: Transcription Silencing by Nucleic Acid Molecules. 11. The Development of Bioactive Triple Helix-Forming Oligonucleotides: Michael M. Seidman, Nitin Puri, Alokes Majumdar, Bernard Cuenoud, Paul S. Miller, and Rowshon Alam. 12. Transcription Factor Decoys: A New Model for Disease Intervention: Michael J. Mann. 13. DNA Damage Produced by 125I-Triplex-Forming Oligonucleotides as a Measure of Their Succesful Delivery into Cell Nuclei: Irina V. Panyutin, Olga A. Sedelnikova, William M. Bonner, Igor G. Panyutin, and Ronald D. Neumann. 14. Targeted Genome Modification via Triple Helix Formation: Jennifer M. Kalish and Peter M. Glazer. Part VI: Functional Genomics—Antisense/RNAi. 15. "Promoter Array" Studies Identify Cohorts of Genes Directly Regulated by Methylation, Copy Number Change, or Transcription Factor Binding in Human Cancer Cells: Yipeng Wang, Jun Hayakawa, Fred Long, Qiuju Yu, Ann H. Cho, Gaelle Rondeau, John Welsh, Shalu Mittal, Ian De Belle, Eileen Adamson, Michael Mcclelland, and Dan Mercola. 16. Application of Expression Genomics for Predicting Treatment Response in Cancer: Khew-Voon Chin, Leah Alabanza, Kazuyuki Fujii, Kazuya Kudoh, Tsunekazu Kita, Yoshihiro Kikuchi, Zachariah E. Selvanayagam, Yick Fu Wong, Yong Lin, and Wei Chung Shih. 17. Stability Regulation of mRNA and the Control of Gene Expression: Chris Cheadle, Jinshui Fan, Yoon S. Cho-Chung, Thomas Werner, Jill Ray, Lana Do, Myriam Gorospe, and Kevin G. Becker. Part VII: Chemosensitivity Enhancement by Antisense and RNAi. 18. Novel MDM2 p53-Independent Functions Identified through RNA Silencing Technologies: Zhuo Zhang, Hui Wang, Mao Li, Elizabeth Rayburn, Sudhir Agrawal, and Ruiwen Zhang. 19. Application of XIAP Antisense to Cancer and Other Proliferative Disorders: Development of AEG35156/ GEM®640: Eric C. Lacasse, Ekambar R. Kandimalla, Peter Winocour, Tim Sullivan, Sudhir Agrawal, John W. Gillard, and Jon Durkin. Part VIII: Nucleic Acid Therapeutics for Human Diseases. 20. Induction of Apoptosis by G3139 in Melanoma Cells: Luba Benimetskaya, Johnathan C. Lai, Anastasia Khvorova, Sijian Wu, Paul Miller, and C A Stein. 21. Zebularine: A Unique Molecule for an Epigenetically Based Strategy in Cancer Chemotherapy: Victor E. Marquez, James A. Kelley, Riad Agbaria, Tisipi Ben-Kasus, Jonathan C. Cheng, Christine B. Yoo, and Peter A. Jones. 22. Chemoprevention with Protein Kinase A RI Antisense in DMBA-Mammary Carcinogenesis: Maria V. Nesterova and Yoon S. Cho-Chung

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Book SynopsisThe structure of DNA varies along its sequence, which can lead to sequence-dependent variations in the fidelity of DNA copying and repair. And because the probability of distinct classes of mutations varies along a DNA sequence, variation that affects fitness will have evolutionary implications, as selection acts on heritable variation. This Annals volume brings together a broad interdisciplinary group of researchers to explore the impact of increasing understanding of DNA structure, repair, replication, and organization on interrelated subjects ranging from evolution, to dependence of the effect of mutagens on environmental and sequence context, to noncanonical forms of information representation in genomes. NOTE: Annals volumes are avaialble for sale as individual books or as a journal. For information on institutional journal subscriptions, please visit http://ordering.onlinelibrary.wiley.com/subs.asp?ref=1749-6632&doi=10.111/(ISSN)1749-6632 ACADEMY MEMBERS: Please contact the New York Academy of Sciences directly to place your order (www.nyas.org). Members of the New York Academy of Science receive full-text access to Annals online and discounts on print volumes. Please visit http://www.nyas.org/MemberCenter/Joun.aspx for more information about becoming a member.Table of ContentsOverview of the creative genome: effects of genome structure and sequence on the generation of variation and evolution 1. Lynn Helena Caporale Genome hyperevolution and the success of a parasite 11. J. David Barry, James P. J. Hall, and Lindsey Plenderleith The tricky path to recombining X and Y chromosomes in meiosis 18. Liisa Kauppi, Maria Jasin, and Scott Keeney Sites of genetic instability in mitosis and cancer 24. Anne M. Casper, Danielle M. Rosen, and Kaveri D. Rajula The genome: an isochore ensemble and it’s evolution 31. Giorgio Bernardi Multiple levels of meaning in DNA sequences, and one more 35. Edward N. Trifonov, Zeev Volkovich, and Zakharia M. Frenkel Evolution of simple sequence repeat-mediated phase variation in bacterial genomes 39. Christopher D. Bayliss and Michael E. Palmer Indirect selection of implicit mutation protocols 45. David G. King G4 motifs in human genes 53. Nancy Maizels Adaptive radiation of venomous marine snail lineages and the accelerated evolution of venom peptide genes 61. Baldomero M. Olivera, Maren Watkins, Pradip Bandyopadhyay, Julita S. Imperial, Edgar P. Heimer de la Cotera, Manual B. Aguilar, Estuardo Lopez Vera, Gisela P. Concepcion, and Arturo Lluisma Integrons and gene cassettes: hotspots of diversity in bacterial genomes 71. Ruth M. Hall Creative deaminases, self-inflicted damage, and genome evolution 79. Silvestro G. Conticello Three-dimensional architecture of the IgH locus facilitates class switch recombination 86. Amy L. Kenter, Scott Feldman, Robert Wuerffel, Ikbel Achour, Lili Wang, and Satyendra Kumar Preaching about the converted: how meiotic gene conversion influences genomic diversity 95. Francesca Cole, Scott Keeney, and Maria Jasin Gross chromosomal rearrangement mediated by DNA replication in stressed cells: evidence from Escherichia coli 103. J.M. Moore, Hallie Wimberly, P.C. Thorton, Susan M. Rosenberg, and P.J. Hastings Implications of genetic heterogeneity in cancer 110. Michael W. Schmitt, Marc J. Prindle, and Lawrence A. Loeb Corrigendum for Ann. N.Y. Acad. Sci. 2009. 1182: 47-57 117.

