 | ISB News Report - February 1997 | |
NEWS FOR THE AGRICULTURAL AND ENVIRONMENTAL BIOTECHNOLOGY COMMUNITY
| ISB News Report - February 1997 | |
NEWS FOR THE AGRICULTURAL AND ENVIRONMENTAL BIOTECHNOLOGY COMMUNITY
In This Issue:
Field Trials Reviewed
Taking Biotechnology to the Community
Resource Added To ISB Web Site
Performance Standards Update
USDA BRARG Grant Abstracts Now on WWW
NAL Digital Conversion Project
For a Better World
International Conference On Plant And Animal Genomes
Potential Allergenicity of Transgenic Foods
Strategic Alliances in the Biotechnology Industry - A 1996 Review
Conducting Bibliographic Searches on the Internet
To fill this informational gap, a number of resource materials have been produced recently for California's Cooperative Extension. A generic talk and slide set was developed which covers various aspects of agricultural biotechnology and its applications. The talk is written in modules which allow the presenter to pick and choose aspects appropriate for the intended audience. It includes a general introduction to the history of foods and agriculture, an explanation of the methods involved using easy-to-understand analogies, an example that contrasts classical and molecular breeding technologies, a look at how biotechnology is already impacting agriculture and finally a look down the biotechnology pipeline highlighting both products on the market and those being developed in laboratories. This resource has been reviewed and modified by a number of county CE personnel, university faculty and private sector and government staff and is available for viewing on-line at http://plantbio.berkeley.edu/~outreach; copies of the slide set can also be ordered at cost. The talk and slide set are currently being expanded to include sections on animal biotechnology, environmental biotechnology, food safety and plants and medicine.
Two other projects have been completed, a 4-H module entitled "Biotechnology and Foods" and an informational commodity-based series called the "ABC (Agricultural Biotechnology for California) Bulletins". The latter is intended to inform county-based CE personnel as well as crop consultants, commodity boards and agribusiness about the current state in a specific commodity of research and product development in biotechnology. These two materials can also be viewed at the Web site listed above. All of these materials are aimed at disseminating information on biotechnology in simple-to-understand, user-friendly format.
Peggy G. Lemaux
Dept. of Plant and Microbial Biology
University of California, Berkeley
lemauxpg@nature.berkeley.edu
Doug King
Doug King
Information Systems for Biotechnology
nbiap@vt.edu
Libraries have traditionally provided society with the means to preserve knowledge that was primarily directed to housing paper copies for materials of factual, cultural and governmental importance. Paper documents were inexpensive, could be read by any knowledgeable individual and were not dependent on any particular hardware or software. Today, if we intend to preserve information in a digital format, we must ensure that future generations will continue to have access despite technological changes in both hardware and software. The long-term solution to the preservation dilemma is to collect the digital information in a universally accepted international standard format (SGML, ISO 8879, Standard Generalized Mark-Up Language). In this way, as technology changes, the basic information remains accessible, independent of specialized hardware or software.
NAL is beginning its digital collection by converting the legacy documents of the Bean Improvement Cooperative (BIC). This project involves 39 volumes of annual reports going back to 1957, four Conference Proceedings and indexes, nearly 5,000 pages of text. Both NAL and BIC share significant benefits from this project. It provides NAL with the opportunity to experiment with building an SGML-based digital collection and provides an unusual opportunity for the Library to directly interact with a user group to develop a product that best meets the user's needs. In turn, BIC members and users worldwide will benefit through preservation and improved access to the cooperative s information.
SGML can provide information consumers with management tools not currently available. In the near future it should be possible to search either within a single document or across a wide range of documents for specific concepts. Search results can then be "resynthesized" into a new document containing only those elements from each article relevant to the user's query. The citation information for each source collated into the output document will be retained. In addition to the BIC documents, we are initiating projects with genetic journals for strawberries, triticale and possibly rice. This aspect of digital information retrieval will be particularly interesting to the genetic research community since a digital core search of genetics journals will allow a search across species.
