Böcker i Methods in Molecular Biology-serien

This volume introduces Translational Bioinformatics as it relates to therapeutic development, and addresses the techniques needed to effectively translate large data sets to relevant biological networks. Chapters detail clinical informatics infrastructure, and leverage pathology, immunology, pharmacology, genomic, proteomic, and metabolomic informatics approaches.   Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, application details for both the expert and non-expert reader, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Translational Bioinformatics for Therapeutic Development: Methods and Protocols aims to ensure success in the study of Translational Bioinformatics.

1. Development and Optimization of Clinical Informatics Infrastructure to Support Bioinformatics at an Oncology CenterRanda M. Perkins and Joseph Markowitz 2. Leveraging Pathology Informatics Concepts to Achieve Discrete Lab Data for Clinical Use and Translational ResearchMandy Flannery O''Leary 3. Cohort Identification for Translational Bioinformatics StudiesTiffany A. Lin, Zeynep Eroglu, Rodrigo Carvajal, and Joseph Markowitz 4. Transitioning Clinical Practice Guidelines into the Electronic Health Record through Clinical PathwaysSharjeel M. Hooda and Karen K. Fields 5. Variable Selection for Time-to-Event DataAi Ni and Chi Song 6. Binary Classification for Failure Risk AssessmentAli Foroughi pour, Ian Loveless, Grzegorz Rempala and Maciej Pietrzak 7. Challenges and Opportunities of Genomic Approaches in Therapeutics DevelopmentJaimie S. Gray and Moray J. Campbell 8. Accessible Pipeline for Translational Research using TCGA: Examples of Relating Gene Mechanism to Disease Specific Outcomes Anders E. Berglund, Ryan M Putney, Jordan H. Creed, Garrick Aden-Buie, Travis A. Gerke, and Robert J. Rounbehler  9. Statistical and Bioinformatics Analysis of Data from Bulk and Single-Cell RNA Sequencing Experiments Xiaoqing Yu, Farnoosh Abbas-Aghababazadeh, Y. Ann Chen, and Brooke L. Fridley 10. Investigating Inter- and Intra-Sample Diversity of  Single-Cell RNA Sequencing DatasetsMeghan C. Ferrall-Fairbanks and Philipp M. Altrock 11. Managing a Large-scale Multi-Omics Project: A Team Science Case Study in ProteogenomicsPaul A. Stewart, Eric A. Welsh, Bin Fang, Victoria Izumi, Tania Mesa, Chaomei Zhang, Sean Yoder, Guolin Zhang, Ling Cen, Fredrik Pettersson, Yonghong Zhang, Zhihua Chen, Chia-Ho Cheng, Ram Thapa, Zachary Thompson, Melissa Avedon, Marek Wloch, Michelle Fournier, Katherine M. Fellows, Jewel M. Francis, James J. Saller, Theresa A. Boyle, Y. Ann Chen, Eric B. Haura, Jamie K. Teer, Steven A. Eschrich, and John M. Koomen 12. Synergistic Drug Combination Prediction by Integrating Multi-omics Data in Deep Learning ModelsTianyu Zhang, Liwei Zhang, Philip R.O. Payne, and Fuhai Li 13. Introduction to Multi-Parametric Flow Cytometry and Analysis of High-Dimensional DataJames Sun, Jodi L. Kroeger, and Joseph Markowitz  14. High Dimensional Flow Cytometry Analysis of Regulatory Receptors on Human T cells, NK cells, and NKT Cells*Ryosuke Nakagawa, Jason Brayer, Nicole Restrepo, James J. Mul├⌐, and Adam W Mailloux  15. Quantitative Analysis of Bile Acid with UHPLC-MS/MSYuan Tian, Jingwei Cai, Erik L. Allman, Philip B. Smith, and Andrew D. Patterson 16. Sample Preparation and Data Analysis for NMR-based MetabolomicsTapas K. Mal, Yuan Tian, and Andrew D. Patterson 

This volume presents the latest techniques used to study germ cell tumors (GCTs), including histopathology;

This volume presents the latest techniques used to study germ cell tumors (GCTs), including histopathology;

This fourth edition provides all new methods on yeast that have not been included in the past three editions. Divided in four parts, chapters guide readers through general applications for genetic manipulation in yeast cells, genome-wide studies, systematically rearrange the yeast chromosomes, and pathway methods. 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.Authoritative and cutting-edge, Yeast Protocol, Fourth Edition aims to compliment previous editions while offering new tools for the yeast research community.

