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Botany: A Lab Manual, Seventh Edition is mapped to match Botany: An Introduction to Plant Biology, Seventh Edition but is the perfect companion for any botany course. Packed with hands-on activities, it engages students and broadens their understanding of plant biology. Now in full color and a convenient lay-flat format, it provides detailed examination of plant structure, plant groups, genetics, classification, and more. Featuring additional case studies and image labeling activities, Botany: A Lab Manual is the clear choice for students digging into this exciting science.
(source: Nielsen Book Data)

• Introduction - An Overview of Practical Electrochemistry Electrochemistry in Equilibrium Electrochemistry with Flowing Current Analytical Electrochemistry Non-Traditional Electrochemistry Electrochemical Energy Conversion and Storage Electrochemical Production Appendix List of Symbols, Acronyms and Abbreviations Index.
• (source: Nielsen Book Data)

Showing how to apply the theoretical knowledge in practice, the one and only compilation of electrochemical experiments on the market now in a new edition. Maintaining its didactic approach, this successful textbook provides clear and easy-to-follow instructions for carrying out the experiments, illustrating the most important principles and applications in modern electrochemistry, while pointing out the potential dangers and risks involved. This second edition contains approximately 25% new material and 20 new experiments, many of which cover electrochemical energy conversion and storage as well as electrochemical equilibrium. With a foreword by R. Daniel Little.
(source: Nielsen Book Data)

• Cloning and identification of recombinant argonaute-bound small RNAs using next-generation sequencing / Pooja Gangras, Daniel M. Dayeh, Justin W. Mabin, Kotaro Nakanishi, and Guramrit Singh
• Quantification of miRNAs co-immunoprecipitated with argonaute proteins using SYBR green-based qRT-PCR / Hong-Duc Phan, Junan Li, Ming Poi, and Kotaro Nakanishi
• Gateway to understanding argonaute loading of single-stranded RNAs : preparation of deep sequencing libraries with in vitro loading samples / Eling Goh and Katsutomo Okamura
• Dumbbell-PCR for discriminative quantification of a small RNA variant / Megumi Shigematsu, Shozo Honda, and Yohei Kirino
• MicroRNA detection by whole-mount in situ hybridization in C. elegans / Yoshiki Andachi and Yuji Kohara
• cCLIP-seq : retrieval of chimeric reads from HITS-CLIP (CLIP-Seq) libraries / Panagiotis Alexiou, Manolis Maragkakis, Zissimos Mourelatos, and Anastassios Vourekas
• Kinetic analysis of small silencing RNA production by human and drosophila dicer enzymes in vitro / Susan E. Liao and Ryuya Fukunaga
• Nucleic acid-binding assay of argonaute protein using fluorescence polarization / Tomohiro Miyoshi
• Reconstitution of RNA interference machinery / Shintaro Iwasaki and Yukihide Tomari
• Single-molecule analysis for RISC assembly and target cleavage / Hiroshi M. Sasaki, Hisashi Tadakuma, and Yukihide Tomari
• Profiling open chromatin structure in the ovarian somatic cells using ATAC-seq / Kensaku Murano, Yuka W. Iwasaki, and Haruhiko Siomi
• Assessing miR-451 activity and its role in erythropoiesis / Dmitry A. Kretov, Andrew M. Shafik, and Daniel Cifuentes
• Functional analysis of microRNAs in neurogenesis during mouse cortical development / Wei Zhang, Xiaoxia Zeng, and Li Zeng
• Cellular approaches in investigating argonaute2-dependent RNA silencing / Cai Zhang, Joonbae Seo, and Takahisa Nakamura
• Genomic tagging of AGO1 using CRISPR/Cas9-mediated homologous recombination / Sanjay Ghosh and Ji-Long Liu
• Accurate profiling and quantification of tRNA fragments from RNA-Seq data : a Vade Mecum for MINTmap / Phillipe Loher, Aristeidis G. Telonis, and Isidore Rigoutsos.

This volume covers methods that analyze various Argonaute proteins from a variety of organisms to help researchers better understand their properties ranging from a molecular level to an organismal level. The chapters in this book explore the following topics: identification and expression analysis of guide nucleic acids and their targets; analysis of biochemical properties of Argonautes; biological functions of Argonautes; and obtaining materials and setting up analysis platforms. 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 authoritative, Argonaute Proteins: Methods and Protocols is a valuable resource for researchers and scientists looking to expand their knowledge of Argonaute proteins and their functions.
(source: Nielsen Book Data)

• Preface... Table of Contents... Contributing Authors...
• 1. Activation-Induced Cytidine Deaminase Aided In Vitro Antibody Evolution Lili An, Chuan Chen, Ruiqi Luo, Yun Zhao, and Haiying Hang
• 2. Analyzing Mouse B-Cell Responses Specific to LCMV Infection Yaxing Hao, Zhirong Li, Yifei Wang, Xiaobing Liu, and Lilin Ye
• 3. Expression of Exogenous Genes in Murine Primary B Cells and B Cell Lines Using Retroviral Vectors Zhiyong Yang and Christopher D. C. Allen
• 4. Biophysical Techniques to Study B Cell Activation: Single Molecule Imaging and Force Measurements Ivan Rey, David A. Garcia, Brittany A. Wheatley, Wenxia Song, and Arpita Upadhyaya
• 5. DNA-Based Probes for Measuring Mechanical Forces in Cell-Cell Contacts: Application to B Cell Antigen Extraction from Immune Synapses Katelyn M. Spillane and Pavel Tolar
• 6. Deriving Quantitative Cell Biological Information from Dye-Dilution Lymphocyte Proliferation Experiments Koushik Roy, Maxim Nikolaievich Shokhirev, Simon Mitchell, and Alexander Hoffmann
• 7. Flow Cytometry Analysis of mTOR Signaling in Antigen-Specific B Cells Qizhao Huang, Haoqiang Wang, Lifan Xu, Jianjun Hu, Pengcheng Wang, Yiding Li, and Lilin Ye
• 8. Ex Vivo Culture Assay to Measure Human Follicular Helper T (Tfh) Cell-Mediated Human B Cell Proliferation and Differentiation Xin Gao, Lin Lin, and Di Yu
• 9. B Cell Receptor Signaling and Compartmentalization by Confocal Microscopy Anurag R. Mishral and Akanksha Chaturvedi
• 10. Investigate Early Activation Events of B Cell Receptor Signaling by Membrane Associated Antigen System and Total Internal Reflection Fluorescence Microscopy Xiaoming Bai, Xiaodong Zhao, and Chaohong Liu
• 11. Imaging the Interactions between B Cells and Antigen-Presenting Cellsal, Jia C. Wang, Madison Bolger-Munro, and Michael R. Gold
• 12. In Vivo Tracking of Particulate Antigen Localization and Recognition by B Lymphocytes at Lymph Nodes Yolanda R. Carrasco
• 13. Study B Cell Antigen Receptor Nano-scale Organization by In Situ Fab Proximity Ligation Assay Kathrin Kla sener, Jianying Yang, and Michael Reth
• 14. Single Particle Tracking of Cell Surface Proteins Laabiah Wasim and Bebhinn Treanor
• 15. The Use of Intravital Two-Photon and Thick Section Confocal Imaging to Analyze B Lymphocyte Trafficking in Lymph Nodes and Spleen Chung Park, Il-Young Hwang, and John H. Kehrl
• 16. Time-lapse Foerster Resonance Energy Transfer Imaging by Confocal Laser Scanning Microscopy for Analyzing Dynamic Molecular Interactions in the Plasma Membrane of B Cells Hae Won Sohn and Joseph Brzostowski
• 17. Understanding of B Cell Receptor Signaling through a Photo-Activatable Antigen Presentation System Jing Wang, Zhengpeng Wan, and Wanli Liur
• 18. Use of Streptolysin O-induced Membrane Damage as a Method of Studying the Function of Lipid Rafts during B Cell Activation Heather Miller and Wenxia Song
• 19. Visualization and Quantitative Analysis of the Actin Cytoskeleton upon B Cell Activation Vid Sustar, Marika Vainio, Pieta K. Mattila.
• (source: Nielsen Book Data)

This volume looks the current advanced protocols used to study aspects of the B cell receptor (BCR). The chapters in this book cover topics such as the mutant of BCR repertoire to understand antibody evolution; interactions between B cells and viruses; mechanical force during BCR activation; B cell signaling using flow cytometry; confocal microscopy, total internal reflection microscopy and intravital two-photon microscopy; and the methods used to study critical cell components related with B cell activation. 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 practical, B Cell Receptor Signaling: Methods and Protocols is a valuable resource for everyone in the scientific community currently working in the B cell field.
(source: Nielsen Book Data)