A simple word search in a SGML file for the term "pods" will return a list of all documents containing that word. Clicking on one of the titles will retrieve the corresponding document, with the specified word highlighted (in this case "pods"). Keyword tagging (the ultimate aim of the BIC project) however, provides more analytical uses, such as creating lists (pathogens and/or sub categories like genetic resistance) and researching relationships between ideas that are not evident in the text (cross species genes / disease resistance).
At this point, only one document at a time can be searched. Once NAL has selected a site-search engine, all of the BIC journals will become available for simultaneous searching. One Web browser currently available to view SGML documents, SoftQuad's Panorama, can be accessed from the BIC homepage (http://www.nal.usda.gov/pgdic/Beans/beansgml.htm). The beta version of Panorama for Windows can be downloaded without charge. It will allow you to view documents on-line but does not allow for downloading or printing; a commercial version of the browser is available with these features.
Michael Tims
Plant Biology Department
University of Maryland
mtims@nal.usda.gov
Susan McCarthy
USDA,ARS National Agricultural Library
smccarth@nal.usda.gov
Specialists from related fields will present progress and results from international projects and programs which are involved in agricultural biotechnology in developing countries. Topics include: building public and private sector linkages; intellectual property, licensing and legal aspects of technology transfer; the role of GATT, NAFTA, the Convention on Biodiversity, and the Uruguay Round/TRIPS; regulatory policies and biosafety guidelines; socio-economic impacts of the new technologies; and, the role of biotechnology in integrated pest management, sustainable agriculture and agronomic systems. The speakers for the conference include federal agency administrators, public and private sector leaders from affiliated research centers, governmental units and corporations.
For registration and fee information, contact Dean Norton, Conference Coordinator, Michigan State University +1-517-353-2290; email global97@pilot.msu.edu.
More than 125 invited presentations and workshop lectures along with 400 poster presentations marked this year s conference. The workshops were essentially commodity based and provided glimpses into recent developments in the genome studies of plants such as rice, cotton, maize, legumes, fruit trees, sugarcane, forest trees, triticaceae, solanaceae, compositae and also of animals such as cattle/sheep, horse, pig, poultry and fish. Detailed genetic maps of these species have been developed using molecular approaches such as RFLP, RAPD, AFLP and microsatellites, and are providing valuable insights into their genome organization and also helping scientists to identify useful genes. Workshops also featured computer applications such as showcasing new software for genome analysis, the World Wide Web sites offering agricultural genome databases and the use of Java programming language that helps in providing interactive content for graphical genome displays.
In his plenary lecture, Bradie Metheny of the Washington FAX newsletter called on agricultural genome researchers to play a more proactive role in explaining the importance of their work to law makers and the general public. He said that such efforts are critical in raising the funding levels for agricultural genome research and in ensuring elevating agricultural productivity through biotechnology. David Cox of Stanford University described the utility of radiation hybrids in developing high resolution genome maps where human cells exposed to radiation are fused to hamster cells to create hybrids with select chromosomes. David Schwartz of New York University talked about optical mapping where DNA molecules are fixed on modified surfaces, cut by restriction enzymes and observed under powerful microscopes to produce high density maps. Glen Evans of University of Texas showed how advanced automation and robotics are being employed by human genome scientists in their quest for high-throughput sequencing. Steven Tanksley of Cornell University explained his group s success in isolating, for the first time, a large segment of tomato chromosome containing quantitative trait loci for fruit weight.
Many plant disease resistance genes have been identified recently and thus further advances made in this area were of considerable interest. Gregory Martin of Purdue University used a novel yeast-two hybrid system to isolate genes encoding proteins involved in plant-pathogen specificity while Pamela Ronald of University of California-Davis described further progress in isolating resistance genes in rice against bacterial blight. As many disease resistance genes across plant species appear to share similar nucleotide sequences, scientists have developed degenerate primers corresponding to such sequences and used PCR to isolate resistance gene analogs in plant species. Saghai Maroof of Virginia Tech and Randy Shoemaker of USDA/ARS have exploited this approach to isolate molecular markers for disease resistance gene clusters in soybean.
Carol Hamilton of Cornell University described a new vector that enables the transfer of multiple foreign genes into plants. The binary bacterial artificial chromosome (BAC) vector is capable of transferring DNA molecules larger than 150 kilobases using Agrobacterium and represents a significant improvement over current methods. This development paves the way for future introduction of multiple genes such as those controlling yield traits into crop plants. Many BAC libraries containing large chromosome pieces derived from crop or animal species were described during the San Diego meeting. Such libraries are helping researchers to identify useful genes through a positional cloning approach.
