Faculty and Student Teams Program

Project Descriptions

Argonne National Laboratory
The Biosciences (BIOS) Division

Requesting applications from science or engineering faculty members at institutions serving students underrepresented in science, engineering, mathematics and technology to work on the following projects.

Project Description

Research in this division is aimed at defining the biological and medical hazards to humans from energy technologies and new energy options. Health-related studies are supported by fundamental research in scientific disciplines, including molecular and cellular biology, crystallography, biophysics, genetics, radiobiology, biochemistry, chemistry, and environmental toxicology. The research involves the integration of findings from investigations at the molecular, cellular, tissue, organ, and whole-animal levels, with the ultimate aim of applying these findings to problems of human health. The Division is organized into two scientific sections (Biophysics, and Functional Genomics), plus a Structural Biology Center that operates two beamlines at the Advanced Photon Source. Each section comprises several research groups with considerable interaction occurring among all groups. Divisional support facilities include an editorial office, a computer center, a biomedical library, and an instrument design and maintenance shop.

Some representative examples of the research projects available for FaST teams are listed below. More detailed information regarding the myriad of research projects occurring at Argonne National Laboratory can be found online in our Research Participation Catalog (http://www.dep.anl.gov/catalog/catalog.htm). The catalog contains the titles and descriptions of almost all research projects underway at Argonne National Laboratory. The catalog is available for downloading OR one can browse the catalog online.

Research Opportunities in the Biosciences Division

            (a) To characterize the mechanisms involved in regulation of gene expression through the development and use of tools for analysis of DNA, RNA, and proteins;

            (b) To deepen understanding of protein stability and protein-protein interaction by using protein engineering techniques;

             (c) To predict protein structure and function from gene sequence data and then use the predictions to select protein targets for structure determination;

            (d) To probe genome sequences with both laboratory and computational techniques in order to discover regulatory pathways relevant to human health, environmental restoration, and energy production;

            (e) To develop the analytical approaches and software required to exploit massively parallel computers for exploration of the three-dimensional structures of proteins; and

            (f) To exploit fully the unique capabilities of Argonne 's Structural Biology Center (SBC) at the APS in exploring currently intractable questions involving reaction mechanisms and molecular structure.

BIOPHYSICS SECTION

A major research goal in biological science is to understand the relationship between the amino acid sequence of a protein and its three-dimensional structure, stability, and function. Because the interactions between the amino acids within a protein obey the same laws of physics that control interactions between proteins, study of the self-association properties of immunoglobulin light chains is relevant to the fundamental properties of all proteins. Antibody light chains are produced in large quantities by patients who have myeloma, a neoplasm. Because the proteins produced by two patients will be similar in three-dimensional structure but will differ in amino-acid sequence, differences in self-association (under various conditions of pH, ionic strength, and temperature) can be related to the physics that determines the protein structure and function. In addition, these studies provide increased understanding of the biophysical properties of these proteins that lead to disease complications in many patients and provide a model system for other, structurally related, protein-based diseases. We are using site-specific mutagenesis, molecular dynamics simulations, and novel bioinformatic approaches to help analyze experimental results.

Protein Crystallography and Molecular Modeling

SBC/APS USER FACILITY

This program applies modern crystallographic methods to rapidly determine structures of biological macromolecules-proteins and nucleic acids-as single molecules, as multicomponent complexes, and complexed with bound ligands. A significant effort in this program is directed toward improving the methods for crystallographic investigation of macromolecular structure, by developing new and better methods and instruments to measure, process, and analyze diffraction data using cryocrystallography. The program operates two advanced x-ray beamlines at the Advanced Photon Source, for tuned, high-throughput, monochromatic x-ray diffraction data collection that is used to determine crystal structures. Crystal structures are being studied of chaperone proteins which direct the folding of protein receptors, important enzymes from pathogenic and thermolphilic organisms, and nucleic acids. Structures of proteins derived from genomic analysis as part of our structural genomic initiative are being determined at this facility. Major equipment includes undulator and bending magnet beamlines, rotating-anode x-ray generator, with imaging plate detector, modern workstations with large capacity data-storage disks, interactive graphics workstations for molecular modeling, HPLC, FPLC, and ectrophoresis equipment, and all necessary facilities and equipment for molecular biology, molecular genetic manipulations of DNA, protein purification and crystallization, and activity assays.

