SBRP Program Description
UCSD's multidisciplinary Superfund Basic Research Program (SBRP) focuses on defining or characterizing important cellular events that occur as a result of toxicant exposure. The basic science seeks to understand the role of crucial signaling pathways and targeted genetic changes that may be tied to the etiology of a toxic episode. Project scientists have developed tools and biological reagents that will aid in biological detection of hazardous contaminants in the environment as well as in developing tools for environmental remediation (bioremediation and phytoremediation).

The Research Translation Core
Translating mechanism-based research and transgenic technologies into new biomolecular methods for hazardous substance detection, risk assessment, and remediation

The Research Translation Core will promote greater understanding and application of biomarkers, biosensors (biomolecules/nanoparticles), bioremediation, phytoremediation and mouse toxicologic models. To move SBRP research from bench to demonstration to commercial use, the Core will help translate the development of new cell lines, transgenic animal models, bioassays, and biomolecular detection systems into applications for exposure monitoring and risk assessment (e.g., new methods of testing for toxicants in water/soil/sediment samples). Through tech transfer and commercial partnerships, SBRP advances in transgenic bioremediation and phytoremediation technologies will be promoted as new biological systems/tools for the environmental restoration of contaminated water, soil and sediments (e.g., transgenic plants that can bioaccumulate heavy metals, bacterial methods to detoxify heavy metals). Promising advances in nanotechnology will spur cross-project collaboration and multidisciplinary efforts to create new fieldable types of biomolecules/nanoparticles that can be used as biosensors for toxin detection.

Project Scientists
(research translation potential: excerpts taken from various sources including SBRP program plan updates, lab web sites, publications, and Bob Tukey')

Michael Karin - Environmental Pollutants & Oxidative Stress: Protective Responses and Animal Models
Develop transgenic mice and cell lines that will be highly sensitive to chemical induced oxidative stress.
The major goal of Karin's lab is to generate mouse models that exhibit altered (increased or decreased) sensitivity to environmental toxins present at Superfund sites. Researchers are creating gene arrays, cell lines and transgenic mice that can be used as biosensors for monitoring exposure to toxicants that cause oxidative stress. Additionally, strains of mice that are deficient in activation of the protective response to oxidative stress are being created. Such mice should be supersensitive to pro-oxidants and thus will facilitate the detection and evaluation of new suspected toxicants and mixtures of chemicals from Superfund Sites for their ability to cause oxidative stress mediated toxicity. Studies during the coming year will test the susceptibility of Ikkß?hep mice to a variety of Superfund site chemicals.

Paul Russell - Yeast Genetics and Stress Response Genes
Use specifically engineered S. pombe strains capable of detecting heavy metals such as arsenic.
Many of the most potent Superfund chemicals and environmental pollutants impart their toxicity by causing oxidative stress. Russell's SBRP project uses yeast genetics and post-genome technologies (e.g. whole genome microarrays and proteomic mass spectrometry) to understand how eukaryotic organisms respond to oxidative stress. The goal is to make fundamental discoveries that will be broadly applicable to human health and bioremediation. The whole genome microarray studies have identified more than 100 genes that are up-regulated in response to oxidative stress. Experiments are planned to understand the functions of a subset of these genes in toxicant response.

Robert Tukey - Environmental Influences of Ah Receptor Ligands on Gene Expression
Developing animal models and cell lines to screen for AhR specific environmental contaminants.
Tukey's lab is investigating the impact of chemicals found at hazardous waste sights on the control and regulation of the Ah or dioxin receptor (AhR), in addition to developing biological models (subcellular biochemical indicators) to access the presence of these contaminants in environmental samples. Two major ubiquitous toxicants, arsenic and polycylic aromatic hydrocarbons (PAH), are being studied. Dr. Tukey's lab has also created a number of key transgenic mice carrying genes that express the human CYP1A1 promoter as well as the entire CYP1A1 gene. Creation of the CYP1A1-luciferase mice is turning out to be a valuable tool for the detection of environmental toxicants that activate the Ah receptor.