One clear message that has come across from comparative studies on genetic maps of crop species is that gene order and gene content even among unrelated plants appears to be similar. Andrew Paterson of Texas A & M University and Jeff Bennetzen of Purdue University elaborated on how such unified genetic maps are helping in our understanding of genome evolution in agricultural plants and how a genetic map from one species would help in the development of maps in other species.
The weed plant Arabidopsis is definitely the darling of many plant genome researchers because of its short life cycle, extremely small genome size and fewer repeat sequences. An international effort to sequence the complete genome of Arabidopsis is now underway. Genes from Arabidopsis can be isolated with relative ease and their availability would help in the rapid isolation of similar genes from crop plants. Many scientists described their progress with the genome analysis of Arabidopsis including the use of Expressed Sequence Tags (EST), the use of advanced computing techniques such as neural networks in such analysis and the international collaborative ventures.
The AFLP markers are clearly gaining popularity among genome researchers as evident by the number of studies using this marker system (See the May 1996 ISB News Report for description of this technique). A workshop on AFLP markers featured Pieter Vos of Keygene, a codeveloper of this technique, who described recent applications of AFLP technology including YAC contig fingerprinting. Keygene also demonstrated their new computer software which helps in the analysis of complex AFLP blots using image analysis.
Abstracts of all the invited presentations, workshop lectures and posters presented at the Plant and Animal Genome V Conference can be viewed on the World Wide Web at http://probe.nalusda.gov:8000/otherdocs/pg/pg5/allabstracts.html.
C. S. Prakash
Center for Plant Biotechnology Research
Tuskegee University
prakash@acd.tusk.edu
Allergenic proteins often share similar properties such as resistance to enzymatic and acid degradation or heat stability. Astwood and coworkers at the Monsanto Company (St. Louis, MO) reported in the October 1996 issue of Nature Biotechnology the development of an assay to evaluate the allergenicity of proteins. This assay is based on the assumption that stability to digestion is a general property of allergenic proteins. The researchers tested the digestive stability of 16 major peanut, soybean, mustard, egg and milk allergens to a simulated gastric fluid (SGF) containing the protease pepsin. Purified allergens such as egg ovalbumin or milk beta-lactoglobulin were stable for 60 minutes in SGF, whereas common plant proteins such as spinach ribulose bis phosphate carboxylase or phosphofructokinase were digested within 15 seconds. The stability of the test proteins to SGF was unchanged when also assayed in the presence of a typical food matrix, such as crude soybean extract. However, not all allergen proteins tested remained intact in SGF. Some allergens such as egg conalbumin were rapidly cleaved into fragments, which were subsequently stable to further digestion. These results demonstrate that stability of the whole protein or protein fragments to SGF digestion can be used as a valid method for assessing the potential allergenicity of a protein.
Reference:
1. Astwood et al. 1996. Nature Biotechnology 14:1269-1273.
Eric A. Wong
Dept. of Animal and Poultry Sciences
Virginia Tech
ewong@vt.edu
Over 70 percent (961) of the actions recorded by IBI in 1996 were in the area of pharmaceuticals, while 6 percent (79) represented actions in the area of plant agriculture and food. Of the ag-related actions, 70 percent were external, involving more than one organization. The largest percentage of these external ag-related actions (20 %) were unspecified joint ventures between organizations, followed by legal actions (18 %), licensing agreements (15 %) and equity investments (11 %). The profile of actions by type is similar to that of the pharmaceutical actions, and shows the importance of strategic alliances to both sectors of the industry. The one exception is the ag-sector's relatively large percentage of legal actions (18%) versus the pharmaceutical sector (6 %). This is likely a reflection, in part, of the substantial proportion of major players in the smaller ag-biotech sector involved in litigation in 1996.