PROTEIN ENGINEERING

This program is aimed at a generalized understanding of how the three-dimensional structure of a membrane protein defines its function. Historically, our work has focused on the bacterial photosynthetic reaction center, a transmembrane protein complex that functions in the process by which light energy is converted into chemical energy. More recently, our research focus has expanded to the development of a generalized system for the heterologous expression, purification, and crystallization of any membrane protein for structure determination or functional characterization. Techniques consistently exercised include gene cloning with plasmid vectors, PCR amplification of DNA sequences, DNA sequencing, protein and DNA gel electrophoresis, protein expression and purification, spectroscopy, bioassay of mutant phenotypes, and protein crystallization. We are in the process of automating many of our routine methodologies using robots recently installed within the division.

STRUCTURAL STUDIES OF MACROMOLECULAR ASSEMBLIES

Recognition of biological macromolecules and their interaction and assembly into larger supermacromolecular structures are at the heart of many important processes in molecular and cellular biology. For example, macromolecular assembly occurs in protein biosynthesis, in the recognition of receptors by protein hormones, in the folding of proteins, and in the recognition of and binding to nucleic acids by proteins that regulate the expression of genetic information. We are studying macromolecular assemblies at the atomic and molecular levels by x-ray crystallography, in particular the protein-protein interactions of molecular chaperones of the hsp60 and hsp70 classes, and large oligomeric enzymes, and protein-nucleic acid complexes. Because the crystals of macromolecular assemblies are usually small and fragile and have large unit cell dimensions, they diffract weakly. Furthermore, these crystals have large, complex structures and their structure determination is experimentally demanding. These studies take advantage of the Advanced Photon Source and the Structural Biology Center and the Midwest Center for Structural Genomics facilities at Argonne . The techniques being used include molecular biology and biochemistry, liquid chromatography and electrophoresis, and synchrotron-based x-ray crystallography. Robotic workstations support purification, crystallization, data collection and structure determination.

HIGH THROUGHPUT APPROACHES TO STUDY PROTEIN FUNCTION

The abundance of genomic sequence data from different organisms provides an opportunity to accelerate our understanding of protein structure and function. However, optimal utilization of this information requires the development of high throughput methods for the generation of expression clones and the evaluation of protein function. We are developing automated methods for high throughput gene cloning and expression, site-specific mutagenesis, and the study of protein function. A Beckman Coulter Core System with integrated liquid handling stations and supporting devices provides the capability  for high throughput production of expression clones for structural genomics and other large-scale programs that aim to characterize protein structure and function. This comprehensive strategy provides an alternative to the single protein approach that has previously dominated cell biology. The current cloning and analysis process spans four days with a maximum linear throughput of 400 targets per production run. The output generated from the expression cloning process is a 96-well plate map that specifies the location of soluble expression clone plasmids. Although developed for structural genomics, the experience gained by implementation of these initial protocols will provide a platform for extension of the system capabilities for application in other growth areas of high throughput molecular biology including site-specific mutagenesis, phage display, and protein interaction studies.

BRIDGI BRIDGING BIOSCIENCE AND NANO-SCIENCE:  DEVELOPING NOVEL TOOLS FOR UNDERSTANDING PROTEIN-LIGAND INTERACTIONS FOR SYSTEMS BIOLOGY

HPUT AA key aspect of the functional characterization of genomes is the understanding and consequent mapping of interactions among proteins and between proteins and ligands at systems level. This project is involved in the development of novel methods to make this mapping possible by engaging the combination of bioscience and nanotechnology. Particular research efforts for this project emphasize the use of single molecule manipulation and detection methods (such as scanning fluorescence correlation spectroscopy) to select ligands directly from combinatorial libraries. Since unveiling the mechanism of protein-ligand interactions plays an important role in elucidating protein functionality, we will also develop new tools to solve the protein binding domain structure using surface enhanced Raman spectroscopy.

