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Signaling Pathways and Summary

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Title: Signaling Pathways and Summary


1
Signaling Pathways and Summary
  • July 3, 2003
  • Signaling lecture
  • Course summary
  • Evaluation process-Dr. Krilowicz (3 pm)
  • Mondays events
  • Student demos of software programs 9-11
  • Evaluations 11-12
  • Visit to Bioinformatics Company 1-2
  • Beach barbeque 2-5

2
What is signal transduction?
  • Conversion of a signal from one physical or
    chemical form into another.
  • In cell biology, commonly refers to the
    sequential process initiated by binding of an
    extracellular signal to a receptor and
    culminating in one or more specific cellular
    responses.

3
What is a signal transduction pathway?
Chemical signals are converted from one type of
signal into another to elicit a molecular
response from the organism. All organisms require
signaling pathways to live.
A?B?C?D?E?F?G
Letters represent chemicals or proteins.
4
What is a second messenger?
  • An intracellular signalling molecule whose
    concentration increases (or decreases) in
    response to binding of an extracellular ligand to
    a cell-surface receptor.

5
Seven levels of regulation of cell growth
An unrepaired mutation in a gene for a DNA-repair
protein, a cell-cycle control protein, or and
anti-apoptosis protein can increase the
likelihood of a cancer developing.
6
Signal Transduction Animations
http//kinase.oci.utoronto.ca/Movies/movies.html

7
Database to deal with signaling pathways (still
in development)
http//www.grt.kyushu-u.ac.jp/spad/index.html
8
One project to organize information of
interacting molecules is KEGG
KEGG (Kyoto Encyclopedia of Genes and Genomes) is
a bioinformatics resource for understanding
higher order functional meanings and utilities of
the cell or the organism from its genome
information. The KEGG project is undertaken in
the Bioinformatics Center, Institute for Chemical
Research, Kyoto University with supports from the
Ministry of Education, Culture, Sports, Science
and Technology (MEXT), the Japan Society for the
Promotion of Science (JSPS), and the Japan
Science and Technology Corporation (JST).
9
Databases of KEGG
  • Metabolic pathways http//www.genome.ad.jp/kegg/ke
    gg2.html - pathway
  • Regulatory pathways
  • Ortholog tables

10
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11
Goals of SoCalBSI
  • 1) Familiarize computer science and molecular
    life science students with bioinformatics
    software programs
  • 2) Introduce programming skills that will enable
    students to independently write programs 
  • 3) Explore the social, moral and ethical issues
    associated with the human genome sequence  
  • 4) Offer career counseling and expose to career
    opportunities
  • 5) Provide research experiences with professional
    bioinformaticists
  • 6) Create opportunities for interactions with
    bioinformaticists
  • 7) Foster long-lasting professional relationships

12
(No Transcript)
13
Course Summary
  • Program Learning Objectives (partial list)
  • Retrieve gene sequence information from GenBank
    and Protein databases
  • Use BLAST program to conduct gene similarity
    searches
  • Align multiple sequences with Clustal W program
  • Predict protein functional motifs with BLIMPs
  • Display and compare 3-D structures of proteins
  • Model protein structure using a homologous
    structure analysis program (Deep View)
  • Write algorithms that will perform a simple
    search of gene sequences stored in a database
  • Understand the statistics used in scoring aligned
    sequences in common programs.
  • Appreciate the ethical issues that developed from
    sequencing the human genome.

14
List of software programs you should be familiar
with
  • PubMed
  • Dotter
  • Needleman-Wunsch global alignment
  • Smith-Waterman local alignment
  • BLAST
  • FASTA
  • Phylip
  • Mascot
  • ChouFasman
  • Kyte-Doolittle
  • GOR
  • Dotter
  • CLUSTAL W
  • BLIMPs
  • PSIPRED
  • DeepView (Swiss PDB viewer)

15
List of databases that we studied
  • Online Mendelian Inheritance of Man
  • MedLine
  • GenBank
  • EMBL
  • DDBJ
  • SWISSPROT
  • Protein Information Resource
  • ProSite
  • BLOCKS
  • Protein Data Bank (PDB)
  • Swiss 2D Gel

16
Concepts in bioinformatics
  • ENTREZ-Suite of connected programs that allow for
    analysis of genes and proteins
  • Modular nature of proteins
  • Sliding window
  • Alignment methods (Local vs. Global)
  • Dynamic programming
  • Statistics (E-value, Z-score, Probabilities,
    Bayes Theorem)

17
Concepts in bioinformatics II
  • Primary and secondary databases
  • Similarity vs. identical amino acids
  • Scoring matrices (PAM, BLOSUM, PSSM)
  • Multiple alignment
  • Guide trees
  • Neural networks
  • Protein structure prediction
  • Developing software program that aligns sequences
    based on scoring matrices

18
Future of bioinformatics
  • Traditionally divided into two camps-users and
    developers
  • SoCalBSI students should have an advantage over
    the typical applicant to graduate school or
    industry position
  • Online Journal of Bioinformatics
  • Bio Inform-a newsletter for bioinformaticists
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