• Part I: Structural Analysis of Bacterial Multidrug Exporters
• 1. High Resolution Crystallographic Analysis of AcrB Using Designed Ankyrin Repeat Proteins (DARPins)
• Heng Keat Tam, Viveka Nand Malviya, and Klaas M. Pos
• 2. Crystallographic Analysis of Drug and Inhibitor-Binding Structure of RND-Type Multidrug Exporter AcrB in Physiologically-Relevant Asymmetric Crystals
• Ryosuke Nakashima, Keisuke Sakurai, and Akihito Yamaguchi
• 3. Crystallographic Analysis of MATE-Type Multidrug Exporter with Its Inhibitors
• Tsukasa Kusakizako, Yoshiki Tanaka, Christopher J. Hipolito, Hiroaki Suga, and Osamu Nureki
• 4. Crystallographic Analysis of the CusBA Heavy-Me tal Efflux Complex of Escherichia coli
• Jared A. Delmar and Edward W. Yu
• 5. Purification of AcrAB-TolC Multidrug Efflux Pump for Cryo-EM Analysis
• Dijun Du, Zhao Wang, Wah Chiu, and Ben F. Luisi
• 6. NMR Spectroscopy Approach to Study the Structure, Orientation, and Mechanism of the Multidrug Exporter EmrE
• Maureen Leninger and Nathaniel J. Traaseth
• 7. Generation of Conformation-Specific Antibody Fragments for Crystallization of the Multidrug Resistance Transporter MdfA
• Frank Jaenecke, Yoshiko Nakada-Nakura, Kumar Nagarathinam, Satoshi Ogasawara, Kehong Liu, Yunhon Hotta, So Iwata, Nor imichi Nomura, and Mikio Tanabe
• Part II: Biochemical and Bioengineering Analysis of Bacterial Multidrug Exporters
• 8. Biochemical Reconstitution and Characterization of Multi-Component Drug Efflux Transporters
• Martin Picard, Elena B. Tikhonova, Isabelle Broutin, Shuo Lu, Alice Verchere, and Helen I. Zgurskaya
• 9. Covalently Linked Trimers of RND (Resistance-Nodulation-Division) Efflux Transporters to Study Their Mechanism of Action: Escherichia coli AcrB Multidrug Exporter as an Example
• Hiroshi Nikaido
• 10. Determining Ligand Path through a Major Drug Transporter, AcrB, in Escherichia coli
• Fasahath Husain and Hiroshi Nikaido
• Part III: Computational Analysis of Bacterial Multidrug Exporters
• 11. Molecular Modeling of Multi-Drug Properties of Resistance Nodulation Division (RND) Transporters
• Pierpaolo Cacciotto, V. K. Ramaswamy, Giuliano Malloci, Paolo Ruggerone, and Attilio V. Vargiu
• 12. A Transcriptomic Approach to Identify Novel Drug Efflux Pumps in Bacteria
• Liping Li, Sasha G. Tetu, Ian T. Paulsen, and Karl A. Hassan
• Part IV: Biomedical Approach for Bacterial Multidrug Exporters
• 13. Regulation of the Expression of Bacterial Multidrug Exporters by Two-Component Signal Transduction Systems
• Kunihiko Nishino
• 14. Study of the Expression of Bacterial Multidrug Efflux Pumps in Anaerobic Conditions
• Jingjing Sun, Ziqing Deng, Danny Ka Chun Fung, and Aixin Yan
• 15. Identification of a Staphylococcus aureus Efflux Pump Regulator Using a DNA-Protein Affinity Technique
• Que Chi Truong-Bolduc and David C. Hooper
• 16. High Throughput Flow Cytometry Screening of Multidrug Efflux Systems
• Mark K. Haynes, Matthew Garcia, Ryan Peters, Anna Waller, Pietro Tedesco, Oleg Ursu, Cristian G. Bologa, Radleigh G. Santos, Clemencia Pinilla, Terry H. Wu, Julie A. Lovchik, Tudor I. Oprea, Larry A. Sklar, and George P. Tegos
• Part V: Advanced Technologies Expected for Application to Multi drug Efflux Transport Studies
• 17. Single-Molecule Analysis of Membrane Transporter Activity by Means of a Microsystem
• Rikiya Watanabe, Naoki Soga, Shin-ya Ohdate, and Hiroyuki Noji
• 18. Large Scale Femtoliter Droplet Array for Single Cell Efflux Assay of Bacteria
• Ryota Iino, Shouichi Sakakihara, Yoshimi Matsumoto, and Kunihiko Nishino
• 19. Reconstitution and Transport Analysis of Eukaryotic Transporters in the Post-Genomic Era
• Hiroshi Omote and Yoshinori Moriyama.
• (source: Nielsen Book Data)

This detailed volume utilizes our current understanding of the structural basis of multidrug recognition and multidrug efflux mechanisms to provide protocols involving these vital intrinsic membrane proteins widely distributed in bacteria. Beginning with protocols for the structural analysis of bacterial multidrug exporters, the book continues with sections on biochemical and bioengineering analysis, computational analysis, biomedical approaches, as well as advanced technologies expected to be applied to multidrug efflux transport studies. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective chapters, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Bacterial Multidrug Exporters: Methods and Protocols serves as an ideal guide to this fast moving field of study.
(source: Nielsen Book Data)

• Part I: Isolation of Bacteriophages
• 1. Isolation of Bacteriophages for Fastidious Bacteria
• Shigenobu Matsuzaki, Jumpei Uchiyama, Iyo Takemura-Uchiyama, Takako Ujihara, and Masanori Daibata
• 2. Isolation of Bacteriophages of the Anaerobic Bacteria Bacteroides
• Cristina Garcia-Aljaro, Maite Muniesa, and Juan Jofre
• 3. Isolation of Bacteriophages for Clinically Relevant Bacteria
• Sanna Sillankorva
• Part II: Characterization of Bacteriophages
• 4. In Vitro Activity against Planktonic and Biofilm Populations Assessed by Flow Cytometry
• Luis Melo, Diana Priscila Pires, and Joana Azeredo
• 5. Observation of Bacteriophage Ultrastructure by Cryo-electron Microscopy
• Ana Cuervo and Jose L. Carrascosa
• 6. Bacteriophage Taxonomy: an Evolving Discipline
• Igor Tolstoy, Andrew M. Kropinski, and J. Rodney Brister
• Part III: Bacteriophage Selection and Cocktail Formulation
• 7. Determination of the Bacteriophage Host Range - Culture Based Approach
• Andrey V. Letarov, and Eugene E. Kulikov
• 8. Recovery and Characterization of Bacteria Resisting Infection by Lytic Bacteriophage
• Libera Latino and Christine Pourcel
• 9. Guidelines to Compose an Ideal Bacteriophage Cocktail
• Maia Merabishvili, Jean-Paul Pirnay, and Daniel De Vos
• Part IV: Biodistribution, Host Interaction and Clinical Application
• 10. Interaction of Bacteriophages with Mammalian Cells
• Zuzanna Kazmierczak and Krystyna Dabrowska
• 11. In Vivo Bacteriophage Biodistribution
• Nicolas Dufour, Raphaelle Delattre, and Laurent Debarbieux
• 12. Interaction of Bacteriophages with the Immune System: Induction of Bacteriophage-specific Antibodies
• Krystyna Dabrowska
• & nbsp--
• 13. Bacteriophage Treatment of Infected Diabetic Foot Ulcers
• Vera V. Morozova, Yulia N. Kozlova, Denis A. Ganichev, and Nina V. Tikunova
• 14. Compassionate Use of Bacteriophage Therapy for Foot Ulcer Treatment as an Effective Step for Moving Toward Clinical Trials
• Randolph Fisha, Elizabeth Kutter, Gordon Wheat, Bob Blasdel, Mzia Kutateladze, and Sarah Kuhl
• Part V: Production, Purification and Bacteriophage Storage
• 15. Bacteriophage Production in Bioreactors
• Maryam Agboluaje and Dominic Sauvage
• 16. Computational Modelling of Bacteriophage Production for Process Optimization
• Konrad Krysiak-Baltyn and Sally L. Gras
• 17. Methods for Bacteriophage Preservation
• Malgorzata B. Lobocka, Aleksandra Glowacka, and Piotr Golec
• Part VI: Safety and Regulation
• 18. Bacteriophage Production in Compliance with Regulatory Requirements
• Jean-Paul Pirnay, Maia Merabishvili, Hilde Van Raemdonck, Daniel De Vos, and Gilbert Verbeken
• 19. Guidelines for Bacteriophage Product Certification
• Alan Fauconnier
• Part VII: New Phage Therapy Approaches
• 20. Nano/micro Formulations for Bacteriophage Delivery
• Pilar Cortes, Mary Cano-Sarabia, Joan Colom, Jennifer Otero, Daniel Maspoch, and Montserrat Llagostera
• 21. Synthetic Biology to Engineer Bacteriophage Genomes
• Ana Rita Costa, Catarina Milho, Joana Azeredo, and Diana Priscila Pires.
• (source: Nielsen Book Data)

This volume details the experimental approaches suitable for isolating and characterizing bacteriophages to formulating bacteriophage medicinal products and clinical application. Chapters guide readers through regulatory compliance and safety aspects of bacteriophage therapy. 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, Bacteriophage Therapy: From Lab to Clinical Practice aims to ensure successful results in the further study of this vital field.
(source: Nielsen Book Data)