1. Use of Yeast Plasmids - Transformation and Inheritance AssaysAnastasiia Mereshchuk, Joyce S.K. Chew, and Melanie J. Dobson 2. Construction of Tight Conditional Mutants Using the Improved Auxin-inducible Degron (iAID) Method in the Budding Yeast Saccharomyces cerevisiaeSeiji Tanaka 3. CRISPR Nickase-Mediated Base Editing in YeastKouichi Kuroda and Mitsuyoshi Ueda 4. Genomic Promoter Shuffling by Using Recyclable CassettesXuelei Tian, Wenqing Zhang, and Wei Xiao 5. Study Essential Gene Functions by Plasmid ShufflingLi Fan and Wei Xiao 6. Scarless Genomic Protein Labeling in Saccharomyces cerevisiaeQian Wang, Yu V. Fu, and Wei Xiao 7. High-Copy Yeast Library Construction and High-Copy Rescue Genetic Screen in Saccharomyces cerevisiae Fanli Zeng and David G. Quintana  8. Genome-Wide Imaging-Based Phenomic Screening Using Yeast (Saccharomyces cerevisiae) Strain CollectionsXiuling Cao, Xuejiao Jin, and Beidong Liu 9. Applications of Oxford Nanopore Sequencing in Schizosaccharomyces pombe Ming He, Xu Chi, and Jie Ren 10. Measuring Genome-Wide Nascent Nucleosome Assembly Using ReIN-MapZhiyun Xu, Jianxun Feng, and Qing Li 11. Targeted Integration of Complex Genetic Elements at Multi-Copy Loci by Golden Gate AssemblyYixuan Zhu and Limin Cao 12. Chromosomal Rearrangements of Synthetic Yeast by SCRaMbLEZhouqing Luo, Shuangying Jiang, and Junbiao Dai 13. Use YeastFab to Construct Genetic Parts and Multicomponent Pathways for Metabolic EngineeringShuangying Jiang, Zhouqing Luo, and Junbiao Dai 14. A Versatile Protocol to Generate Translocations in Yeast Genomes using CRISPR/Cas9Nicolas Agier, Aubin Fleiss, St├⌐phane Delmas, and Gilles Fischer15. Yeast Nucleoplasmic Extracts and an Application to Visualize Chromatin Assembly on Single Molecules of DNA Yong Wang and Yu V. Fu 16. Assays for Autophagy III: Observing Dynamic Protein TraffickingJing Zhu and Zhiping Xie 17. Isolation of Aged Yeast Cells Using Biotin-Streptavidin Affinity PurificationXuejiao Jin, Xiuling Cao, and Beidong Liu 18. High-Throughput Rapid Yeast Chronological Lifespan AssayAbd-Al-Wahab A. Khawaja, Zach R. Belak, Christopher H. Eskiw, and Troy A. A. Harkness 19. Long-Term Imaging and Dynamic Analysis of Cytoophidia in YeastShanshan Zhang, Hui Li, and Ji-Long Liu 20. Monitoring 5''-end Resection at Site-specific Double-strand Breaks by Southern Blot AnalysisHaoyang Peng, Simin Zhang, and Xuefeng Chen   

This volume details practical procedures on the latest DNA vaccine technology. Chapters guide readers through methods and protocols on DNA vaccine design, the adjuvant influence, production and purification methodologies, delivery systems, and approaches of the influence of DNA vaccines in the immunological response performance and in the cancer immunotherapy. 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. Authoritative and cutting-edge, DNA Vaccines: Methods and Protocols aims to ensure successful results in the further study of this vital field.

