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• 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)

• 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.
(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)

• Overview of recent therapeutics advances for duchenne muscular dystrophy / Jean K. Mah
• Clinical manifestations and overall management strategies for duchenne muscular dystrophy / Takeshi Tsuda
• Cardiac involvement in duchenne muscular dystrophy and related dystrophinopathies / Sophie I. Mavrogeni, George Markousis-Mavrogenis, Antigoni Papavasiliou, George Papadopoulos, and Genovefa Kolovou
• Characterization of the inflammatory response in dystrophic muscle using flow cytometry / Jenna M. Kastenschmidt, Ileen Avetyan, and S. Armando Villalta
• Imaging analysis of the neuromuscular junction in dystrophic muscle / Stephen J.P. Pratt, Shama R. Iyer, Sameer B. Shah, and Richard M. Lovering
• System biology approach : gene network analysis for muscular dystrophy / Federica Censi, Giovanni Calcagnini, Eugenio Mattei, and Alessandro Giuliani
• Proteomic profiling of the dystrophin-deficient brain / Sandra Murphy and Kay Ohlendieck
• Probing the pathogenesis of duchenne muscular dystrophy using mouse models / Alexander Morrison-Nozik and Saptarsi M. Haldar
• Exon skipping therapy using phosphorodiamidate morpholino oligomers in the mdx52 mouse model of duchenne muscular dystrophy / Shouta Miyatake, Yoshitaka Mizobe, Hotake Takizawa, Yuko Hara, Toshifumi Yokota, Shinichi Takeda, and Yoshitsugu Aoki
• Designing effective antisense oligonucleotides for exon skipping / Takenori Shimo, Rika Maruyama, and Toshifumi Yokota
• Identification of splicing factors involved in DMD exon skipping events using an in vitro RNA binding assay / Julie Miro, Cyril F. Bourgeois, Mireille Claustres, Michel Koenig, and Sylvie Tuffery-Giraud
• Use of antisense oligonucleotides for the treatment of duchenne muscular dystrophy / Karima Relizani and Aurelie Goyenvalle
• PMO delivery system using bubble liposomes and ultrasound exposure for duchenne muscular dystrophy treatment / Yoichi Negishi, Yuko Ishii, Kei Nirasawa, Eri Sasaki, Yoko Endo-Takahashi, Ryo Suzuki, and Kazuo Maruyama
• Proton nuclear magnetic resonance (1H NMR) spectroscopy-based analysis of lipid components in serum/plasma of patients with duchenne muscular dystrophy (DMD) / Niraj Kumar Srivastava
• Test of antifibrotic drugs in a cellular model of fibrosis based on muscle-derived fibroblasts from duchenne muscular dystrophy patients / Simona Zanotti and Marina Mora
• Flow cytometry-defined CD49d expression in circulating T-lymphocytes is a biomarker for disease progression in duchenne muscular dystrophy / Wilson Savino, Fernanda Pinto-Mariz, and Vincent Mouly
• Advanced methods to study the cross talk between fibro-adipogenic progenitors and muscle stem cells / Luca Tucciarone, Usue Etxaniz, Martina Sandona , Silvia Consalvi, Pier Lorenzo Puri, and Valentina Saccone
• AAV6 vector production and purification for muscle gene therapy / Christine L. Halbert, James M. Allen, and Jeffrey S. Chamberlain
• From gRNA identification to the restoration of dystrophin expression : a dystrophin gene correction strategy for duchenne muscular dystrophy mutations using the CRISPR-induced deletion method / Benjamin Duchene, Jean-Paul Iyombe-Engembe, Joel Rousseau, Jacques P. Tremblay, and Dominique L. Ouellet.

This volume explores experimental approaches used to study Duchenne muscular dystrophy (DMD), an X-linked degenerative skeletal muscle disease caused by mutations in the dystrophin gene. Including the latest progress and scientific achievements, the book covers recent discoveries achieved through in vivo gene editing which have proven to be promising in restoring dystrophin expression, at least in ameliorating skeletal muscle symptoms, and the contents focus on "Omics" techniques in gene expression, protein expression, miRNAs, and long non-coding RNA analysis, as well as experimental studies of the structural/functional changes affecting the skeletal and cardiac muscles and ongoing preclinical studies and clinical trials. 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, Duchenne Muscular Dystrophy: Methods and Protocols serves as a guide for researchers exploring the complicated nature of dystrophin in the hope of helping the victims of this disorder.
(source: Nielsen Book Data)

• Use of animal models and techniques in glaucoma research : introduction / Harry A. Quigley - - Hypertonic saline injection model of experimental glaucoma in rats / John C. Morrison, Elaine C. Johnson, and William O. Cepurna
• Microbead occlusion model of ocular hypertension in mice / David J. Calkins, Wendi S. Lambert, Cathryn R. Formichella, William M. McLaughlin, and Rebecca M. Sappington-- Ocular hypertension/glaucoma in minipigs : episcleral veins cauterization and microbead occlusion methods / Elena Vecino, Haritz Urcola, Alejando Bayon, and Sansar C. Sharma
• Noninvasive intraocular pressure measurement in animals models of glaucoma / Yan Hu and John Danias
• High-throughput binocular pattern electroretinograms in the mouse / Tsung-Han Chou, Jonathon Toft-Nielsen, and Vittorio Porciatti
• Visual evoked potentials in glaucoma and alzheimer's disease / Elisa Cerri, Carlotta Fabiani, Chiara Criscuolo, and Luciano Domenici
• Investigation of the functional retinal output using microelectrode arrays / G€unther Zeck
• Quantitative proteomic analysis of human aqueous humor using iTRAQ 4plex labeling / Anna Trzeciecka, Padmanabhan Pattabiraman, Maria Carmen Piqueras, Carol Toris, and Sanjoy K. Bhattacharya
• Shotgun Sshingolipid analysis of human aqueous humor / Anna Trzeciecka, Ulises Arbelo, Arturo Barron, Genea Edwards, Sruthi Sampathkumar, Carol Toris, and Sanjoy K. Bhattacharya
• Assessment of aqueous humor dynamics in the rodent by constant flow infusion / J. Cameron Millar, Tien N. Phan, and Iok-Hou Pang
• Methods for analyzing endoplasmic reticulum stress in the trabecular meshwork of glaucoma models / Prabhavathi Maddineni, Ramesh B. Kasetti, and Gulab S. Zode
• Quantification of scleral biomechanics and collagen fiber alignment / Ian C. Campbell, Joseph M. Sherwood, Darryl R. Overby, Bailey G. Hannon, A. Thomas Read, Julia Raykin, and C. Ross Ethier
• Biolistic labeling of retinal ganglion cells / Luca Della Santina and Yvonne Ou
• Anterograde tract tracing for assaying axonopathy and transport deficits in glaucoma / Samuel D. Crish and Brett R. Schofield
• In vitro and in vivo methods for studying retinal ganglion cell survival and optic nerve regeneration / Yuqin Yin and Larry I. Benowitz
• 3D histomorphometric reconstruction and quantification of the optic nerve head connective tissues / Hongli Yang, Juan Reynaud, Howard Lockwood, Galen Williams, Christy Hardin, Luke Reyes, Stuart K. Gardiner, and Claude F. Burgoyne
• Visualizing astrocytes of the optic nerve / Daniel Sun
• Investigation of microRNA expression in experimental glaucoma / Hari Jayaram, Diana C. Lozano, Elaine C. Johnson, and John C. Morrison
• Utilizing RNA-seq to identify differentially expressed genes in glaucoma model tissues, such as the rodent optic nerve head / Diana C. Lozano, Dongseok Choi, Hari Jayaram, John C. Morrison, and Elaine C. Johnson
• Single-cell dissociation and characterization in the murine retina and optic nerve / Hee Joo Choi, Rui Wang, and Tatjana C. Jakobs.

This detailed volume introduces the reader to current methods in glaucoma research, in particular those that make use of animal disease models. Given that the retinal ganglion cells damaged and destroyed by glaucoma do not regenerate after lowering the intraocular pressure, new therapeutic approaches that protect ganglion cells directly is a vital research goal that this volume's contents aim to aid scientists in developing. 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, Glaucoma: Methods and Protocols serves as a useful guide for both ophthalmologists in clinical practice and researchers in the field.
(source: Nielsen Book Data)

