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.htmVideo 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!

Nature v. 409 Feb. 15, 2001 and Science v. 291, Feb. 16, 2001We have ~30,000-40,000

genes

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

7

DNA Chip Technology (Affymetrix, Agilent, etc.) can help find new drugs for cancer therapy

The color of the spot indicates which genes are being turned on. Yellow = gene is on (in both conditions)

mRNA

ssDNA is added to chip

Each spot on chip has ssDNA (20-mers) from

a different gene

UV light

Thousands of genes can be

analyzes at one time

“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)*These people are in highest demand* Highest Demand. 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”

– LIMS (lab information management sys)– EST clustering– Sequence analysis & annotation– Etc., etc. . . . .

per Russ Altman of Stanford’s Biomedical Informatics Training Program

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

TGT AAT AGT TAT ATT TTCATT ATA AAT TGT GTT TGT AGA CAT CAT AAA TTT AAAACA TGG CTT TTT AAC CTGATA AAT CCT ACG AAT ATTTGT AAT AGT TAT GTT ATTGCA GTA AGT ACC GTT TGT ATT ATA AAT TGT GTT CTG

TGT AAT AGT TAT ATT TTCATT ATA AAT TGT GTT TGT AGA CAT CAT AAA TTT AAAACA TGG CTT TTT AAC CTGATA AAT CCT ACG AAT ATTTGT AAT AGT TAT GTT ATTGCA GTA AGT ACC GTT TGT ATT ATA AAT TGT GTT CTG

Which genes are turned off then on ? Courtesy of Dr. Young Moo Lee

Sequence to Structure to Function:

Homology Implies

Function

3D Structure

Secondary Structure

Protein Sequence

DNA Sequence

Evolu

tionary

Con

serv

atio

n

3D Active Site

(databases)Molecular Simulations Inc. San Diego, CA

Most

Least