FUNCTIONAL GENOMICS SECTION

PROTEOMICS

Two-dimensional gel electrophoresis coupled with computerized image and data analysis is being used to characterize the normal protein composition of cells and to detect changes in response to environmental pressures. Current studies are focused on the analysis and identification of proteins produced by microorganisms. In addition to two-dimensional gel electrophoresis of proteins (isoelectric focusing combined with sodium dodecyl sulfate polyacrylamide gel electrophoresis), this project involves the use of image and data analysis algorithms, World Wide Web databases, and mass spectrometry. The construction and maintenance of interactive Internet databases is an important part of the data presentation for this project.

Our laboratory is conducting research into the interaction of trace metals such as copper and zinc with proteins and how these interactions change during cellular processes to affect protein activity. It is our contention that metal:protein are regulated dynamically during numerous cellular processes and such regulations may act as a form of post-translational regulation of a protein’s structure and function. As a system of study, we are using several models of angiogenesis, the process by which new blood capillaries are formed. It is well-known that angiogenesis is high sensitive, both in vitro and in vivo, to bioavailable copper. We are employing and developing numerous methodologies to investigate dynamism in the metalloproteome during endothelial cell angiogenesis. These include use of the Advanced Photon Source for high resolution x-ray fluorescence metal mapping in situ, development of separative methodologies for metalloproteins, and isolation and identification of novel metalloproteins used by these cells as they undergo morphogenetic differentiation.

biochemical toxicology

This research program is designed to investigate health effects of toxic metals to which humans may be environmentally or occupationally exposed. One research area focuses on the role of pregnancy, lactation, or ovariectomy in the susceptibility of animals to bone loss after cadmium exposure. Mechanisms of cadmium action on bone are studied in isolated bone cells in culture. Molecular pathways of cadmium action are investigated for specific genes known to influence bone resorption and by gene expression microarray to identify unknown genes. Another research area focuses on the biochemical pathways for toxic heavy metals, including their uptake and tissue deposition. The role of metallothionein, a metal-binding protein, is studied using normal and metallothionein-deficient mice. Measurements of calcium and cadmium content in tissues are performed using atomic absorption spectroscopy.

ANTIBODY ENGINEERING

With the recent completion of two hundred sequenced bacterial and six eukaryotic genomes, the scientific community is entering a “post-genomics era”. To add value to this accomplishment, the community’s attention is now directed at determining the function of the thousands of gene products, proteins, in each cell. Traditionally, one valuable type of reagent that is widely used to probe cells and learn when the protein is synthesized, where it is localized, and what it is associated with in the cell is the antibody. However, it typically takes two to three months to generate rabbit or mouse antibodies to each individual protein, and there is limited control by the investigator on the quality of the antibodies generated by the immunized animals. To overcome the limitations of antibody generation and to meet the need for thousands of antibodies, we utilize phage-display to isolate high-affinity and selectively generate designer antibodies to any protein. Such antibodies will be used to 1) affinity purify the target proteins from cells, and then identify interacting proteins through gel electrophoresis and mass spectrometry, 2) promote crystallization of proteins for x-ray diffraction studies at the Advanced Photon Source (APS), and 3) format the antibodies as arrays onto glass slides, with which one can measure the concentrations of many proteins simultaneously in cells, as they respond to stimuli or become diseased.

A major project within this laboratory is analysis of the mechanism by which small molecules bind to proteins. In spite of the fact that multiple three dimensional pictures have been obtained of protein-ligand pairings, the pace of rational drug design has been hindered by a lack of global coherent rules underlying small molecule-protein interactions. By studying the pattern of virally-presented combinatorial peptides binding to common metabolites such as ATP and glucose, and correlation those sequences with three dimensional structures of known metabolite/protein pairs, we aim to create a database of peptide sequences which are predictive for metabolite binding in known protein sequences. Information derived from this work can eventually be extended to combinatorial chemistry-derived drugs predict potential targets within the human body prior to clinical trials.