• Preface Table of Contents Contributing Authors Part I Surveillance, Diagnosis and Classification of hemorrhagic fever viruses
• 1. Global Spread of Hemorrhagic Fever Viruses: Predicting PandemicsJean Paul Gonzalez, Marc Souris, and Willy Valdivia-Granda
• 2. An Approach to the Identification and Phylogenetic Analysis of Emerging and Hemorrhagic Fever Viruses Francisco J. Diaz, Luis Paternina, and Juan D. Rodas
• 3. Preliminary Classification of Novel Hemorrhagic Fever-Causing Viruses Using Sequence-Based Pairwise Sequence Comparison (PASC) Analysis Yiming Bao and Jens H. Kuhn
• 4. Epidemiological Surveillance of Viral Hemorrhagic Fevers with Emphasis on Clinical Virology Carolina Montoya-Ruiz and Juan D. Rodas
• 5. Diagnostics for Lassa Fever: Detecting Host Antibody Responses Maria S. Salvato, Igor S. Lukashevich, Sandra Medina-Moreno, and Juan Carlos Zapata
• 6. Sampling Design and Mosquito Trapping for Surveillance of Arboviral Activity Luis E. Paternina and Juan D. Rodas
• 7. Epidemiological Surveillance of Rodent-Borne Viruses (Roboviruses) Juan D. Rodas, Andres Londono, and Sergio Solari Part II Structural Studies and Reverse Genetics of Hemorrhagic Fever Viruses
• 8. Entry Studies of New World Arenaviruses Maria Guadalupe Martinez, Maria Belen Forlenza, Nelida A. Candurra, and Sandra M. Cordo
• 9. Studies of Lassa Virus Cell Entry Antonella Pasquato, Antonio Herrador Fernandez, and Stefan Kunz
• 10. A Cell-Cell Fusion Assay to Assess Arenavirus Envelope Glycoprotein Membrane-Fusion Activity Joanne York and Jack H. Nunberg
• 11. Assays to Assess Arenaviral Glycoprotein Function Junjie Shao, Xiaoying Liu, Yuying Liang, and Hinh Ly
• 12. Expression and X-Ray Structural Determination of the Nucleoprotein of Lassa Fever Virus Xiaoxuan Qi, Wenjian Wang, Haohao Dong, Yuying Liang, Changjiang Donga, and Hinh Ly
• 13. Assays to Demonstrate the Roles of Arenaviral Nucleoproteins (NP) in Viral RNA Synthesis and in Suppressing Type I Interferon Qinfeng Huang, Junjie Shao, Yuying Liang, and Hinh Ly
• 14. Intracellular Detection of Viral Transcription and Replication using RNA FISH Michael E. Lindquist and Connie S. Schmlajohn
• 15. Hemorrhagic Fever Virus Budding Studies Ronald N. Harty Part III In Vivo Models of Hemorrhagic Fever Virus Infection
• 16. Murine Models for Viral Hemorrhagic Fever Rosana Gonzalez-Quintial and Roberto Baccala
• 17. Testing Experimental Therapies in a Guinea Pig Model for Hemorrhagic Fever Gary Wong, Yuhai Bi, Gary Kobinger, George F. Gao, and Xiangguo Qiu
• 18. A Primate Model for Viral Hemorrhagic Fever Maria S. Salvato, Igor S. Lukashevich, Yida Yang, Sandra Medina-Moreno, Mahmoud Djavani, Joseph Bryant, and Juan C. Zapata
• 19. A Primary Human Liver Cell Culture Model for Hemorrhagic Fever Viruses Mahmoud Djavani Part IV Immune Assays and Vaccine Production for Hemorrhagic Fever Viruses
• 20. Protocol for the Production of a Vaccine Against Argentine Hemorrhagic Fever Ana Maria Ambrosio, Mauricio Andres Mariani, Andrea Soledad Maiza, Graciela Susana Gamboa, Sebastian Edgardo Fossa, and Alejando Javier Bottale
• 21. Detection of Virus-Antibody Immune Complexes in Secondary Dengue Virus Infection Meng Ling Moi, Tomohiko Takasaki, and Ichiro Kurane
• 22. Future Approaches to DNA Vaccination Against Hemorrhagic Fever VirusesJohn J. Suschak and Connie S. Schmaljohn Part V Host Responses to Viral Hemorrhagic Fever
• 23. Identifying Restriction Factors for Hemorrhagic Fever Viruses: Dengue and Junin Federico Giovannoni, Jose Rafael Pena Carcamo, Maria Laura Morell, Sandra Myriam Cordo, and Cybele Carina Garcia
• 24. Determining the Virus Life-Cycle Stage Blocked by an Antiviral Claudia S. Sepulveda, Cybele C. Garcia, and Elsa B. Damonte
• 25. Retrovirus-Based Surrogate Systems for BSL-2 High-Throughput Screening of Antivirals Targeting BSL-3/4 Hemorrhagic Fever-Causing Viruses Sheli R. Radoshitzky, Veronica Soloveva, Dima Gharaibeh, Jens H. Kuhn, and Sina Bavari
• 26. Protocols to Assess Coagulation following In Vitro Infection with Hemorrhagic Fever Viruses Melissa L. Tursiella, Shannon L. Taylor, and Connie S. Schmaljohn.
• (source: Nielsen Book Data)

This volume presents protocols that analyze and explore hemorrhagic fever viruses (HFV). This book is divided into 5 parts: Part I begins with an overview on predicting viral pandemics and then covers methods for surveillance, diagnosis, and classification of HFV. This includes an antibody capture method using Lassa virus antigens. Part II discusses structural studies and reverse genetics of HFV. The chapters in this part describe envelope glycoprotein membrane fusion studies, arenavirus nucleocapsid protein, and the use of virus-like-particles to study viral egress. Part III explores in vivo models of HFV infections, and contains chapters on murine, guinea pig, and primate models for HFV, and methods to obtain a subset of primary human liver cells that can be cultured long-term. Part IV looks into immune assays and vaccine production for HFV. The chapters in this section cover the attenuated vaccine for Argentine HFV, detecting virus-antibody immune complexes in secondary dengue infections, and DNA vaccination. Part V discusses host responses to viral hemorrhagic fever, and contains chapters on identifying host restrictions to Junin or Dengue infection, and a cell-culture method to assess coagulation after HFV 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. Thorough and cutting-edge, Hemorrhagic Fever Viruses: Methods and Protocols is a valuable resource for scientists and researchers who want to bridge the gap between virus recognition in surveillance and understanding host responses to infection.
(source: Nielsen Book Data)

• Noncoding RNAs in DNA damage response : opportunities for cancer therapeutics / Wani Arjumand, Asia Asiaf, and Shiekh Tanveer Ahmad
• MicroRNAs in breast cancer : diagnostic and therapeutic potential / Asia Asiaf, Shiekh Tanveer Ahmad, Wani Arjumand, and Mohammad Afzal Zargar
• Involvement of miRNAs and pseudogenes in cancer / Lutfi Tutar, Aykut Ozgur, and Yusuf Tutar
• MicroRNAs reprogram tumor immune response / Wei Cao, Wenfang Cheng, and Wei Wu
• Apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like gene expression, RNA editing, and MicroRNAs regulation / Wei Cao and Wei Wu
• MicroRNAs change the landscape of cancer resistance / Jun Zhu, Wei Zhu, and Wei Wu
• MicroRNA, noise, and gene expression regulation / Wei Wu
• Deep sequencing reveals a microRNA expression signature in triple-negative breast cancer / Yao-Yin Chang, Liang-Chuan Lai, Mong-Hsun Tsai, and Eric Y. Chuang
• Detection of plasma microRNA signature in osteosarcoma patients / Wendy Allen-Rhoades and Jason T. Yustein
• Identification of E6/E7-dependent microRNAs in HPV-positive cancer cells / Anja Honegger, Daniela Schilling, Holger Sultmann, Karin Hoppe-Seyler, and Felix Hoppe-Seyler
• Combination of anti-miRNAs oligonucleotides with low amounts of chemotherapeutic agents for pancreatic cancer therapy / Marta Passadouro and Henrique Faneca
• Evaluation of microRNA delivery in vivo / Rikki A.M. Brown, Kirsty L. Richardson, Felicity C. Kalinowski, Michael R. Epis, Jessica L. Horsham, Tasnuva D. Kabir, Marisa H. De Pinho, Dianne J. Beveridge, Lisa M. Stuart, Larissa C. Wintle, and Peter J. Leedman
• Angiogenesis analysis by in vitro coculture assays in transwell chambers in ovarian cancer / Ali Flores-Perez, Dolores Gallardo Rinc on, Erika Ruiz-Garcıa, Raquel Echavarria, Laurence A. Marchat, Elizbeth Alvarez-Sanchez, and Cesar Lopez-Camarillo
• Application of individual qPCR performance parameters for quality control of circulating microRNA data / Anna Brunet-Vega, Marıa Elisa Quılez, Marıa Jose Ramırez-Lazaro, and Sergio Lario
• Construction of multi-potent microRNA sponge and its functional evaluation / Suhwan Chang
• MicroRNA sequencing data analysis toolkits / Wei Wu.

This volume details basic principles of experimental and computational methods for the study of microRNAs in cancer research and, therefore, provides a firm grounding for those who wish to develop further applications. 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, MicroRNA and Cancer: Methods and Protocols, Second Edition aims to ensure successful results in the further study of this vital field.
(source: Nielsen Book Data)

• Free flow zonal electrophoresis for fractionation of plant membrane compartments prior to proteomic analysis / Bronwyn J. Barkla
• Isolation and purity assessment of membranes from Norway spruce / Enni Vaisanen, Junko Takahashi, Luis A. Jimenez Barboza, Xianbao Deng, Teemu H. Teeri, Kurt V. Fagerstedt, Sabine Luthje, and Anna K€arkonen
• Nuclear proteome : isolation of intact nuclei, extraction of nuclear proteins, and 2-DE analysis / Aarti Pandey, Subhra Chakraborty, and Niranjan Chakraborty
• Identification of plant nuclear proteins based on a combination of flow sorting, SDS-PAGE, and LC-MS/MS analysis / Ivo Chamrad, Jana Urinovska, Beata Petrovska, Hana Jerabkova, Rene Lenobel, Jan Vrana, Jaroslav Dolezel, and Marek Sebela
• Isolation, purity assessment, and proteomic analysis of nuclei / Setsuko Komatsu
• Proteomic analysis of rice golgi membranes isolated by floating through discontinuous sucrose density gradient / Kazusato Oikawa, Takuya Inomata, Yoshitoshi Hirao, Tadashi Yamamoto, Marouane Baslam, Kentaro Kaneko, and Toshiaki Mitsui
• Analyzing the vacuolar membrane (tonoplast) proteome / Miwa Ohnishi, Katsuhisa Yoshida, and Tetsuro Mimura
• Preparation of membrane fractions (envelope, thylakoids, grana, and stroma lamellae) from arabidopsis chloroplasts for quantitative proteomic investigations and other studies / Lucas Moyet, Daniel Salvi, Martino Tomizioli, Daphne Seigneurin-Berny, and Norbert Rolland
• Isolation of intact thylakoid membranes from heterocysts of filamentous, nitrogen-fixing cyanobacteria / Ann Magnuson and Tanai Cardona
• Targeted quantification of isoforms of a thylakoid-bound protein : MRM method development / Roque Bru-Martınez, Ascensi on Martınez-Marquez, Jaime Morante-Carriel, Susana Selles-Marchart, Marıa Jose Martınez-Esteso, Jose Luis Pineda-Lucas, and Ignacio Luque
• Sample preparation for analysis of the plant mitochondrial membrane proteome / Christine Schikowsky, Beate Thal, Hans-Peter Braun, and Holger Eubel
• Plasma membrane proteomics of Arabidopsis suspension-cultured cells associated with growth phase using Nano-LC-MS/MS / Bin Li, Daisuke Takahashi, Yukio Kawamura, and Matsuo Uemura
• Mini-scale isolation and preparation of plasma membrane proteins from potato roots for LC/MS analysis / Anna M. Jozefowicz, Andrea Matros, Katja Witzel, and Hans-Peter Mock
• Assay of plasma membrane H+-ATPase in plant tissues under abiotic stresses / Małgorzata Janicka, Anna Wdowikowska, and Grazyna Kłobus
• Absolute quantitation of in vitro expressed plant membrane proteins by targeted proteomics (MRM) for the determination of kinetic parameters / Carsten Rautengarten, Berit Ebert, and Joshua L. Heazlewood
• MSE for label-free absolute protein quantification in complex proteomes / Stefan Helm and Sacha Baginsky
• Identification and characterization of plant membrane proteins using ARAMEMNON / Rainer Schwacke and Ulf-Ingo Flugge
• VANTED : a tool for integrative visualization and analysis of -omics data / Anja Hartmann and Anna Maria Jozefowicz.