• 1. Genotyping Strains of Lyme Disease Agents Directly From Ticks, Blood, or Tissue
• Alan G. Barbour and Vanessa J. Cook
• 2. Species Identification and Phylogenetic Analysis of Borrelia burgdorferi Sensu Lato using Molecular Biological Methods
• Gabriele Margos, Isabell Notter, and Volker Fingerle
• 3. Generation of Mammalian Host-adapted Borrelia burgdorferi by Cultivation in Peritoneal Dialysis Membrane Chamber Implantation in Rats
• Melissa J. Caimano
• 4. Co-immunoprecipitation for Identifying Protein-protein Interactions in Borrelia Burgdorferi
• Henna Iqbal, Darrin R. Akins, and Melisha R. Kenedy
• 5. Characterization of Borrelia burgdorferi Binding to Mammalian Cells and Extracellular Matrix
• Yi-Pin Lin and John M. Leong
• 6. Analysis of Lipids and Lipid Rafts in Borrelia
• Alvaro Toledo, Zhen Huang, Jorge Benach, and Erwin London
• 7. Trace Element AnalysisofBorrelia burgdorferi by Inductively Coupled Plasma-Sector Field Mass Spectrometry
• Xin Li, Peng Wang, Anthony Lutton, and John Olesik
• 8. Identification and Characterization of Borrelia burgdorferiComplement-binding Proteins
• Peter Kraiczy
• 9. Artificial Infection of Ticks with Borrelia burgdorferi using a Microinjection Method and their Detection in vivo using Quantitative PCR Targeting flaB RNA
• Alexis A. Smith, Xiuli Yang, Erol Fikrig, and Utpal Pal
• 10. Borrelia burgdorferi Microarray Analysis
• Radha Iyer and Ira Schwartz
• 11. Borrelia burgdorferi Transcriptome Analysis by RNA-sequencing
• Lybecker M and Henderson KC
• 12. Selection of Borrelia burgdorferi Promoter Sequences Active during Mammalian Infection Using In Vivo Expression Technology
• Philip P. Adams and Mollie W. Jewett
• 13. Analysis of DNA and RNA Binding Properties of Borrelia burgdorferi Regulatory Proteins
• J. Seshu , Trever C. Smith II, Ying-Han Lin, S.L. Rajasekhar Karna, Christine L. Miller, and Tricia Van Laar
• 14. Identification of Acetylated Proteins in Borrelia burgdorferi
• Youyun Yang, Alan Wolfe, and X. Frank Yang
• 15. Genetic Transformation and Complementation
• D. Scott Samuels, Dan Drecktrah, and Laura S. Hall
• 16. Genome-wide Mutagenesis in Borrelia burgdorferi
• Tao Lin and Lihui Gao
• 17. Generation of Conditional Mutants in Borrelia burgdorferi
• Jacob I. Latham and Jon S. Blevins
• 18. Detection of Bioluminescent Borrelia burgdorferi from in vitro Jenny A. Hyde and Jon T. Skare
• 19. Analysis of Borrelia burgdorferi Proteome and Protein-protein Interactions
• Xiuli Yang, Meghna Thakur, Juraj Koci, Alexis A. Smith, Preeti Singh, Xuran Zhuang, Kamoltip Promnares, Yan Wang, Ozlem Buyuktanir, and Utpal Pal
• 20. Two Photon Intravital Microscopy of Lyme Borrelia in Mice
• Alexia A. Belperron, Jialing Mao, and Linda K. Bockenstedt
• 21. Investigating Human Dendritic Cell Immune Responses to Borrelia burgdorferi
• Lauren M.K. Mason and Joppe W.R. Hovius
• 22. Phagocytosis Assays for Borrelia burgdorferi
• Juan Anguita, Ana Carreras-Gonzalez, and Nicolas Navasa
• 23. Measuring Borrelia burgdorferi Motility and Chemotaxis
• Kai Zhang and Chunhao Li
• 24. In vitro Models of Cutaneous Inflammation
• Quentin Bernard, Benoit Jaulhac, and Nathalie Boulanger
• 25. Magnetic Isolation of Phagosomes Containing Toll like Receptor Ligands
• Tanja Petnicki-Ocwieja and Linden T. Hu
• 26. Xenodiagnosis using Ixodes scapularis Larval Ticks in Humans
• Siu-Ping Turk, Carla Williams, and Adriana Marques
• 27. Recombinant E. coli Dualistic Role as an Antigen-adjuvant Delivery Vehicle for Oral Immunization
• Maria Gomes-Solecki and Luciana Richer.
• (source: Nielsen Book Data)

This volume details protocols that broadly cover many aspects of basic and translational research on Borrelia burgdorferi. Chapters guide readers through epidemiology and ecology, cultivation, cell structure, physiology, genomics and transcriptomics, proteomics, animal infection, pathogenesis and host responses, and vaccines. These essential protocols incorporate the most recent, practical, and innovative research tools aiding new and experienced researchers in their studies involving the biology, pathogenesis, and prevention of B. burgdorferi infection. 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, Borrelia burgdorferi: Methods and Protocols aims to ensure successful results in the further study of this vital field of biomedical research.
(source: Nielsen Book Data)

• Methods for cytogenetic chromosome barcoding and chromosome painting in Brachypodium distachyon and its relative species / Dominika Idziak-Helmcke and Alexander Betekhtin
• Transcriptional and posttranscriptional regulation of drought stress treatments in Brachypodium leaves / Edoardo Bertolini, Mario Enrico Pè, and Erica Mica
• Brachypodium distachyon long noncoding RNAs : genome-wide identification and expression analysis / Concetta De Quattro, Erica Mica, Mario Enrico Pè, and Edoardo Bertolini
• Highly efficient and reproducible Fusarium spp. inoculation method for Brachypodium distachyon / Anuj Rana, Aneesh Karunakaran, Timothy L. Fitzgerald, Rosalie Sabburg, Elizabeth A.B. Aitken, Robert J. Henry, Jonathan J. Powell, and Kemal Kazan
• Tissue culture (somatic embryogenesis)-induced Tnt1 retrotransposon-based mutagenesis in Brachypodium distachyon / Upinder S. Gill, Juan C. Serrani-Yarce, Hee-Kyung Lee, and Kirankumar S. Mysore
• Methods for xyloglucan structure analysis in Brachypodium distachyon / Lifeng Liu
• Genomic approaches to analyze alternative splicing, a key regulator of transcriptome and proteome diversity in Brachypodium distachyon / Sonia Irigoyen, Renesh H. Bedre, Karen-Beth G. Scholthof, and Kranthi K. Mandadi
• Information resources for functional genomics studies in Brachypodium distachyon / Keiichi Mochida and Kazuo Shinozaki
• Methods for functional transgenics : development of highly efficient transformation protocol in Brachypodium and its suitability for advancing Brachypodium transgenics / Ron Vunsh
• Molecular markers in whole genome evolution of Brachypodium / Xin-chun Mo, De-quan Zhang, Can Kou, and Ling-juan Yin
• Estimate codon usage bias using codon usage analyzer (CUA) / Zhenguo Zhang and Gaurav Sablok
• Identification of pseudogenes in Brachypodium distachyon chromosomes / Salvatore Camiolo and Andrea Porceddu
• TILLING in Brachypodium distachyon / Louise de Bang, Anna Maria Torp, and Søren K. Rasmussen
• Method for the large-scale identification of phasiRNAs in Brachypodium distachyon / Kun Yang, Xiaopeng Wen, and Gaurav Sablok
• Evaluation of genome-wide markers and orthologous markers in Brachypodium distachyon / Gaurav Sablok, Suresh B. Mudunuri, Korneliya Gudys, Kranthi Chennamsetti, G.P. Saradhi Varma, and Miroslaw Kwasniewski
• Protocol for coexpression network construction and stress-responsive expression analysis in Brachypodium / Sanchari Sircar, Nita Parekh, and Gaurav Sablok
• Whole genome DNA methylation analysis using next-generation sequencing (BS-seq) / I-Hsuan Lin
• Application of tissue culture and transformation techniques in model species Brachypodium distachyon / Bahar Sogutmaz Ozdemir and Hikmet Budak.