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Book SynopsisWith the world population growth, food demand grows. Aquatic foods provide high quality protein, essential for human health. It is clearly visible that the production of aquatic organisms using aquaculture will have to increase, to the extent that the fishery productivity holds steady over the past few years, even increasing fishing effort. The total production of aquatic organisms by-catch (including fish, molluscs, crustaceans, etc.) represents 83.5 million tonnes in the year 2014, with a stable production for some years. On the other hand, aquaculture has grown enough in recent years. In the year 2006 the total output of aquatic organisms through cultivation was approximately 45 million tonnes in 2014 the production over 73 million tones. Since the establishment and technical domain about reproduction and hatchery of marine fish, has begun a process of genetic improvement, as the best individuals were selected for mating and reproduction in search of the best possible offspring. According to Dunham et al. (2000), breeding programs began in the 1960s. Molecular-based knowledge emerged in the 1980s and has continued to gain momentum. Efforts are now well established in traditional selective breeding, biotechnology and molecular genetics of finfish, and are rapidly developing for aquatic invertebrate domestication.Genetic improvement is the theory that aims to find the animals that produce the best offspring generation after generation, increasing the population average to some trait. The main objectives of the breeding programs are: increase animal health and increase productivity and product quality. However, on aquaculture, breeding programs are not common, and in many species the production is based only on the capture of wild animals. This can be explained, primarily because of the complexity of the reproductive cycle; the rapid increase of inbreeding in breeding stocks; and the few knowledge of the theory of genetic improvement for researchers, educators, etc. In addition to all this, the breeding programs of aquatic organisms face severe problems compared to terrestrial animals. The genetic improvement for aquatic organisms really is a challenging path ahead of us, for that we shall seek to carry out research to help this area to develop, benefiting the entire aquaculture chain.

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Book Synopsis* Provides specific examples of germplasm research related to climate change threats * Edited by internationally renowned experts in the field * The final chapter of the book draws a synthesis of the many issues raised within the bookTable of Contentsa: Preface 1: Food Security, Climate Change and Genetic Resources 2: Genetic Resources and Conservation Challenges under the Threat of Climate Change 3: Climate Projections 4: Effects of Climate Change on Potential Food Production and Risk of Hunger 5: Regional Impacts of Climate Change on Agriculture and the Role of Adaptation 6: International Mechanisms for Conservation and Use of Genetic Resources 7: Crop Wild Relatives and Climate Change 8: Climate Change and On-farm Conservation of Crop Landraces in Centres of Diversity 9: Germplasm Databases and Informatics 10: Exploring ‘Omics’ of Genetic Resources to Mitigate the Effects of Climate Change 11: Harnessing Meiotic Recombination for Improved Crop Varieties 12: High Temperature Stress 13: Drought 14: Salinity 15: Response to Flooding: Submergence Tolerance in Rice 16: Effects of Climate Change on Plant–Insect Interactions and Prospects for Resistance Breeding Using Genetic Resources"

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Book SynopsisMaintaining food security in the face of human population increase and climate change is one of the critical challenges facing us in the 21st Century. Utilisation of the full range of agrobiodiversity will be a necessary tool in addressing this challenge. In this book a team of international contributors review all aspects of utilization and conservation of crop wild relative (CWR) and landrace (LR) diversity as a basis for crop improvement and future food security. Enhancing Crop Genepool Use covers four key areas: · Characterization techniques - novel 'omics' techniques and predictive tools that can be used to identify adaptive traits and expedite plant breeding. · Conservation strategies - how to develop national, regional and global CWR and LR conservation strategies, how better to target conservation to meet the needs of the plant breeding community, and how to integrate CWR and LR diversity into existing biodiversity conservation programmes. · Facilitating CWR and LR use - pre-breeding using 'exotic' germplasm, meeting breeders' needs, integrating the conservation and user communities, and policy enhancement. · Informatics development - improving characterization, trait and conservation data management and accessibility, and inter-information system operability. This book will appeal to a wide array of specialists and postgraduate students, such as those working in the fields of agrobiodiversity conservation and use, conservation, ecology, botany, genetics, plant breeding and agriculture.Table of ContentsPart I: Breeder's use of exotic germplasm 1: Using phenomics and genomics to unlock landrace and wild relative diversity for crop improvement 2: Pre-domesticating wild relatives as new sources of novel genetic diversity 3: Unravelling quinoa domestication with wild ancestors 4: Screening wild Vigna species and cowpea (Vigna unguiculata) landraces for sources of resistance to Striga gesnerioides 5: Wild Lactuca saligna a rich source of variation for lettuce breeding 6: Capturing wild relative and landrace diversity for crop improvement using a new selection tool to exploit genetic resources in durum wheat Part II: Improving access to PGRFA 7: How the Focused Identification of Germplasm Strategy (FIGS) is used to mine plant genetic resources collections for adaptive traits 8: Predictive characterization methods for accessing and using CWR diversity 9: Keeping a finger on the pulse: monitoring the use of CWR in crop improvement Part III: CWR conservation 10: Joining up the dots: a systematic perspective of crop wild relative conservation and use 11: Europe’s crop wild relative diversity: from conservation planning to conservation action 12: An approach for in situ gap analysis and conservation planning on a global scale 13: The distributions and ex situ conservation of crop wild relatives: a global approach 14: National strategies for the conservation of crop wild relatives 15: Crop wild relatives, a priority in Jordan? - developing a national strategy for the conservation of plant diversity in Jordan using a participatory approach 16: Establishing systematic crop wild relative conservation within the United Kingdom 17: Optimized site selection for the in situ conservation of forage CWRs: a combination of community and genetic level perspectives 18: Developing a crop wild relative conservation strategy for Finland 19: Developing national crop wild relative in situ conservation strategy for Lithuania: creation of national CWR inventory and its prioritization 20: Priorities for conservation of crop wild relatives at Indian National Genebank 21: Strategies for detecting climate adaptations in the wild pearl millet for future breeding use 22: Assessment of the conservation status of Mesoamerican crop species and their wild relatives in light of climate change Part IV: LR conservation 23: Landrace conservation of maize in Mexico and evolutionary breeding 24: Use of spontaneous sexually-produced new landraces of a vegetatively propagated crop of the Andes (Oxalis tuberosa Mol.) to enhance in situ conservation 25: A long-term systematic monitoring framework for on-farm conserved potato landrace diversity 26: A European in situ (on-farm) conservation and management strategy for landraces 27: Using landraces in agriculture, food and cooking: experiences around a big city in Southern Europe 28: Hungarian strategies for the conservation of crop wild relative and landrace diversity 29: Assessment of Italian landrace density and species richness: useful criteria for developing in situ conservation strategies 30: Chickpea wild relatives and landraces of Georgia 31: Landrace inventories and recommendations for in situ conservation in Finland Part V: Community-based conservation and use 32: Community biodiversity management (CBM): A participatory methodology that integrates empowerment, livelihoods and on-farm management of agrobiodiversity 33: Evolutionary Plant Breeding: A method for rapidly increasing on-farm biodiversity to support sustainable livelihoods in an era of climate change 34: Value chain development: a silver bullet for agrobiodiversity conservation and use? Part VI: PGR conservation and use policy 35: Moving slowly towards the light: a review of efforts to create a global system for PGRFA over the last half century 36: On the conservation and sustainable use of plant genetic resources in Europe: a stakeholder analysis 37: Towards an improved European Plant Germplasm System 38: Impact of the genetic resources policy landscape on food security: an assessment of the Genetic Resources and Intellectual Property Rights Programme 39: What do we have to lose? Monitoring crop genetic diversity Part VII: Conservation informatics 40: Improved utilization of crop diversity for rationalized breeding using data interoperability 41: Implementation of a PGR Global Documentation System in Portugal 42: The GRIN-Taxonomy Crop Wild Relative Inventory