Mortality in over 90% of cancer patients is the result not of the effects of the primary lesion, but the crowding out of normal cells by metastatic tumor cells at secondary sites within the body. Cellular migration of tumors is dependent upon both the successful disruption of cell-cell contacts at the primary site and the erection of proper scaffolding at the secondary site(s). A major step in scaffolding construction must include the attraction of new blood vessels (or angiogenesis) to feed and oxygenate the new tumor. These new vessels are primarily built with a class of cells called endothelial cells, which are one of the very few cell types in mammals that have the ability to migrate post-embryonically. Our group is using a systems biology approach to identify the major protein players involved in endothelial cell migration, differentiation, and morphogenesis in order to develop a new class of side effect-free anti-cancer drugs.

Our recently acquired ability to decode the genomes of both uni- and multi-cellular organisms (including man) has given us the blueprint for understanding biological processes at a level not before possible. The conversion of sequence information into the who, what, where, when, how and why of any one biological process, however, will require the simultaneous application of a number of intersecting methodologies. Knowledge of the three dimensional structure of a protein will in turn frequently translate into functional information, allowing for the elucidation of unexpected links in biological pathways not as amenable to discovery by the more traditional hypothesis-driven research methods.

Small angle x-ray scattering (SAXS) of proteins and macromolecular complexes in solution has been shown to reliably yield information about the size and shape of proteins. More recently it has been demonstrated by our group that wide angle scattering patterns (WAXS) obtained at high flux third generation synchrotron beam lines are not only sensitive to protein conformation states, but the scattering patterns generated can be quantitatively compared to detailed structural models. This data, made possible by third generation synchrotron sources, provides a rich source of structural information that has not yet been exploited. Given the broad range of conditions and particle sizes amenable to solution x-ray scattering, a combination of HTP SAXS and WAXS analysis downstream from a large-scale protein production facility has the potential to generate information on the size, shape and structural class (i.e. fold) of every expressed protein.

This project proposes to establish and standardize a SAXS/WAXS protocol to collect structural data on a large number of proteins; construct a database of small and wide angle scattering patterns; and to use this data to assign a structural class to each of the proteins studied. The long term goal is a high throughput method for experimentally assigning the structural class of every protein that can be expressed from a genome. This work will require the high brilliance focused undulator beams at the Advanced Photon Source (APS) that generate a flux density 100-fold greater than those of second generation sources.

microbiology

Microbes can convert agricultural feedstocks, such as sugars derived from corn, into valuable chemicals, and have long been exploited for this ability. Efforts are now in progress to expand their use to include the production of larger-volume, less-expensive chemicals through new "green" processes. At Argonne, modern techniques in microbiology, genetic engineering, and enzymology are applied in "metabolic engineering", in which metabolic pathways are altered by adjusting gene expression or introducing new enzymes, thereby channeling metabolites to the desired end products. Another major activity of the Microbiology Group involves a collaboration with structural biologists in determining the structures of diverse microbial proteins. This project, funded by NIH, seeks to accelerate greatly the rate at which protein structures can be solved, as well as provide a complete library of potential protein structures. In that effort, we have developed new expression vectors and novel cell culture methods that facilitiate high-throughput production of proteins. Additional vectors under development promise to improve the solubility of expressed proteins and to allow their production in host cells other than E. coli.

Microbes can convert cheap, renewable resources to valuable products and have long been exploited for this ability. Efforts are now in progress to expand their use to include the production of larger-volume, less-expensive chemicals. New processes and products to be developed will reduce both dependency on petroleum and the environmental liabilities of some industrial chemicals. At Argonne , modern techniques in microbiology, genetic engineering, and enzymology, as well as classical approaches, are being applied in this effort. Addition of foreign genes or alteration of gene expression, called "metabolic engineering", attempts to alter the metabolic pathways of the microbes to produce different chemicals. Site-specific mutagenesis of proteins attempts to change the specificity or stability of enzymes to create novel catalysts that will carry out useful reactions not performed by naturally occurring enzymes. Strains developed by these approaches are evaluated in laboratory scale fermentations, which are then optimized for production of the desired metabolites.