This volume presents protocols for Brachypodium genomics in numerous areas ranging from marker development, trait evolution, functional genomics, metabolomics, transcriptomics, genomics, and tilling. This book also explores techniques to study the widening genetic base of Brachypodium that will help researchers better understand the model plant using NGS technologies. 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, Brachypodium Genomics: Methods and Protocols is a valuable resource for bench-oriented molecular biologists and computational biologists working towards further evolving this field.
(source: Nielsen Book Data)

• 1. Introduction to Cancer Stem Cells: Past, Present, and Future
• David Bakhshinyan, Ashley A. Adile, Maleeha A. Qazi, Mohini Singh, Michelle M. Kameda-Smith, Nick Yelle, Chirayu Chokshi, Chitra Venugopal, and Shiela K. Singh
• 2. Surface Markers for the Identification of Cancer Stem Cells
• Vinod Gopalan, Farhadul Islam, and Alfred King-yin Lam
• 3. The Role of CD44 and Cancer Stem Cells
• Liang Wang, Xiangsheng Zuo, Keping Xie, and Daoyan Wei
• 4. Evaluation and Isolation of Cancer Stem Cells Using ALDH Activity Assay
• Luigi Mele, Davide Liccardo, and Virginia Tirino
• 5. Isolation of Cancer Stem Cells by Side Population Method
• Masayuki Shimoda, Masahide Ota, and Yasunori Okada
• 6. Self-Renewal and CSCs In Vitro Enrichment: Growth as Floating Spheres
• Pooja Mehta, Caymen Novak, Shreya Raghavan, Maria Ward, and Geeta Mehta
• 7. In Vitro Tumorigenic Assay: The Tumor Spheres Assay
• Hui Wang, Anna Paczulla, Martina Konantz, and Claudia Lengerke
• 8. In Vitro Tumorigenic Assay: Colony Forming Assay for Cancer Stem Cells
• Vijayalakshmi Rajendran and Mayur Vilas Jain
• 9. Xenograft as In Vivo Experimental Model
• Manuela Porru, Luca Pompili, Carla Caruso, and Carlo Leonetti
• 10. How to Assess Drug Resistance in Cancer Stem Cells
• Maria Laura De Angelis, Ruggero De Maria, and Marta Baiocchi
• 11. Tumor Tissue Analogs for Assessment of Radioresistance in Cancer Stem Cells
• Meenakshi Upreti
• 12. Generation of In Vitro Model of Epithelial Mesenchymal Transition (EMT) Via the Expression of a Cytoplasmic Mutant Form of Promylocytic Leukemia Protein (PML)
• Anna Di Biase, Amanda K. Miles, and Tarik Regad
• 13. Identification and Isolation of Cancer Stem Cells Using NANOG-EGFP Reporter System
• Magdalena E. Buczek, Stephen P. Reeder, and Tarik Regad
• 14. Determination of miRNAs from Cancer Stem Cells Using a Low Density Array Platform
• Hiromichi Kawasaki, Angela Lombardi, and Michele Caraglia
• 15. Assessing DNA Methylation in Cancer Stem Cells
• Sudipto Das, Bruce Moran, and Antoinette S. Perry
• 16. Histones Acetylation and Cancer Stem Cells (CSCs)
• Vivian Petersen Wagner, Manoela Domingues Martins, and Rogerio Moraes Castilho
• 17. Immunohistochemistry for Cancer Stem Cells Detection: Principles and Methods
• Martina Intartaglia, Rosalaura Sabetta, Monica Gargiulo, Giovanna Roncador, Federica Zito Marino, and Renato Franco
• 18. Circulating Tumor Cells
• Sebastian A. Garcia, Jurgen Weitz, and Sebastian Schoelch.
• (source: Nielsen Book Data)

This detailed volume gathers a comprehensive collection of methods, protocols, and procedures used for the identification, characterization, and selection of cancer stem cells. These include surface marker expression, side population, spheres formation, ALDH activity, and numerous others. 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 protocols, and expert tips and troubleshooting advice to avoid potential pitfalls. Comprehensive and practical, Cancer Stem Cells: Methods and Protocols provides researchers with the techniques they will need in order to pursue vital research into this complex field of study.
(source: Nielsen Book Data)

• Detection of combinatorial mutational patterns in human cancer genomes by exclusivity analysis / Hua Tan and Xiaobo Zhou
• Discovering altered regulation and signaling through network-based integration of transcriptomic, epigenomic, and proteomic tumor data / Amanda J. Kedaigle and Ernest Fraenkel
• Analyzing DNA methylation patterns during tumor evolution / Heng Pan and Olivier Elemento
• MicroRNA networks in breast cancer cells / Andliena Tahiri, Miriam R. Aure, and Vessela N. Kristensen
• Identifying genetic dependencies in cancer by analyzing siRNA screens in tumor cell Line Panels / James Campbell, Colm J. Ryan, and Christopher J. Lord
• Phosphoproteomics-based profiling of kinase activities in cancer cells / Jakob Wirbel, Pedro Cutillas, and Julio Saez-Rodriguez
• Perseus : a bioinformatics platform for integrative analysis of proteomics data in cancer research / Stefka Tyanova and Juergen Cox
• Quantitative analysis of tyrosine kinase signaling across differentially embedded human glioblastoma tumors / Hannah Johnson and Forest M. White
• Prediction of clinical endpoints in breast cancer using NMR metabolic Profiles / Leslie R. Euceda, Tonje H. Haukaas, Tone F. Bathen, and Guro F. Giskeødega°rd
• Stochastic and deterministic models for the metastatic emission process : formalisms and crosslinks / Christophe Gomez and Niklas Hartung
• Mechanically coupled reaction-diffusion model to predict glioma growth : methodological details / David A. Hormuth II, Stephanie L. Eldridge, Jared A. Weis, Michael I. Miga, and Thomas E. Yankeelov
• Profiling tumor infiltrating immune cells with CIBERSORT / Binbin Chen, Michael S. Khodadoust, Chih Long Liu, Aaron M. Newman, and Ash A. Alizadeh
• Systems biology approaches in cancer pathology / Aaron DeWard and Rebecca J. Critchley-Thorne
• Bioinformatics approaches to predict drug responses from genomic sequencing / Neel S. Madhukar and Olivier Elemento
• Robust optimization approach to cancer treatment under toxicity uncertainty / Junfeng Zhu, Hamidreza Badri, and Kevin Leder
• Modeling of interactions between cancer stem cells and their microenvironment : predicting clinical response / Mary E. Sehl and Max S. Wicha
• Methods for high-throughput drug combination screening and synergy scoring / Liye He, Evgeny Kulesskiy, Jani Saarela, Laura Turunen, Krister Wennerberg, Tero Aittokallio, and Jing Tang.

This book comprises protocols describing systems biology methodologies and computational tools, offering a variety of ways to analyze different types of high-throughput cancer data. Chapters give an overview over data types available in large-scale data repositories and state-of-the-art methods used in the field of cancer systems biology. 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 practical, Cancer Systems Biology : Methods and Protocols aims to ensure successful results in the further study of this vital field. The chapters "Identifying Genetic Dependencies in Cancer by Analyzing siRNA Screens in Tumor Cell Line Panels", "Perseus: A Bioinformatics Platform for Integrative Analysis of Proteomics Data in Cancer Research" and "Phosphoproteomics-based Profiling of Kinase Activities in Cancer Cells" are available open access under a CC BY 4.0 license via link.springer.com.
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• 1. Molecular Regulation of Cellular Quiescence: A Perspective from Adult Stem Cells and Its Niches
• Wai-Kin So and Tom H. Cheung
• 2. An In Vitro Model of Cellular Quiescence in Primary Human Dermal Fibroblasts
• Mithun Mitra, Linda D. Ho, and Hilary A. Coller
• 3. Flow Cytometric Detection of G0 in Live Cells by Hoechst 33342 and Pyronin Y Staining
• Ayad Eddaoudi, Stephanie Louise Canning, and Itaru Kato
• 4. Using Carboxy Fluorescein Succinimidyl Ester (CFSE) to Identify Quiescent Glioblastoma Stem-Like Cells
• Hassan Azari, Loic P. Deleyrolle, and Brent A. Reynolds
• 5. Isolation of Neural Stem and Progenitor Cells from the Adult Brain and Live Imaging of Their Cell Cycle with the FUCCI System
• Alexandra Chicheportiche, Martial Ruat, Francois D. Boussin, and Mathieu Daynac
• 6. Determination of Histone 2B-Green Fluorescent Protein (GFP) Retention in Intestinal Stem Cells
• Kevin R. Hughes and Yashwant R. Mahida
• 7. Detecting Hematopoietic Stem Cell Proliferation Using BrdU Incorporation
• Katie A. Matatall, Claudine S. Kadmon, and Katherine Y. King
• 8. Cell Cycle Analysis by Mass Cytometry
• Gregory K. Behbehani
• 9. Preparation and Analysis of Saccharomyces cerevisiae Quiescent Cells
• Marla M. Spain, Sarah G. Swygert, and Toshio Tsukiyama
• 10. Identifying Quiescent Stem Cells in Hair Follicles
• Christine N. Rodriguez and Hoang Nguyen
• 11. Single EDL Myofiber Isolation for Analyses of Quiescent and Activated Muscle Stem Cells
• Caroline E. Brun, Yu Xin Wang, and Michael A. Rudnicki
• 12. Investigating Cellular Quiescence of T Lymphocytes and Antigen-Induced Exit from Quiescence
• Kai Yang and Hongbo Chi
• 13. Retroviral Transduction of Quiescent Murine Hematopoietic Stem Cells
• Chun Shik Park and H. Daniel Lacorazza
• 14. Analysis of Murine Hematopoietic Stem Cell Proliferation During Inflammation
• Emilie Jalbert and Eric M. Pietras
• 15. A Facile, In Vitro 384-Well Plate System to Model Disseminated Tumor Cells in the Bone Marrow Microenvironment
• Johanna M. Buschhaus, Kathryn E. Luker, and Gary D. Luker
• 16. Distinguishing States of Arrest: Genome-Wide Descriptions of Cellular Quiescence Using ChIP-Seq and RNA-Seq Analysis
• Surabhi Srivastava, Hardik Gala, Rakesh K. Mishra, and Jyotsna Dhawan
• 17. Analysis of lncRNA-Protein Interactions by RNA-Protein Pull-Down Assay and RNA Immunoprecipitation (RIP)
• Holger Bierhoff
• 18. Analysis of MicroRNA-Mediated Translation Activation of In Vitro Transcribed Reporters in Quiescent Cells
• Syed I.A. Bukhari, Samuel S. Truesdell, and Shobha Vasudevan
• 19. Genome-Wide Identification of Transcription Factor Binding Sites in Quiescent Adult Neural Stem Cells
• Shradha Mukherjee and Jenny Hsieh
• 20. Study Quiescence Heterogeneity by Coupling Single-Cell Measurements and Computer Modeling
• Jungeun Sarah Kwon, Xia Wang, and Guang Yao.
• (source: Nielsen Book Data)