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Book SynopsisAdvances in research and development reveal the immense diversity and potential of marine genetic resources. Under international law, no specific regime applies to these complex and paradoxical objects of use. The Law of the Sea Convention sets a framework that is partly inadequate for this new category of resources. The Biodiversity Convention and the Nagoya Protocol only address the genetic resources of national areas. Patents allow their holder to exercise a monopoly on exploiting biotechnological creations to extensive claims, questioning the common nature of biodiversity and related knowledge. They hinder research and the objectives of biodiversity law. The legal and practical rules of physical and functional access vary in geometry. They focus on the valorization of research results, crystallizing conflicts of interest between suppliers and users. Sustainable research and development is essential to the knowledge and protection of marine biodiversity. The qualification of marine genetic resources in common, standard contractual tools, distributed research and development infrastructures, negotiation of an agreement on sustainable use and conservation of biodiversity beyond the limits of national jurisdiction, would To remove these inconsistencies.Table of ContentsForeword ix Introduction xi Chapter 1. The Scientific Representation of the Living World: A Dual Concept Between Nature’s and Humans’ Shares 1 1.1. Natural sciences: the given living world 2 1.1.1. Taxonomy: the observation of the living world 2 1.1.2. Systematics: the identification of the living world 10 1.2. Life sciences: the constructed living world 18 1.2.1. Biological sciences: the exploration of the living world 18 1.2.2. Bio-technosciences: the instrumentalization of the living world 25 Part 1. Singular Objects Moving Toward Reservation 35 Chapter 2. Exploitable Raw Materials 37 2.1. Genetic material: natural resources defined according to their conditions of appropriation 38 2.1.1. Appropriable natural things 41 2.1.2. Things on the verge of exclusive appropriation 45 2.2. Marine genetic resources: biological resources defined according to their destination 58 2.2.1. Traditional marine living resources exploited for food and industrial purposes 59 2.2.2. New marine biological resources searched for the purposes of scientific and biotechnological valorization 63 Chapter 3. Patentable Biotechnological Inventions 75 3.1. The patentability of life of any origin: an established principle 80 3.1.1. The uncontested patentability of inventions of microorganic origin 81 3.1.2. The logical acceptance of the patentability of inventions of macroorganic origin 87 3.2. The patentability of life in all its forms: a questionable reality 98 3.2.1. An overall commodification of the living world 99 3.2.2. A gradual privatization of research in life sciences 109 Part 2. Global Objects Moving Toward Sharing 117 Chapter 4. Residual Res Communes 119 4.1. Res communes due to disinterest 120 4.1.1. Non-appropriable things as a matter of principle 121 4.1.2. Things of common use 134 4.2. Common resources at risk 137 4.2.1. The tragedy of the genetic pool 138 4.2.2. The tragedy of the scientific “anticommons” 151 Chapter 5. Reconstructing the Commons 157 5.1. Renewal of the commons in a context of global interdependencies 160 5.1.1. Global public goods: a theoretical and global approach to the commons 162 5.1.2. Common-pool resources: a concrete and nuanced approach to the commons 166 5.2. An attempt to apply renewed figures of the commons to marine biodiversity and associated knowledge 172 5.2.1. A desirable communitarization 172 5.2.2. A communitarization difficult to implement 186 Conclusion 197 Appendices 199 Appendix 1. Classical Marine Bioprospecting: Biochemistry and Genetic Engineering 201 Appendix 2. Modern Marine Bioprospecting: Metagenomics 203 Appendix 3. The Drug Research and Development Steps 205 Appendix 4. Risk Assessment in the Bioprospecting Process 207 Appendix 5. Aleatory Component Comparison in Fishing and Bioprospecting 209 Appendix 6. Patent Claims Over Genes of Marine Origin 211 Appendix 7. Illustrative Database on Marine Biotechnological Innovations 213 Bibliography 231 Index 263