This volume provides comprehensive and detailed protocols that discuss proteomic techniques, plant endosomes, and isolation of organelles and subcellular fractions. The chapters in this book explore numerous plant species and cover topics, such as isolation and purity assessment of membranes from Norway spruce; proteomic analysis of nuclei; analyzing the vacuolar membrane (tonoplast) proteome; isoforms of a thylakoid-bound protein; assay of plasma membrane H+-ATPase in plant tissue under abiotic stresses; and identification and characterization of plant membrane proteins using ARAMEMNON. 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. Practical and thorough, Plant Membrane Proteomics: Methods and Protocols is a valuable resource that promotes the use of plant membrane proteomics to develop the future of the field.
(source: Nielsen Book Data)

• Part I: Detection and Quantification of Quorum Sensing Signal Molecules
• 1. Use of Whole Cell Bioassays for Screening Quorum Signaling, Quorum-Interference, and Biofilm Dispersion
• Starla G. Thornhill and Robert J.C. McLean
• 2. Detection of 2-Alkyl-4-Quinolones Using Biosensors
• Matthew P. Fletcher, Stephen P. Diggle, Miguel Camara, and Paul Williams
• 3. "Hot Stuff": The Many Uses of a Radiolabel Assay in Detecting Acyl-Homoserine Lactone Quorum Sensing Signals
• Amy L. Schaefer, Caroline S. Harwood, and E. Peter Greenberg
• 4. Liquid Chromatography/Mass Spectrometry (LC/MS) for the Detection and Quantification of -Acyl-L-Homoserine Lactones (AHLs) and 4-Hydroxy-2-Alkylquinolines (HAQs)
• Francois Lepine, Sylvain Milot, Marie-Christine Groleau, and Eric Deziel
• 5. Detection of the Bacterial Quorum Sensing Signaling Molecules N-Acyl Homoserine Lactones (HSL) and N-Acyl-Homoserine (HS) with an Enzyme-Linked Immunosorbent Assay (ELISA) and via Ultrahigh Performance Liquid Chromatography Coupled to Mass Spectrometry (UHPLC-MS)
• Michael Rothballer, Jenny Uhl, Josie Kunze, Philippe Schmitt-Kopplin, and Anton Hartmann
• 6. Biosensors for the Detection and Quantification of AI-2 Class Quorum Sensing Compounds
• Sathish Rajamani and Richard Sayre
• 7. Detection of Agr-Type Autoinducing Peptides Produced by Staphylococcus aureus
• Ewan J. Murray and Paul Williams
• 8. Ultra Performance Liquid Chromatography/Mass Spectrometry for the Detection and Quantification of Diffusible Signal Factor (DSF)-Family Quorum Sensing Signals
• Lian Zhou, Shuang Sun, Wei Zhang, and Ya-Wen He
• 9. Rapid Electrochemical Detection of Pseudomonas aeruginosa Signaling Molecules by Boron-Doped Diamond Electrode
• Alyah Buzid, John H.T. Luong, F. Jerry Reen, Fergal O'Gara, Jeremy D. Glennon, and Gerard P. McGlacken
• 10. Detection and Quantification of Butyrolactones from Streptomyces
• Marc Biarnes-Carrera, Rainer Breitling, and Eriko Takano
• Part II: Methods for the Studying of Quorum Sensing at the Molecular, Physiological, and Population Level
• 11. Fluorescence Quenching Studies of γ-Butyrolactone Binding Protein (CprB) from Streptomyces coelicolor A3(2)
• Jessy Mariam and Ruchi Anand
• 12. Methods to Study Solo/Orphan Quorum Sensing Receptors
• Vittorio Venturi, Sujatha Subramoni, Anice Sabag-Daigle, and Brian M.M. Ahmer
• 13. Enzymatic Assays to Investigate Acyl-Homoserine Lactone Autoinducer Synthases
• Daniel Shin and Rajesh Nagarajan
• 14. Global Expression Analysis of Quorum Sensing-Controlled Genes by RNAseq
• Charlotte D. Majerczyk
• 15. Identification of AHL- and BDSF-Controlled Proteins in Burkholderia cenocepacia by Proteomics
• Yilei Liu, Gabriella Pessi, Katharina Riedel, and Leo Eberl
• 16. Imaging N-Acyl Homoserine Lactone Quorum Sensing In Vivo
• Louise Dahl Hultqvist, Maria Alhede, Tim Holm Jakobsen, Michael Givskov, and Thomas Bjarnsholt
• 17. Assessing Pseudomonas aeruginosa Autoinducer Effects on Mammalian Epithelial Cells
• Jake Everett, Rebecca Gabrilska, Kendra Rumbaugh, and Elena Vikstroem
• 18. Animal Models for Pseudomonas aeruginosa Quorum Sensing Studies
• Damien Maura, Arunava Bandyopadhaya, and Laurence G. Rahme
• 19. Methods to Study Quorum Sensing-Dependent Virulence and Movement of Phytopathogens In Planta
• Shulamit Manulis-Sasson and Laura Chalupowicz
• 20. Differential Equations Models to Study Quorum Sensing
• Judith Perez-Velazquez and Burkhard A. Hense
• Part III: Identification and Characterization of Anti-Quorum Sensing Agents
• 21. Qualitative and Quantitative Determination of Quorum Sensing Inhibition In Vitro
• Tim Holm Jakobsen, Maria Alhede, Louise Dahl Hultqvist, Thomas Bjarnsholt, and Michael Givskov
• 22. A Co-Culture-Based Approach for Screening Campaigns Aimed at Identifying Novel Pseudomonas aeruginosa Quorum Sensing Inhibitors
• Giordano Rampioni, Giulia Giallonardi, Francesca D'Angelo, and Livia Leoni
• 23. A Culture-Dependent Method for the Identification of Quorum Quenching Enzymes of Microbial Origin
• Kaihao Tang and Xiao-Hua Zhang
• 24. Directed Evolution of Quorum Quenching Enzymes: A Method for the Construction of a Directed Evolution Platform and Characterization of a Quorum-Quenching Lactonase from Geobacillus kaustophilus
• Maybelle Kho Go, Jeng Yeong Chow, and Wen Shan Yew
• 25. Generation of High-Sensitivity Monoclonal Antibodies Specific for Homoserine Lactones
• Soumya Palliyil
• 26. Identification of AI-2 Quorum Sensing Inhibitors in Vibrio harveyi through Structure-Based Virtual Screening
• Tianyu Jiang, Peng Zhu, Lupei Du, and Minyong Li
• 27. Identification of Staphylococcal Quorum Sensing Inhibitors by Quantification of o-Hemolysin with High Performance Liquid Chromatography
• Cassandra L. Quave and Alexander R. Horswill.
• (source: Nielsen Book Data)

This detailed volume provides scientists interested in quorum sensing with a broad spectrum of methods and protocols useful for studying bacterial communication processes at the chemico-physical, molecular, and physiological level. Divided into three sections, the content covers detection and quantification of quorum sensing signal molecules, methods for the studying of quorum sensing at the molecular, physiological, and population level, as well as identification and characterization of anti-quorum sensing agents. 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 cutting-edge, Quorum Sensing: Methods and Protocols serves as a comprehensive guide to the most important methodology currently available in the field.
(source: Nielsen Book Data)