Palmer Taylor - Organophosphate Pesticide Exposure: Analysis of Disposition in the Body and Target Inactivation in Relation to Gene Expression
Utilize chemically engineered acetyl-cholinesterase as a tool for monitoring the presence of organophosphates.
The use of organophosphate based pesticides in California is of serious concern because of its extensive use and the potential of human exposure. Dr. Taylor’s laboratory has been developing detection systems to quantitate exposure to organophosphates. Dr. Taylor’s laboratory has been developing technology for a fluorescence sensor for detection of organophosphate interactions with acetylcholinesterase.These detection systems, along with the development of unique transgenic mice to analyze for acetylcholinestease sensitivity, are being developed as a tool for detection of organophosphates in the environment. This information is in the early stages of patent development. The UCSD Superfund program feels that this work is pivotal since it will establish not only an analytical tool but also a biological tool to access organophosphate exposure. The state of California is one of the heaviest users of insecticides, and organophosphate runoff and potential exposure to workers as well as surrounding communities is of significant concern. This work is laying the foundation for the development of tools that can be implemented for future risk assessment.

Julian Schroeder- Phytochelatin Synthase and Resistance to Heavy Metals
Develop transgenic plants expressing PCS genes for bioremediation of heavy metal contaminated soils.
The Schroeder lab discovered that the biological heavy metal chelators, named phytochelatins, are transported from roots to leaves of plants and that transgenic phytochelatin expression enhances accumulation of cadmium in plant leaves (Gong, Lee and Schroeder, 2003). This work will be exploited in the future to determine if these transgenic plants can be used to bioaccumulate heavy metals. Dr. Schroeder's laboratory is using microarrays and promoter luciferase reporter transgenics to construct heavy metal reporter lines which can signal exposure to specific heavy metals as well as their transfer through the plant. Patents on these new discoveries are being processed at UCSD.

Bradley Tebo- Bacterial Genes and Proteins Involved in Redox Transformation of Metals
Utilize anaerobic Cr (VI)-reducing bacteria for bioremediation.
Heavy metals are found as contaminants in many surface and subsurface waters as a result mostly of industrial activity but also due to natural processes (arsenic is an example of a naturally occurring metal contaminant). Bacteria are able to catalyze the transformation of some toxic metals to less toxic and/or less mobile states. We are currently pursuing two strategies to harness the natural activity of bacteria to detoxify heavy metals. One involves the direct microbial reduction of Cr(VI) (a toxic and soluble metal) to Cr(III) (a less toxic and insoluble metal). The other involves the bacterial oxidation of Mn(II) to produce high surface area, highly reactive manganese oxides with tremendous capacity for scavenging heavy metals and degrading organic compounds.

Ronald M. Evans Professor, Gene Expression Laboratory New to the SBRP.
Proposes using PXR and CAR humanized mice, develop unique cell lines and animal models to identify PXR/CAR specific toxicants.
Excerpt from a lab publication: The humanized mouse system represents a major step toward generating a humanized rodent toxicologic model and thus provides an advanced way to explore the interface between the environment and the human genome. These xenobiotic receptors and genetically engineered animals, in conjunction with the completion of the human genome project, should greatly facilitate our understanding of the complexity of the xenobiotic response and its implication in pharmaceutical development including drug profiling, toxicity analysis, and drug-drug interaction.
Wen Xie and Ronald M. Evans THE JOURNAL OF BIOLOGICAL CHEMISTRY Vol. 276, No. 41, Issue of October 12, pp. 37739–37742, 2001.

Sangeeta N. Bhatia
Microscale Tissue Engineering
Develop microscale, zonated liver tissues to study liver function following exposure to environmental toxicants.
Dr. Bhatia is new to the SBRP. Her work focuses on Microscale Tissue Engineering and development of Biological Micro-Electo-Mechanical Systems. Use of microfabrication techniques for control of cellular microenvironment. Micro- and Nanotechnology tools developed in Dr. Sangeeta Bhatia's lab will be integrated
with biomarker platforms developed in the SBRP labs. For example, incorporation of fluorescently-modified acetylcholinesterase (Taylor) into photopatterned hydrogels may enable the fabrication of sensor arrays on an enclosed microscope slide. (# 3 at http://mtel.ucsd.edu/publications/index.asp ). These arrays may allow fingerprinting of organophosphates in the field via changes in fluorescence. Bhatia and her colleagues hypothesize that the incorporation of these enzymes in a hydrated environment (hydrogel) rather than immobilized on a rigid surface will preserve their conformation and activity. The ability to photopattern the hydrogels shall allow formation of arrays of 'sensors' with each spot containing a different modification of acetylcholinesterase enabling the parallel, continuous interrogation of small volume samples. Similarly, BioMEMS tools developed in Dr. Bhatia's laboratory combined with fluorescent reporters in transgenic animals developed by Dr. Tukey and Dr. Evans (of P450 IA1 and CAR activity) may allow miniaturization and integration of biomarker analysis (i.e. 'lab-on-a-chip' platforms). For example, hepatocytes isolated from the livers of transgenic animals should fluoresce upon exposure to relevant toxicants. Immobilization of live cells on chip platforms should therefore enable continuous interrogation of small volume samples. See (Biomems- http://mtel.ucsd.edu/research/index.asp) for more info.