terrestrial ecology

The ability of plants to adapt or respond to a changing environment is dependent on homeostatic capacities that minimize the cost of growth and biomass allocation. Plants’ responses to environmental stresses, such as nutrient limitation or anthropogenic effects such as elevated CO₂, suggest that they have a centralized system of stress response involving changes in nutrient and water use, carbon allocation, hormonal balances, and reliance on mycorrhizal fungi. Our research addresses mechanisms controlling plants with obligate and facultative dependency on the mycorrhizal symbiosis and the relative importance of these mechanisms in various plant life forms. Our overall objective is to determine whether a major mechanism of control is the balance between photo-assimilate supply to the roots and the host’s need for nutrients. To address this objective, two general questions will be investigated:  (1) what are the mechanisms controlling photo-assimilate allocation to the fungus and nutrient inflow to the plant? (2) Will the host’s dependence on supplied nutrients influence its ability to adjust to a changing environment? (3) Does a relationship exist between net C gain of the host and the amount and activity of mycorrhizal fungi?

terrestrial CARBON PROCESSES

Concerns over rising concentrations of atmospheric CO₂ have increased interest in the capacity of soil to serve as a carbon sink. The amount of carbon stored in world soils is estimated at more than twice the carbon in vegetation or in the atmosphere. Thus, even relatively small changes in soil carbon storage per unit area could have a significant impact on the global carbon balance. Soil carbon may be stabilized because of its biochemical recalcitrance or by incorporation into organomineral complexes with clays. Soil structure also plays a dominant role in controlling microbial access to substrates and, thus, relatively labile organic material can be physically protected from decomposition by incorporation into soil aggregates. This project is researching the biological mechanisms involved in the formation, stabilization, and degradation of aggregates and how the aggregation process, in turn, influences soil carbon dynamics. This information is necessary (1) to identify management practices that maximize soil carbon sequestration and (2) to determine the potential for terrestrial ecosystems to serve as a sink for elevated concentrations of atmospheric CO₂. This project involves application of soil physical and biological fractionation techniques and stable isotope measurements to samples obtained from elevated CO₂ experiments and sites with long-term plots representing alternative land management strategies.

synchrotron-based environmental research

This research program in synchrotron-based environmental research is aimed at exploring applications of new advances in x-ray physics to understanding problems in environmental science. The principal goal of this program is to address general issues concerning the bioavailability of contaminants in the environment, with a particular emphasis on the mobility, uptake mechanisms, transformations, and toxicity of metals and organic chemicals in natural soils. Research projects include both the study of bulk samples by using x-ray absorption spectroscopy and the study of microscopic samples and spatial variations on the micron length scale by using x-ray fluorescence imaging, phase contrast imaging, and x-ray absorption spectroscopy with micron-sized spots. Particular research interests within the group include:  (1) the investigation of mineral-microbe interactions so as to better understand the role of these interactions in the fate and transport of heavy metal contaminants; and (2) the study of newly created, highly-reactive materials for the selective removal of radioactive contaminants from DOE waste storage tasks.

Applicants Responsibilities and Relationship to Project

Applicants will receive support under the Department of Energy Faculty and Student Team (FaST) Research Program to work collaboratively with the project research team at the Laboratory for up to 10 weeks during the year starting during the summer of 2006. Summer and academic year visits to Argonne Lab will be scheduled by mutual agreement between the Research Project Directors at Argonne National Laboratory (ANL) and the successful applicant. Faculty will be expected to identify students from their campus to participate in the Undergraduate Research Participation programs offered by the Department of Energy at ANL. Ideally, faculty will provide some mentorship and/or advising support to students during the summer research activities. It is expected that the faculty member will become an integral part of the research team working on this project and will support the project through the academic year on her or his campus.

Qualifications of Ideal Candidate

Support and Financial Commitments

See Financial Information.

For More Information contact:

http://www.dep.anl.gov