• Preface... Table of Contents... Contributing Authors...
• 1. The Secret Life of RNA: Lessons from Emerging Methodologies Caroline Medioni and Florence Besse
• 2. Quantification of 2'-O-Me Residues in RNA using Next-Generation Sequencing (Illumina RiboMethSeq Protocol) Lilia Ayadi, Yuri Motorin, and Virginie Marchand
• 3. Identifying the m6A Methylome by Affinity Purification and Sequencing Phillip J. Hsu and Chuan He
• 4. PARIS: Psoralen Analysis of RNA Interactions and Structures with High Throughput and Resolution Zhipeng Lu, Jing Gong, and Qiangfeng Cliff Zhang
• 5. Axon-TRAP-RiboTag: Affinity-Purification of Translated mRNAs from Neuronal Axons in Mouse In Vivo Toshiaki Shigeoka, Jane Jung, Christine E. Holt, and Hosung Jung
• 6. LCM-Seq: A Method for Spatial Transcriptomic Profiling using Laser Capture Microdissection Coupled with PolyA-Based RNA Sequencing Susanne Nichterwitz, Julio Aguila Benitez, Rein Hoogstraaten, Qiaolin Deng, and Eva Hedlund
• 7. Spatial Transcriptomics: Constructing a Single-Cell Resolution Transcriptome-Wide Expression Atlas Kaia Achim, Hernando Martinez Vergara, and Jean-Baptiste Pettit
• 8. Single mRNA Molecule Detection in Drosophila Shawn C. Little and Thomas Gregor
• 9. Detection and Automated Analysis of Single Transcripts at Subcellular Resolution in Zebrafish Embryos L. Carine Stapel, Coleman Broaddus, and Nadine L. Vastenhouw
• 10. Super-Resolution Single Molecule FISH at the Drosophila Neuromuscular Junction Joshua S. Titlow, Lu Yang, Richard M. Parton, Ana Palanca, and Ilan Davis
• 11. Detection of mRNA and Associated Molecules by ISH-IEM on Frozen Sections Catherine Rabouille
• 12. Hybridization Chain Reaction for Direct mRNA Detection without Nucleic Acid Purification Yao Xu and Zhi Zheng
• 13. In Situ Detection of MicroRNA Expression with RNAscope Probes Viravuth P. Yin
• 14. Padlock Probes to Detect Single Nucleotide Polymorphisms Tomasz Krzywkowski and Mats Nilsson
• 15. Quantifying Gene Expression in Living Cells with Ratiometric Bimolecular Beacons Yantao Yang, Mingming Chen, Christopher K. Krueger, Andrew Tsourkas, and Antony K. Chen
• 16. Optimizing Molecular Beacons for Intracellular Analysis of RNA Mingming Chen, Yantao Yang, Christopher K. Krueger, and Antony K. Chen
• 17. Live Imaging of Nuclear RNPs in Mammalian Complex Tissue with ECHO-liveFISH Dan Ohtan Wang
• 18. In Vivo Visualization and Function Probing of Transport mRNPs using Injected FIT Probes Jasmine Chamiolo, Imre Gaspar, Anne Ephrussi, and Oliver Seitz
• 19. Visualizing RNA in Live Bacterial Cells using Fluorophore- and Quencher-Binding Aptamers Murat Sunbul, Ankita Arora, and Andres Jaschke
• 20. Method for Imaging Live-Cell RNA using an RNA Aptamer and a Fluorescent Probe Shin-ichi Sato, Kenji Yatsuzuka, Yousuke Katsuda, and Motonari Uesugi
• 21. RNA Live Imaging in the Model Microorganism Ustilago maydis S. Zander, K. Muntjes, and M. Feldbrugge
• 22. Real-Time Fluorescence Imaging of Single-Molecule Endogenous Non-Coding RNA in Living Cells Hideaki Yoshimura and Takeaki Ozawa
• 23. Live Imaging of mRNA Synthesis in Drosophila Hernan G. Garcia and Thomas Gregor
• 24. Imaging Newly Transcribed RNA in Cells by Using a Clickable Azide-Modified UTP Analog Anupam A. Sawant, Sanjeev Galande, and Seergazhi G. Srivatsan
• 25. Detection of the First Round of Translation: The TRICK Assay Franka Voigt, Jan Eglinger, and Jeffrey A. Chao
• 26. Imaging Translation Dynamics of Single mRNA Molecules in Live Cells Suzan Ruijtenberg, Tim A. Hoek, Xiaowei Yan, and Marvin E. Tanenbaum
• 27. Systematic Detection of Poly(A)+ RNA-Interacting Proteins and Their Differential Binding Miha Milek and Markus Landthaler
• 28. Isolation and Characterization of Endogenous RNPs from Brain Tissues Rico Schieweck, Foong yee Ang, Renate Fritzsche, and Michael A. Kiebler
• 29. Individual Nucleotide Resolution UV Cross-Linking and Immunoprecipitation (iCLIP) to Determine Protein-RNA Interactions Christopher R. Sibley
• 30. RNA Tagging: Preparation of High-Throughput Sequencing Libraries Christopher P. Lapointe and Marvin Wickens
• 31. RAP-MS: A Method to Identify Proteins that Interact Directly with a Specific RNA Molecule in Cells Colleen A. McHugh and Mitchell Guttman.
• (source: Nielsen Book Data)

This volume introduces different concepts and methods of detecting RNA in biological material in a variety of model systems. The chapters in this book discuss methods that will answer numerous biological questions that arise in the study of RNAs. Some of the topics covered in this book are single mRNA molecule detection in embryos and neurons; detection of mRNA and associated molecules by ISH-IEM on frozen sections; optimizing molecular beacons for intracellular analysis of RNA; imaging translation dynamics of single mRNA molecules in live cells; preparation of high-throughput sequencing libraries; and capturing RNA binding proteins in embryos and in cell-culture. 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, RNA Detection: Methods and Protocols is a valuable resource for novel and experiences scientist in the expanding field of RNAs.
(source: Nielsen Book Data)

• Simple protocol to isolate, characterize, and expand dental pulp stem cells / Federica Di Scipio, Andrea Elio Sprio, Maria Elisabetta Carere, Zhiqian Yang, and Giovanni Nicolao Berta
• Derivation of mesenchymal stem cells from embryonic stem cells : a non-variable and inexhaustive source of adult stem cells / Glen Lester Sequiera, Niketa Sareen, Ejlal Abu El-Rub, and Sanjiv Dhingra
• Compact bone-derived multipotent mesenchymal stromal cells (MSCs) for the Tteatment of Sjogren's-like disease in NOD mice / Ghada Abu Elghanam, Younan Liu, Saeed Khalili, Dongdong Fang, and Simon D. Tran
• Manipulating the proliferative potential of cardiomyocytes by gene transfer / Giulia Prosdocimo and Mauro Giacca
• Assessment of energy metabolic changes in adipose tissue-derived stem cells / Ghazaleh Hajmousa and Martin C. Harmsen
• Isolation and in vitro characterization of epidermal stem cells / Kasper S. Moestrup, Marianne S. Andersen, and Kim B. Jensen
• Endothelial progenitor cells : procedure for cell isolation and applications / Garikipati V.N. Srikanth and Raj Kishore
• Therapeutic application of placental mesenchymal stem cells reprogrammed neurospheres in spinal cord injury of SCID / Vikram Sabapathy, Franklin Jebaraj Herbert, and Sanjay Kumar
• Therapeutic application of human wharton jelly mesenchymal stem cells in skin injury of SCID / Vikram Sabapathy, Balasubramanian Sundaram, and Sanjay Kumar
• Isolation, characterization, and expansion of cancer stem cells / Luke A. Torre-Healy, Artem Berezovsky, and Justin D. Lathia
• Cardiac progenitor cell extraction from human auricles / Paolo Di Nardo and Francesca Pagliari
• Isolation and culture of satellite cells from mouse skeletal muscle / Antonio Musarò and Silvia Carosio
• Isolation of stromal stem cells from adipose tissue / Maria Prat, Francesca Oltolina, Silvia Antonini, and Andrea Zamperone
• Human-induced pluripotent stem cell-derived mesenchymal stem cells as an individual-specific and renewable source of adult stem cells / Glen Lester Sequiera, Sekaran Saravanan, and Sanjiv Dhingra
• Simplified and systematic method to isolate, culture, and characterize multiple types of human dental stem cells from a single tooth / Mohammed Bakkar, Younan Liu, Dongdong Fang, Camille Stegen, Xinyun Su, Murali Ramamoorthi, Li-Chieh Lin, Takako Kawasaki, Nicholas Makhoul, Huan Pham, Yoshinori Sumita, and Simon D. Tran
• Measurement of autophagy by flow cytometry / Silvia Zappavigna, Angela Lombardi, Gabriella Misso, Anna Grimaldi, and Michele Caraglia
• Echocardiography-guided intramyocardial injection method in a murine model / Kay Maeda, Rick Seymour, Marc Ruel, and Erik J. Suuronen
• Noninvasive assessment of cell fate and biology in transplanted mesenchymal stem cells / Federico Franchi and Martin Rodriguez-Porcel
• Methods for long-term storage of murine bone marrow-derived mesenchymal stem cells / Niketa Sareen, Ejlal Abu-El-Rub, Glen Lester Sequiera, Meenal Moudgil, and Sanjiv Dhingra
• Therapeutic application of adult stem cells in the heart / Taylor A. Johnson and Dinender K. Singla
• Patient-derived and intraoperatively formed biomaterial for tissue engineering / Shalmli U. Joshi, Rares O. Barbu, Melissa Carr-Reynolds, Brian Barnes, and Syam P. Nukavarapu
• Three-dimensional printed scaffolds with multipotent mesenchymal stromal cells for rabbit mandibular reconstruction and engineering / Dongdong Fang, Michael Roskies, Mohamed-Nur Abdallah, Mohammed Bakkar, Jack Jordan, Li-Chieh Lin, Faleh Tamimi, and Simon D. Tran
• Optimal environmental stiffness for stem cell mediated ischemic myocardium repair / Honghai Liu, Christian Paul, and Meifeng Xu
• Assessment of MiRNA regulation of endothelial progenitor cell mediated angiogenesis / Darukeshwara Joladarashi and Prasanna Krishnamurthy
• Stem cell exosomes : cell-freetherapy for organ repair / Mohsin Khan and Raj Kishore.

This volume contains a collection of protocols from some of the major laboratories involved in stem cell research across the world. The research discussed in this book covers topics such as: isolating, characterizing and expanding dental pulp stem cells; manipulating the proliferative potential of cardiomyocytes by gene transfer; isolation of stromal stem cells from adipose tissue; noninvasive assessment of cell fat and biology in transplanted mesenchymal stem cells; and cell-free therapy for organ repair. 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, Adult Stem Cells: Methods and Protocols is a valuable resource for helping researchers transform the study of stem cells into an industrialized process that will supply patients with efficient, safe, and cost-effective cell treatments.
(source: Nielsen Book Data)