Part I: Vector design For vaccination1. A Novel Cre Recombinase Mediated In Vivo Minicircle (CRIM) DNA Vaccine Platform for Veterinary ApplicationYanlong Jiang, Guilian Yang, and Chunfeng Wang 2. Vaccination with Messenger RNA - a Promising Alternative to DNA VaccinationIstv├ín Tomb├ícz, Drew Weissman, and Norbert Pardi 3. Impact of a Plasmid DNA-Based Alphavirus Vaccine on Immunization Efficiency Kenneth Lundstrom Part II: DNA Vaccine Adjuvants and Immunostimulatory Response 4. CpG Oligonucleotides as Vaccine AdjuvantsNeslihan Kayraklioglu, Begum Horuluoglu, and Dennis M. Klinman 5. Molecular Adjuvants for DNA Vaccines: Application, Design, Preparation and FormulationAilar Sabbaghi and Amir Ghaemi 6. Assessing Antigen-specific Cellular Immune Responses Upon HIV/SIV Plasmid DNA Vaccination in the Non-human Primate ModelXintao Hu, Barbara K. Felber, and Antonio Valentin Part III          Biotechnological Processes to Obtain DNA Vaccines7. Enhanced Biosynthesis of Plasmid DNA from Escherichia coli Applying Experimental Design Lu├¡s A. Passarinha 8. Primary Purification of Plasmid DNA Using Differential Isopropanol PrecipitationAlexandra Wagner, A. Rita Silva-Santos, Sara Sousa Rosa, Sophie Gierak, Ana M. Azevedo, and Duarte Miguel F. Prazeres 9. Scale-Up of Plasmid DNA Downstream Process Based on Chromatographic Monoliths Urh ─îernigoj and Ale┼í ┼átrancar 10. Purification of Plasmid DNA by Multimodal Chromatography A. Rita Silva-Santos, Sara Sousa Rosa, Duarte Miguel F. Prazeres, and Ana M. Azevedo 11. Minicircle DNA Vaccine Purification and E7 Antigen Expression AssessmentAna M. Almeida, Dalinda Eus├⌐bio, Jo├úo A. Queiroz, Fani Sousa, and ├éngela Sousa Part IV:         DNA Vaccine Delivery 12. Tumor-Specific CD8+ T Cell Responses Induced by DNA VaccinationPablo C├íceres-Morgado and Alvaro Lladser 13. Therapeutic DNA Vaccine Against HPV16-Associated CancerMeihua Yu and Janin Chandra 14. Bulk and Microfluidic Synthesis of Stealth and Cationic-Liposomes for Gene Delivery ApplicationsLucimara Gaziola de la Torre, Amanda da Costa e Silva de Noronha Pessoa, Bruna Gregatti de Carvalho, Thiago Bezerra Taketa, Ismail Es, and Gabriel Perli 15. Conception of Plasmid DNA and Polyethylenimine Delivery Systems with Potential Application in DNA Vaccines FieldDiana Costa, ├éngela Sousa, R├║ben Faria, Ana Raquel Neves, and Jo├úo A. Queiroz 16. Main Features of DNA Based Vectors for Use in Lactic Acid Bacteria and Update ProtocolsNina D. Coelho-Rocha, Fernanda A. L. Barroso, La├¡sa M. Tavares, Ester S. S. dos Santos, Vasco Azevedo, Mariana M. Drumond, and Pamela Mancha-Agresti Part V:           DNA Vaccine Transfer to Clinical Trials17. Ethics of DNA Vaccines Transfer for Clinical Research Ana Cristina Ramalhinho and Miguel Castelo-Branco 18. Preparation of an Academic Clinical TrialPreparation of an academic clinical trialAna Cristina Ramalhinho and Miguel Castelo-Branco

This book provides an overview of methods and experimental protocols that are currently used to analyze the presence and abundance of non-canonical DNA nucleotides in different biological systems. Focusing particularly on the newly discovered and less studied DNA modifications that are enzymatically produced and are likely to play specific roles in various biological processes, the volume explores chromatography- and mass spectrometry-based techniques for the detection and quantification of DNA modifications, antibody-based approaches to study their spatial distribution in different cells and tissues, and methods to analyze their genomic distribution with the help of bioinformatics tools that interrogate the corresponding datasets. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and comprehensive, DNA Modifications: Methods and Protocols serves as an ideal guide to research scientists and PhD students in this rapidly developing discipline, and, thus, will ultimately contribute to deciphering the roles of non-canonical DNA nucleotides in different biological systems.

