completion of the Department of Energys Human Genome Project
indicates the remarkable progress scientists have made in understanding
the genetic basis of life. The Genomes to Life Program, the successor
to the Human Genome Project, has an even more ambitious goal: to
understand life in a comprehensive and integrated manner. The initiative
is an example of systems biology, the study of tissues as integrated
systems rather than as isolated parts, such as individual genes,
proteins, or chemical reactions.
of experiments on isolated chemical pathways or proteins laid the
foundation for the study of complex biological systems. Now, the
increasing interest in systems biology reflects the fact that we
do not yet have a comprehensive understanding of how a cell functions,
says Livermore physicist Andrew Quong. He says that progress in
systems biology requires a multidisciplinary effort involving experts
in biology, biochemistry, molecular biology, chemistry, physics,
and computer science. Only when experts from various disciplines
work together on a computational model can we begin to understand
the interactions between genes and the thousands of subcellular
components and chemical reactions, many of them linked in subtle
ways to one another, says Quong.
advanced computational modelsbased on sound chemical and physical
principles and new laboratory experimentsrunning on the fastest
supercomputers will permit scientists to visualize and understand
the complex interactions and changes within a simulated cell. For
example, a scientist will one day be able to predict a cells
response to different mixes of nutrients or exposure to a drug or
a toxin from a pathogen.
notes that widely used, but relatively simple circuit diagrams treat
cellular processes as dimensionless electrical circuits. Previous
attempts at computational models have treated only a small set of
chemical reactions. By contrast, Livermore scientists use models
that combine many more reactions, and, where possible, they extend
the simulations to realistically portray a cell in three dimensions.
project is to develop a three-dimensional (3D) model of calcium
ion transport within epithelial cells, which line all body cavities,
including the lungs, digestive track, and kidneys. The research
is funded by the Laboratory Directed Research and Development program.
Calcium ions are fundamental signaling ions in cells and play a
role in many cellular processes, from cell division to muscle contraction.
Quongs research is among the first attempts at modeling cellular
processes to take advantage of massively parallel supercomputers,
which use many microprocessors working in tandem.
research builds on Livermores experience in computational
biology, supercomputing, biosecurity, and multiscale modeling of
materials and chemical reactions. The effort also involves laboratory
experiments done by Livermore biologists to supply essential data
for the developing model.
immediate payoff from the research will be increased understanding
of a key cellular function, but the Livermore team hopes that the
model will lead to new insights into the interactions between pathogens
(viruses or bacteria) and human host cells. These insights will
likely result in advances to control and prevent disease as well
as initiatives in homeland security to detect and thwart any attempt
at biological terrorism.
||Waves of calcium ions are
believed to be an important signaling mechanism as they move
within and across epithelial cells. The waves are coordinated
by inositol-1,4,5-triphosphate (IP3), which binds to certain
cell receptors. The diagram illustrates the flow of calcium
and IP3 molecules from (a) one cell to (b) its neighbors.
Learning from High Explosives
Quongs team is modeling the flow of calcium
ions inside kidney epithelial cells using ALE3D, a computer code
originally developed at Lawrence Livermore for studying the detonation
of high explosives. ALE3D is part of the family of codes belonging
to the Advanced Simulation and Computing program, an element of
the National Nuclear Security Administrations Stockpile Stewardship
Program to ensure the safety and reliability of the nations
A code for high explosives
might not seem applicable for mimicking cellular processes. However,
the codes flexibility allows it to model chemical reactions
and ions within a cell much as it tracks chemical reactions and
the transport of molecules and ions created by chemical explosives.
Team member and chemist
Albert Nichols notes that the chemistry and underlying physics in
both a functioning cell and a high-explosives detonation are the
same. Some adjustments must be made, however, for enzymes, which
are not found in inorganic systems. Nichols also points out that
in models of purely chemical systems, reactions move toward thermodynamic
equilibrium, whereas in a cell, equilibrium means death.
For the cell study, ALE3D
tracks waves of calcium ions within a 3D mesh that corresponds to
the volume of several adjoining epithelial cells. Our goal
is to track the flow of calcium ions at any point in space inside
the cell, says Quong.
Epithelial cells are barriers
that protect the body from the external world and inhibit and control
the movement of water, molecules, and ions across these barriers.