• Pathophysiology of alpha-1 antitrypsin deficiency liver disease / Jeffrey H. Teckman and Keith S. Blomenkamp
• Pathophysiology of alpha-1 antitrypsin lung disease / Michael Kalfopoulos, Kaitlyn Wetmore, and Mai K. ElMallah
• Measuring and interpreting serum AAT concentration / Leslie J. Donato, Melissa R. Snyder, and Dina N. Greene
• AAT phenotype identification by isoelectric focusing / Dina N. Greene, M.C. Elliott-Jelf, and David G. Grenache
• Laboratory diagnosis by genotyping / Irene Belmonte, Luciana Montoto, and Francisco Rodrıguez-Frıas
• Genotyping protocol for the alpha-1 antitrypsin (PiZ) mouse model / Alisha M. Gruntman
• Elastase-induced lung emphysema models in mice / Bela Suki, Erzsebet Bartolak-Suki, and Patricia R.M. Rocco
• Assessing structure-function relations in mice using the forced oscillation technique and quantitative histology / Harikrishnan Parameswaran and Bela Suki
• Practical methods for assessing emphysema severity based on estimation of linear mean intercept (Lm) in the context of animal models of alpha-1 antitrypsin deficiency / Airiel M. Davis, Kristen E. Thane, and Andrew M. Hoffman
• Design, cloning, and in vitro screening of artificial miRNAs to silence alpha-1 antitrypsin / Florie Borel and Christian Mueller
• Methods to identify and characterize siRNAs targeting serpin A1 in vitro and in vivo using RNA interference / Stuart Milstein, Kun Qian, Linying Zhang, and Alfica Sehgal
• Knockdown of Z mutant alpha-1 antitrypsin in vivo using modified DNA antisense oligonucleotides / Mariam Aghajan, Shuling Guo, and Brett P. Monia
• Immunohistochemistry staining for human alpha-1 antitrypsin / Dongtao A. Fu and Martha Campbell-Thompson-- Periodic acid-schiff staining with diastase / Dongtao A. Fu and Martha Campbell-Thompson
• Protocol for directed differentiation of human induced pluripotent stem cells (iPSCs) to a hepatic lineage / Joseph E. Kaserman and Andrew A. Wilson
• Isolation of kupffer cells and hepatocytes from a single mouse liver / Marcela Aparicio-Vergara, Michaela Tencerova, Cecilia Morgantini, Emelie Barreby, and Myriam Aouadi
• Alpha-1 antitrypsin transcytosis and secretion / Angelia D. Lockett
• Measuring the effect of histone deacetylase inhibitors (HDACi) on the secretion and activity of alpha-1 antitrypsin / Chao Wang, Marion Bouchecareilh, and William E. Balch
• Expression and purification of active recombinant human Alpha-1 antitrypsin (AAT) from Escherichia coli / Beena Krishnan, Lizbeth Hedstrom, Daniel N. Hebert, Lila M. Gierasch, and Anne Gershenson
• Quantification of total human alpha-1 antitrypsin by sandwich ELISA / Qiushi Tang, Alisha M. Gruntman, and Terence R. Flotte
• Quantification of murine AAT by direct ELISA / Andrew Cox and Christian Mueller
• Quantification of Z-AAT by a Z-specific "sandwich" ELISA / Florie Borel, Qiushi Tang, and Christian Mueller
• Semiquantitation of monomer and polymer alpha-1 antitrypsin by centrifugal separation and assay by western blot of soluble and insoluble components / Keith S. Blomenkamp and Jeffrey H. Teckman
• Electrophoresis- and FRET-based measures of serpin polymerization / Sarah V. Faull, Anwen E. Brown, Imran Haq, and James A. Irving
• Therapeutics : alpha-1 antitrypsin augmentation therapy / Michael Campos and Jorge Lascano
• Therapeutic options in alpha-1 antitrypsin deficiency : liver transplantation / Nedim Hadzic
• Therapeutics : gene therapy for alpha-1 antitrypsin deficiency / Alisha M. Gruntman and Terence R. Flotte.

This volume provides protocols that expand on the latest alpha-1-antitrypsin (AAT) research. The chapters in this book are divided in to three sections: Part I is dedicated to patient-oriented research; part II discusses animal models; and Part III focuses on in vitro studies. 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, Alpha-1 Antitrypsin Deficiency: Methods and Protocols is a valuable resource for researchers, students, and clinican-scientists interested in AAT deficiency, as well as anyone working in the fields of pulmonology and hepatology.
(source: Nielsen Book Data)

• Part I: Properties, Design, Synthesis and Characterization of AMPs
• 1. Antimicrobial Peptides: An Introduction Evan F. Haney, Sarah C. Mansour, and Robert E.W. Hancock
• 2. Tools for Designing Amphipathic Helical Antimicrobial Peptides Davor Juretic, Damir Vukicevic, and Alessandro Tossi
• 3. Chemical Synthesis of Antimicrobial Peptides Lena Munzker, Alberto Oddo and Paul R. Hansen
• 4. Microwave-Assisted Synthesis of Antimicrobial Peptides Suhas Ramesh, Beatriz G. de la Torre, Fernando Albericio, Hendrik G. Kruger, and Thavendran Govender
• 5. High Performance Liquid Chromatography and Mass Spectrometry-Based Design of Protolytically Stable Antimicrobial Peptides Mojtaba Bagheri and Robert E. W. Hancock
• 6. Determination of Structure and Micellar Interactions of Small Antimicrobial Peptides by Solution-State NMR Reinhard Wimmer and Lars Erik Uggerhoj
• 7. Mass Spectrometry Approaches for Determining the Structure of Antimicrobial Peptides Jiongyu Liu and Jianping Jiang Part II: Studying Interactions of AMPs with Model Membranes and Bacteria
• 8. Molecular Dynamics Simulation and Analysis of the Antimicrobial Peptides-Lipid Bilayers Interactions Shima Arasteh and Mojtaba Bagheri
• 9. Calorimetry Methods to Study Membrane Interactions and Perturbations Induced by Antimicrobial Host Defense Peptides Mauricio Arias, Elmar J. Prenner and Hans J. Vogel
• 10. Fluorescence and Absorbance Spectroscopy Methods to Study Membrane Perturbations by Antimicrobial Host Defense Peptides Mauricio Arias and Hans J. Vogel
• 11. Applying Fluorescence Correlation Spectroscopy to Investigate Peptide-Induced Membrane Disruption Kasper Kristensen, Jonas R. Henriksen, and Thomas L. Andresen
• 12. Macromolecule Biosynthesis Assay and Fluorescence Spectroscopy Methods to Explore Antimicrobial Peptide Mode(s) of Action Bimal Jana, Kristin Renee Baker, and Luca Guardabassi
• 13. Using Confocal Microscopy and Computational Modeling to Investigate the Cell Penetrating Properties of Antimicrobial Peptides Gabriel Del Rio, Edda Klipp, and Andreas Herrmann
• 14. Atomic Force Microscopy Study of the Interactions of Indolicidin with Model Membranes and DNA Peter Fojan and Leonid Gurevich
• 15. Protocols for studying the interaction of MSI-78 with the Membranes of Whole Gram-positive and Gram-negative Bacteria by NMR Nury P. Santisteban , M. R. Morrow, and V. Booth
• 16. Preparation of membrane models of Gram-negative bacteria and their interaction with Antimicrobial Peptides studied by CD and NMR Rickey P. Hicks
• 17. Studying the Interaction of Magainin 2 and Cecropin A with E. coli Bacterial Cells using Circular Dichroism Concetta Avitabile, Luca Domenico D'Andrea and Alessandra Romanelli
• 18. Studying the Mechanism of Membrane Permeabilization induced by Antimicrobial Peptides using Patch-clamp Techniques Giorgio Rispoli
• 19. Assays for Identifying Inducers of the Antimicrobial Peptide LL-37 Frank Nylen, Peter Bergman, Gudmundur H. Gudmundsson, and Birgitta Agerberth
• 20. Methods for Elucidating the Mechanism of Action of Proline-rich and other Non-lytic Antimicrobial Peptides Monica Benincasa, Giulia Runti, Mario Mardirossian, Renato Gennaro, and Marco Scocchi
• 21. The Interaction of Antimicrobial Peptides with the Membrane and Intracellular Targets of Staphylococcus Aureus Investigated by ATP-leakage, DNA-binding Analysis and the Expression of a LexA Controlled Gene, recA Sanne Gottschalk and Line Elnif Thomsen Part III: Assaying Selected Biological Activities of AMPs
• 22. Methods for Investigating Biofilm Inhibition and Degradation by Antimicrobial Peptides Li-av Segev-Zarko and Yechiel Shai
• 23. Protocols for Studying Inhibition and Eradication of Bacterial Biofilms by Antimicrobial Peptides Vijayalekshmi Sarojini"p>
• 24. Protocols for Studying Antimicrobial Peptides (AMPs) as Anti-cancer Agents Laurence Madera and David W. Hoskin
• 25. Using Oral and Colon Cancer Cells for studying the Anti-cancer properties of Antimicrobial peptides Teerakul Arpornsuwan, Wimolpak Sriwai, Hathaitip Sritanaudomchai, and Sittiruk Roytrakul
• 26. Using Disease-Associated Enzymes to Activate Antimicrobial Peptide Prodrugs <Eanna B. Forde, Graeme Kelly, Hisham Makki, Zahraa Al-Sharshahi, Deirdre Fitzgerald-Hughes, and Marc Devocelle
• 27. Anti-inflammatory Properties of Antimicrobial Peptides and Peptidomimetics: LPS and LTA Neutralization Sarah Line Skovbakke and Henrik Franzyk
• 28. Protocols for Screening Antimicrobial Peptides That Influence Virulence Gene Expression in Staphylococcus aureus Martin Saxtorph Bojer, Mara Baldry, and Hanne Ingmer
• 29. Methods for in vitro Analysis of Antimicrobial Activity and Toxicity of Anti-keratitis Peptides: Bacterial Viability in tears, MTT and TNF-a release assays Floriana Cappiello, Bruno Casciaro, Satya Sree Kolar, Hasna Baidouri, Alison McDermott, and Maria Luisa Mangoni
• 30. Methods for In Vivo/ex-vivo Analysis of Antimicrobial Peptides in Bacterial Keratitis: siRNA Knockdown, Colony Counts, Myeloperoxidase, Immunostaining, and RT-PCR Assays Satya Sree Kolar, Hasna Baidouri, Maria Lusia Mangoni, and Alison M. McDermott
• 31. Haemolytic Activity of Antimicrobial Peptides Alberto Oddo and Paul R. Hansen.
• (source: Nielsen Book Data)

This volume provides basic and advanced laboratory protocols for the non-specialist and the experienced researcher. Chapters are divided into three parts covering synthesis and characterization of AMPs, studying the interaction of AMPs with model systems or bacteria, and assaying selected biological activities of AMPs. 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, Antimicrobial Peptides: Methods and Protocols aims to ensure successful results in the further study of this vital field.
(source: Nielsen Book Data)