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Book SynopsisThis book constitutes a fascinating and in-depth analysis of the significance of the requirement of industrial application within gene patenting and how this influences innovation in Europe and the US. The author addresses an area normally overlooked in biotechnology patenting due to the predominance of the ethical debate and, in doing so, produces a unique approach to dealing with concerns in this field. Patenting Genes: The Requirement of Industrial Application is the result of extensive research into the legal history of the industrial application requirement as well as exploration of the broad range of decisions on DNA patentability. This requirement has taken a prominent role within DNA patenting decisions in Europe since the 1998 Biotech Directive, which Dr Diaz Pozo argues has worked efficiently to control claims to human gene sequences and encouraged progress in genetic research. A broad selection of decisions on the patentability of DNA in both European Union and US courts is discussed, emphasizing the mirroring of the European approach in US cases. Academics and students of patent law and biotechnology innovation, as well as policy formulators, will find this book of great interest and value. Activists and practitioners interested in the patentability of human gene inventions in Europe and the US will also benefit from this original work.Trade Review'This insightful and accessible book provides a uniquely thorough examination of the European requirement of industrial application and the determination of the scope of protection of gene patents. It is a scholarly work of the highest quality and rewards readers with its clear and accessible approach to the often overlooked legal issues surrounding the patentability of biotechnological inventions on grounds of industrial application. The book is highly recommended for academics and for practitioners alike.' --(Duncan Matthews, Queen Mary University of London, UK)'This book provides a valuable contribution to the understanding of industrial application in patent law. It shows how - with the evolvement of biotechnology patent law - a formerly obscure patentability requirement became a key tool for patent law policy. A detailed discussion of the Biotechnology Directive, as well as in-depth analysis of EPO and CJEU jurisprudence, makes this book worthwhile reading for any IP lawyer concerned with patent law.' --(Herbert Zech, University of Basel, Switzerland)Table of ContentsContents: 1. Introduction 2. Genetic inventions and patent law in Europe 3. The European requirement of industrial application 4. The industrial applicability of human genetic inventions 5. The requirement of industrial application and the interpretation of the exclusion of human genetic discoveries from patent protection 6. The requirement of industrial application and the determination of the scope of protection of gene patents 7. Human gene patents, patent clusters and innovative progress 8. Conclusion Index

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Book SynopsisSince the first edition of this book was published in 2002, the field of quantitative genetics, genomics and breeding has changed markedly. In response, only four chapters have been updated for this new edition, and the remaining 16 chapters are entirely new. This book presents state-of-the-art, authoritative chapters on contemporary issues in the broad areas of quantitative genetics, genomics and plant breeding. Section 1 (Chapters 2 to 12) emphasizes the application of genomics, and genome and epigenome editing techniques, in plant breeding; bioinformatics; quantitative trait loci mapping; and the latest approaches of examining and exploiting genotype-environment interactions. Section 2 (Chapters 13 to 20) represents the intersection of breeding, genetics and genomics. This section describes the use of cutting-edge molecular breeding and quantitative genetics techniques in wheat, rice, maize, root and tuber crops and pearl millet. Overall, the book focuses on using genomic information to help evaluate traits that can combat biotic/abiotic stresses, genome-wide association mapping, high-throughput genotyping/phenotyping, biofortification, use of big data, orphan crops, and gene editing techniques. The examples featured are taken from across crop science research and cover a wide geographical base. This book contains: chapters by expert authors from six continents; state-of-the-art information on topical areas relative to crop improvement; coverage of genome-editing techniques.Table of Contents1: Vignettes of the History of Genetics Section I: Quantitative Genetics: Plant Breeding, Bioinformatics, Genome Editing and G × E Interaction 2: Food and Health: The Role of Plant Breeding 3: The Importance of Plant Pan-genomes in Breeding 4: Genome Editing Technologies for Crop Improvement 5: Epigenome Editing in Crop Improvement 6: Bioinformatics and Plant Breeding 7: Bioinformatics Approaches for Pathway Reconstruction in Orphan Crops — A New Paradigm 8: Advances in QTL Mapping and Cloning 9: Genotype–Environment Interaction and Stability Analyses: An Update 10: Biplot Analysis of Multi-environment Trial Data 11: Design and Analysis of Multi-year Field Trials for Annual Crops 12: Advances in the Definition of Adaptation Strategies and Yield-stability Targets in Plant Breeding Section II: Intersection of Breeding, Genetics and Genomics: Crop Examples 13: Prediction with Big Data in the Genomic and High-throughput Phenotyping Era: A Case Study with Wheat Data 14: Quantitative Genetics in Improving Root and Tuber Crops 15: Genomic Selection in Rice: Empirical Results and Implications for Breeding 16: Novel Breeding Approaches for Developing Climate-resilient Rice 17: Quantitative Genetics, Molecular Techniques and Agronomic Performance of Provitamin-A Maize in Sub-Saharan Africa 18: Developments in Genomics Relative to Abiotic Stress-tolerance Breeding in Maize During the Past Decade 19: Exploiting Alien Genetic Variation for Germplasm Enhancement in Brassica Oilseeds 20: Biofortified Pearl Millet Cultivars Offer Potential Solution to Tackle Malnutrition in India

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Book SynopsisBridging the gap between genome and phenotype, the transcriptome is a molecular-level snapshot of the act of living. Transcriptomics shows which genes are expressed into proteins in a specific tissue of a specific organism at a specific time and condition. This book gives an account of the extraordinary diversity of ways transcriptomics has been and can be utilised in basic and applied entomological research. It encompasses a vast range of disciplines within entomology, applying transcriptomics to the study of over one million described species of insects. It covers a vast range of disciplines from phylogenomics to pest management, from ecology to physiology, and from behavior to evolutionary biology. The book covers the breadth and depth of transcriptomics use in research to showcase the utility of this technology in all disciplines. Research examples in the book are relevant to fish, birds, plants, and fungi, as well as insects and other arthropods, helping scientists in any field, using any system, to understand what transcriptomics can do for them. The book: Introduces transcriptomics theory and practice for researchers of all levels wishing to gain an insight into how to apply these techniques to their own fields. Showcases the myriad ways transcriptomics can be used to answer biological questions. Is written by a team of international experts describing their own experiences, giving guidance for applying it to the reader's own work. Reviews how transcriptomics research has helped entomologists push their fields further and make new discoveries.Table of Contents1: Harnessing Transcriptomics to Study Insect Biology – Kyle M Lewald, Joanna C. Chiu 2: From Reads to Genes – Chengran Zhou, Guanliang Meng, Shanlin Liu 3: Transcriptomics in Pest Management Research - Antonino Malacrinò 4: Aphid Transcriptomics—Past, Present and Future – Sampurna Sattar, Gary A Thompson 5: Transcriptomic Research on Honey Bee-Associated Pathogens – James P. Tauber 6: Cytochrome P450s in the Era of Transcriptomics - Bernarda Calla, May R Berenbaum 7: Whole-body Transcriptome of the Douglas-fir Seed Chalcid, Megastigmus spermotrophus, Reveals Ecological and Evolutionary Insights. - Amber R Paulson, Jürgen Ehlting, Patrick von Aderkas, Steven J. Perlman. 8: Differential Transcriptome Profiling for Identification of Cellulose Degrading Enzymes in Ctenolepisma longicaudata - Ratnasri Pothula, Brian R. Johnson, William E. Klingeman, Matthew Huff, Margaret E. Staton, Juan Luis Jurat-Fuentes 9: Using RNA-Seq to Help Identify Functions in Unknown Organs - Matan Shelomi 10: A practical guide for functional transcriptomics: A case study in RNA interference and qPCR to understand the explosive chemistry of Brachinus bombardier beetles (Coleoptera: Carabidae). - Aman Gill, Melanie Gee, Kipling Will