Part I: Introduction 1. Modified Forms of Cytosine in Eukaryotes: DNA (De)Methylation and Beyond            Maria Eleftheriou and Alexey Ruzov 2. Evidence for Non-Cytosine Epigenetic DNA Modifications in Multicellular Eukaryotes: An Overview            Paige Lowe, Ryszard Olinski, and Alexey Ruzov 3. Mass Spectrometry-Based Analysis of DNA Modifications: Potential Applications in Basic Research and Clinic            Ryszard Olinski, Rafal Rozalski, and Daniel Gackowski 4. Mapping DNA Methylation in Mammals: The State of the Art            Antonio Lentini and Colm E. Nestor Part II: Detection and Quantification of DNA Modifications Using Mass Spectrometry and Capillary Gel Electrophoresis 5. Detection of Modified Bases in Bacteriophage Genomic DNA            Yan-Jiun Lee and Peter R. Weigele 6. Liquid Chromatography-Mass Spectrometry Analysis of Cytosine Modifications            Nan Dai and Ivan R. Corr├¬a Jr. 7. Detection of DNA Methylation in Genomic DNA by UHPLC-MS/MS            Konstantinos Boulias and Eric Lieberman Greer 8. Quantification of DNA Modifications Using Two-Dimensional Ultra-Performance Liquid Chromatography Tandem Mass-Spectrometry (2D-UPLC-MS/MS)            Marta Starczak, Maciej Gawronski, Ryszard Olinski, and Daniel Gackowski 9. MS Analysis of DNA Modifications in Urinary/Body Fluids            Aleksandra Skalska, Agnieszka Siomek-Gorecka, Ryszard Olinski, and Rafal Rozalski 10. Preparation of Internal Standards for 2D-UPLC-MS/MS Quantification of Non-Canonical DNA Bases            Marta Starczak, Aleksandra Skalska, Rafal Rozalski, Ryszard Olinski, and Daniel Gackowski 11. Detection of TET-Oxidized 5-Methylcytosine Bases by Capillary Gel Electrophoresis            Romualdas Vaisvila, Lise Hunault, and Lana Saleh Part III: Assessing the Levels and Spatial Distribution of DNA Modifications Using Antibody-Based Approaches 12. Immunochemical Detection of Modified Cytosine Species in Mammalian Preimplantation Embryos            Tie-Bo Zeng and Piroska E. Szab├│ 13. Immunochemical Detection of Modified Cytosine Species in Lampbrush Chromatin            Garry T. Morgan 14. Detection of Low-Abundance DNA Modifications Using Signal Amplification-Based Immunocytochemistry            Abdulkadir Abakir and Alexey Ruzov 15. Immunohistochemical Detection of Modified Cytosine Bases in Rodent Brain            Marcus D. Wallis and Rebecca C. Trueman 16. Immunohistochemical Detection of 5-Hydroxymethylcytosine and 5-Ca

This updated edition emphasizes the benefits of structural genomics to the wider structural research community with a diverse range of applicable methods.

This updated edition emphasizes the benefits of structural genomics to the wider structural research community with a diverse range of applicable methods.

This volume provides a varied selection of current methods and molecular probes used to generate, image and quantify ROS production and lipid peroxidation. Chapters guide readers through methods and protocols on in silico modelling of ROS dynamics in biological systems and a breaking proposal. 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. Authoritative and cutting-edge,  Reactive Oxygen Species: Methods and Protocols aims to ensure successful results in the further study of this vital field.