• Assaying radiosensitivity of ataxia-telangiectasia / Hailiang Hu, Shareef Nahas, and Richard A. Gatti
• Assaying for radioresistant DNA synthesis, the hallmark feature of the intra-S-phase checkpoint using a DNA fiber technique / Amanda W. Kijas and Martin F. Lavin
• ATM gene mutation detection techniques and functional analysis / Guillaume Rieunier, Catherine Dubois D'Enghien, Alice Fievet, Dorine Bellanger, Dominique Stoppa-Lyonnet, and Marc-Henri Stern
• HTRF assay for the protein kinase ATM / Phillip Adams, Jonathan Clark, Simon Hawdon, Jennifer Hill, and Andrew Plater
• ATM kinase inhibitors : HTS cellular imaging assay using cellomics ArrayScan VTI platform / Catherine Bardelle and Joanna Boros
• Image-based high content screening : automating the quantification process for DNA damage-induced foci / Yi Chieh Lim
• Analyzing ATM function by electroporation of endonucleases and immunofluorescence microscopy / Keiji Suzuki
• Quantitative and dynamic imaging of ATM kinase activity by bioluminescence imaging / Shyam Nyati, Grant Young, Brian Dale Ross, and Alnawaz Rehemtulla
• Zn(II)-Phos-Tag SDS-PAGE for separation and detection of a DNA damage-related signaling large phosphoprotein / Eiji Kinoshita, Emiko Kinoshita-Kikuta, and Tohru Koike
• Identification of ATM protein kinase phosphorylation sites by mass spectrometry / Mark E. Graham, Martin F. Lavin, and Sergei V. Kozlov
• Studies of ATM kinase activity using engineered ATM sensitive to ATP analogues (ATM-AS) / Masato Enari, Yuko Matsushima-Hibiya, Makoto Miyazaki, and Ryo Otomo
• Functional characterization of ATM kinase using acetylation-specific antibodies / Yingli Sun and Fengxia Du
• Identification of ATM-interacting proteins by co-immunoprecipitation and Glutathione-S-Transferase (GST) pull-down assays / Amanda L. Bain, Janelle L. Harris, and Kum Kum Khanna
• ATM activation and H2AX phosphorylation induced by genotoxic agents assessed by flow- and laser scanning cytometry / Hong Zhao, H. Dorota Halicka, Jorge Garcia, Jiangwei Li, and Zbigniew Darzynkiewicz
• Peptide immunoaffinity enrichment with targeted mass spectrometry : application to quantification of ATM kinase phospho-signaling / Jeffrey R. Whiteaker, Lei Zhao, Regine M. Schoenherr, Jacob J. Kennedy, Richard G. Ivey, and Amanda G. Paulovich
• Mass spectrometry-based proteomics for quantifying DNA damage-induced phosphorylation / Marina E. Borisova, Sebastian A. Wagner, and Petra Beli
• Statistical analysis of ATM-dependent signaling in quantitative mass spectrometry phosphoproteomics / Ashley J. Waardenberg
• ChIP technique to study protein dynamics at defined DNA double strand breaks / Jie Wen and Patrick Concannon
• Studies of the DNA damage response by using the Lac Operator/Repressor (LacO/LacR) tethering system / Rossana Piccinno, Marta Cipinska, and Vassilis Roukos
• Imaging of fluorescently tagged ATM kinase at the sites of DNA double strand breaks / Anthony J. Davis, Shih-Ya Wang, David J. Chen, and Benjamin P.C. Chen
• Live cell imaging to study real-time ATM-mediated recruitment of DNA repair complexes to sites of ionizing radiation-induced DNA damage / Burkhard Jakob and Gisela Taucher-Scholz
• Analyzing heterochromatic DNA double strand break (DSB) repair in response to ionizing radiation / Karolin Klement and Aaron A. Goodarzi
• Phenotypic analysis of ATM protein kinase in DNA double-strand break formation and repair / Elisabeth Mian and Lisa Wiesmüller
• Monitoring DNA repair consequences of ATM signaling using simultaneous fluorescent readouts / Adrian Wiegmans
• Noncanonical ATM activation and signaling in response to transcription-blocking DNA damage / Jurgen A. Marteijn, Wim Vermeulen, and Maria Tresini
• Study of ATM phosphorylation by Cdk5 in neuronal cells / Hua She and Zixu Mao
• DNA damage response in human stem cells and neural descendants / Jason M. Beckta, Bret R. Adams, and Kristoffer Valerie
• Patient-specific stem cell model to investigate the neurological phenotype observed in ataxia-telangiectasia / Romal Stewart, Gautam Wali, Chris Perry, Martin F. Lavin, Francois Féron, Alan Mackay-Sim, and Ratneswary Sutharsan
• Lentiviral reprogramming of A-T patient fibroblasts to induced pluripotent stem cells / Sam Nayler, Sergei V. Kozlov, Martin F. Lavin, and Ernst Wolvetang
• Monitoring the ATM-mediated DNA damage response in the cerebellum using organotypic cultures / Efrat Tal and Yosef Shiloh.

Ataxia-telangiectasia (A-T) is a rare and severe genetic disorder affecting children. A-T is a multisystem disease characterized by progressive neurodegeneration, immunodeficiency and cancer predisposition. This detailed volume explores the ever expanding field of research into the ATM (ataxia-telangiectasia, mutated) gene and the role played by ATM kinase in DNA damage signaling and diverse cellular processes. What follows is a handy desktop reference for both seasoned A-T researchers and postgraduate students, as it demonstrates the breadth of recent developments in A-T studies. 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. Both classic and cutting-edge techniques are described, including ATM gene mutation detection, assays for radiosensitivity and radioresistant DNA synthesis, new methods to measure ATM kinase activity by imaging microscopy and high content screening as well as proteomics, phosphoproteomics and bioinformatics approaches to decipher ATM-dependent signalling pathways. Additional methods include generation of patient-specific stem cells and approaches to study ATM functions in the nervous system. Comprehensive and practical, ATM Kinase: Methods and Protocols aims to ignite and attract the interest of colleagues from diverse fields to A-T research in an effort to bring their expertise and fresh ideas to resolve many A-T puzzles still waiting to be pieced together and to alleviate the suffering of A-T children and their families.
(source: Nielsen Book Data)

• 1 Some thoughts on experimental design / Claudio D. Stern
• 2 Comparative genomics as a foundation for evo-devo studies in birds / Phil Grayson, Simon Y.W. Sin, Timothy B. Sackton, and Scott V. Edwards
• 3 A step-by-step guide to assemble a reptilian genome / Asier Ullate-Agote, Yingguang Frank Chan, and Athanasia C. Tzika
• 4 Genomic and transcriptomic analyses of avian sex chromosomes and sex-linked genes / Jilin Zhang, Jing Li, and Qi Zhou
• 5 Systems biology analyses in chicken : workflow for transcriptome and ChIP-seq analyses using the chicken skin paradigm / Yung-Chih Lai, Randall B. Widelitz, and Cheng-Ming Chuong
• 6 Application of a CAGE method to an avian development study / Ruslan Deviatiiarov, Marina Lizio, and Oleg Gusev
• 7 CRISPR/Cas9 in the chicken embryo / Valérie Morin, Nadège Véron, and Christophe Marcelle
• 8 Fluorescent quail : a transgenic model system for the dynamic study of avian development / David Huss and Rusty Lansford
• 9 Lentiviral-mediated transgenesis in songbirds / Wan-chun Liu, Marian Hruska-Plochan, and Atsushi Miyanohara
• 10 In ovo electroporation methods in chick embryos / Hidekiyo Harada, Minoru Omi, and Harukazu Nakamura
• 11 Genetic manipulation of the avian urogenital system using in ovo electroporation / Claire E. Hirst, Olivier Serralbo, Katie L. Ayers, Kelly N. Roeszler, and Craig A. Smith
• 12 Enhancer analyses using chicken embryo electroporation / Masanori Uchikawa, Naoko Nishimura, Makiko Iwafuchi-Doi, and Hisato Kondoh
• 13 Transgene introduction into the chick limb bud by electroporation / Shogo Ueda, Takayuki Suzuki, and Mikiko Tanaka
• 14 Chicken induced pluripotent stem cells : establishment and characterization / Aurelie Fuet and Bertrand Pain
• 15 Isolation and characterization of chicken primordial germ cells and their application in transgenesis / Jae Yong Han and Bo Ram Lee
• 16 Handling of gametes for in vitro insemination in birds / Shusei Mizushima, Mei Matsuzaki, and Tomohiro Sasanami
• 17 In vitro and ex ovo culture of reptilian and avian neural progenitor cells / Wataru Yamashita, Toyo Shimizu, and Tadashi Nomura
• 18 Lifting the veil on reptile embryology : the veiled chameleon (Chamaeleo calyptratus) as a model system to study reptilian development / Raul E. Diaz Jr., Federica Bertocchini, and Paul A. Trainor
• 19 Model clades versus model species : Anolis lizards as an integrative model of anatomical evolution / Thomas J. Sanger and Bonnie K. Kircher
• 20 The feather model for chemo- and radiation therapy-induced tissue damage / Zhicao Yue and Benhua Xu
• 21 An early chick embryo culture device for extended continuous observation / Hans-Georg Sydow, Tobias Pieper, Christoph Viebahn, and Nikoloz Tsikolia
• 22 A sensitive and versatile in situ hybridization protocol for gene expression analysis in developing amniote brains / Pei-Shan Hou, Takuma Kumamoto, and Carina Hanashima
• 23 Somitogenesis and axial development in reptiles / Cindy Xu, Mariana B. Grizante, and Kenro Kusumi
• 24 MicroCT imaging on living alligator teeth reveals natural tooth cycling / Randall B. Widelitz, Alaa Abdelhamid, M. Khalil Khan, Amr Elkarargy, Cheng-Ming Chuong, and Ping Wu.

