Handbook of Systems Toxicology. Edition No. 1

Table of Contents

VOLUME

Contributors ix

Preface xvii

Acknowledgments xix

Abbreviations and Acronyms xxi

Part One - Toxicogenomics

1 Toxicogenomics: An Overview with Special Reference to Genetic and Genomic Approaches to the Identification of Toxic Effects
Mayukh Banerjee and Ashok K. Giri

2 Toxicogenomics – Applications in Systems Toxicology
Pius Joseph

3 System Toxicology Approaches for Evaluating Chemical Carcinogenicity
Heidrun Ellinger-Ziegelbauer and Jiri Aubrecht

4 Effect of p53 Genotype on Gene Expression and DNA Adducts in ENU-Exposed Mice
Rohan Kulkarni, Dayton M. Petibone, Ching-Wei Chang, James J. Chen, William H. Tolleson, William B. Melchior, Mona I. Churchwell, Frederick A. Beland and Suzanne M. Morris

5 Application of Ecotoxicogenomics for Understanding Mode of Action of Chemicals and Species Extrapolation
Hajime Watanabe, Yasuhiko Kato and Taisen Iguchi

Part Two - Nutrigenomics

6 A Community-Based Participatory Research/Translational Biomedical Research Strategy for Personalizing Nutrition, Medicine, and Healthcare
Anna Williams, Carolyn Wise, Dalia Lovera, Beverly McCabe-Sellers, Margaret Bogle and Jim Kaput

7 Role of the Endocannabinoid System in Systems Toxicity
Constantinos Pistos and Stamatios Theocharis

Part Three - Genomic Technology

8 Integrative Analysis of Microarray Data: A Path for Systems Toxicology
Axel Rasche, Reha Yildirimman and Ralf Herwig

9 Application of Systems Biology in Neurotoxicological Studies During Development
Cheng Wang, Lei Guo, Tucker A. Patterson and William Slikker

10 Mitochondria-Specific Mouse Gene Array and its Application in Toxicogenomics
Varsha G. Desai

11 Integration of Systems Toxicology into Drug Discovery
Mark Fielden

12 Systems Toxicology: A Valuable Tool for Early Prediction and Mechanistic Assessment of Liver Toxicity of Food-Related Products
Saura C. Sahu

Part Four - Proteomic Technology

13 Mass Spectrometry-Based Proteomics in Systems Toxicology
Li-Rong Yu, Yuan Gao and Donna L. Mendrick

14 Applications of Proteomic Technologies to Toxicology
Yue Ge, Maribel Bruno and Heidi Foth

15 Application of Quantitative Proteomic Approaches to Toxicology
T.S. Keshava Prasad and Raghothama Chaerkady

16 Use of Proteomic and Metabolomic Techniques in Ecotoxicological Research
Maria S. Sep´ulveda, Kimberly J. Ralston-Hooper, Brian C. Sanchez, Amber Hopf-Jannasch, Stephanie D. Baker, Naomi Diaz and Jiri Adamec

17 Application of Proteomics to Study Mechanisms of Toxicity and Dose–Response Relationships of Chemical Exposure
Zheying Zhu and Robert J. Edwards

Part Five - Metabolomic Technology

18 Metabolomics in Systems Toxicology: Towards Personalized Medicine
Laura K. Schnackenberg, Jinchun Sun and Richard D. Beger

19 Species-Metabolite Relation Database KNApSAcK and Its Multifaceted Retrieval System, KNApSAcK Family
Hiroki Takahashi, Aki Hirai, Masayuki Shojo, Kaori Matsuda, Aziza Kawsar Parvin, Hiroko Asahi, Kensuke Nakamura, Md. Altaf-Ul-Amin and Shigehiko Kanaya

20 Biomarkers for the Assessment of Acetaminophen-Induced Liver Injury
Wimal Pathmasiri, Rodney W. Snyder, Jason P. Burgess, James A. Popp, Timothy R. Fennell and Susan J. Sumner

21 Application of Metabonomic Approach inTarget Organ Toxicity
Athina Zira and Stamatios Theocharis

Part Six - Bioinformatics and Chemoinformatics

22 Toxicoinformatics for Systems Toxicology
Lyle D. Burgoon

23 Chemoinformatics and its Applications
Vetrivel Umashankar and Subramanian Gurunathan

24 Biomarker Discovery: Introduction to Statistical Learning and Integrative Bioinformatics Approaches
Dirk Repsilber and Marc Jacobsen

Part Seven - Systemics

25 Mechanistic Investigation of EMD335823s Hepatotoxicity Using Multiple Omics Profiling Technologies
Alexandra Sposny, Christina S. Schmitt and Philip G. Hewitt