1. Introduction to in silico Modeling to Study ROS DynamicsJana Schleicher 2. Assessment of ROS Production in Mitochondria of Live CellsPlamena R. Angelova, Albena T. Dinkova-Kostova, and Andrey Y. Abramov 3. Measurement of Superoxide Production in Acute Hypoxia by Fixed-Cell MicroscopyPablo Hernansanz-Agust├¡z, Carmen Choya-Foces, and Antonio Mart├¡nez-Ruiz 4. A Photodynamic Tool to Promote a Sustained, ROS-Dependent Growth of Human Hair Follicles in ex vivo CultureMar├¡a I. Calvo-S├ínchez, Sandra Fern├índez-Martos, and Jes├║s Espada 5. Singlet Oxygen and Protochlorophyllide Detection in Arabidopsis thalianaLiangsheng Wang and Tatjana Kleine 6. Characterization of oxidative lipidomics and autophagy induction in Chlamydomonas reinhardtii under abiotic stressCristina Ortega-Villasante, ├üngel Bar├│n-Sola, Margarita Toledo-Basantes, Flor Mart├¡nez, and Luis E. Hern├índez 7. Fluorescence Detection of Increased Reactive Oxygen Species Levels in Saccharomyces cerevisiae at the Diauxic Shift Abhishek Sinha and Elah Pick 8. Flow Cytometry and Confocal Microscopy for ROS Evaluation in Fish and Human SpermatozoaVanesa Robles, Marta F. Riesco, Juan M. Mart├¡nez-V├ízquez, and David G. Valcarce 9. Measurement of Reactive Oxygen Species In Semen Samples Using ChemiluminescenceT├ónia R. Dias 10. Methods to Unravel Pathways of Reactive Oxygen Species in the Photodynamic Inactivation of BacteriaNatalia S. Gsponer and Edgardo N. Durantini 11. Revealing ROS Production by Antibiotics and Photosensitizers in Biofilms. A Fluorescence Microscopy ApproachSol R. Mart├¡nez  and Andr├⌐s M. Durantini 12. EPR Spectroscopy as a Method for ROS Quantification in SkinSilke B. Lohan, Daniela Ivanov, Nadine Sch├╝le, Bastian Berger, Stephanie Albrecht, and Martina C. Meinke 13. Detection of Superoxide Radical in Adherent Living Cells by Electron Paramagnetic Resonance (EPR) Spectroscopy Using Cyclic Nitrones Kahina Abbas, Nikola Babi─ç, and Fabienne Peyrot 14. Singlet Oxygen Quantum Yield Determination Using Chemical AcceptorsRoger Bresol├¡-Obach, Joaquim Torra, Renzo P. Zanocco, Antonio L. Zanocco, and Santi Nonell 15. A General Method to Establish the Relative Efficiency of Different Sonosensitizers to Generate ROS for SDTViviana Grosso, Alejandro Senz, and Arnaldo T. Soltermann  16. Lipid Peroxidation Assay using BODIPY-phenylbutadiene Probes:A Methodological OverviewJuan C. Stockert  17. Use of Fluorescent Probes to Detect ROS in Photodynamic TherapySulbha K Sharma and Michael R Hamblin 

This detailed new edition provides a comprehensive collection of protocols applicable to all members of the Coronavirinae sub-family currently and that are also transferrable to other fields of virology.

This detailed new edition aims to provide a range of methods and protocols for studying vascular morphogenesis in vivo and in vitro to reflect up-to-date advances in the field.

This detailed new edition aims to provide a range of methods and protocols for studying vascular morphogenesis in vivo and in vitro to reflect up-to-date advances in the field.

This detailed book aims to provide readers with critical information to accomplish the synthesis of nanosystems for the purpose of supramolecular entities complexing with drugs, targeted drug delivery system characterization, as well as the study of the physical-chemical interactions that govern the stability and properties of these systems.

This detailed book aims to provide readers with critical information to accomplish the synthesis of nanosystems for the purpose of supramolecular entities complexing with drugs, targeted drug delivery system characterization, as well as the study of the physical-chemical interactions that govern the stability and properties of these systems.

Authoritative and practical, Polypeptide Materials: Methods and Protocols serves to reflect the inter-disciplinary nature of molecular biology as well as the importance of developing innovative measurement methods to advance this vital area of research.

Authoritative and practical, Polypeptide Materials: Methods and Protocols serves to reflect the inter-disciplinary nature of molecular biology as well as the importance of developing innovative measurement methods to advance this vital area of research.

This book addresses the major periodontal pathogens implicated as causal agents in periodontal disease, including Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, Fusobacterium nucleatum, Aggregatibacter actinomycetemcomitans, and Prevotella spp.