This detailed volume explores methods and protocols that aim to increase our understanding of how cells enter a quiescent state during homeostasis and how cells exit quiescence and re-enter differentiating cell divisions to restore damaged tissues, essential for developing new approaches in regenerative medicine in the future. The chapters in this book were designed to address cellular quiescence in prokaryote and eukaryote organisms, detection of quiescence (Hoechst/pyronin Y, FUCCI, CFSE, BrdU, H2B-GFP, CyTOF), quiescence in stem cells (skin, intestinal, neuronal, hematopoietic), genomic regulation (gene expression, transcription factors, lncRNA, RNA methylation), as well as analysis of the heterogeneity of quiescence by computer modeling. 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 practical, Cellular Quiescence: Methods and Protocols offers a broad view of basic and cutting-edge technology to inspire research in this emerging field of cell biology.
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• 1. Targeted Deletion of Hsf1, 2 and 4 Genes in Mice
• Xiongjie Jin, Binnur Eroglu, Demetrius Moskophidis, and Nahid F. Mivechi
• 2. Role of Heat Shock Factors in Stress-induced Transcription
• Murshid, A., Prince T., Ben Lang, and Calderwood, S. K.
• 3. Monitoring of the Heat Shock Response with a Real-time Luciferase Reporter
• Toshiki Kijima, Takanori Eguchi, Len Neckers, and Thomas L. Prince
• 4. Quantitative Profiling of Chaperone/client Interactions with LUMIER Assay
• Mikko Taipale
• 5. Measurement of chaperone-mediated effects on Polyglutamine Protein Aggregation by the Filter Trap Assay
• Maria A.W.H. van Waarde-Verhagen and Harm H. Kampinga
• 6. Fluorescent-linked Enzyme Chemoproteomic Strategy (FLECS) for Identifying HSP70 Inhibitors
• Haystead, T.A.J.
• 7. A High-throughput Screen for Inhibitors of the Hsp90-Chaperone Machine
• Jason Davenport, Lakshmi Galam, and Robert L. Matts
• 8. Primary Colorectal Cells Culture as a Translation Research Model
• Sheah Lin Lee, Nina Claire Dempsey-Hibbert, Dale Vimalachandran, Terence David Wardle, Paul A Sutton, and John H. H. Williams
• 9. Cell Death and Survival Assays
• Alexander E. Kabakov and Vladimir L. Gabai
• 10. Detecting the Potential Pharmacological Synergy of Drug Combination by Viability Assays In Vitro
• Benjamin K. Gibbs and Carole Sourbier
• 11. Proteomic Profiling of Hsp90 Inhibitors
• Sudhakar Voruganti, Jake T. Kline, Maurie J. Balch, Janet Rogers, Robert L. Matts, and Steven D. Hartson
• 12. Analysis of HspB1 (Hsp27) Oligomerization and Phosphorylation Patterns and its Interaction with Specific Client Polypeptides
• Andre-Patrick Arrigo
• 13. Nucleotide Exchange Factors for Hsp70 Chaperones
• Heike Rampelt, Matthias P. Mayer, and Bernd Bukau
• 14. Determination of Hsp90 Activity through Activation of Glucocorticoid Receptors in Yeast
• Michael Reidy
• 15. Bacterial Hsp90 ATPase Assays
• Joel R. Hoskins, Sue Wickner, and Shannon M. Doyle
• 16. Detecting Post-translational Modifications of Hsp90
• Rebecca A. Sager, Mark R. Woodford, Len Neckers, and Mehdi Mollapour
• 17. Chromatin Immunoprecipitation (ChIP) of Heat Shock Protein 90 (Hsp90)
• Aneliya Yoveva and Ritwick Sawarkar
• 18. A Workflow Guide to RNA-seq Analysis of Chaperone Function and Beyond
• Benjamin J. Lang, Kristina M. Holton, Jianlin Gong, and Stuart K. Calderwood
• 19. Computational Modeling of the Hsp90 Interactions with Cochaperones and Small Molecule Inhibitors
• Gennady M. Verkhivker
• 20. Computational Analysis of the Chaperone Interaction Networks
• Shwani Kumar, Kamran Rizzolo, Sandra Zilles, Mohan Babu, and Walid A. Houry
• 21. Immunohistochemistry of Human Hsp60 in Health and Disease: From Autoimmunity to Cancer
• Francesco Cappello, Everly Conway de Macario, Francesca Rappa, Giovanni Zummo, and Alberto J. L. Macario
• 22. Immunohistochemical and Flow Cytometric Analysis of Intracellular and Membrane-bound Hsp70, as a Putative Biomarker of Glioblastoma Multiforme, using the cmHsp70.1 Monoclonal Antibody
• Stefan Stangl, Gemma A. Foulds, Helena Fellinger, Geoffrey J. Pilkington, A. Graham Pockley, and Gabriele Multhoff
• 23. Detection and Analysis of Extracellular Hsp90 (eHsp90)
• Stephanie Cortes, Alexander Baker-Williams, Mehdi Mollapour, and Dimitra Bourboulia
• 24. Molecular Chaperone Receptors
• Ayesha Murshid, Jimmy Theriault, Jianlin Gong, and Stuart K. Calderwood
• 25. Creation of Recombinant Chaperone Vaccine using Large Heat Shock Protein for Antigen-targeted Cancer Immunotherapy
• Chunqing Guo, John R. Subjeck, and Xiang-Yang Wang
• 26. A Novel Heat Shock Protein 70-based Vaccine Prepared from DC-Tumor Fusion Cells Desheng Weng, Stuart K. Calderwood, and Jianlin Gong
• 27. Hsp70: A Cancer Target Inside and Outside the Cell Christophe Boudesco, Sebastien Cause, Gaetan Jego, and Carmen Garrido
• 28. Evidence for Hsp90 Cochaperones in Regulating Hsp90 Function and Promoting Client Protein Folding
• Marc B. Cox and Jill L. Johnson
• 29. Clinical Evaluation and Biomarker Profiling of Hsp90 Inhibitors
• Akira Yuno, Min-Jung Lee, Sunmin Lee, Yusuke Tomita, David Rekhtman, Brittni Moore, and Jane B. Trepel.
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This volume is a compilation of laboratory protocols and methodology required for the study of molecular chaperones and the cellular stress response. Chapters detail stress response in Hsf1, Hsf2 and Hsf4 knockout mice, mapping HSP interaction networks, the LUminescence-based Mammalian IntERactome (LUMIER), Hsp70 biology, protein folding activity of Hsp90, cytotoxicity of HSP inhibitors, computational approaches for modeling allosteric Hsp90 interactions, HSPs in immunity and vaccine development , and biologies of Hsp70 and Hsp90. 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 practical, Chaperones: Methods and Protocols aims to ensure successful results in the further study of this vital field.
(source: Nielsen Book Data)

• ChIP and ChIP-related techniques : expanding the fields of application and improving ChIP performance / Neus Visa and Antonio Jordan-Pla
• Considerations on experimental design and data analysis of chromatin immunoprecipitation experiments / Antonio Jordan-Pla and Neus Visa
• How to combine ChIP with qPCR / Patrik Asp
• Analysis of protein-DNA interaction by chromatin immunoprecipitation and DNA tiling microarray (ChIP-on-chip) / Hui Gao and Chunyan Zhao
• Chromatin immunoprecipitation from mouse embryonic tissue or adherent cells in culture, followed by next-generation sequencing / Mario A.F. Soares and Diogo S. Castro
• Chromatin RNA immunoprecipitation (ChRIP) / Tanmoy Mondal, Santhilal Subhash, and Chandrasekhar Kanduri
• DNA accessibility by MNase digestions / Ann-Kristin Ostlund Farrants
• Characterization of the nucleosome landscape by micrococcal nuclease-sequencing (MNase-seq) / Wieteke Anna Maria Hoeijmakers and Richard Bartfai
• ChIP-re-ChIP : co-occupancy analysis by sequential chromatin immunoprecipitation / Timothy V. Beischlag, Gratien G. Prefontaine, and Oliver Hankinson
• Sm-ChIPi : single-molecule chromatin immunoprecipitation imaging / Roubina Tatavosian and Xiaojun Ren
• Chromatin immunoprecipitation of skeletal muscle tissue / Amarjit Saini and Carl Johan Sundberg
• Chromatin immunoprecipitation assay in the hyperthermoacidophilic crenarchaeon, Sulfolobus acidocaldarius / Kun Wang and Ann-Christin Lindas
• Using intra-ChIP to measure protein-DNA interactions in intracellular pathogens / Brett R. Hanson and Ming Tan
• Native chromatin immunoprecipitation-sequencing (ChIP-Seq) from low cell numbers / Teodora Ribarska and Gregor D. Gilfillan
• MOBE-ChIP : probing cell type-specific binding through large-scale chromatin immunoprecipitation / Shenqi Wang and On Sun Lau
• Multiplexed ChIP-Seq using direct nucleosome barcoding : a tool for high-throughput chromatin analysis / Christophe D. Chabbert, Sophie H. Adjalley, Lars M. Steinmetz, and Vicent Pelechano
• Analysis of ChIP-seq data in R/Bioconductor / Ines de Santiago and Thomas Carroll
• Spike-in normalization of ChIP data using DNA-DIG-antibody complex / Andrea B. Eberle.

