Table of contents for

There are six main pages plus other smaller pages:

1. home page (logic & experimental design)
2. proteins;
3. cDNA & mRNA;
4. antibodies;
5. DNA & genes;
6. bioinformatics
7. Dictionary: A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

• links to related sites
• other pages

• The contents of each page is provided below, and links to each section are provided.

• Introduction and Purpose
• Overview / Point of view
• Organization of web site (the purpose of the different pages)
• Goals of this site
• How to make comments or send additions to the site

• Why study proteins
• The value of protein purification
• The Logic of Protein Purification
  • Assays
  • Sources
• The strategy and logic of protein purification
• Criteria for purity
• The generality of purification to constant specific activity
• Fractionation of proteins and the value of SDS gels.
• An illustration of strategic decisions and luck in protein purification
• Summary

• Forward
• Some key terms ('cloning' and 'library')
• Cloning strategy
  • cDNA libraries
  • making cDNA
  • Incorporating cDNA into the vector
  • Screening
  • Designing a probe
  • Test for specificity
  • Getting full length cDNAs
• Other methods of isolating cDNAs
  • Cloning from expression libraries
  • Complementation
  • Expression on the cell surface
  • Functional cloning of receptors
  • Homology screening
  • PCR-based screens
  • Plus/minus screening and differential display
  • Two hybrid screening
• Why Isolate cDNAs (expression, localization, sequence info, genetics, expression, in vivo function, for purification, making antibodies and others)
• cDNAs and Experimental Design

• Scope and objective
• Antibodies
• Antigens
• Thinking about antibody-antigen interactions
• Making polyclonal antibodies (antiserum)
• Making monoclonal antibodies
• Uses of antibodies
• Antibody Specificity
• Suitability of antibodies for different purposes

• Forward (moving between genes & genetics and mRNAs & proteins)
• Why is it important to understand the molecular structure of genes?
• How are genomic clones isolated?
  • Using a cDNA
  • From genetic information
• Promoter analysis-the goals
• functional assays of promoters
  • Defining the structure of cis-acting sequences by a functional assay
  • Reporter genes
  • Defining the limits of cis-acting sequences
  • Transfections; understanding differences between stable & transient
  • Some transfection procedures
• DNA protein interactions
  • Identification of transcription factors
  • Foot print analysis
  • Gel shift analysis
• Structure function analysis of promoters
• From DNA sequence to genetic analysis (knock outs, knock ins, conditional knockouts, & transgenes)
  • Genetics vs
  • Reverse genetics
  • Genetic systems
  • How to make mice deficient in the product of a known gene
    • Part one, making a mutation by homologous recombination
    • Part two, getting the mutation into the germ line
    • Making a mutant animal by genetic selection of mutant ES cells
  • Conditional knock outs
    • By regulated, site-specific recombination
    • Conditional expression of a transgene
  • Making subtle mutations/knock-ins
  • Transgenes/ producing animals with an added gene product

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Bioinformatics page

• Introduction to bioinformatics
• Relationship of Bioinformatics to other pages on this site
• Bioinformatics and Experimental approaches
  • 1. Bridging among protein, DNA, and RNA sequences
  • 2. Searching for related sequences in other organisms
  • 3. Searching for functional patterns in proteins and nucleic acids
  • 4. Determine if there are known interactions among proteins
  • 5. Structural studies and predictions
  • 6. Managing data
• Bioinformatics and Scientific communication
  • 7. Getting in touch with the scientific literature
  • 8. Identifying reagents and protocols for their use from biotechnology companies
  • 9. Becoming aware of meetings where scientists exchange information and ideas
  • 10. Find funding opportunities for your ideas and find out what others are doing or want to do.
  • 11. Make a killing on the market.

Dictionary: A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

• gene disruption by homologous recombination
• Knock out mice
• Screening Methods For Detection Of Unknown Point Mutations
• Addition of an epitope to a protein coding sequence: FLAG-tag