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Book SynopsisThe genetic improvement of fish for aquaculture and related fisheries has seen huge advances over recent years. Building upon the previous two editions of Aquaculture and Fisheries Biotechnology: Genetic Approaches, this 3rd edition offers a presentation of traditional selective breeding, modern genetic biotechnology, genomics, gene transfer and gene editing, and the latest developments in genetic biotechnology such as epigenetics, xenogenesis and genome-wide association study coupled with commercial application, the impact of government regulation and expectations for the future. It provides a firm grounding in relevant aspects of classical genetics, before focusing on particular aspects such as sex reversal and breeding as applied in aquaculture and fisheries. It also explores how more recent molecular genetics, genomics and biotechnology techniques can be used and combined in improvement programmes for fish and aquaculture species. A glossary explains the latest terminology used in biotechnology and genetics.This book will be useful for research scientists and students in marine biotechnology, aquaculture biotechnology, and fish genetics and breeding.

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Book SynopsisGenome sequencing has become a basic tool of plant and animal breeding. Reduced costs have allowed the sequencing of thousands of plant lines or cultivars, leading to previously unobtainable insights into genetic impacts during breeding and generating large numbers of novel candidate breeding genes. This book summarizes the impacts that the genome sequencing revolution has had on agriculture with reference to applications across species and locations. It explains new techniques and their use in understanding epigenetics, breeding and conservation. It is a useful resource for scientists wanting to learn how different fields of agriculture have adapted novel genome sequencing technologies to their requirements, and for those wanting to transfer technologies and lessons learned from one field of agriculture to another.This book is a useful resource for students and researchers in biotechnology, genetics, genomics and breeding.

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Book SynopsisRNA interference (RNAi) has the potential to make major contributions towards sustainable crop production and protection with minimal environmental impacts compared to other technologies. RNAi is being developed and exploited both within plants (i.e. host-induced gene silencing, HIGS) and/or as topical applications (e.g. spray-induced gene silencing, SIGS) for targeting pest and pathogen genes and for manipulating endogenous gene expression in plants. Chapters by international experts review current knowledge on RNAi, methods for developing RNAi systems in GM plants and applications for crop improvement, crop production and crop protection. Chapters examine both endogenous systems in GM plants and exogenous systems where interfering RNAs are applied to target plants, pests and pathogens. The biosafety of these different systems is examined and methods for risk assessment for food, feed and environmental safety are discussed. Finally, aspects of the regulation of technologies exploiting RNAi and the socio-economic impacts of RNAi technologies are discussed.Table of ContentsChapter 1: Introduction to RNAi in Plant Production and Protection. Bruno Mezzetti, Jeremy Sweet and Lorenzo Burgos Chapter 2: Gene silencing to induce pathogen-derived resistance in plants. Zhen Liao, Elena Zuriaga, Ángela Polo and Maria L. Badenes Chapter 3: Exogenous application of small RNAs as a tool for gene function discovering. Barbara Molesini and Tiziana Pandolfini Chapter 4: The “Trojan Horse” approach for successful RNA interference in inscects. Dimitrios Kontogiannatos, Anna Kolliopoulou and Luc Swevers. Chapter 5: Biogenesis and functional RNAi in fruit-trees. Michel Ravelonandro and Pascal Briard Chapter 6: Gene silencing or gene editing: the pros and cons. Huw D Jones Chapter 7: Application of RNAi technology in Forest Trees. Matthias Fladung, Hely Haggman and S. Sutela Chapter 8: Host-induced gene silencing and spray-induced gene silencing for crop protection against viruses. Angela Ricci, Silvia Sabbadini, Laura Miozzi, Bruno Mezzetti and Emanuela Noris. Chapter 9: Small talk and large impact: the importance of small RNA molecules in the fight of plant diseases. Kristian Persson Hodén and Christina Dixelius Chapter 10: dsRNA stability during external applications – an overview. Ivelin Pantchev, Goritsa Rakleova and Atanas Atanassov Chapter 11: Boosting dsRNA delivery in plant and insect cells with peptide- and polymer-based carriers: cases-based current status and future perspectives. Kristof de Schutter, Olivier Christiaens, Clauvis Nji Tizi Taning and Guy Smagghe Chapter 12: Environmental safety assessment of RNAi plants for pest control. Salvatore Arpaia, Olivier Christiaens, Paul Henning Krogh, Kimberly Parker and Jeremy Sweet Chapter 13: Food and feed safety assessment of RNAi plants and products. Hanspeter Naegeli, Gijs Kleter and Antje Dietz-Pfeilstetter Chapter 14: Regulatory aspects of RNAi in plant production. Werner Schenkel and Achim Gathmann Chapter 15: The Economics of RNAi technology in plant breeding: from the innovation landscape to consumer acceptance. Dario Frisio and Vera Ventura Chapter 16: Communication challenges of RNAi and selected communication messages from iPLANTA for dissemination. Hilde-Gunn Opsahl-Sorteberg