This up-to-date volume includes protocols that illustrate the broad use of chromatin immunoprecipitation (ChIP) and ChIP-related methods in a variety of biological research areas. The collection also includes protocols designed to improve the performance of ChIP for specific applications. Written in the highly successful Methods in Molecular Biology series format, chapters include introduction to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, as well as tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Chromatin Immunoprecipitation: Methods and Protocols features techniques, including bioinformatic analysis of ChIP data, will be of interest to a very broad research community in the fields of biochemistry, molecular biology, microbiology, and biomedicine.
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• Detection and reconstruction of circular RNAs from transcriptomic data / Yi Zheng and Fangqing Zhao
• Deep computational circular RNA analytics from RNA-seq data / Tobias Jakobi and Christoph Dieterich
• Genome-wide circRNA profiling from RNA-seq data / Daphne A. Cooper, Mariela Cortés-López, and Pedro Miura
• Analysis of circular RNAs using the web tool CircInteractome / Amaresh C. Panda, Dawood B. Dudekula, Kotb Abdelmohsen, and Myriam Gorospe
• Characterization and validation of circular RNA and their host gene mRNA expression using PCR / Andreas W. Heumüller and Jes-Niels Boeckel
• Detecting circular RNAs by RNA fluorescence in situ hybridization / Anne Zirkel and Argyris Papantonis
• Single-molecule fluorescence in situ hybridization (FISH) of circular RNA CDR1as / Christine Kocks, Anastasiya Boltengagen, Monika Piwecka, Agnieszka Rybak-Wolf, and Nikolaus Rajewsky
• Highly efficient strategy for overexpressing circRNAs / Dawei Liu, Vanessa Conn, Gregory J. Goodall, and Simon J. Conn
• Constructing GFP-based reporter to study back splicing and translation of circular RNA / Yun Yang and Zefeng Wang
• Northern blot analysis of circular RNAs / Tim Schneider, Silke Schreiner, Christian Preusser, Albrecht Bindereif, and Oliver Rossbach
• Nonradioactive northern blot of circRNAs / Xiaolin Wang and Ge Shan
• Characterization of circular RNA concatemers / Thomas B. Hansen
• Characterization of circular RNAs (circRNA) associated with the translation machinery / Deniz Bartsch, Anne Zirkel, and Leo Kurian
• Synthesis and engineering of circular RNAs / Sonja Petkovic and Sabine Müller
• Preparation of circular RNA in vitro / Naoko Abe, Ayumi Kodama, and Hiroshi Abe
• Discovering circRNA-microRNA interactions from CLIP-seq data / Xiao-Qin Zhang and Jian-Hua Yang
• Identification of circRNAs for miRNA targets by argonaute2 RNA immunoprecipitation and luciferase screening assays / Yan Li, Bing Chen, and Shenglin Huang.

This volume provides established approaches for identifying, characterizing, and manipulating circRNAs in vitro, in vivo, and in silico. Chapters highlight the breakthroughs and the challenges in this new field of research. 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 practical, Circular RNAs: Methods and Protocols aims to useful and informative for further study into this vital field.
(source: Nielsen Book Data)

• Gene phylogenies and orthologous groups / Joao C. Setubal and Peter F. Stadler
• Pan-genome storage and analysis techniques / Tina Zekic, Guillaume Holley, and Jens Stoye
• Comparative genomics for prokaryotes / Joao C. Setubal, Nalvo F. Almeida, and Alice R. Wattam
• Assembly, annotation, and comparative genomics in PATRIC, the all bacterial bioinformatics resource center / Alice R. Wattam, Thomas Brettin, James J. Davis, Svetlana Gerdes, Ronald Kenyon, Dustin Machi, Chunhong Mao, Robert Olson, Ross Overbeek, Gordon D. Pusch, Maulik P. Shukla, Rick Stevens, Veronika Vonstein, Andrew Warren, Fangfang Xia, and Hyunseung Yoo
• Phylogenomics / Jose S.L. Patane, Joaquim Martins-JR, and Joao C. Setubal
• Comparative genome annotation / Stefanie Konig, Lars Romoth, and Mario Stanke
• Practical guide for comparative genomics of mobile genetic elements in prokaryotic genomes / Danillo Oliveira Alvarenga, Leandro M. Moreira, Mick Chandler, and Alessandro M. Varani
• Comparative metagenomics / Andrew Maltez Thomas, Felipe Prata Lima, Livia Maria Silva Moura, Aline Maria da, Silva, Emmanuel Dias Neto, and Joao C. Setubal
• Genome rearrangement analysis : cut and join genome rearrangements and gene cluster preserving approaches / Tom Hartmann, Martin Middendorf, and Matthias Bernt
• Whole genome duplication in plants : implications for evolutionary analysis / David Sankoff and Chunfang Zheng
• Sequence-based synteny analysis of multiple large genomes / Daniel Doerr and Bernard M.E. Moret
• Family-free genome comparison / Daniel Doerr, Pedro Feijao, and Jens Stoye
• Comparative methods for reconstructing ancient genome organization / Yoann Anselmetti, Nina Luhmann, Severine Berard, Eric Tannier, and Cedric Chauve
• Comparative RNA genomics / Rolf Backofen, Jan Gorodkin, Ivo L. Hofacker, and Peter F. Stadler
• Bioinformatic approaches for comparative analysis of viruses / Deyvid Amgarten and Chris Upton
• Comparative genomics of gene loss and gain in Caenorhabditis and other nematodes / Christian Rodelsperger
• Comparative genomics in Drosophila / Martin Oti, Attilio Pane, and Michael Sammeth
• Comparative genomics in Homo sapiens / Martin Oti and Michael Sammeth.

This volume provides broad coverage of computational and mathematical techniques and concepts related to the field of comparative genomics. The topics covered in the chapters range from those concerned with general techniques and concepts that apply to all organisms to others that are more specialized, covering specific biological systems such as viruses, Drosophila, and Homo sapiens. Written in the highly successful Methods in Molecular Biology series format, by authors who are active researchers in the field, many chapters include step-by-step procedures, which illustrate practical applications of the techniques described. Cutting-edge and thorough, Comparative Genomics: Methods and Protocols should be useful to students and researchers in the continually growing and exciting field of comparative genomics.
(source: Nielsen Book Data)

• Current and future challenges in GPCR drug discovery / Sid Topiol
• Characterization of ligand binding to GPCRs through computational methods / Silvana Vasile, Mauricio Esguerra, Willem Jespers, Ana Oliveira, Jessica Sallander, Johan Aqvist, and Hugo Gutierrez-de-Teran
• Breakthrough in GPCR crystallography and its impact on computer-aided drug design / Antonella Ciancetta and Kenneth A. Jacobson
• Structural framework for GPCR chemogenomics : what's in a residue number? / Marton Vass, Albert J. Kooistra, Stefan Verhoeven, David Gloriam, Iwan J.P. de Esch, and Chris de Graaf
• GPCR homology model generation for lead optimization / Christofer S. Tautermann
• GPCRs : what can we learn from molecular dynamics simulations? / Naushad Velgy, George Hedger, and Philip C. Biggin
• Methods of exploring protein-ligand interactions to guide medicinal chemistry efforts / Paul Labute
• Exploring GPCR-ligand interactions with the fragment molecular orbital (FMO) method / Ewa I. Chudyk, Laurie Sarrat, Matteo Aldeghi, Dmitri G. Fedorov, Mike J. Bodkin, Tim James, Michelle Southey, Roger Robinson, Inaki Morao, and Alexander Heifetz
• Molecular basis of ligand dissociation from G protein-coupled receptors and predicting residence time / Dong Guo and Adriaan P. IJzerman
• Methodologies for the examination of water in GPCRs / Andrea Bortolato, Benjamin G. Tehan, Robert T. Smith, and Jonathan S. Mason
• Methods for virtual screening of GPCR targets : approaches and challenges / Jason B. Cross
• Approaches for differentiation and interconverting GPCR agonists and antagonists / Przemysław Miszta, Jakub Jakowiecki, Ewelina Rutkowska Maria Turant, Dorota Latek, and Sławomir Filipek
• Opportunities and challenges in the discovery of allosteric modulators of GPCRs / Damian Bartuzi, Agnieszka A. Kaczor, and Dariusz Matosiuk
• Challenges and opportunities in drug discovery of biased ligands / Ismael Rodrıguez-Espigares, Agnieszka A. Kaczor, Tomasz Maciej Stepniewski, and Jana Selent
• Synergistic use of GPCR modeling and SDM experiments to understand ligand binding / Andrew Potterton, Alexander Heifetz, and Andrea Townsend-Nicholson
• Computational support of medicinal chemistry in industrial settings / Daniel F. Ortwine
• Investigating small-molecule ligand binding to G protein-coupled receptors with biased or unbiased molecular dynamics simulations / Kristen A. Marino and Marta Filizola
• Ligand-based methods in GPCR computer-aided drug design / Paul C.D. Hawkins and Gunther Stahl
• Computational methods used in hit-to-lead and lead optimization stages of structure-based drug discovery / Alexander Heifetz, Michelle Southey, Inaki Morao, Andrea Townsend-Nicholson, and Mike J. Bodkin
• Cheminformatics in the service of GPCR drug discovery / Tim James
• Modeling and deorphanization of orphan GPCRs / Constantino Diaz, Patricia Angelloz-Nicoud, and Emilie Pihan.

