Performing Department
(N/A)
Non Technical Summary
Who are the customers of the service that will be developed through this proposed SBIR project Government laboratories (USDA ARS) as well as university laboratories and small companies will have need of this service-consultation and data collection for a fee, in order to commercialize products of biotechnology. The ability of the laboratory, whether public or private, to move the product toward commercialization depends critically on the ease and cost of deregulation if the product is to be grown in the agricultural sector. Currently, no service is available which fills this need. The alternative to this joint venture concept is each entity from the specialty crop perspective doing its own deregulation petition. Clearly this has not been conducive to success since few or no petitions for non-regulated status from the specialty crop sector have been submitted to the USDA-APHIS. Moreover, the Specialty Crop Regulatory Assistance was initiated to serve this purpose. The vision of SCRA is: Enhanced public good through biotechnology: Increased diversity of specialty crops, traits, and crop developers. The associated mission is: Facilitating regulatory clearance for biotechnology-derived specialty crops. The groundwork for the SCRA service organization has been laid, but funding and services have not been developed. One of the barriers to the development of the SCRA is that cooperative funding from diverse small company entities is not easy to orchestrate, particularly when funds are limited as in the current economic environment. However, the services that would be provided by the SCRA would increase sales and revenues, allowing the entity to have funds to move the SCRA project forward. In this "Catch 22", a new paradigm is necessary to move the project forward. This joint venture concept is being developed to assist the SCRA in achieving its goals. Our efforts on this project could help the SCRA develop a "regulatory atlas" which is a goal of the SCRA. While the atlas per se is not the target of this proposal, the process will help to develop different scenarios that could be used for the creation of a regulatory atlas. The public stands to benefit the most from this project because new products utilizing biotechnology that make foods/feeds/horticultural products with new traits will be available. This is important as there are many such products under development. Moreover, the confidence with which these products are embraced will be high because an independent organization will be responsible for data collection, analysis and interpretation. The benefit to the public is also in the realm of more affordable foods (manufactured with fewer inputs) and more nutritious foods.
Animal Health Component
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Research Effort Categories
Basic
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Applied
100%
Developmental
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Goals / Objectives
Objectives: 1. Construct a regulatory plan for a model crop with a biotechnology-derived trait. The plan will include a description of the necessary data and services to help a company begin the process of deregulating a biotechnology-derived specialty crop. Corn with cellulase will be the model. 2. Mine literature and databases for data describing the variation in 1) composition of corn seed, 2) target protein safety and 3) growth parameters 3. Mine data for a second and possibly third crop based on search terms corresponding to those for the cellulase-producing corn. 4. Collect data on seed composition and growth parameters for normal dent corn and transgenic corn expressing cellulases. 5. Develop a business strategy for a joint venture modeled as a contract research organization (CRO). Expected Outputs: The deliverables from Phase I include prospecting and feasibility as follows: 1. Outlines of two model regulatory plans, one for a specialty application of a commodity crop and another for a specialty crop with an input trait will be developed. 2. Results of the literature and data mining approach for establishing baseline data for determining the range of normal values for corn seed composition and field performance will be tested. These data must be usable for comparison against data collected regarding a transgenic crop of interest. 3. A business strategy for moving the services organization forward will be further developed.
Project Methods
1. Develop a regulatory plan for a specialty crop. Petitions to achieve non-regulated status for each transgenic crop have data sets that have common elements. In addition, some target proteins within those crops, for example pharmaceutical proteins or industrial proteins/enzymes, require analyses that will have to be done in addition to the transgenic crop characteristic analyses. The actual plan will differ somewhat depending on the protein incorporated and the intended use. It is important to build a model plan from which to design the correct experimental approach. 2. Design software for data mining: Stage 1: Define sources. The first stage is a listing of information sources: PubMed, PubMedCentral, Agricola, Biological Abstracts, Chemical abstracts, NCBI, Maize Genome Database, and International Life Sciences Institute. This list can be embedded into the software that will be developed. This will enable them to be accessed by the software as often as desired without further attention from users and developers. Stage 2: Establish queries. A list of queries will be developed for the purpose of retrieving records that may contain information useful in determining the ranges of values of those characteristics of interest to the deregulation of transgenic crops. Stage 3: Extract and organize data into sets and graphs through computer and human decision-making. Text and database records that have been retrieved need further processing to be useful. We must extract specific data from larger records. The data needed are those that address the specific crop plant characteristics of interest that are necessary to analyze for deregulation. While the field of information retrieval accesses appropriate records, the field of information extraction (IE) pulls out the needed facts from within unstructured data and partially structured data. Stage 4: Text and Data mining. The necessary outcome of the text and data mining phase is the body of facts stated in the literature about desired crop characteristics. Long lists of individual facts must be summarized, organized, and presented properly to realize their intrinsic value. The data, a set of evidence consisting of individual facts identified from the literature, will be mined in a process of evidence combination to identify ranges of normal variation for crop characteristics. 3. Gather Seed compositional analysis and field perfomance data on control and cellulase corn to determine if transgenic data fit into the normal range of parameters: Total protein; Total lipid determination; Total carbohydrate determination; Total soluble protein extracted in phosphate buffered saline (PBS), acid, base and alcohol; PBS soluble protein analyzed on 2D gels. Collect data on inbreds and hybrids in Arkansas, summer 2009. Average height, diseases observed and percent coverage, percent lodging, and yield will be recorded. 4. Develop a business strategy that encompasses the concepts developed in this project modeled as a contract research organization (CRO).