This book addresses the major periodontal pathogens implicated as causal agents in periodontal disease, including Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, Fusobacterium nucleatum, Aggregatibacter actinomycetemcomitans, and Prevotella spp.

This volume explores the latest techniques used to study and understand chromatin reprogramming in embryos and germ cells. Various culture systems are presented, which consist of invaluable tools to investigate many developmental processes. This book also looks at methods for direct examination of DNA, RNA, and proteins in embryos, along with low-input and single-cell assays for exploring these features at the genome-wide scale. 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 thorough, Epigenetics Reprogramming During Mouse Embryogenesis: Methods and Protocols is a valuable resource for any scientist and researcher looking to make new discoveries in this fascinating field of chromatin reprogramming. 

Preface...Table of Contents...Contributing Authors...1.Ex Vivo Culture for Preimplantation Mouse Embryo to Analyse PluripotencyKatia Boutourlinsky, Nicolas All├¿gre, and Claire Chazaud2.Microfabricated Device for High Resolution Imaging of Preimplantation EmbryosSandrine Vandormael-Pournin, Emmanuel Frachon, Samy Gobaa, and Michel Cohen-Tannoudji3. In Vitro Culture of Mouse Blastocyst to the Egg Cylinder Stage via Mural Trophectoderm ExcisionHatice O. Ozguldez and Ivan Bedzhov4. Spatially Organized Differentiation of Mouse Pluripotent Stem Cells on Micropatterned SurfacesSophie M. Morgani and Anna-Katerina Hadjantonakis 5. Mouse Primordial Germ Cells: In Vitro Culture and Conversion to Pluripotent Stem Cell LinesMalgorzata Borkowska and Harry G. Leitch6. Generation of Primordial Germ Cell-Like Cells in Small and Large ScalesWolfram H. Gruhn and Ufuk G├╝nesdogan7. Genome-Scale CRISPR Screening for Regulators of Cell Fate TransitionsValentina Carlini, Kristjan H. Gretarsson, and Jamie A. Hackett8. Somatic Reprogramming by Nuclear Transfer Vincent Brochard and Nathalie Beaujean9. Targeted Transgenic Mice using CRISPR/Cas9 TechnologyFatima El Marjou, Colin Jouhanneau, and Denis Krndija10. Whole-Mount Immunofluorescence Staining of Early Mouse EmbryosFrederick C. K. Wong  11. Investigating the Inner Cell Mass of the Mouse Blastocyst by Combined Immunofluorescence Staining and RNA Fluorescent In Situ HybridizationMaud Borensztein 12. Mapping of Chromosome Territories by 3D-Chromosome Painting during Early Mouse DevelopmentKatia Ancelin, Yusuke Miyanari, Olivier Leroy, Maria-Elena Torres-Padilla, and Edith Heard13. Deciphering the Early Mouse Embryo Transcriptome by Low-Input RNA-seqRaquel P├⌐rez-Palacios, Patricia Fauque, Aur├⌐lie Teissandier, and D├⌐borah Bourc''his14. Studying DNA Methylation Genome-Wide by Bisulfite Sequencing from Low Amounts of DNA in MammalsAmbre Bender, Hala Al Adhami, Thomas Dahlet, and Michael Weber15. Profiling DNA Methylation Genome-Wide in Single CellsAntonio Galvao and Gavin Kelsey 16. Tracking Histone Modifications in Embryos and Low Input Samples using Ultrasensitive STAR ChIP-seqBingjie Zhang, Xu Peng, Feng Xu, and Wei Xie17. Chromatin Profiling in Mouse Embryonic Germ Cells by CUT&RUNSrinivasa Abishek Prakash and Joan Barau 18. DamID to Map Genome-Protein Interactions in Pre-Implantation Mouse EmbryosMrinmoy Pal, Kim de Luca, Jop Kind, and Maria-Elena Torres-Padilla19. Understanding Chromosome Structure during Early Mouse Development by Single-Cell Hi-C AnalysisNo├⌐mie Ranisavljevic, Maud Borensztein, and Katia Ancelin 20. Bioinformatic Analysis of Single Cell Hi-C Data from Early Mouse EmbryoSamuel Collombet, Yuvia A. P├⌐rez-Rico, Katia Ancelin, Nicolas Servant, and Edith Heard Subject Index List...