This volume discusses recent advances in avian and reptilian biology that have caused this diverse field to re-emerge. The chapters in this book are divided into 4 parts: genomics and transcriptomics, genetic manipulation, stem cells, and new model systems. Part I details how to perform genomic and transcriptomic analyses in birds and reptiles; Part II highlights technological advancements in avian genetic manipulation; Part III focuses on methods to handle pluripotent cells; and part IV looks at the emerging models in avian and reptilian developmental 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.Cutting-edge and comprehensive, Avian and Reptilian Developmental Biology: Methods and Protocols explores a variety of approaches and different sauropsid models that will help facilitate communication and collaboration among researchers, which in turn will progress this field forward.
(source: Nielsen Book Data)

• Fuel of the Bacterial Flagellar Type III Protein Export Apparatus
• Interactions of Flagellar Structural Subunits with the Membrane Export Components Machinery
• Fluorescent Microscopy Techniques to Study Hook Length Control and Flagella Formation
• Coupling of Flagellar Gene Expression with Assembly in Salmonella enterica
• Dynamic Measures of Flagellar Gene Expression
• Purification and Characterization of the Bacterial Flagellar Basal Body from Salmonella enterica
• Design and Preparation of the Fragment Proteins of the Flagellar Components Suitable for X-Ray Crystal Structure Analysis
• Structural Analysis of the Flagellar Component Proteins in Solution by Small Angle X-Ray Scattering
• Structural Study of the Bacterial Flagellar Basal Body by Electron Cryomicroscopy and Image Analysis
• Structure of the MotA/B Proton Channel
• Mechanism of Stator Assembly and Incorporation into the Flagellar Motor
• Rotation Measurements of Tethered Cells
• Tracking the Movement of a Single Prokaryotic Cell in Extreme Environmental Conditions
• Measurements of the Rotation of the Flagellar Motor by Bead Assay
• Measurements of Ion-Motive Force Across the Cell Membrane
• Stoichiometry and Turnover of the Stator and Rotor
• Direct Imaging of Intracellular Signaling Molecule Responsible for the Bacterial Chemotaxis
• In Situ Structural Analysis of the Spirochetal Flagellar Motor by Cryo-Electron Tomography
• Motility of Spirochetes
• Structure of the Sodium-Driven Flagellar Motor in Marine Vibrio
• Chemotactic Behaviors of Vibrio Cholerae Cells
• Purification of Fla2 Flagella of Rhodobacter sphaeroides
• Dynamics in the Dual Fuel Flagellar Motor of Shewanella oneidensis MR-1
• Ion Selectivity of the Flagellar Motors Derived from the Alkaliphilic Bacillus and Paenibacillus Species
• Measurement of Free-Swimming Motility and Magnetotactic Behavior of Magnetococcus massalia Strain MO-1.

This volume examines the structure and dynamics of the bacterial flagellum using bacterial genetics, molecular biology, biochemistry, structural biology, biophysics, cell biology, and molecular dynamics simulation. The chapters are divided into 4 parts: Part I describes flagellar type III protein exports, assembly, and gene regulation in S. enterica; Part II explains how to isolate the flagella from the bacterial cell bodies, and further explains how to conduct high-resolution structural and functional analyses of the flagellar motor; Part III talks about how to measure flagellar motor rotation over a wide range of external load, how to measure ion motive force across the cytoplasmic membrane, and how to measure dynamic properties of the flagellar motor proteins by fluorescence microscopy with single molecule precision; and Part IV explores the structure and function of Spirochetal, Vibrio, Shewanella, and Magnetococcus flagellar motors. 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, The Bacterial Flagellum: Methods and Protocols aims to provide valuable and vital research to aid in the investigation of the bacterial flagellum resulting from various bacterial species.

• MicroRNAs, long noncoding RNAs, and their functions in human disease / Min Xue, Ying Zhuo, and Bin Shan
• MicroRNA expression : protein participants in microRNA regulation / Valeria M. King and Glen M. Borchert
• Viral microRNAs, host microRNAs regulating viruses, and bacterial microRNA-like RNAs / Sara-Elizabeth Cardin and Glen M. Borchert
• MicroRNAs : biomarkers, diagnostics, and therapeutics / Weili Huang
• Relational databases and biomedical big data / N.H. Nisansa D. de Silva
• Semantic technologies and bio-ontologies / Fernando Gutierrez
• Genome-wide analysis of microRNA-regulated transcripts / David Chevalier and Glen M. Borchert
• Computational prediction of microRNA target genes, target prediction databases, and web resources / Justin T. Roberts and Glen M. Borchert
• Exploring microRNA : target regulatory interactions by computing technologies / Yue Hu, Wenjun Lan, and Daniel Miller
• Limitations of existing approaches in improving microRNA target prediction accuracy / Rasiah Loganantharaj and Thomas A. Randall
• Genomic regulation of microRNA expression in disease development / Feng Liu
• Next-generation sequencing for microRNA expression profile / Yue Hu, Wenjun Lan, and Daniel Miller
• Handling high-dimension (high-feature) microRNA data / Yue Hu, Wenjun Lan, and Daniel Miller
• Effective removal of noisy data via batch effect processing / Ryan G. Benton
• Logical reasoning (inferencing) on microRNA data / Jingsong Wang
• Machine learning techniques in exploring microRNA gene discovery, targets, and functions / Sumi Singh, Ryan G. Benton, Anurag Singh, and Anshuman Singh
• Involvement of microRNAs in diabetes and its complications / Bin Wu and Daniel Miller
• MicroRNA regulatory networks as biomarkers in obesity : the emerging role / Lihua Zhang, Daniel Miller, Qiuping Yang, and Bin Wu
• Expression of microRNAs in thyroid carcinoma / Gaohong Zhu, Lijun Xie, and Daniel Miller.

This thorough volume provides an in-depth introduction to and discussion of microRNAs (miRs) and their targets, miR functions, and computational techniques applied in miR research, thus serving the need for a comprehensive book focusing on miR target genes, miR regulation mechanisms, miR functions performed in various human diseases, and miR databases/knowledgebases. Without prior knowledge of the area of study, computational biologists, computer scientists, bioinformaticians, bench biologists, as well as clinical investigators will find it easy to follow the techniques in this collection. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detailed implementation advice that ensures successful results. Accessible and practical, Bioinformatics in MicroRNA Research functions as an ideal guide for researchers of all backgrounds to explore this vital area of study.
(source: Nielsen Book Data)

• Volume 1: Optical-based detectors
• Localized surface plasmon resonance (LSPR)-coupled fiber-optic nanoprobe for the detection of protein biomarkers / Jianjun Wei, Zheng Zeng, and Yongbin Lin
• Ultra-sensitive surface plasmon resonance detection by colocalized 3D plasmonic nanogap arrays / Wonju Lee, Taehwang Son, Changhun Lee, Yongjin Oh, and Donghyun Kim
• Two-dimensional surface plasmon resonance imaging system for cellular analysis / Tanveer Ahmad Mir and Hiroaki Shinohara
• Immunosensing with near-infrared plasmonic optical fiber gratings / Christophe Caucheteur, Clotilde Ribaut, Viera Malachovska, and Ruddy Wattiez
• Biosensing based on magneto-optical surface plasmon resonance / Sorin David, Cristina Polonschii, Mihaela Gheorghiu, Dumitru Bratu, and Eugen Gheorghiu
• Nanoplasmonic biosensor using localized surface plasmon resonance spectroscopy for biochemical detection / Diming Zhang, Qian Zhang, Yanli Lu, Yao Yao, Shuang Li, and Qingjun Liu
• Plasmonics-based detection of virus using sialic acid functionalized gold nanoparticles / Changwon Lee, Peng Wang, Marsha A. Gaston, Alison A. Weiss, and Peng Zhang
• MicroRNA biosensing with two-dimensional surface plasmon resonance imaging / Ho Pui Ho, Fong Chuen Loo, Shu Yuen Wu, Dayong Gu, Ken-Tye Yong, and Siu Kai Kong
• Gold nanorod array biochip for label-free, multiplexed biological detection / Zhong Mei, Yanyan Wang, and Liang Tang
• Resonant waveguide grating imager for single cell monitoring of the invasion of 3D speheroid cancer cells through matrigel / Nicole K. Febles, Siddarth Chandrasekaran, and Ye Fang
• Label-free biosensors based on bimodal waveguide (BiMW) interferometers / Sonia Herranz, Adrian Fernandez Gavela, and Laura M. Lechuga
• DNA-directed antibody immobilization for robust protein microarrays : application to single particle detection DNA-directed antibody immobilization / Nese Lortlar Unlu, Fulya Ekiz Kanik, Elif Seymour, John H. Connor, and M. Selim Unlu
• Reflectometric interference spectroscopy / Guenther Proll, Goran Markovic, Peter Fechner, Florian Proell, and Guenter Gauglitz
• Hypermulticolor detector for quantum-antibody based concurrent detection of intracellular markers for HIV diagnosis / Annie Agnes Suganya Samson and Joon Myong Song
• Low-cost charged-coupled device (CCD) based detectors for Shiga toxins activity analysis / Reuven Rasooly, Ben Prickril, Hugh A. Bruck, and Avraham Rasooly
• Smartphone-enabled detection strategies for portable PCR-based diagnostics / Aashish Priye and Victor M. Ugaz
• Streak imaging flow cytometer for rare cell analysis / Joshua Balsam, Hugh Alan Bruck, Miguel Ossandon, Ben Prickril, and Avraham Rasooly
• Rapid detection of microbial contamination using a microfluidic device / Mustafa Al-Adhami, Dagmawi Tilahun, Govind Rao, Chandrasekhar Gurramkonda, and Yordan Kostov
• Resonance energy transfer-based nucleic acid hybridization assays on paper-based platforms using emissive nanoparticles as donors / Samer Doughan, M. Omair Noor, Yi Han, and Ulrich J. Krull
• Enhanced performance of colorimetric biosensing on paper microfluidic platforms through chemical modification and incorporation of nanoparticles / Ellen Flavia Moreira Gabriel, Paulo T. Garcia, Elizabeth Evans,Thiago M.G. Cardoso, Carlos D. Garcia, and Wendell K.T. Coltro
• Smartphone-based colorimetric reader for human C-reactive protein immunoassay / A.G. Venkatesh, Thomas van Oordt, E. Marion Schneider, Roland Zengerle, Felix von Stetten, John H.T. Luong, and Sandeep Kumar Vashist
• Novel colorimetric PCR-based biosensor for detection and quantification of hepatitis B virus / Li Yang, Mei Li, Feng Du, Gangyi Chen, Afshan Yasmeen, and Zhuo Tang
• CCD camera detection of HIV infection / John R. Day
• "Dipstick" colorimetric detection of metal ions based on immobilization of DNAzyme and gold nanoparticles onto a lateral flow device / Debapriya Mazumdar, Tian Lan, and Yi Lu
• Liposome-enhanced lateral-flow assays for clinical analyses / Katie A. Edwards, Ricki Korff, and Antje J. Baeumner
• Development of dual quantitative lateral flow immunoassay for the detection of mycotoxins / Yuan-Kai Wang, Ya-Xian Yan, and Jian-He Sun.

