Transcript Let`s investigate some of the Hot Areas of Life Sciences in more detail:

Let’s investigate some of the Hot
Areas of Life Sciences in more detail:
• Genomics
– Human Genome Project
– Use of Microarrays or DNA
chips
• Bioinformatics
– Merging biology with
computer science
• Proteomics
– “functional genomics”
Conversations with Professor Bruce Hammock,
UC Davis Professor, Principal Investigator for the SuperFund Project,
Director of the NIH Training Program in Biomolecular Technology &
National Academy Science member:
http://www.niehs.nih.gov/dert/video/hammock.htm
Video Presentations
Dr. Hammock speaks of his early attraction to science and early influences.
What do you think is your most important or exciting scientific discovery?
Remarks regarding the mission and history of the National Academy of Sciences.
The importance of educating the lay public about science and environmental health.
His impressions on the writings of E. O. Wilson and science writers for the public.
What is the most important motivating factor to get young people interested in science?
How did your career in science develop?
What motivates you as a scientist and mentor?
On exciting and emerging fields of science. (He loves metabolomics!!)
A Rough Draft of the Human Genome in
2001 was just the Beginning!
We have ~30,000-40,000 genes
Nature v. 409 Feb. 15, 2001 and Science v. 291, Feb. 16, 2001
The Human Genome Project is
nearly complete!
• What does it all mean?
• How can I store all this genetic code (>3
billion bases)?
• How can I access related databases?
• How can we share data in other databases
over the web?
• What do these ~30,000 genes do?
• Are there related genes in other life
forms?
Biologists need Help from Computer
Scientists and Mathematicians!
TIGR is a good
public database for
looking at gene
sequences from a
number of species..
This allows
scientists to do
comparative
genomics (look for
similarities in the
DNA of other
species)
Comparative Genomics will speed the
Discovery Process for New Drugs:
Scientific American
July 2000
DNA Chip Technology (Affymetrix, Agilent, etc.)
can help find new drugs for cancer therapy
Each spot on chip has
ssDNA (20-mers) from
a different gene
mRNA
ssDNA is added to chip
Thousands of
genes can be
analyzes at one
time
UV light
The color of the spot indicates which genes are being
turned on. Yellow = gene is on (in both conditions)
7
“14 Letters that Spell the Future”
• Washington Post (Aug 2, 2001)
• Bioinformatics is the new buzzword!
• It is difficult to define but a good one is:
“The art and science of using computational tools
to find answers to biological questions”
Bioinformatics:
“The Evolution of Tools”
From the New Yorker
Bioinformatics – Three Levels
•
•
•
•
1. USERS (AS/BS level)
of Information
of Tools
of Instrumentation
In-Silico (Computer)
Modeling
2. INTERPRETERS (BS/MS)
• of Information
•
•
•
•
•
•
•
3. DEVELOPERS*
of Information
of Tools
of Instrumentation
of Architecture/Storage
of Algorithms
of Modeling Strategies
of Visualization Methods
Per Pete Smietana, PhD (bioinformaticist)
*TheseDemand.
people are
in highest
demand
* Highest
Usually
PhD level
Get Schooled for Bioinformatics:
• Biology
– Know basics & Have sense of biological
experimentation and public databases (NCBI,
TIGR, etc.)
• Computer Science
– Programming (C/C++/Perl scripting)
– Database construction (UNIX/LINUX)
– Algorithm design
• Math/Statistics
– Probability, Experiment design, Machine
learning
• Ethics
• “Core Bioinformatics”
per Russ Altman of Stanford’s
Biomedical Informatics Training
Program
–
–
–
–
LIMS (lab information management sys)
EST clustering
Sequence analysis & annotation
Etc., etc. . . . .
The Challenge of Proteomics
Complex Proteome(s)
• Multiple Proteins for
each Gene due to
splicing
• Varied and fragile
nature of proteins
• Quantitative and
Qualitative changes
of the proteome
• Structural and
Functional
Proteomics Studies
Per Tina Settineri, Ph.D., Applied Biosystems
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Which genes are turned off then on ?
Courtesy of Dr. Young Moo Lee
TTC
TGT
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Sequence to Structure to Function:
Homology Implies
Function
Least
Evolutionary Conservation
Most
3D Active Site
3D Structure
Secondary Structure
Protein Sequence
DNA Sequence
Molecular Simulations Inc. San Diego, CA
(databases)