This detailed second edition presents a wide variety of marine invertebrate model systems, from cephalochordata to holothurians, along with novel experimental protocols for taking advantage of their unique properties.

This detailed second edition presents a wide variety of marine invertebrate model systems, from cephalochordata to holothurians, along with novel experimental protocols for taking advantage of their unique properties.

This Open Access volume provides readers with an open access protocol collection and wide-ranging recommendations for preclinical renal MRI used in translational research.

This updated book explores a wide repertoire of tools and approaches that have been created, modified, and applied to the study of L. monocytogenes, forming the basis of our understanding of the bacterium today. Many of these key experimental techniques are gathered together herein. The volume presents aspects such as clinical disease and host-pathogen interactions, as well as the study of biofilms which present a significant challenge for control of the organism in the food processing environment. The topics covered in this edition also include sampling in order to isolate Listeria, methods for their identification and characterization, methods for gene manipulation, and methods for control of the organism. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and up-to-date, Listeria monocytogenes: Methods and Protocols, Second Edition aims to contribute toward the harmonization of methods used to study this important bacterium, and to be of particular interest to Listeria research both in relation to food association and control as well as clinical microbiology.

Part I: Detection, Quantification, and Confirmation 1. Traditional Methods of Analysis for Listeria monocytogenes            Rui Magalh├úes, Cristina Mena, V├ónia Ferreira, Gon├ºalo Almeida, Joana Silva, and Paula Teixeira 2. MALDI-ToF MS: A Rapid Methodology for Identifying and Subtyping Listeria monocytogenes            Snehal R. Jadhav, Rohan M. Shah, and Enzo A. Palombo 3. Sample Preparation for qPCR Detection of Listeria from Food            Patrick Mester, Anna Kristina Witte, and Peter Rossmanith 4. qPCR Validation on the Basis of the Listeria monocytogenes prfA Assay            Anna Kristina Witte, Patrick Mester, and Peter Rossmanith Part II: Subtyping Approaches 5. Serotype Assignment by Sero-Agglutination, ELISA, and PCR            Lisa Gorski 6. Pulsed-Field Gel Electrophoresis (PFGE) Analysis of Listeria monocytogenes            Karen Hunt and Kieran Jordan 7. Multi-Locus Sequence Typing (MLST) and Whole Genome Sequencing (WGS) of Listeria monocytogenes and Listeria innocua            Beatrix Stessl, Martin Wagner, and Werner Ruppitsch Part III: Genotypic and Phenotypic Characterization 8. High-Throughput Characterization of Listeria monocytogenes Using the OmniLog Phenotypic Microarray            Laura Luque-Sastre, Kieran Jordan, S├⌐amus Fanning, and Edward M. Fox 9. High-Throughput Screening of Biofilm Formation of Listeria monocytogenes on Stainless Steel Coupons Using a 96-Well Plate Format            Jessica A. Gray, P. Scott Chandry, John P. Bowman, and Edward M. Fox 10. Confocal Laser Microscopy Analysis of Listeria monocytogenes Biofilms and Spatially Organized Communities            Maud Darsonval, Marina Gr├⌐goire, Julien Deschamps, and Romain Briandet 11. Extraction and Preparation of Listeria monocytogenes Subproteomes for Mass Spectrometry Analysis            Tiago Santos and Michel H├⌐braud Part IV: Strain Manipulation 12. Extraction and Analysis of Plasmid DNA from Listeria monocytogenes            Aidan Casey and Olivia McAuliffe 13. Generation of Nonpolar Deletion Mutants in Listeria monocytogenes Using the "SOEing" Method            Kathrin Rychli, Eva Harter, Caitriona M. Guinane, Karen Daly, Colin Hill, and Paul D. Cotter 14. Mutant Construction and Integration Vector-Mediated Genetic Complementation in Listeria monocytogenes            Cameron Parsons, Reha Azizoglu, Driss Elhanafi, and Sophia Kathariou