. TECH TRANSFER
Dr. Donna Shaw, a senior licensing officer from out office has been specifically assigned to facilitate the writing and processing of new inventions from SBRP researchers. This proactive approach is more effective than our past reliance on the SBRP reseachers' own initiatives to contact TechTIPS for processing of their ideas. Dr.Shaw will work closely with Dr. Keith Pezzoli -- the PI of the SBRP's Research Translation Core -- to help spur the transfer of technology per the NIEHS mandate. Dr. Shaw will also participate in our monthly PI meetings to identify potential opportunities for technology transfer of ideas to the private sector. UCSD recognizes the importance of fostering the commercial development and utilization of technologies that result from research activities on campus for the public good. TechTIPS has been promoting and facilitating this process since 1994. TechTIPS will organize technology showcases, entrepreneurs/innovators forum, intellectual property awareness seminars and educational workshops that will invite and attract both academic and industry representatives. Innovations from SBRP will be highlighted to encourage broad utilization.

Patent updates
New information related to patents for UCSD includes newly submitted and pending patents as follows:

Project 1 – Karin
We have disclosed the proprietary mouse strains we have generated to the Tech Transfer Office at UCSD. The disclosures include: Ikkß conditional deletion (the Ikkß-floxed mouse), mice lacking IKKß in intestinal epithelial cells and mice lacking IKKß in liver cells.

Project 4 – Tukey
The development of new transgenic mice response to Ah receptor ligands have been disclosed to the Tech Transfer Office at UCSD.

Project 7 - Taylor
The University of California, San Diego has taken a patent position on the “Fluorescence Ligand Binding Assay of the Acetylcholine Binding Protein and Analogs of Ligand-Gated Ion Channels,” SD2003-085-1.

Project 8 - Schroeder
A submitted patent on the use of phytochelatin synthases was issued by the US patent office: Phytochelatin Synthases and Uses Therefore. P.A. Rea, O.K. Vatamaniuk, S. Mari, Y-P. Lu, J.I. Schroeder, E.J. Kim, S. Clemens, U.S. Patent Number 6,489,537 B1 (patent issued 12/2002).

Highlight from a SBRP document (a good example of the fruits of tech transfer)
Commercial Application of the CALUX Bioassay for Use in Detecting Dioxin and Related Chemicals

NIEHS SBRP | A LEGACY IN MULTIDISCIPLINARY RESEARCH Volume I SECTION 1 | PAGE 23 Michael S. Denison, Ph.D., University of California - Davis Commercial Application of the CALUX Bioassay for Use in Detecting Dioxin and Related Chemicals 1 patent received as a result of SBRP-funded research SBRP-funded researchers have developed, validated, and patented a cell bioassay system (known as CALUX) that is sensitive, specific, quick, and inexpensive. This recombinant cell bioassay has been engineered to respond to dioxin-like HAHs and PAHs, with the activation of gene expression, specifically that of fireflyluciferase. Xenobiotic Detection Systems (XDS), Inc., a biotech company in North Carolina, has combined the CALUX bioassay system with a rapid chemical extraction procedure to develop a sensitive combination system for the detection of dioxins and dioxin-like chemicals in extracts of biological, environmental, and food and feed samples. After reviewing the validation results, the U.S. Food and Drug Administration (FDA) licensed the CALUX screening technology from XDS for critical evaluation as a rapid screening method for dioxins and related chemicals in food and feed. The FDA is in the initial phase of incorporating the bioassay into their food/feed screening program, and introducing such innovative techniques in FDA-sponsored laboratories. In addition, the technology has been licensed to companies in Japan and Belgium, and XDS is using it extensively to screen dioxins in a wide variety of matrices sent to them by governmental, commercial, academic, and public organizations. The USEPA has also expressed interest in licensing the CALUX screening technology. An application for USEPA approval of the assay will be submitted shortly. With USEPA approval, the bioassay should gain a significantly greater commercial and regulatory use.