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Book SynopsisDocuments and critically analyses the photographs that helped strengthen as well as bring down the Eugenics Movement. Using a large body of racial-type images and a variety of historical and archival sources, and concentrating mainly on developments in Britain, the USA and Nazi Germany, the author argues that photography, as the most powerful visual medium of the late nineteenth and early twentieth centuries, was vital to the Eugenics Movement's success -- not only did it allow eugenicists to identify the people with superior and inferior hereditary traits, but it helped publicise and lend scientific authority to eugenicists' racial theories. The author further argues for a strong connection between the racial-type photographs that eugenicists created and the photographic images produced by nineteenth-century anthropologists and prison authorities, and that the photographic works of contemporary liberal anthropologists played a significant role in the Eugenics Movement's downfall. Besides adding to our knowledge of photography's crucial role in helping to authorise and implement some of the most controversial social policies of modern times, this book makes a major contribution to our understanding of the history of racism. Most accounts of eugenics have been written by history of science scholars, with an emphasis on the history of science and medicine. In contrast, "Picture Imperfect" looks at eugenics from the standpoint of its most significant cultural data -- racial-type photography, investigating the techniques, media forms, and styles of photography used by eugenicists, and relating these to their racial theories and their social policies and goals. Indeed, the visual archive was crucially constitutive of eugenic racial science because it helped make many of its concepts appear both intuitive as well as scientifically legitimate. Discussion of the history of the eugenics movement encompasses a wide narrative, including Nazi history, US politics, criminology and prison studies, and propaganda.Trade Review"This book makes a significant contribution to an underexamined and important topic. Eugenics had an immense (mainly negative) impact on twentieth-century social and political history, and as Anne Maxwell demonstrates this was in large part because of its use of modern visual technologies, particularly photography. This story should not be allowed to disappear from cultural memory and Anne Maxwell's careful and path-breaking scholarship will do much to keep it there." -- Simon During, Johns Hopkins University.Table of ContentsIntroduction; Racial-type Photographs in the Colonial Period; The Degenerate Face: Nineteenth-Century Prison Photographs; The Eugenics Movement Begins: Galton and the Races of Britain; Building a Healthy Nation: Eugenic Images in the United States, 1890-1935; Creating the Master Race: Photography and Racial Selection in Germany; Sub-Human Versus the Master Race: Racial-Type Photographs and Nazi Party Propaganda; Eugenics Under Fire: the Racial-type Imagery of Boas, Du Bois, Huxley and Hadden; Conclusion; Index.

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Book SynopsisDocuments and critically analyses the photographs that helped strengthen as well as bring down the Eugenics Movement. Using a large body of racial-type images and a variety of historical and archival sources, and concentrating mainly on developments in Britain, the USA and Nazi Germany, the author argues that photography, as the most powerful visual medium of the late nineteenth and early twentieth centuries, was vital to the Eugenics Movement's success -- not only did it allow eugenicists to identify the people with superior and inferior hereditary traits, but it helped publicise and lend scientific authority to eugenicists' racial theories. The author further argues for a strong connection between the racial-type photographs that eugenicists created and the photographic images produced by nineteenth-century anthropologists and prison authorities, and that the photographic works of contemporary liberal anthropologists played a significant role in the Eugenics Movement's downfall. Besides adding to our knowledge of photography's crucial role in helping to authorise and implement some of the most controversial social policies of modern times, this book makes a major contribution to our understanding of the history of racism. Most accounts of eugenics have been written by history of science scholars, with an emphasis on the history of science and medicine. In contrast, "Picture Imperfect" looks at eugenics from the standpoint of its most significant cultural data -- racial-type photography, investigating the techniques, media forms, and styles of photography used by eugenicists, and relating these to their racial theories and their social policies and goals. Indeed, the visual archive was crucially constitutive of eugenic racial science because it helped make many of its concepts appear both intuitive as well as scientifically legitimate. Discussion of the history of the eugenics movement encompasses a wide narrative, including Nazi history, US politics, criminology and prison studies, and propaganda.Trade Review"This book makes a significant contribution to an underexamined and important topic. Eugenics had an immense (mainly negative) impact on twentieth-century social and political history, and as Anne Maxwell demonstrates this was in large part because of its use of modern visual technologies, particularly photography. This story should not be allowed to disappear from cultural memory and Anne Maxwell's careful and path-breaking scholarship will do much to keep it there." -- Simon During, Johns Hopkins University.Table of ContentsIntroduction; Racial-type Photographs in the Colonial Period; The Degenerate Face: Nineteenth-Century Prison Photographs; The Eugenics Movement Begins: Galton and the Races of Britain; Building a Healthy Nation: Eugenic Images in the United States, 1890-1935; Creating the Master Race: Photography and Racial Selection in Germany; Sub-Human Versus the Master Race: Racial-Type Photographs and Nazi Party Propaganda; Eugenics Under Fire: the Racial-type Imagery of Boas, Du Bois, Huxley and Hadden; Conclusion; Index.

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Book SynopsisRecent advances in plant genomics and molecular biology have revolutionized our understanding of plant genetics, providing new opportunities for more efficient and controllable plant breeding. Successful techniques require a solid understanding of the underlying molecular biology as well as experience in applied plant breeding. Bridging the gap between developments in biotechnology and its applications in plant improvement, Molecular Plant Breeding provides an integrative overview of issues from basic theories to their applications to crop improvement including molecular marker technology, gene mapping, genetic transformation, quantitative genetics, and breeding methodology.Table of Contents1: Introduction 2: Molecular Breeding Tools: Markers and Maps 3: Molecular Breeding Tools: Omics and Arrays 4: Populations in Genetics and Breeding 5: Plant Genetic Resources: Management, Evaluation and Enhancement 6: Molecular Dissection of Complex Traits: Theory 7: Molecular Dissection of Complex Traits: Practice 8: Marker-assisted Selection: Theory 9: Marker-assisted Selection: Practice 10: Genotype-by-environment Interaction 11: Isolation and Functional Analysis of Genes 12: Gene Transfer and Genetically Modified Plants 13: Intellectual Property Rights and Plant Variety Protection 14: Breeding Informatics 15: Decision Support Tools

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Book SynopsisQuantitative Trait Loci (QTL) is a topic of major agricultural significance for efficient livestock production. This advanced-level textbook covers all the statistical methods that have been used or proposed for detection and analysis of QTL and marker- and gene- assisted selection in animal genetics and breeding, as well as new advances that have revolutionized the field since the first edition.Trade Review"...the book is certainly a must-have for anyone involved in the statistical analysis of QTL studies in livestock... and (is) a useful textbook for advanced undergraduate and postgraduate students" - Chris Haley, Roslin Institute, on the first edition."Table of Contents1: Principles of Parameter Estimation 2: Random and Fixed Effects, the Mixed Model 3: Historical Overview 4: Experimental Designs to Detect QTL, Generation of Linkage Disequilibrium 5: QTL Parameter Estimation for Crosses between Inbred Lines 6: Advanced Statistical Methods for QTL Detection and Parameter Estimation 7: Analysis of QTL as Random Effects 8: Statistical Power to Detect QTL, and Parameter Confidence Intervals 9: Optimization of Experimental Designs 10: Fine Mapping of QTL 11: Complete Genome QTL Scans: The Problem of Multiple Comparisons 12: Multiple Trait QTL Analysis 13: Principles of Selection Index and Traditional Breeding Programmes 14: Marker-assisted Selection:Theory 15: Marker-assisted Selection : Results of Simulation Studies 16: Marker-assisted Introgression

