 | ISB News Report - March 1997 | |
NEWS FOR THE AGRICULTURAL AND ENVIRONMENTAL BIOTECHNOLOGY COMMUNITY
Release of this issue was delayed to include news on sheep cloning
| ISB News Report - March 1997 | |
NEWS FOR THE AGRICULTURAL AND ENVIRONMENTAL BIOTECHNOLOGY COMMUNITY
Release of this issue was delayed to include news on sheep cloning
In This Issue:
Dolly: The Science Behind the Sensation
New Workshops Offered
Court Finds Only One Sense in Making Viral Antisense Constructs
First Gene for Resistance to an Animal Pest Identified in Plants
Growers Endorse Herbicide Resistance, Recognize Need for Responsible Use
Biotech in the Dirt: Soil Remediation by Engineered Microbes
Will Transgenics Companies Benefit Financially from Cloning Breakthrough?
ISB Adopts New Search Software for News Report Articles
In the February 27 issue of Nature, Ian Wilmut's group at the Roslin Institute in Edinburgh report the first successful birth of a mammal after transfer of a nucleus from an adult tissue to an enucleated egg. This remarkable achievement follows their report a year ago (Nature, March 7, 1996) of the birth of lambs after transfer of nuclei from cultured embryo-derived cells. In the latest study, the researchers established three new cell lines derived from a Poll Dorset 9-day old embryo, a Black Welsh day-26 fetus and the mammary gland of a 6-year old Finn Dorset ewe in the last trimester of pregnancy. Nuclei were recovered from quiescent cells at passages 3 to 8 and introduced into enucleated eggs. Induction of quiescence was shown in the 1996 report to be important for "reprogramming" the nucleus to allow successful development.
Lambs were born to surrogate mothers from embryos reconstructed with nuclei derived from all of the cell types. Of the embryos reconstructed with a nucleus from mammary tissue, less than 12% were able to develop to a transferrable stage, and only about 3% of these transferred embryos resulted in a live birth. A high rate of fetal loss was observed, but this is not unexpected for the development of any new technology.
Of the eight lambs born in the study, one died minutes after birth, but all displayed the morphological characteristics and, more importantly, the polymorphic genetic loci of the breed used as the nucleus donor. However, it is important to point out that the one "cloned" sheep from the mammary-derived nucleus was likely not a true clone of the donor ewe. Because the genetic makeup of a cell consists of DNA not only from the nucleus but also from the cytoplasmic mitochondria, a true clone would need to have mitochondria from the donor ewe as well as the nucleus.
Although the technology for cloning animals by embryo splitting has been available for a few years, the method does not allow performance testing of the animal prior to cloning. The real potential benefit of the technological breakthrough of Wilmut's group is the ability to clone animals with proven performance. For agriculture, this could mean the replication of a limited number of superior animals from an elite herd. Caution must be exercised with this technology to avoid excessively narrowing the genetic base of domesticated species, which would increase potential susceptibility to disease.
Eric A. Wong
Department of Animal and Poultry Sciences
Virginia Tech
ewong@vt.edu
Information Systems for Biotechnology, the program that brings you this News Report every month, has developed two new workshops for agriculture and environmental biotechnology professionals.
"Oversight of Recombinant DNA Research: From the Lab to the Greenhouse to the Field" is a one-day course on the regulations that apply to recombinant DNA organisms under laboratory containment, greenhouse confinement, or released into the environment. This is an introductory course for new faculty and research staff and a refresher course for biosafety officers and members of institutional biosafety committees. The emphasis is on recombinant DNA organisms used in agriculture and environmental applications; the course does not address medical, pharmaceutical, or fermentation technology applications.
Topics include the latest NIH Guidelines for laboratory research and greenhouse experiments, and procedures and requirements under current and proposed USDA and EPA rules for biotechnology products. Participants learn which agencies have jurisdiction over various types of genetically engineered organisms and what is required for compliance with their rules. The course uses a participatory format with discussions and exercises; information resources and reference materials are be provided.
"The Biosafety Review Process" is a one-day orientation to risk assessment and risk management for the environmental release of genetically modified organisms. It is designed for anyone involved in planning, conducting, reviewing or overseeing field tests. The course takes a science-based approach to identifying environmental issues associated with small- and large-scale releases of genetically engineered plants and microorganisms.
The review process is presented as a systematic evaluation to identify potential environmental concerns and use appropriate experimental design to manage the risk or reduce it to an acceptable level. Participants gain experience in biosafety review by working through examples of proposed field tests. Various decision support tools are discussed, and supplemental reference materials are provided.