Quong notes that a pathogens first interaction with a human
is with epithelial cells, so understanding the signaling and ion
transport pathways in these cells has important applications to
human health and protecting against bioterrorist attacks.
From among the large family
of different epithelial cells, the team decided on those found in
the kidney. These cells
can be grown easily in culture. Also, they have a roughly cubic
shape, with one highly specialized side facing the outside environment.
This asymmetric design can be represented realistically with ALE3D.
Systems biology demands innovative experiments and instrumentation.
Although not new to chemists, secondary ion mass spectrometry
(SIMS) is beginning to be applied by biologists. With
its extreme sensitivity (a few parts per billion) and
spatial resolution (50 to 100 nanometers), SIMS is a powerful
SIMS uses a stream
of energetic ions that bombard the surface of a material
under investigation. Upon impact, these ions generate
positively and negatively charged ions, which are gathered
by electrically charged lenses, imaged, and identified.
mass spectrometers are typically used in industry to characterize
materials and to examine the surface of semiconductors
and polymers. Livermores three machines are used
to map the surfaces of mirrors and optics for the Department
of Energys National Ignition Facility, now under
construction at Livermore.
SIMS is unique
because it can yield a map of any selected molecules or
ions of interest. This is an important feature for biological
applications because the alternative in many cases requires
homogenizing many cells and then testing for the presence
of the molecules or ions. The result is an average of
a cell population, with no information about location
within a cell.
processes are dependent upon spatial localization,
says Livermore biochemist Judy Quong. Quong is the principal
investigator of a Laboratory Directed Research and Development
project studying the application of SIMS to subcellular
imaging. One area of research seeks to determine the distribution
of PhIP (2-amino-1-methyl-6-phenyl-imidazo[4,5-b]pyridine)
in cells. One of the mutagenic compounds known as heterocyclic
is a carcinogen that has been consistently demonstrated
to cause dose-dependent mammary and prostate tumors in
rats. Another area of research is using SIMS to determine
the spatial resolution of isotopically labeled cancer
drugs in cells. Improved understanding of the distribution
and cancer drugs in cells could lead to more effective
Working with physicists
Ian Hutcheon and Kuang Jen Wu, Quong uses two different
mass spectrometers, a recently acquired static time-of-flight
secondary ion mass spectrometer and a dynamic secondary
ion mass spectrometer. The Laboratory will be acquiring
a new nanoscale dynamic secondary ion mass spectrometer
(NanoSIMS), which has a spatial resolution of 50 to 100
nanometers and greater sensitivity than Livermores
current dynamic instrument. NanoSIMS will be only the
second such machine in the nation dedicated to biological
Because SIMS can
detect any element, it is an ideal technique for helping
physicist Andrew Quongs team locate calcium that
is sequestered in cellular organelles, specialized cell
parts analogous to an organ. SIMS will be able to generate
a horizontal and vertical profile of the calcium distribution
within frozen cells. The results will be compared to those
gained from standard laboratory methods that use radioisotopes
in live cells to locate calcium.
says she is hopeful that more Livermore biologists will
take advantage of SIMSs capabilities. Were
trying to introduce biologists to new techniques that
are normally used only by chemists and materials scientists.
locate the three-dimensional position of calcium ions
before they are released in a wave, the modeling team
will be using secondary ion mass spectrometry (SIMS).
Unlike electron microscopy, SIMS can detect any ion or
molecule of choice, as seen in these images. (a) A scanning
electron microscope image of clusters of human epithelial
cells indicated by the arrows. Although the image shows
the morphology of the cells, it cannot reveal the presence
of selected molecules. (b) An image of the same cells
taken by a secondary ion mass spectrometer shows the location
of phosphocholine, a molecule found in cell membranes.
(c) A SIMS image of the same cells shows that the PhIP
mutagen is also present in this cell membrane.
on Calcium Waves
In simulating the transport
of calcium ions in kidney epithelial cells, the model includes the
movement of inositol-1,4,5-triphosphate (called IP3) molecules because
they coordinate the release of calcium ions in waves. The waves,
lasting several seconds each, are believed to be an important signaling
mechanism as they move within and across epithelial cells. By binding
to receptors, which are folded proteins located within the cell,
IP3 molecules trigger the release of calcium.