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Book SynopsisThe understanding of pig genetics and genomics has advanced significantly in recent years, creating fresh insights into biological processes. This comprehensive reference work discusses pig genetics and its integration with livestock management and production technology to improve performance. Fully updated throughout to reflect advances in the subject, this new edition also includes new information on genetic aspects of domestication, colour variation, genomics and pig breeds, with contributions from international experts active in the field.Table of Contents1: Systematics and Evolution of the Pig 2: Genetic Aspects of Pig Domestication 3: Molecular Genetics of Coat Colour Variation 4: Genetics of Morphological Traits and Inherited Disorders 5: Molecular Genetics 6: Immunogenetics 7: Cytogenetics and Chromosome Maps 8: Pig Genomics 9: Behaviour Genetics of the Domestic Pig 10: Biology and Genetics of Reproduction 11: Transgenics and Modern Reproductive Technologies 12: Developmental Genetics 13: Pig Genetic Resources 14: Genetics of Performance Traits 15: Genetics of Meat Quality and Carcass Traits 16: Genetic Improvement of the Pig 17: Pigs as a Model for Biomedical Sciences 18: Breeds of Pigs 19: Standard Genetic Nomenclature of the Pig, with Glossaries 20: Index

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Book SynopsisFood legumes are important constituents of human and animal nutrition, supplying high quality proteins crucial for a balanced diet. These crops also play an important role in low-input agricultural production systems by fixing atmospheric nitrogen. Despite systematic and continuous breeding efforts by legume researchers all over the world, substantial genetic gains have not been achieved. These issues require immediate attention, and overall, a paradigm shift is needed in breeding strategies to strengthen our traditional crop improvement programs. To this end, Biology and Breeding of Food Legumes provides extensive information on their history, origin, evolution and botany, as well as breeding objectives and procedures, nutritional improvement, industrial uses, post-harvest technology and recent developments made through biotechnological intervention.Table of Contents1: History, Origin and Evolution 2: Domestication 3: Biology of Food Legumes 4: Breeding for Improvement of Cool Season Food Legumes 5: Breeding for Improvement of Warm Season Food Legumes 6: Distant Hybridization and Alien Gene Introgression 7: Polyploidy 8: Cytology and Molecular Cytogenetics 9: Molecular Cytogenetics in Physical Mapping of Genomes and Alien Introgressions 10: Micropropagation 11: Androgenesis and Doubled-Haploid Production in Food Legumes 12: Genetic Transformation 13: Male Sterility and Hybrid Production Technology 14: Mutagenesis 15: Breeding for Biotic Stresses 16: Breeding for Abiotic Stresses 17: Legume Improvement in Acidic and Less Fertile Soils 18: Molecular Breeding Approach in Managing Abiotic Stresses 19: Trait Mapping and Molecular Breeding 20: Improving Protein Content and Nutrition Quality 21: Underutilized Food Legumes: Potential for Multipurpose Uses 22: Legumes as a Model Plant Family 23: Plant Genetic Resources and Conservation of Biodiversity 24: Seed Dormancy and Viability 25: Postharvest Technology 26: Value Addition and International Trade

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Book SynopsisNow available in paperback, Molecular Plant Breeding provides an integrative overview of issues from basic theories to their applications to crop improvement. Chapters include discussions of breeding methodology, quantitative genetics, genomics and bioinformatics and present statistical issues related to gene mapping, marker-assisted selection and genotype by environment interactions in clear and concise language. Providing an integrated profile of molecular breeding in plants, this book will be an essential resource for researchers and students involved in plant biology and breeding, genetics and applied genomics.Table of Contents1: Introduction 2: Molecular Breeding Tools: Markers and Maps 3: Molecular Breeding Tools: Omics and Arrays 4: Populations in Genetics and Breeding 5: Plant Genetic Resources: Management, Evaluation and Enhancement 6: Molecular Dissection of Complex Traits: Theory 7: Molecular Dissection of Complex Traits: Practice 8: Marker-assisted Selection: Theory 9: Marker-assisted Selection: Practice 10: Genotype-by-environment Interaction 11: Isolation and Functional Analysis of Genes 12: Gene Transfer and Genetically Modified Plants 13: Intellectual Property Rights and Plant Variety Protection 14: Breeding Informatics 15: Decision Support Tools