ISB will conduct the courses onsite at the request of interested academic, government, and/or corporate institutions. There is a $75 per person registration fee for each course. Host institutions should be able to guarantee a minimum of ten participants and arrange local meeting space and audio-visual equipment. For additional information or to schedule one or both workshops, contact Dr. Pat Traynor at 540-231-2620, or email traynor@nbiap.biochem.vt.edu.
On January 18, 1984, Marcia Vincent wrote in her laboratory notebook about an experiment in which a viral gene fragment was inserted into a cloning vector in either the sense or antisense orientation. Does the notebook entry evidence the conception of a method for producing a virus-resistant plant using antisense expression to inhibit translation of viral RNA? This is one question recently decided in the affirmative by the U.S. Court of Appeals for the Federal Circuit in Kridl v. McCormick (1).
Kridl concerned an interference between the patent application of Jean C. Kridl and Robert M. Goodman (assigned to Calgene, Inc.) and the patent application of Francis P. McCormick, Kenneth A. Barton, and William Swain (assigned to Agracetus, Inc.). An interference is an administrative proceeding in the U.S. Patent and Trademark Office (USPTO) to decide which of two or more inventors was the first to invent. The interference proceeding is based upon the principle that two patents must not be granted for the same inventive concept. In this case, the USPTO examiner had decided that the Kridl and McCormick patent applications contained claims for the same invention. The USPTO Board's job was to find which group was the first to invent the commonly claimed invention.
Under U.S. patent law, the act of invention is viewed as consisting of a conception of the complete invention and a reduction to practice of the invention, which may be "constructive" (i.e., filing a patent application) or "actual." An actual reduction to practice requires the physical production of a composition or apparatus that works for the intended purpose or the actual carrying out of the steps of a process invention. Here, the USPTO Board had determined that McCormick et al. had been the first to conceive of the invention and the first to constructively reduce to practice by filing a patent application. The Board based their conclusion, in part, upon the January 18, 1984, entry in the laboratory notebook of Marcia Vincent, who was working with an inventor of the McCormick group.
On appeal, Kridl et al. argued that the evidence corroborating the McCormick group's conception was not legally sufficient to establish that they had conceived plants. They grounded this argument on the principle that the complete conception of an invention requires comprehension of the invention's utility (2). To support their position, Kridl et al. hypothesized that the McCormick group may have intended to use the antisense constructs described in the lab notebook as experimental controls, or that they may have designed the experiments for producing DNA constructs in the sense orientation.
While the Federal Circuit agreed that McCormick et al. had not presented evidence explicitly corroborating conception of the utility of the invention, the court observed that antisense constructs in plants were not known by January of 1984. The court opined, therefore, that using the unique antisense constructs as experimental controls would have been illogical, and that it would have been wasteful to try to produce sense constructs using a method that also generated antisense constructs. So, the Federal Circuit agreed with the Board's conclusion that one skilled in the art would have seen only one meaningful use for the antisense constructs described in Marcia Vincent's notes: a means for imparting viral resistance to plants or plant cells by inhibiting translation of viral mRNA.
Emphasizing that the utility of the invention need not always be explicitly corroborated, the court found that the antisense constructs "speak for themselves" because their only logical utility was to confer viral resistance. Of course, one cannot rely on the favorable inferences of a court. As a routine matter, therefore, it is a prudent practice to immortalize the objective of experiments in a laboratory notebook as evidence of inventive activity.
References:
1.Kridl v. McCormick, No. 96-1339 [Interference No. 102-613] (Fed. Cir., Feb. 5, 1997).
2.Rey-Bellet v. Engelhardt, 493 F.2d 1380 (CCPA 1974).
Phillip B.C. Jones
Foley and Lardner, Madison, WI
pbcj@globaldialog.com
The past three years saw a flurry of reports from biotechnology researchers as they began locating plant genes for resistance to pathogens such as fungi, virus and bacteria. Now comes another first - a plant gene conferring resistance to a nematode has been found. In a study published in the journal Science, Christian Jung of the University of Kiel in Germany along with colleagues in Denmark and the Netherlands describe the identification of a nematode resistance gene from wild beets (1). The scientific community is justifiably upbeat about this finding as it represents the first major step towards development of nematode resistant crop varieties using biotechnology. Availability of engineered crops would help minimize the use of toxic chemicals or economically unfavorable crop rotations, which presently are used to control these pests (2).