Also notable were the differences in the types of companies taking part in strategic actions. Actions between biotechnology firms made-up 30 percent of all external pharmaceutical actions as compared to actions between biotechnology firms and larger diversified companies, which comprised 56 percent of the pharmaceutical actions. In contrast, less than 15 percent of ag-biotech actions were between biotechnology firms, while 67 percent involved biotechnology firms and a larger diversified company. This difference is partially due to the existence of top-tier biopharmaceutical firms such as Amgen, Genentech, Genzyme, and Chiron that are much more like large diversified corporations but are still classified as biotechnology firms, and doing many deals with other smaller biotechnology firms. It also demonstrates the direction that the ag-biotech sector has been moving, with larger diversified corporations like Monsanto looking to access technology as part of building value into its agriculture business through biotechnology. The alliance model is not likely to change in 1997.
[Note on IBI's Actions Database: Although international in scope, the most complete coverage in the database is of U.S. companies. This is because most of the information resources used by IBI to collect data are U.S.-based, and with the United States still home to the highest number of dedicated biotechnology firms in the world, many of the strategic actions involve U.S. companies. The database intends to cover the major business actions of biotechnology companies, but there are types of actions for which coverage is not intended to be as complete (e.g., patents, university alliances, and scientific breakthrough), and IBI makes subjective decisions about what to include.]
William O. Bullock
Inst. for Biotechnology Information, LLC
Research Triangle Park, NC
http://www.biotechinfo.com
Entrez is more than just a database of 1.3 million citations. It is a comprehensive information retrieval system that integrates the MEDLINE molecular biology subset and databases of nucleotide and protein sequences, genomes and 3D structures. Thus with a few clicks, users can not only find titles of papers with blazing speed, but also receive the abstract and download protein and nucleotide sequences of genes mentioned in the papers. Entrez also links you to related papers for every citation and provides a "glossary" type explanation of key words.
To navigate to the MEDLINE subset of Entrez, click on "Entrez" under the "NCBI Services" and then choose the "Search Molecular Biology Subset of MEDLINE". You will be provided with a simple and user- friendly interface where you can search with key words, author names or gene symbols; more advanced searches including Boolean search (AND, NOT, or OR) are permitted.
Uncover is a document delivery service run by a private company whose database indexes thousands of titles daily in the science, technology, and medical fields. Uncover can be found on the Web (http://www.Carl.Org/uncover) while a text-based interface is available through telnet (database.Carl.Org). Uncover maintains 8 million citations from nearly 17,000 journals; 5,000 citations are added daily. The user interface is simple and you can search using key words, journal titles or author names. Uncover returns your query with complete citations but does not provide abstracts except for occasional summaries. For many journals, you can browse through each issue's Table of Contents. The search for citations is free, and you can receive full-text documents by fax for about $10 to $15, often within one hour. For a $25 annual fee, Uncover also provides an electronic alert service that regularly emails the Table of Contents from up to 50 journals of your choice.
For searching titles in agricultural subjects (including biotechnology), the Integrated System for Information Services (ISIS) from the USDA's National Agricultural Library (NAL) is your best bet. The ISIS cannot be accessed through the Web yet, although the NAL is hoping to have a Web interface soon. ISIS can be reached by telnet (opac.nal.usda.gov); enter "isis" at the login prompt. In the menu, choose "4" for "Accessing Journal Article Citation Database" and then enter the command "/IND". Boolean searches are permitted and abstracts are available for many recent citations. ISIS includes the popular AGRICOLA database, a vast repository of practically everything published in agricultural research. Unlike the friendly interface of the Web, navigating through the text-based ISIS with its arcane interface can be frustrating as it is necessary to remember the search commands. ISIS can thus be rather unforgiving to the novice, but the NAL provides search tips and a list of commands for ISIS on its Web site (http://www.nal.usda.gov/isis).
C. S. Prakash
The material in this News Report is compiled by NBIAP's Information Systems for Biotechnology, a joint project of USDA/CSREES and the Virginia Polytechnic Institute and State University. It does not necessarily reflect the views of the U.S. Department of Agriculture or of Virginia Tech. The News Report may be freely photocopied or otherwise distributed without charge. P.L. Traynor, Editor.
Information Systems for Biotechnology, 120 Engel Hall, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061-0308, tel: 540-231-2620, fax: 540-231-2614, email: traynor@nbiap.biochem.vt.edu
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