New views of life
The genomes of the human, mouse, fruit fly, a worm, a weed,
and many microbes have been mapped and sequenced. We
now have the parts lists for these organisms. We are learning
that many of the parts—the genes that direct cell machinery to
produce proteins—are related, from organism to organism.
Researchers are now trying to figure out what these parts do in
relationship to each other (systems biology) and how they vary
among species and individuals within each species. Then researchers can write the
operating manuals. The rewards will be great.
"One long-term goal of this research is to develop
targeted drugs that are effective for a specific
disease," says Michelle Buchanan, director of
ORNL's Chemical and Analytical Sciences Division.
"To design these therapeutic drugs, you need detailed
knowledge about the many molecular-level processes
that occur within a cell." Acquiring such knowledge is
not an easy task.
"We frequently hear about new human genes that
play a role in cancer and diseases of the heart, central
nervous system, and other organs," says Reinhold
Mann, director of ORNL's Life Sciences Division.
"Some diseases can be traced to one altered DNA
base pair in a particular gene. However, genome
characteristics or changes that make some people
more likely to get sick involve complex, intricately
timed, and balanced interactions among a variety of genes and other signals encoded in
the genome. Our current state of knowledge of how the genome is interpreted to
provide the diversity of life is extremely limited."
ORNL researchers use various technologies to characterize DNA and proteins. This image shows the order of chemical bases in a strand of DNA. The bases are labeled with dyes that fluoresce in different colors when exposed to laser light. The sequence was obtained by gel electrophoresis in a PE Biosystems DNA-sequencing machine at ORNL.
"The next step," says Buchanan, "is to identify which genes turn on to make particular
proteins. Then we must identify the protein complexes, or protein machines, in which
proteins work together in the cell to carry out specific roles and help perform life's most
essential functions. These protein complexes are involved in signaling pathways that tell
cells what to do and allow them to communicate with each other."
Characterizing the roles of protein machines in cells is the objective of DOE's
"Genomes to Life" initiative. This knowledge will help scientists predict how cells and
their genes will respond to changes in the environment, such as exposure to a toxin.
Some of this knowledge will be obtained at DOE's Center for Structural and Molecular
Biology at ORNL. Scientists at this user center directed by Buchanan will obtain
information about protein interactions through mass spectrometry, computational
biology, and small-angle neutron scattering (SANS). SANS will be conducted using the
planned Bio-SANS instrument that is to be completed at ORNL's High Flux Isotope
Reactor in 2003. Various studies of proteins and other biological materials are also
planned. These studies will be conducted using biological instruments at the Spallation
Neutron Source, to be completed in 2006 at ORNL.
Research by Oak Ridge biological scientists is aimed at learning which genes are
expressed when certain microrganisms are exposed to environmental toxins or radiation.
DOE is interested in funding microbial research partly because microbes can help
remediate mixed waste sites by converting toxic metals from the soluble to the insoluble
state to help keep them on-site.
In addition, there is great interest in learning about the proteins that are expressed by
microbes under various conditions. ORNL's experts in mass spectrometry can identify
proteins by determining their molecular weight and amino-acid sequence and comparing
this information with that in a protein database. In this way, they can find protein
signatures and then work backwards to determine the gene sequence coding for that
protein, thus identifying the gene that was expressed, say, as a result of exposure to a
A protein can have as many as 200 modifications in response to the actions of other
proteins or environmental influences. These post-translational modifications (PTM),
such as the addition of a phosphate or carbohydrate to a protein, can change the
protein's activity. For example, if a PTM is present on a regulatory protein A, it
becomes a misshapen key that no longer fits into Protein B, preventing it from turning
on a downstream gene, possibly causing miscommunication between cells. Mass
spectrometry is an excellent tool for identifying proteins that have been modified.
ORNL researchers seek to understand complex biological systems at the organism as
well as the molecular and cellular levels, says Mann. To understand how
hormone-mimicking chemicals can affect development, ORNL researchers are studying
gene and protein expression in see-through embryos of zebrafish. They are also trying
to identify the genes that enable trees to produce better wood products and fuels and
store more carbon from the air. To understand the functions of genes in mammals,
ORNL researchers are determining which genes are expressed in the skin of mice and
which mouse genes in their mutant form cause maladies also found in humans, such as
polycystic kidney disease, obesity, chronic hereditary tyrosinemia, and epilepsy.
Researchers use microarrays (gene chips) and computational tools for these expression
studies. For example, our experimental researchers collaborate with our computational
biology experts, who make sense out of gene ex-pression data using super-computers.
They are practicing the discipline of bioinformatics, the study of genetic and other
biological information using computational and statistical techniques.
Yun You examines the image of a mouse embryo magnified in an optical microscope. The image is captured by a difital camera and then transferred to a computer.
"Knowing functions of all genes in the genome,
by itself, will not lead to understanding the
processes of a living organism," Mann says.
"The reason is the biological system's
complexity. Expression of genes can be
regulated in a virtually unlimited number of
ways, depending on location in the body, time
in the development of the organism, and
environmental conditions and exposures.
"Certain protein complexes can bind to specific
locations in an organism's genome, thereby
controlling the expression of a gene sometimes
far away from these binding sites. The number
of these regulatory protein complexes is finite, perhaps some 10,000, but taken together
with the number of genes and regulatory binding sites in the genome, there is a
combinatorial explosion that works against any brute force approach solely based on
experimental research. That is why collaborations between experimenters and
computational biologists are so important. They are a hallmark of biological
investigations at ORNL."
Computational biology researchers in ORNL's Life Sciences Division have identified
many genes in bacterial, mouse, and human genomes and have computationally
analyzed the human genome using an ORNL-developed gene-finding computer
program. They have written and used assembly programs and analysis tools to produce
draft sequences of the 300 million DNA base pairs in chromosomes 19, 16, and 5 for
DOE's Joint Genome Institute (JGI). They have also analyzed 25 complete microbial
genomes (52,000 genes) and many JGI draft microbial genomes (1000 genes/day).
They have predicted the structures of proteins (100 proteins/day) from amino-acid
sequences using an ORNL-developed, protein-threading computer program.
The section's programmers have written algorithms and developed other tools to make
it easier for biologists to use computers to find genes and make sense out of the rising
flood of biological data. These data are produced in studies of biochemical pathways
and processes, cellular and developmental processes, tissue and organism physiology,
and ecological processes and populations. Through ORNL's user-friendly Genome
Channel Web site, its Genomic Integrated Supercomputing Toolkit, and the IBM
super-computer at DOE's Center for Computational Sciences, the international biology
community, including pharmaceutical industry researchers and academics, have easily
obtained genetically meaningful interpretations of their DNA sequences and other data.
ORNL's Web site is popular in the biological community (150,000 sessions per month).
Thanks to ORNL's interdisciplinary approach to complex biology using state-of-the-art
technologies, we believe we have the right stuff to better understand the stuff of life.