Integrated Genomics (PDF)

Preface. Author biographies. Acknowledgments. List of figures. 1 Introduction to basic laboratory genetics. 1.1 Transferring and handling C. elegans. 1.2 Introduction to laboratory genetics. 2 Gene expression analysis using transgenic animals. 2.1 Transgenic gene expression analysis in C. elegans: lacZ staining. 2.2 Transgenic gene expression analysis in C. elegans: GFP analysis. 3 Creation and testing of transgenic yeast for use in protein-protein interaction screening. 3.1 Small-scale transformation of S. cerevisiae. 3.2 Transformation of S. cerevisiae to test for non-specific interaction. 3.3 Assaying for protein-protein interaction by reporter gene expression. 4 Yeast two-hybrid screening. 4.1 Protein-protein interaction screening of a C. elegans cDNA library. 4.2 Assaying for protein-protein interaction by reporter gene expression. 5 Isolation and identification of interacting proteins. 5.1 Preparation of electrocompetent E. coli. 5.2 Isolation of DNA from yeast and electroporation of E. coli. 5.3 Small-scale isolation of plasmid DNA from E. coli: the mini-prep. 5.4 Sequencing of two-hybrid library plasmid DNA vectors. 6 Using bioinformatics in modern science. 6.1 DNA sequence chromatogram. 6.2 BLASTing your sequence. 6.3 Evaluating sequence results and choosing an RNAi target. 6.4 Bioinformatics practice questions. 7 Generation of an RNAi vector. 7.1 Small-scale isolation of genomic DNA from C. elegans. 7.2 PCR amplification of target gene sequence from C. elegans genomic DNA. 7.3 Preparations for cloning to generate RNAi vector. 7.3.1 Agarose gel electrophoresis. 7.3.2 Removal of dNTPs from PCR reaction. 7.3.3 Restriction enzyme digestion of PCR product and C. elegans RNAi vector. 7.4 Gel purification of DNA and ligation of vector and PCR-amplified DNA. 7.4.1 Preparative agarose gel electrophoresis. 7.4.2 Gel purification of DNA from agarose gel. 7.4.3 Ligation of vector and PCR-amplified DNA. 7.5 Transformation of ligation reactions. 7.6 PCR screening of

Guy A. Caldwell, Ph.D., is an Assistant Professor in the
Department of Biological Sciences at The University of Alabama in
Tuscaloosa, where since 1999, he has held an undergraduate
professorial appointment from the Howard Hughes Medical
Institute. In 2001, Dr. Caldwell was named a Basil O'Connor
Scholar of The March of Dimes Birth Defects Foundation for his
research into the molecular basis of childhood birth defects of the
brain. Dr. Caldwell is a recipient of grants from The March of
Dimes, National Institutes of Health, the Dystonia Medical Research
Foundation, American Parkinson's Disease Association,
Parkinson's Disease Foundation, and the National Parkinson
Foundation. In January 2003, The Caldwell lab was selected as one
of only 11 worldwide to represent the research goals of The Michael
J. Fox Foundation for Parkinson's Research in their Protein
Degradation Grant Initiative. For his combined teaching and
research efforts, Dr. Caldwell was also chosen as the recipient of
a 2003 CAREER award from the National Science Foundation, the most
prestigious honor for young faculty bestowed by that organization.
He is the author of 2 editions of a widely adopted textbook in
biotechnology sold worldwide in 3 languages by Harcourt. He
currently teaches courses in Molecular Genomics, Neuronal Signaling
Mechanisms, General Biology, and an acclaimed seminar on the
societal impact of the Human Genome Project.

Shelli N. Williams, B.Sc., is a doctoral candidate in the
Department of Biological Sciences at The University of Alabama in
Tuscaloosa, where she has attended the university as an
undergraduate and graduate student since 1997. Following her
early graduation magna cum laude from the university, Ms.
Williams began her graduate work in the laboratory of Dr. Guy A.
Caldwell. She has experience teaching introductory biology
courses to both major and non-major students and has served as
teaching assistant for a senior level discovery-based

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