26 Application of DNA Microarray in Studies of Herbal Dietary Supplements
Lei Guo, James C. Fuscoe, P. Fu and Nan Mei

27 Unravelling Sex Differences in Drug-Induced Liver Injury
Weida Tong, Qiang Shi, William Salminen, Minjun Chen, Hong Fang, Ayako Suzuki and Donna L. Mendrick

28 Commonality and Stochasticity in Systems Toxicology
Yoko Hirabayashi and Tohru Inoue

29 Immunotoxicogenomics: A Systems Approach
Rob J. Vandebriel, Henk van Loveren, Kirsten A. Baken and Jeroen L.A. Pennings

30 Systems Biology: Integrating'-Omics'-Oriented Approaches to Determine Foodborne Microbial Toxins
Om V. Singh, Nagathihalli S. Nagaraj and Prashant Gabani

31 Epigenomic Analysis inToxicology
Toshikazu Ushijima, Eriko Okochi-Takada and Hideyuki Takeshima

Author Index I

Subject Index III

VOLUME

Contributors ix

Preface xvii

Acknowledgments xix

Abbreviations and Acronyms xxi

Part Eight - Image Analysis, Sequencing and Systems Modeling

32 Sequencing Technology Advances and Toxicology
Luke D. Ratnasinghe

33 Next-Generation Sequencing: A Revolutionary Tool for Toxicogenomics
Zhenqiang Su, Baitang Ning, Hong Fang, Huixiao Hong, Roger Perkins, Weida Tong and Leming Shi

34 Systems Toxicology Modeling for Prediction in Humans
Cristiano Migliorini, Thierry Lave, Neil J. Parrott, Micaela Reddy, Hans Peter Grimm, Robert C. Penland, Antoine Soubret, Gabriel Helmlinger, Anna Georgieva and Klaas P. Zuideveld

35 In Silico Tools for Molecular Modeling
Vetrivel Umashankar and Subramanian Gurunathan

36 In Silico Toxicology Prediction Using Toxicogenomics Data
Yasushi Okuno, Yohsuke Minowa, Hiroshi Yamada, Yasuo Ohno and Tetsuro Urushidani

37 Systems Modeling in Developmental Toxicity
Thomas B. Knudsen and Rob DeWoskin

38 Multiscale Integration of Toxicokinetic and Toxicodynamic Processes: From Cell and Tissue to Organ and “Whole Body” Models
Panos G. Georgopoulos, Sastry Isukapalli, Ioannis P. Androulakis, Marianthi G. Ierapetritou and William J. Welsh

39 Biomarkers of System Response to Therapeutic Intervention
Ludmila Danilova and Michael F. Ochs

Part Nine - Nanotechnology

40 Nanotoxicology
Yinfa Ma and Weisheng Lin

41 Toxicology of Engineered Metal Nanoparticles
Giovanni Bernardini, Anna Giulia Cattaneo, Enrico Sabbioni, Mario Di Gioacchino, Maurizio Chiriva-Internati and Rosalba Gornati

42 Multifunctional Nanomaterials for Biomedical Applications: The Onset of Nanomedicine
Yang Xu, Meena Mahmood and Alexandru S. Biris

43 Nanotoxicology: A Brief Overview and Discussion of the Current Toxicological Testing In Vitro and Suggestions for Future Research
Martin J. D. Clift, Fabian Blank, Peter Gehr and Barbara Rothen-Rutishauser

44 Toxicity of Selenium Compounds and Nano-Selenium Particles
Jinsong Zhang and Julian E. Spallholz

45 In Vivo Toxicity Studies of Metal and Metal Oxide Nanoparticles
Andrea Adamcakova-Dodd, Peter S. Thorne and Vicki H. Grassian

46 The Role of Oxidative Stress in Nanotoxicology
Christie M. Sayes, Nivedita Banerjee and Amelia A. Romoser

47 Health Effects of Nanoparticles
Armelle Baeza-Squiban, Sonja Boland, Salik Hussain and Francelyne Marano

48 Systems Toxicological Approach to the Risk Assessment of Nanomaterials
Sang-Hee Jeong, Wan-Seob Cho, Ji-Eun Kim and Myung-Haing Cho

Part Ten - Regulatory Applications

49 Implementing Systems Toxicologyin Drug Development for Regulatory Decision Making
Joseph F. Sina and Frank D. Sistare

Author Index I

Subject Index III

Authors

Saura C. Sahu From Genomics to In Vitro and In Vivo Models. Daniel A. Casciano University of Arkansas - Medical Science.