Description
This second edition volume presents a selection of cellular and molecular techniques that can be adapted to cover a range of applications and diseases. The book is divided into three sections: saliva and oral diseases, molecular biosciences, and cell and tissues. The first section contains chapters that discuss proteomic analyses by mass spectrometry and NMR-based metabolomics that can be used to not only study saliva, but also to assess other oral fluids such as gingival crevicular fluid. The second section contains chapters that profile oral microbial communities, quantitative real-time PCR, and adhesion of yeast and bacteria to oral surfaces. The third section deals with a range of approaches that enable the behavior of cells and tissues in both health and disease to be analyzed at the molecular level. 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, Oral Biology: Molecular Techniques and Applications, Second Edition is a useful resource for oral biologists at all levels (students, early career researchers, and experienced veterans), and it provides a ready reference to new techniques and approaches that can be used to answer numerous specific scientific questions that may lead to a deeper understanding and treatments of oral diseases. Preface… Table of Contents… Contributing Authors… Part I Saliva and Other Oral Fluids 1. Salivary Diagnostics using Purified Nucleic Acids Paul D. Slowey 2. RNA Sequencing Analysis of Salivary Extracellular RNA Blanca Majem, Feng Li, Jie Sun, and David T.W. Wong 3. Qualitative and Quantitative Proteomic Analysis of Oral Fluids in Health and Periodontal Disease by Mass Spectrometry Erdjan Salih 4. Antioxidant Micronutrients and Oxidative Stress Biomarkers Iain L.C. Chapple, Helen R. Griffiths, Mike R. Milward, Martin R. Ling, and Melissa M. Grant 5. NMR-Based Metabolomics of Oral Biofluids Horst Joachim Schirra and Pauline J. Ford 6. Gene Therapy of Salivary Diseases Bruce J. Baum, Sandra Afione, John a. Chiorini, Ana P. Cotrim, Corinne M. Goldsmith, and Changyu Zheng Part II Molecular Biosciences 7. The Oral Microbiota in Health and Disease: An Overview of Molecular Findings Jos F. Siqueira, Jr., and Isabela N. Ras 8. Microbial Community Profiling using Terminal Restriction Fragment Length Polymorphism (T-RFLP) and Denaturing Gradient Gel Electrophoresis (DGGE) Jos F. Siqueira, Jr., Mitsuo Sakamoto, and Alexandre S. Rosado 9. Analysis of 16S rRNA Gene Amplicon Sequences using the QIIME Software Package Blair Lawley and Gerald W. Tannock 10. Adhesion of Yeast and Bacteria to Oral Surfaces Richard D. Cannon, Karl M. Lyons, Kenneth Chong, Kathryn Newsham-West, Kyoko Niimi, and Ann R. Holmes 11. Quantitative Analysis of Periodontal Pathogens by Real-Time Polymerase Chain Reaction M Jos Marin, Elena Figuero, David Herrera, and Mariano Sanz 12. Methods to Study Antagonistic Activities Among Oral Bacteria Fengxia Qi and Jens Kreth 13. Natural Transformation of Oral Streptococci by Use of Synthetic Pheromones Gabriela Salvadori, Roger Junges, Rabia Khan, Heidi A. mdal, Donald Morrison, and Fernanda C. Petersen 14. Markerless Genome Editing in Competent Streptococci Roger Junges, Rabia Khan, Yanina Tovpeko, Heidi A. mdal, Fernanda C. Petersen, and Donald A. Morrison 15. Tools and Strategies for Analysis of Genome-Wide and Gene-Specific DNA Methylation Patterns Aniruddha Chatterjee, Euan J. Rodger, Ian M. Morison, Michael R. Eccles, and Peter A. Stockwell 16. Generating Multiple Base-Resolution DNA Methylomes using Reduced Representation Bisulfite Sequencing Aniruddha Chatterjee, Euan J. Rodger, Peter a. Stockwell, Gwenn Le Me, and Ian M. Morison 17. A Protocol for the Determination of the Methylation Status of Gingival Tissue DNA at Specific CpG Islands Trudy J. Milne 18. Genome-Wide Expression Analysis of Periodontal Cells and Tissues Moritz Kebschull, Claudia Hlsmann, Per Hoffmann, and Panos N. Papapanou 19. Differential Expression and Functional Analysis of High-Throughput -Omics Data Using Open Source Tools Moritz Kebschull, Julia M. Fittler, Ryan T. Demmer, and Panos N. Papapanou 20. Exploring Genome-Wide Expression Profiles Using Machine Learning Techniques Moritz Kebschull and Panos N. Papapanou Part III Cells and Tissues 21. Embryonic Explant Culture: Studying Effects of Regulatory Molecules on Gene Expression in Craniofacial Tissues Katja Nrhi 22. Oral Epithelial Cell Culture Model for Studying the Pathogenesis of Chronic Inflammatory Disease Mike R. Milward, Martin R. Ling, Melissa M. Grant, Iain L.C. Chapple 23. Fabrication and Characterization of Decellularized Periodontal Ligament Cell Sheet Constructs Amro Farag, Cedryck Vaquette, Dietmar W. Hutmacher, P. Mark Bartold, and Saso Ivanovski 24. A Method to Isolate, Purify and Characterize Human Periodontal Ligament Stem Cells Krzysztof Mrozik, Stan Gronthos, Songtao Shi, and P. Mark Bartold 25. Constructing Tissue Microarrays: Protocols and Methods Considering Potential Advantages and Disadvantages for Downstream Use Lynne Bingle, Felipe P. Fonseca, and Paul M. Farthing 26. Growing Adipose-Derived Stem Cells under Serum-Free Conditions Diogo G. Zanicotti and Dawn E. Coates 27. Quantitative Real-Time Gene Profiling of Human Alveolar Osteoblasts Dawn E. Coates, Sobia Zafar, and Trudy J. Milne 28. Proteomic Analysis of Dental Tissue Microsamples Jonathan E. Mangum, Jew C. Kon, and Michael J. Hubbard 29. Characterization, Quantification and Visualization of Neutrophil Extracellular Traps Phillipa C. White, Ilaria J. Chicca, Martin R. Ling, Helen J. Wright, Paul R. Cooper, Mike R. Milward, and Iain L.C. Chapple
