Preface

v

Contributors

xi

Section I

Saliva Studies

1

Gene Therapy of Salivary Diseases   Bruce J. Baum, Janik Adriaansen, Ana P. Cotrim, Corinne M. Goldsmith, Paolo Perez, Senrong Qi, Anne M. Rowzee, and Changyu Zheng

3

2

Collection, Storage, and Processing of Saliva Samples for Downstream Molecular Applications   Bradley Stephen Henson and David T. Wong

21

3

Proteomic Analysis of Saliva: 2D Gel Electrophoresis, LC-MS/MS, and Western Blotting   Shen Hu, Jiang Jiang, and David T. Wong

31

4

Transcriptomic Analyses of Saliva   Viswanathan Palanisamy and David T. Wong

43

Section II

Oral Microbiology

5

The Oral Microbiota: General Overview, Taxonomy, and Nucleic Acid Techniques   José F. Siqueira Jr. and Isabela N. Rôças

55

6

Microbial Community Profiling Using Terminal Restriction Fragment Length Polymorphism (T-RFLP) and Denaturing Gradient Gel Electrophoresis (DGGE)   José F. Siqueira Jr., Mitsuo Sakamoto, and Alexandre S. Rosado

71

7

Protocols to Study the Physiology of Oral Biofilms   José A. Lemos, Jacqueline Abranches, Hyun Koo, Robert E. Marquis, and Robert A. Burne

87

8

Adhesion of Yeast and Bacteria to Oral Surfaces   Richard D. Cannon, Karl M. Lyons, Kenneth Chong, and Ann R. Holmes

103

9

Quantitative Analysis of Periodontal Pathogens by ELISA and Real-Time Polymerase Chain Reaction   Stephen M. Hamlet

125

10

Bacterial Viability Determination in a Dentinal Tubule Infection Model by Confocal Laser Scanning Microscopy   Abdul Aziz, Dikesh Parmar, Andrew McNaughton, and Geoffrey R. Tompkins

141

11

Characterization of Anti-competitor Activities Produced by Oral Bacteria   Fengxia Qi and Jens Kreth

151

12

Natural Transformation of Oral Streptococci   Fernanda, Cristina Petersen and Anne Aamdal Scheie

167

13

Use of In Vivo-Induced Antigen Technology (IVIAT) to Identify Virulence Factors of Porphyromonas gingivalis   Shannon M. Wallet, Jin Chung, and Martin Handfield

181

14

Oral Bacterial Genome Sequencing Using the High-Throughput Roche Genome Sequencer FLX System   Nicholas C.K. Heng and Jo-Ann L. Stanton

197

15

Use of a Yeast-Based Membrane Protein Expression Technology to Overexpress Drug Resistance Efflux Pumps   Erwin Lamping and Richard D. Cannon

219

Section III

Cells and Tissues

16

Explant Culture of Embryonic Craniofacial Tissues: Analyzing Effects of Signaling Molecules on Gene Expression   Katja Närhi and Irma Thesleff

253

17

A Method to Isolate, Purify, and Characterize Human Periodontal Ligament Stem Cells   Krzysztof Mrozik, Stan Gronthos, Songtao Shi, and P. Mark Bartold

269

18

Preclinical Methods for the Evaluation of Periodontal Regeneration In Vivo

285

19

Proteomic Analysis of Dental Tissue Microsamples   Jonathan E. Mangum, Jew C. Kon, and Michael J. Hubbard

309

20

Immunological Techniques: ELISA, Flow Cytometry, and Immunohistochemistry   Pauline J. Ford

327

21

Analysis of Immune Responses to Purified Recombinant Antigens of Periodontal Pathogens   Koichi Tabeta and Kazuhisa Yamazaki

345

22

Single Strand Conformation Polymorphism Analysis for the Diagnosis of T-Cell Clonality in Periodontal Disease   Kazuhisa Yamazaki and Harue Ito

359

23

Real-Time PCR Focused-Gene Array Profiling of Gingival and Periodontal Ligament Fibroblasts   Patty Chou and Trudy J. Milne

373

24

The Use of Gene Arrays in Deciphering the Pathobiology of Periodontal Diseases   Morits Kebschull and Panos N. Papapanou

385

25

Bioinformatics Techniques in Microarray Research: Applied Microarray Data Analysis Using R and SAS Software   Ryan T. Demmer, Paul Pavlidis, and Panos N. Papapanou

395

Subject Index

419