None of the cultivated sugar beet varieties exhibits resistance to cyst nematodes, so breeders have had to work with wild beet species in their breeding programs. The resulting plants, although resistant, do not perform well in the field because associated 'weedy' genes are also introduced from the wild beets. Wild beets are not closely related to cultivated species and consequently their chromosomes do not pair. Thus, Jung and colleagues could not use recombination mapping, an approach normally used in locating genes. Instead, they sought to identify the hybrid beet lines carrying small chromosomal translocation segments from wild beets. According to Jung, this was a laborious study where many breeding lines had to be tested by molecular marker analysis.
Fortunately, they discovered a satellite DNA sequence which hybridized only to the wild beet but not the cultivated sugar beet chromosome. Using this as a probe, scientists identified among resistant plants one which had the smallest chromosome segment from the wild species. Eventually the nematode resistance gene (Hs1pro-1) was identified from a cDNA library through cross hybridization with a yeast artificial chromosome library of the resistant plant.
When the new gene was introduced into a susceptible beet variety using Agrobacterium rhizogenes, the resulting hairy roots were resistant to cyst nematodes, thus confirming the phenotype of the gene. Further proof that scientists had isolated the actual resistance gene came when resistant roots re-transformed with an anti-sense construct of the gene became susceptible to nematodes. The gene appears to be expressed primarily in roots where its activity increases when the plant is challenged by the soil-borne pests. Nematodes attempting to feed on resistant plants face the risk of their mouth parts being degraded.
The predicted protein sequence of the newly discovered gene was similar in many ways to other disease resistance genes found in plants. Jung comments on his study, "The practical value is clear: breeders now have the opportunity to produce nematode resistant beet varieties, avoiding the 'deleterious' genes from the wild beets which are located on the translocations. This is a straightforward approach for beet breeding". The group hopes to have transgenic plants soon and are optimistic that their finding opens up new avenues for developing nematode resistant varieties in other crops such as oil seed rape. As these tiny worms cause billions of dollars in damage to many agricultural crops world wide, such optimism would hopefully translate into future relief for farmers in their fight against this agricultural pest.
References:
1. Cai, D. et al. 1997. Positional cloning of a gene for nematode resistance in sugar beet. Science 275:832-834
2. Moffat, A. S. 1997. First nematode- resistance gene found. Science 275:757.
C. S. Prakash
Center for Plant Biotechnology Research
Tuskegee University
prakash@acd.tusk.edu
Crops that have been genetically engineered to be herbicide resistant are making the transition from research station to the grower's field. An indication of how they are being received by state extension specialists and farmers was given recently in a number of papers presented at meetings of the Southern Weed Science Society (Jan. 20-22) and the Weed Science Society of America (Feb. 3-6).
At these meetings, university and agrochemical industry personnel working in all aspects of weed control present their research results and discuss issues related to weed science. Due to the confidential nature of industry research, though, most reports are presented by scientists working in the public sector such as university or government. Research reported at these meetings tends to concentrate on new approaches to weed control, and the optimization and adaptation of existing methods to local conditions in each state. The conferences thus provide a barometer of emerging trends and practices in weed science, and this year was remarkable for the number of presentations dealing with field testing of transgenic herbicide resistant crops. This technology has been much heralded for years, and we are now beginning to see how it works under field conditions.
There has been continued increase in the range of crops that have been genetically engineered to be herbicide resistant, and in the number of herbicide 'families' for which such engineered crops exist. During these two conferences, field tests on transgenic varieties of four major crops and five herbicide classes were reported. The crops being tested, soybean, corn, cotton, and rice, are the major field crops that comprise a high percentage of U.S. acreage, and thus represent maximum profits to the companies that supply the seeds and herbicides. Each of these crops has been engineered for resistance to one or more herbicides, although separate lines were used for each herbicide so no crop resistant to multiple herbicide classes has been made.
Most engineering efforts have incorporated resistance to either glyphosate (soybean, corn, and cotton) or glufosinate (soybean, corn and rice). The agronomic advantage of creating resistance to these chemicals lies in the fact that both of these herbicides are normally non-selective, i.e. they will kill all weeds and crops, so conferring resistance to the crop alone results in an extremely efficient herbicide. Therefore, several of the presentations dealt with the topic of how to use these herbicides for effective weed control in their new role and how they might replace the need for existing herbicides.