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Book SynopsisThis book comprises the first volume of a series which reports the outcomes of the European Union Concerted Action Programme on Genetic Hearing Impairment. The aim is to bring together clinical geneticists and audiologists, as well as basic scientists and other clinicians with a general interest in this field, to standardise the audiological and terminological approaches and publish state of the art interdisciplinary studies.Table of ContentsPreface. Contributors. Part I Gene therapy. Chapter 1 Gene therapy for hearing disorders - AK Lalwani, GJ Carvalho, JJ Han and AN Mhatre. Part II Radiology. Chapter 2 Radiology of inner ear defects - PD Phelps. Part III Computer Systems Chapter 3 An Internet database on genetic non-syndromal hearing impairments - M. Mazzoli, L. Saggin, SD Hatzopouilos and A Martini. Chapter 4 A decision support system for the diagnosis of syndromal genetic hearing impairment - S Crino, A D'Amico, S Grisanti and G Grisanti. Part IV Epidemiology Chapter 5 Epidemiology of hereditary hearing impairment in childhood - preliminary estimates from the European Union - A Parving, RJC Admiraal, F Apaydin, E Arslan, A Davis, O Dias, H Fortnum, G Grisanti, M Gross, M Hess, K Konradsson, G Lina-Granade, VE Newton, C O'Donovan, E Orzan, M Sorri, D Stephens, MD Tsakanikox, M Waagenaar and K Welzl-Müller. Chapter 6 The German Registry for Hearing Impairment in Children: preliminary results - A Cherechevskaia, A Costa, E Rosztok, M Hess and M Gross. Chapter 7 Recessive hearing impairment in two birth cohorts in western Sicily - G Grisanti, AM Amodeo, S Crino and E Martines. Chapter 8 Aetiology of hearing impairment in children borth in northern Finland ijn 1975-1979 and in 1985-1989 (Abstract) - E Maki-Torkko, P Lindholm, M Vayrynen and M Sorri. Part V Audiovestibular tests. Chapter 9 Audiometric criteria for linkage analysis in genetic hearing impairment - FL Wuyts, PH Van de Heyning an F Declau. Chapter 10 Audioscan notches in carriers of genetic hearing impairment - F Zhao, D Stephens, R Meredith and VE Newton. Chapter 11 Cochlear irregulatities in obligate carriers of recessive genetic hearing impairment and in control subjects - G Lina-Granade, M Kreiss, T Gelas, L Collet and A Morgon. Chapter 12 Three-dimensional video-oculography for the detection of genetic vestibular dysfunction at the level of the threee semicircular canals and the otoliths (Abstract) - FL Wuyts, PH Van de Heyning, H Kingma, L Bourmans and D Van Dyck. Part VI Non-syndromal autosomal recessive hearing impairment. Chapter 13 Homozygosity mapping applied to hereditary hearing impairment - localizing recessive deafness genes - RJH Smith, A Ramesh, CR Srikumari Srisailapathy, K Fukushima, S Wayne, A Chen, L Van Laer, J Ashley, RIZ Zbar, M Lovett and G Van Camp. Chapter 14 A Turkish kindred with autosomal recessive non-syndromal hearing impairment segregates DFNB9 (Abstract) - SM Leal, E Vitale, F Apaydin, Y Hu, C Barnwell, M Iber, T Kandogan, U Braendle, HP Zenner, M Schwalb and O Cura. Chapter 15 Assessment of the contribution of the loci DFNA1-10 and DFNB1-9 in inherited hearing impairment in two populations: The United Arab Emirates and the British Pakistani populations (Abstract) - KA Brown, G Karban, G Parry, LL Moynihan, AH Janjua, LI Al-Gazali, VE Newton, AF Markham and RF Mueller. Part VII Non-syndromal autosomal dominant hearing impairment. Chapter 16 Hereditary dominant non-syndromal progressive hearing impairment in a large family in southern Italy - A Bojano, L Califano and P Capparuccia. Chapter 17 Autosomal dominant non-syndromal progressive sensorineural hearing impairment: audiological evalution of a Dutch DFNA2 family (Abstract) - H Kunst, HAM Marres, PLM Huygen, P Coucke, P Willems and CWRJ Cremers. Chapter 18 Autosomal dominant congenital severe sensorineural hearing impairment - localization of a disease gene to chromosome 11q by linkage in an Austrian family (Abstract) - K Kirschhofer, JBN Kenyon, DM Hoover, P Franz, K Weopoltshammer, F Wachtler and WJ Kimberling. Part VIII X-Linked hearing impairment Chapter 19 Identification of a novel locus for non-syndromal X-linked sonsorineural impairment (DFN6) on Xp22 (Abstract) - I del Castillo, M Villamar, M Sarduy, L Romero, C Herraiz, F Javier Hernandez, M Rodriguez, I Borras, A Montero, J Bellon, M Cruz Tapia and F Moreno. Part IX Mitochondrial hearing impairment Chapter 20 Nuclear candidate genes for 'mitochondrial deafness' - HT Jacobs, ZH Shah, V Migliosi, SK Lehtinen, A Rovio and K O'Dell. Chapter 21 A mitochondrial point mutation at position 7472 causes early onset hearing impairment and late onset neurological symptoms. Report of a Dutch and a comparison with a Sicilian family - RJH Ensink, PLM Huygen, HAM Marres, K Verhoeven, G Van Camp and GW Padberg. Chapter 22 Genetic study of mitochondrially inherited sensorineural hearing impairment in eight large families from Spin and Cuba - M Sarduy, I del Castillo, M Villamar, L Romero, C Heraiz, F Javier Hernandex, M Cruz Tapia, C Magarino, D Menendez del Castillo, I Menendez-Alejo, R Ramirez, B Arellano, C Morales, J Bellon and F Moreno. Chapter 23 Hearing impairment in mitochondrial point mutation - E Orzan, L Bartolomei, V Magnavita and E Arslan. Chapter 24 Prevalence of the base pair 3243 mutation of the tRNALeu gene in the mitochondrial DNA in a population-based cohort of patients with sensorineural hearing impairment (Abstract) - S Uimonen, I Hassinen, M Sorri and K Majamaa. Part X Syndromal conditions Chapter 25 Otorhinolaryngological manifestations of Stickler syndrome linked to chromosome 6 near the COL11A2 gene - RJC Admiraal, HG Brunner, PLM Huygen and CWRJ Cremers. Chapter 26 Dominant hemifacial microsomia in a four-general pedigree - A McInerney, R Winter and M Bitner-Glindzicz. Chapter 27 Variability of expression of sensorineural hearing loss in Usher syndrome: report of a family - D Zanetti and AR Antonelli. Chapter 28 Mpv 17 - Glomerulosclerosis gene is essential for inner ear function - AM Meyer zum Gottesberge, B Eschen, A Reuter, L Kintrup and H Weiher. Chapter 29 Cloning of a cadidate gene for hearing defects in CATCH 22 syndrome (Abstract) - A Pizzuti, G Novelli, A Ratti, F Amati, A Mari, G Calabrese, S Nicolis, V Silani, B Marino, G Scarlato, S Ottolenghi, R Mingarelli and B Dallapiccola. References. Index.

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Book SynopsisCystic fibrosis (CF) is one of the most common genetic diseases, affecting about 70,000 people throughout the world, with over 1,000 new cases diagnosed each year. This book describes the symptoms of CF including lung disease, digestive problems, pancreatic insufficiency, liver disease, intestinal obstruction, and infertility. It explains how CF is caused by mutations in the CFTR gene encoding a protein ion channel that maintains the balance of salt and water in the lungs and other organs. The book presents CF as an autosomal recessive disease that can arise in families with no prior history of CF. The reader will learn about treatments and therapies for CF, including antibiotics for infections, medicines for improved digestion, respiratory therapy, and pancreatic enzyme replacement. The book describes promising new pharmaceutical discoveries that enable personalized medicine for the treatment of CF. It evaluates the prospects for curing CF through gene therapy and explains how genome editing may be used in the future to correct the CFTR gene mutations underlying CF.

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