Although there have been
other models of calcium waves, they have been limited to one or
two dimensions. Says Quong, Were constructing for the
first time a 3D model that is consistent with experimental data
and is based upon valid physiology and chemistry.
One goal of the Livermore
model is to accurately reflect where calcium is stored within the
cell prior to being released as part of a wave. Calcium ions are
often found sequestered in certain organelles, specialized cell
parts analogous to organs. A series of laboratory experiments on
kidney epithelial cells, grown by Livermore molecular biologist
Michael Thelen, will reveal the location of calcium-containing organelles.
The experiments will use
antibodies labeled with fluorescent dyes to measure and visualize
the calcium. The data will then be fed into the model.
is also planning to image live cells with a confocal microscope.
This type of microscope focuses light in a narrow plane, thereby
allowing images of progressively deeper slices through a live cell.
The observations will be compared with those gathered from secondary
ion mass spectrometry (SIMS) imaging. (See the box above.)
Although the model is still
incomplete, Quong has successfully used it to perform simulations
based on published data from laboratory studies of kidney epithelial
cells. The simulations model a group of several cells measuring
about 25 micrometers in diameter. They show the initiation of calcium
waves within a single cell and the propagation of the waves through
neighboring cells. The simulations, with a resolution of about 1
micrometer, were completed on several Livermore supercomputers processing
the flow of ions in epithelial cells may help scientists treat kidney
and lung diseases, says Quong. For example, calcium concentration
affects the movement of cilia (tiny brushes) that are found in lung
epithelial cells. The cilia catch and move pathogens and foreign
particles that are trapped in mucus secreted by the cells. However,
people suffering from cystic fibrosis, the most common genetic defect
among Caucasians, produce abnormally thick mucus that can make breathing
difficult and inhibit the movement and effectiveness of the cilia.
The thick mucus is believed to be caused by the faulty transport
of sodium and chloride ions in and out of the cells. This variable
of ion transport will be incorporated into the model.
|A Livermore code simulating
the flow of calcium ions compares favorably to experimental
images of calcium ion waves. (a) An image from confocal microscopy
taken by Japanese scientists captures a wave of calcium ions
(bound to a red dye) that began in one epithelial cell and spread
to its neighbors. (Image reprinted with permission from Science
284, May 28, 1999, 1529. Copyrighted 1999, American Association
for the Advancement of Science.) (b) The Livermore code simulates
a wave of calcium ions (in red) triggered by the cell located
in the center. The simulated cells measure about 25 micrometers
across. The white lines represent cell membranes and the missing
portions indicate gaps in the membrane where calcium ions pass
from one cell to another.
Livermore model is pointing the way toward a new approach to understanding
how cells operate and diseases begin and progress. The eventual
result will likely make the biological sciences more predictive.
A cell has so many interacting pathways that we must understand
how everything is related, and computational models can help us
do that, says Quong.
models of chemical pathways in the cell are important to both human
health and national security. Indeed, the research directly supports
Livermores national security mission by helping scientists
study issues related to biosecurity, such as the effects of pathogens
on cell function and hostpathogen interactions.
Our long-range goal
is to develop tools for homeland security and health care,
Quong says. Understanding the interactions between a host cell and
a pathogen will help scientists learn how to shut off bacterial
toxin production, defeat genetically engineered organisms, defend
against new antibiotic-resistant microbes, predict a host cells
response to infections, defend agriculture against pathogens, and
develop new drug delivery systems.
Computational models, once
reserved for phenomena such as explosions and material fracture
but now used for cells and their processes, are sure to become an
important tool for scientists, health professionals, and those guarding
our national security.
The 3D epithelial cell modeling team consists of Michael Colvin,
Aaron Golumbfskie, Kenneth Kim, Alison Kubota, Christopher Mundy,
Albert Nichols, Andrew Quong, Judy Quong, and Michael Thelen.
Key Words: Advanced
Simulation and Computing program, ALE3D code, biosecurity, calcium
ion waves, confocal microscope, cystic fibrosis, Genomes to Life
Program, homeland security, Human Genome Project, secondary ion
mass spectrometry (SIMS), systems biology.
For further information contact Andrew Quong (925) 422-5641 (firstname.lastname@example.org).