• Volume 2: Electrochemical, bioelectronic, piezoelectric, cellular and molecular biosensors
• Reagentless, screen-printed amperometric biosensor for the determination of glutamate in food and clinical applications / G. Hughes, R.M. Pemberton, P.R. Fielden, and J.P. Hart
• Electrochemical DNA sensing system using modified nanoparticle probes for detecting methicillin-resistant Staphylococcus aureus / Hiroaki Sakamoto, Yoshihisa Amano, Takenori Satomura, and Shin-ichiro Suye
• Electrochemical lateral flow paper strip for oxidative-stress induced DNA damage assessment / Jared Leichner, Mehenur Sarwar, Amirali Nilchian, Xuena Zhu, Hongyun Liu, Shaomin Shuang, and Chen-zhong Li
• Application of a nanostructured enzymatic biosensor based on fullerene and gold nanoparticles to polyphenol detection / Cristina Tortolini, Gabriella Sanzo, Riccarda Antiochia, Franco Mazzei, and Gabriele Favero
• Screen-printed all-polymer aptasensor for impedance based detection of influenza A virus / Julie Kirkegaard and Noemi Rozlosnik
• Microfluidic arrayed Lab-On-A-Chip for electrochemical capacitive detection of DNA hybridization events / Hadar Ben-Yoav, Peter H. Dykstra, William E. Bentley, and Reza Ghodssi
• Enzymatic detection of traumatic brain injury related biomarkers / Brittney A. Cardinell and Jeffrey T. La Belle
• Bacterial detection using peptide-based platform and impedance spectroscopy / Hashem Etayash, Thomas Thundat, and Kamaljit Kaur
• Fabrication of lab-on-paper using porous Au-Paper electrode : application to tumor marker electrochemical immunoassays / Shenguang Ge, Yan Zhang, Mei Yan, Jiadong Huang, and Jinghua Yu
• Electrochemical biosensors combined with isothermal amplification for quantitative detection of nucleic acids / Miyuki Tabata, Bo Yao, Ayaka Seichi, Koji Suzuki, and Yuji Miyahara
• Mini-electrochemical system with integrated micropipet tip and pencil graphite electrode for measuring cytotoxicity / Dong-Mei Wu, Xiao-Ling Guo, Qian Wang, Jin-Lian Li, Ji-Wen Cui, Shi Zhou, and Su-E Hao
• All-electrical graphene DNA sensor array / Jeffrey Abbott, Donhee Ham, and Guangyu Xu
• Extended gate field-effect transistor biosensors for point-of-care testing of uric acid / Weihua Guan and Mark A. Reed
• Highly sensitive glucose sensor based on organic electrochemical transistor with modified gate electrode / Xudong Ji and Paddy K.L. Chan
• Fabrication of hydrogenated diamond metal-insulator-semiconductor field-effect transistors / Jiangwei Liu and Yasuo Koide
• Light-addressable potentiometric sensor for odorant detection using single bioengineered olfactory sensory neurons as sensing element / Chunsheng Wu, Liping Du, Yulan Tian, Xi Zhang, and Ping Wang
• Piezoelectric cantilever biosensors for label-free, real-time detection of DNA and RNA / Alexander P. Haring, Ellen Cesewski, and Blake N. Johnson
• Electrochemical quartz crystal nanobalance (EQCN) based biosensor for sensitive detection of antibiotic residues in milk / Sunil Bhand and Geetesh K. Mishra
• Development of novel piezoelectric biosensor using PZT ceramic resonator for detection of cancer markers / Li Su, Chi-Chun Fong, Pik-Yuan Cheung, and Mengsu Yang
• Finger-powered electro-digital-microfluidics / Cheng Peng and Y. Sungtaek Ju
• Monitoring the cellular binding events with quartz crystal microbalance (QCM) biosensors / Abdul Rehman and Xiangqun Zeng
• Piezoelectric plate sensor (PEPS) for analysis of specific KRAS point mutations at low copy number in urine without DNA isolation or amplification / Ceyhun E. Kirimli, Wei-Heng Shih, and Wan Y. Shih
• Synthetic cell-based sensors with programmed selectivity and sensitivity / Elvis Bernard and Baojun Wang
• Dynamic antibiotic susceptibility test via a 3D microfluidic culture device / Zining Hou, Yu An, and Zhigang Wu
• Aptasensors for detection of avian influenza virus H5N1 / Yanbin Li and Ronghui Wang
• Optical and electrochemical aptasensors for sensitive detection of streptomycin in blood serum and milk / Mohammad Ramezani, Khalil Abnous, and Seyed Mohammad Taghdisi
• Lateral flow biosensor for the detection of single nucleotide polymorphisms / Lingwen Zeng and Zhuo Xiao
• Loop-mediated isothermal amplification and LFD combination for detection of Plasmodium falciparum and Plasmodium vivax / Darin Kongkasuriyachai, Suganya Yongkiettrakul, Wansika Kiatpathomchai, and Narong Arunrut
• Characterization of in vivo selected bacteriophage for the development of novel tumor-targeting agents with specific pharmacokinetics and imaging applications / Jessica Newton-Northup and Susan L. Deutscher
• Microfluidic "Pouch" chips for immunoassays and nucleic acid amplification tests / Michael G. Mauk, Changchun Liu, Xianbo Qiu, Dafeng Chen, Jinzhao Song, and Haim H. Bau
• Functionalized vesicles by microfluidic device / Derek Vallejo, Shih-Hui Lee, and Abraham Lee
• Filtration and analysis of circulating cancer associated cells from the blood of cancer patients / Cha-Mei Tang, Peixuan Zhu, Shuhong Li, Olga V. Makarova, Platte T. Amstutz, and Daniel L. Adams
• Inkjet-printed paper fluidic devices for onsite detection of antibiotics using surface-enhanced raman spectroscopy / Stephen M. Restaino, Adam Berger, and Ian M. White
• High resolution microultrasound (μUS) investigation of the gastrointestinal (GI) tract / Thineskrishna Anbarasan, Christine E.M. Demore, Holly Lay, Mohammed R.S. Sunoqrot, Romans Poltarjonoks, Sandy Cochran, and Benjamin F. Cox.

This volume provides comprehensive and detailed technical protocols on current biosensor and biodetection technologies and examples of their applications and capabilities. Chapters in Biosensors and Biodetection: Methods and Protocols, Volume 1: Optical-Based Detectors, Second Edition chapters focus on direct and indirect optical detectors including surface plasmon resonance, interferometric sensors, charge-coupled device (CCD) based detectors, spectrometry, and many other cutting-edge optical biosensors technologies. Written in the format of the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, tips on troubleshooting and avoiding known pitfalls, and step-by-step, readily reproducible laboratory protocols. Authoritative and practical, Biosensors and Biodetection: Methods and Protocols, Volume 1: Optical-Based Detectors, Second Edition offers descriptions of major technologies by leading experts in the field in extensive technical detail. The aim of the book is to make biosensors more accessible and understandable to engineers, students, medical professionals, molecular biologists, chemical, and physical science researchers developing biosensor technologies, allowing readers to both understand the technology and to construct similar devices.
(source: Nielsen Book Data)

• Protocol for extraction and isolation of brassinosteroids from plant tissues / Danuše Tarkowská and Miroslav Strnad
• Synthetic protocol for AFCS : a biologically active fluorescent castasterone analog conjugated to an alexa fluor 647 dye / Johan M. Winne, Niloufer G. Irani, Jos Van den Begin, and Annemieke Madder
• Physiological analysis of brassinosteroid responses and sensitivity in rice / Hongning Tong and Chengcai Chu
• Light regulation of brassinosteroid signaling components : checking regulation of protein stability in darkness / Claudia Corvalán and Sunghwa Choe
• Approaches to study light effects on brassinosteroid sensitivity / Sandi Paulišić, Maria José Molina-Contreras, Irma Roig-Villanova, and Jaime F. Martínez-García
• Technical framework for studying the signaling nexus of brassinosteroids and immunity / Rosa Lozano-Durán and Youssef Belkhadir
• Identification of brassinosteroid target genes by chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) and RNA-sequencing / Trevor Nolan, Sanzhen Liu, Hongqing Guo, Lei Li, Patrick Schnable, and Yanhai Yin
• Quantitation of cell type-specific responses to brassinosteroid by deep sequencing of polysome-associated polyadenylated RNA / Kristina Vragović, Elizabeth Bartom, and Sigal Savaldi-Goldstein
• Methods for modeling brassinosteroid-mediated signaling in plant development / David Frigola, Ana I. Caño-Delgado, and Marta Ibañes
• Quantitative microscopic analysis of plasma membrane receptor dynamics in living plant cells / Yu Luo and Eugenia Russinova
• Analysis of in vitro DNA interactions of brassinosteroid-controlled transcription factors using electrophoretic mobility shift assay / Simon J. Unterholzner, Wilfried Rozhon, and Brigitte Poppenberger
• Identification of brassinosteroid signaling complexes by coimmunoprecipitation and mass spectrometry / Walter van Dongen, Luc van Heerde, Sjef Boeren, and Sacco C. de Vries
• Simplified enrichment of plasma membrane proteins from Arabidopsis thaliana seedlings using differential centrifugation and Brij-58 treatment / Carina A. Collins, Michelle E. Leslie, Scott C. Peck, and Antje Heese
• Probing activation and deactivation of the BRASSINOSTEROID INSENSITIVE1 receptor kinase by immunoprecipitation / Sara Martins, Grégory Vert, and Yvon Jaillais
• Primary root of Sorghum bicolor (L. Moench) as a model system to study brassinosteroid signaling in crops / David Blasco-Escámez, Fidel Lozano-Elena, Norma Fàbregas, and Ana I. Caño-Delgado
• Brassinosteroid action in plant abiotic stress tolerance / Priti Krishna, Bishun D. Prasad, and Tawhidur Rahman.

This detailed volume compiles state-of-the-art methodologies for the study of brassinosteroid hormones, contributed by recognized researchers in the field, in order to bring together different experimental and theoretical biology techniques for addressing the questions of how brassinosteroids function in Arabidopsis and other agriculturally valuable species, such as rice and sorghum. 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, Brassinosteroids: Methods and Protocols assesses a wide range of appealing methodologies for experts as well as researchers with a general interest in hormone signaling in plants.
(source: Nielsen Book Data)