This volume looks at modern computational strategies and techniques used in GPCR drug discovery including structure and ligand-based approaches and cheminformatics. The chapters in this book describe how these approaches can be applied to address key drug discovery issues, such as receptor structure modelling, function and dynamics, prediction of protein-water-ligand interactions and binding kinetics, free energy of binding, interconversion between agonists and antagonists, deorphanization of GPCRs, and the discovery of biased and allosteric modulators. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary software and tools, step-by-step, readily reproducible modelling protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and unique, Computational Methods for GPCR Drug Discovery is a valuable resource for structural and molecular biologists, computational and medicinal chemists, pharmacologists, and drug designers.
(source: Nielsen Book Data)

• Two-dimensional gel electrophoresis and 2D-DIGE / Paula Meleady
• Comparative DIGE proteomics / Kay Ohlendieck
• 2D-DIGE and fluorescence image analysis / Elisa Robotti and Emilio Marengo
• DIGE analysis software and protein identification approaches / Abduladim Hmmier and Paul Dowling
• Native DIGE : efficient tool to elucidate protein interactomes / Diksha Dani and Norbert A. Dencher
• Comparative two-dimensional fluorescence gel electrophoresis / Doreen Ackermann and Simone Konig
• DIGE-based phosphoproteomic analysis / Taras Stasyk and Lukas Alfons Huber
• DIGE saturation labeling for scarce amounts of protein from formalin-fixed paraffin-embedded (FFPE) tissue / Paul Dowling
• Comparative 3-sample DIGE analysis of skeletal muscles / Kay Ohlendieck
• DIGE analysis of ProteoMiner fractionated serum/plasma samples / Sandra Murphy and Paul Dowling
• DIGE analysis of human tissues / Cecilia Gelfi and Daniele Capitanio
• DIGE analysis of animal tissues / Alessio Di Luca, Ruth Hamill, Anne Maria Mullen, and Giuliano Elia
• Rapid 2D DIGE proteomic analysis of mouse liver / Shotaro Kamata and Isao Ishii
• Proteomic analysis of lung tissue by DIGE / Jarlath E. Nally and Simone Schuller
• Comparative testis tissue proteomics using 2-dye versus 3-dye DIGE analysis / Ashling Holland
• DIGE analysis of fish tissues / Joanna Nynca, Mariola A. Dietrich, and Andrzej Ciereszko
• Protein digestion for DIGE analysis / Sandra Murphy and Kay Ohlendieck
• Subcellular fractionation for DIGE-based proteomics / Sandra Murphy
• DIGE analysis of immunodepleted plasma / Paul Dowling and Kay Ohlendieck
• Elucidating cellular metabolism and protein difference data from DIGE proteomics experiments using enzyme assays / Andrew Dowd
• Enzyme assay methods to validate DIGE proteomics data / Andrew Dowd
• Immunoblot analysis of DIGE-based proteomics / Martin Landsberger and Heinrich Brinkmeier
• Immunofluorescence microscopy for DIGE-based proteomics / Rustam R. Mundegar, Margit Zweyer, and Dieter Swandulla.

This volume provides a comprehensive study of this key method of gel-based proteomics. Chapters in Difference Gel Electrophoresis: Methods and Protocols detail methods on principles of differential protein labeling, two-dimensional gel electrophoresis, techniques on optimized proteomic workflows, advanced mass spectrometry for protein identification, application of basic biological research, and applied biomarker discovery. 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, Difference Gel Electrophoresis: Methods and Protocols aims to ensure successful results in the further study of this vital field.
(source: Nielsen Book Data)

• Identification of disease susceptibility alleles in the next generation sequencing era / Johanna K. DiStefano and Christopher B. Kingsley
• Induced pluripotent stem cells in disease modeling and gene identification / Satish Kumar, John Blangero, and Joanne E. Curran
• Development of targeted therapies based on gene modification / Taylor M. Benson, Fatjon Leti, and Johanna K. DiStefano
• What can we learn about human disease from the nematode C. elegans / Javier Apfeld and Scott Alper
• Microbiome sequencing methods for studying human diseases / Rebecca M. Davidson and L. Elaine Epperson
• Emerging role of long noncoding RNAs in human disease / Johanna K. DiStefano
• Identification of disease-related genes using a genome-wide association study approach / Tobias Wohland and Dorit Schleinitz
• Whole genome library construction for next generation sequencing / Jonathan J. Keats, Lori Cuyugan, Jonathan Adkins, and Winnie S. Liang
• Whole exome library construction for next generation sequencing / Winnie S. Liang, Kristi Stephenson, Jonathan Adkins, Austin Christofferson, Adrienne Helland, Lori Cuyugan, and Jonathan J. Keats
• Optimized methodology for the generation of RNA-sequencing libraries from low-input starting material : enabling analysis of specialized cell types and clinical samples / Kendra Walton and Brian P. O'Connor
• Using fluidigm C1 to generate single-cell full-length cDNA libraries for mRNA sequencing / Robert Durruthy-Durruthy and Manisha Ray
• MiSeq : a next generation sequencing platform for genomic analysis / Rupesh Kanchi Ravi, Kendra Walton, and Mahdieh Khosroheidari
• Methods for CpG methylation array profiling via bisulfite conversion / Fatjon Leti, Lorida Llaci, Ivana Malenica, and Johanna K. DiStefano
• miRNA quantification method using quantitative polymerase chain reaction in conjunction with Cq method / Fatjon Leti and Johanna K. DiStefano
• Primary airway epithelial cell gene editing using CRISPR-Cas9 / Jamie L. Everman, Cydney Rios, and Max A. Seibold
• RNA interference to knock down gene expression / Haiyong Han
• Using luciferase reporter assays to identify functional variants at disease-associated loci / Anup K. Nair and Leslie J. Baier
• Physiologic interpretation of GWAS signals for type 2 diabetes / Richard M. Watanabe
• Identification of Genes for Hereditary Hemochromatosis / Glenn S. Gerhard, Barbara V. Paynton, and Johanna K. DiStefano
• Identification of driver mutations in rare cancers : the role of SMARCA4 in small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) / Jessica D. Lang and William P.D. Hendricks
• Rise and fall and rise of linkage analysis as a technique for finding and characterizing inherited influences on disease expression / Ettie M. Lipner and David A. Greenberg.

This volume presents detailed laboratory procedures in an easy to follow format that can be carried out with success by investigators lacking previous exposure to a specific research method. Chapter guide readers through the application of molecular approaches to disease gene identification and overviews, and case studies are also presented. 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 practical, Disease Gene Identification: Methods and Protocols, Second Edition aims to help with the identification and characterization of many more disease-related genes and provide novel, and effective strategies for disease treatment and prevention.
(source: Nielsen Book Data)

• Summary of the biological processes, disease-associated changes, and clinical applications of DNA methylation / Gitte Brinch Andersen and Jorg Tost
• Considerations for design and analysis of DNA methylation studies / Karin B. Michels and Alexandra M. Binder
• Quantification of global DNA methylation levels by mass spectrometry / Agustin F. Fernandez, Luis Valledor, Fernando Vallejo, Maria Jesus Canal, and Mario F. Fraga
• Antibody-based detection of global nuclear DNA methylation in cells, tissue sections, and mammalian embryos / Nathalie Beaujean, Juliette Salvaing, Nur Annies Abd Hadi, and Sari Pennings
• Whole-genome bisulfite sequencing using the Ovation® ultralow methyl-seq protocol / Christian Daviaud, Victor Renault, Florence Mauger, Jean-Francois Deleuze, and Jorg Tost
• Tagmentation-based library preparation for low DNA input whole genome bisulfite sequencing / Dieter Weichenhan, Qi Wang, Andrew Adey, Stephan Wolf, Jay Shendure, Roland Eils, and Christoph Plass
• Post-bisulfite adaptor tagging for PCR-free whole-genome bisulfite sequencing / Fumihito Miura and Takashi Ito
• Multiplexed reduced representation bisulfite sequencing with magnetic bead fragment size selection / William P. Accomando Jr. and Karin B. Michels
• Low input whole-genome bisulfite sequencing using a post-bisulfite adapter tagging approach / Julian R. Peat and Sebastien A. Smallwood
• Methyl-CpG-binding domain sequencing : MBD-seq / Karolina A. Aberg, Robin F. Chan, Linying Xie, Andrey A. Shabalin, and Edwin J.C.G. van den Oord
• HELP-based DNA methylation assays / John M. Greally
• Comprehensive whole DNA methylome analysis by integrating MeDIP-seq and MRE-seq / Xiaoyun Xing, Bo Zhang, Daofeng Li, and Ting Wang
• Digital restriction enzyme analysis of methylation (DREAM) / Jaroslav Jelinek, Justin T. Lee, Matteo Cesaroni, Jozef Madzo, Shoudan Liang, Yue Lu, and Jean-Pierre J. Issa
• Nucleosome occupancy and methylome sequencing (NOMe-seq) / Fides D. Lay, Theresa K. Kelly, and Peter A. Jones
• Bisulphite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) / Clare Stirzaker, Jenny Z. Song, Aaron L. Statham, and Susan J. Clark
• Guide to illumina beadChip data analysis / Michael C. Wu and Pei-Fen Kuan
• Microdroplet PCR for highly multiplexed targeted bisulfite sequencing / H. Kiyomi Komori, Sarah A. LaMere, Traver Hart, Steven R. Head, Ali Torkamani, and Daniel R. Salomon
• Multiplexed DNA methylation analysis of target regions using microfluidics (fluidigm) / Martyna Adamowicz, Klio Maratou, and Timothy J. Aitman
• Large-scale targeted DNA methylation analysis using bisulfite padlock probes / Dinh Diep, Nongluk Plongthongkum, and Kun Zhang
• Targeted bisulfite sequencing using the seqCap epi enrichment system / Jennifer Wendt, Heidi Rosenbaum, Todd A. Richmond, Jeffrey A. Jeddeloh, and Daniel L. Burgess
• Multiplexed and sensitive DNA methylation testing using methylation-sensitive restriction enzymes "MSRE-qPCR" / Gabriel Beikircher, Walter Pulverer, Manuela Hofner, Christa Noehammer, and Andreas Weinhaeusel
• Quantitative DNA methylation analysis at single-nucleotide resolution by pyrosequencing / Florence Busato, Emelyne Dejeux, Hafida El abdalaoui, Ivo Glynne Gut, and Jorg Tost
• Methylation-specific PCR / Joao Ramalho-Carvalho, Rui Henrique, and Carmen Jeronimo
• Quantitation of DNA methylation by quantitative multiplex methylation-specific PCR (QM-MSP) assay / Mary Jo Fackler and Saraswati Sukumar
• Methylight and digital methyLight / Mihaela Campan, Daniel J. Weisenberger, Binh Trinh, and Peter W. Laird
• Quantitative region-specific DNA methylation analysis by the EpiTYPER technology / Sonja Kunze
• Methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) / Cathy B. Moelans, Lilit Atanesyan, Suvi P. Savola, and Paul J. van Diest
• Methylation-sensitive high resolution melting (MS-HRM) / Dianna Hussmann and Lise Lotte Hansen
• Hairpin bisulfite sequencing : synchronous methylation analysis on complementary DNA strands of individual chromosomes / Pascal Giehr and Jorn Walter
• Helper-dependent chain reaction (HDCR) for selective amplification of methylated DNA sequences / Susan M. Mitchell, Keith N. Rand, Zheng-Zhou Xu, Thu Ho, Glenn S. Brown, Jason P. Ross, and Peter L. Molloy
• DNA methylation analysis from blood spots : increasing yield and quality for genome-wide and locus-specific methylation analysis / Akram Ghantous, Hector Hernandez-Vargas, and Zdenko Herceg
• DNA methylation analysis of free-circulating DNA in body fluids / Maria Jung, Glen Kristiansen, and Dimo Dietrich
• Tet-assisted bisulfite sequencing (TAB-seq) / Miao Yu, Dali Han, Gary C. Hon, and Chuan He
• Multiplexing for oxidative bisulfite sequencing (oxBS-seq) / Kristina Kirschner, Felix Krueger, Anthony R. Green, and Tamir Chandra
• Affinity-based enrichment techniques for the genome-wide analysis of 5-hydroxymethylcytosine / John P. Thomson and Richard R. Meehan.

This third edition volume expands on the previous editions by providing a comprehensive update on the available technologies required to successfully perform DNA methylation analysis. The different technologies discussed in this book analyze the global DNA methylation contents, comprehensive analyses using various NGS based methods for genome-wide DNA methylation analysis, along with precise quantification of DNA methylation levels on single CpG positions. The chapters in this book are divided into 7 parts: an introduction to the field along with tips on study design and data analysis; global DNA methylation levels; genome-wide DNA methylation analysis; highly multiplexed target regions; locus-specific DNA methylation analysis; DNA methylation analysis of specific biological samples; and hydroxymethylation. 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, DNA Methylation Protocols, Third Edition is a valuable resource for postdoctoral investigators and research scientists who work with different aspects of genetics, and cellular and molecular biology, as well as clinicians who are involved in diagnostics or treatment of diseases with epigenetic components.
(source: Nielsen Book Data)

• Preface... Table of Contents... Contributing Authors...
• 1- Type IA DNA Topoisomerases: A Universal Core and Multiple Activities Florence Garnier, Helene Debat, and Marc Nadal
• 2- Topoisomerase I and Genome Stability: The Good and The Bad Jang-Eun Cho and Sue Jinks-Robertson
• 3- DNA Topoisomerases as Targets for Antibacterial Agents Hiroshi Hiasa
• 4- DNA Supercoiling Measurement in Bacteria Yingting Liu, Zhi-Chun Hua, and Fenfei Leng
• 5- DNA Catenation Reveals the Dynamics of DNA Topology during Replication Alicia Castan, Pablo Hernandez, Dora B. Krimer, and Jorge B. Schvartzman
• 6- Mapping E. coli Topoisomerase IV Binding and Activity Sites Hafez El Sayyed and Olivier Espeli
• 7- The Use of Psoralen Photobinding to Study Transcription-Induced Supercoiling Fedor Kouzine, Laura Baranello, and David Levens
• 8- Immunoprecipitation of RNA:DNA Hybrids from Budding Yeast Aziz El Hage and David Tollervey
• 9- Detect
• ion of oriC-Independent Replication in Escherichia coli Cells Makisha Martel, Aurelien Balleydier, Julien Brochu, and Marc Drolet
• 10- Single-Molecule Magnetic Tweezer Analysis of Topoisomerases Kathryn H. Gunn, John F. Marko, and Alfonso Mondragon
• 11- Synthesis of Hemicatenanes for the Study of Type IA Topoisomerases Shun-Hsiao Lee, Tao-shih Hsieh, and Grace Ee-Lu Siaw
• 12- An Assay for Detecting RNA Topoisomerase Activity Muzammil Ahmad, Dongyi Xu, and Weidong Wang
• 13- Studying TDP1 Function in DNA Repair Shih-Chieh Chiang, Kirsty Liversidge, and Sherif F. El-Khamisy
• 14- Topoisomerase II Chromatin Immunoprecipitation Kayleigh A. Smith, Ian G. Cowell, and Caroline A. Austin
• 15- Analyzing Mitotic Chromosome Structural Defects after Topoisomerase II Inhibition or Mutation Juan F. Gimenez-Abian, Andrew B. Lane, and Duncan J. Clarke
• 16- Monitoring the DNA Topoisomerase II Checkpoint in Saccharomyces cerevisiae Katherine Furniss, Amit C. J. Vas, Andrew Lane, and Duncan J. Clarke
• 17- Studying Topoisomerase 1-Mediated Damage at Genomic Ribonucleotides Jessica S. Williams and Thomas A. Kunkel
• 18- A Fluorescence-Based Assay for Identification of Bacterial Topoisomerase I Poisons Thirunavukkarasu Annamalai, Bokun Cheng, and Yuk-Ching Tse-Dinh
• 19- Fluoroquinolone-Gyrase-DNA Cleaved Complexes Gan Luan and Karl Drlica
• 20- Detection of Topoisomerase Covalent Complexes in Eukaryotic Cells Jay Anand, Yilun Sun, Yang Zhao, Karin C. Nitiss, and John L. Nitiss
• 21- Visualization and Quantification of Topoisomerase-DNA Covalent Complexes Using the Trapped in Agarose Immunostaining (TARDIS) Assay Ian G. Cowell and Caroline A. Austin
• 22- Study of Plasmid-Mediated Quinolone Resistance in Bacteria George A. Jacoby.
• (source: Nielsen Book Data)

This volume looks at the evolution of the topo field over the last year and discusses how DNA topoisomerases are directly and indirectly involved in numerous cellular processes. The chapters in this book cover various topics, such as type 1 topos with an evolutionary perspective; antimicrobial agents targeting topos; experimental protocols related to DNA topology, including a basic technique to measure DNA supercoiling in bacteria; protocols for in vitro studies, including assays to detect RNA topo activity; topo inhibitors; and a study of plasmid-mediated quinolone resistance in bacteria. 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, DNA Topoisomerases: Methods and Protoc ols is intended for specialists and non-specialists with an overview of selected hot topics in the field, and the latest protocols to study DNA topology, topoisomerases functions and inhibition by various compounds.
(source: Nielsen Book Data)