The assertion that herbicide resistant crops can reduce the total amount of herbicides applied to a field appeared to be borne out by research. Because glyphosate and glufosinate kill most weeds effectively, use of one of these herbicides alone was able to control weeds equal to or better than standard mixtures of two or three different, more selective chemicals. Even difficult weed situations such as quackgrass in corn and sicklepod in soybean were controlled effectively. In fact, many presentations demonstrated greater than 95% control of weeds with the new technology. Since neither glyphosate nor glufosinate have residual activity after application, researchers recommended a second application of the herbicide to achieve best results in some cases, but even then the number of different herbicides and amount of labor expended by a farmer would likely be less than under current methods, with no loss of effectiveness. It is also noteworthy that researchers found no advantage to application rates higher than those currently used for these herbicides.
The other major advantage of using glyphosate or glufosinate resistant crops is their role in no-till agriculture. Minimizing or eliminating tillage of fields stops soil erosion and reduces pesticide runoff to non-agricultural land, but weeds soon become a major problem in such a system if herbicides are not used aggressively. Reports from growers of glyphosate resistant corn or soybean in no-till situations confirmed that use of the transgenics can give farmers the upper hand in weed control with lower herbicide inputs.
Genes for resistance to other herbicides have also been introduced into major crops. For example, a variety of corn has been engineered for resistance to sethoxydim, an herbicide lethal to grass species but not broadleaf weeds. The benefit of this development is that sethoxydim has fewer environmental drawbacks than chemicals such as atrazine which currently are used to control grass weeds in corn. However, because sethoxydim controls only part of the potential weed spectrum, other herbicides must still be used to control broadleaf weeds.
Additional research reports concerned soybeans resistant to the sulfonylurea class of herbicides, and corn resistant to the imidazolinone class, both of which inhibit the same enzymatic step in plant biosynthesis of branched chain amino acids. Both classes contain several herbicides with specific crop/weed selectivities, so the development of these new resistant crop varieties merely creates expanded uses for these already popular herbicides.
The engineered crops appear to be received very favorably by growers. Given the results of the field tests, it is not surprising that a survey of farmers who have used glyphosate- resistant soybeans were extremely positive, with over 60% planning to increase their production of this variety the following year. However, there was also another message sounded at the conferences, and this was a warning that we must not rely on any one method for weed control.
The number of herbicide resistant weeds increases each year, and stands currently at 180 species world-wide. Development of new resistances will accelerate if the variety of herbicides and other weed control methods decreases due to the wide scale adoption of herbicide resistant crops. Already 26 weeds resistant to members of the sulfonylurea and imidazolinone classes are known, and last year the first report of glyphosate resistance in annual ryegrass was found (1).
Another environmental consideration reported at the conferences was the ability of the bar gene, which confers resistance to glufosinate, to be transferred by pollen in simple outcrossing from rice to red rice, a troublesome weed in some rice production areas. In this case the trait would not need to occur naturally and be selected for over several generations, so a high level of resistance could develop in a very short time. A warning was sounded by Stephen Powles in a keynote address to the Weed Science Society of America. He emphasized that the only way to control weeds in the long term will be through the integration of multiple, distinct weed control methods. It appears certain that the agronomic advantages of herbicide resistant crops will ensure their importance in the near future, but without careful use they may rapidly be rendered obsolete by the emergence of resistant weeds.
Reference:
1. Pratley, J. 1996, as cited in Gressel, J. 1996. Resistant Pest Management 8:2-5.
Jim Westwood
International Research and Development
Virginia Tech
westwood@vt.edu
Bioremediation of environmental contaminants using genetically engineered microorganisms (GEMs) holds tremendous potential, but many issues remain to be resolved before this method is adopted widely. Priority areas for current research include improving microbial strains, improving bioanalytical methods for measuring processes, and developing analytical techniques for better understanding, control, and optimization of environmental and reactor systems. Scientists working at Oak Ridge National Laboratory (ORNL) started an ambitious experiment last October which should provide some "illuminating" results.
Gary Sayler, University of Tennessee, and Robert Burlage, ORNL, are principal investigators in a study of the degradation of polyaromatic hydrocarbons (PAHs) in soil using a genetically modified bacterium. The PAHs naphthalene, phenanthrene, and anthracene are considered priority pollutants; their occurrence in soils typically is due to spills or leaks of fossil fuels. The current phase of the research project simulates bioremediation of landfill disposal and leaching scenarios. The project is the first to entail release of a GEM into the environment for the purpose of enhancing biodegradation and bioremediation. It examines in situ GEM activity, movement, and process optimization, using bioluminescent sensing technology.
Strains of Pseudomonas fluorescens possessing a metabolic pathway for degradation of naphthalene were isolated from PAH- contaminated soil and, in earlier work (1), were genetically engineered with the lux genes from Vibrio fischeri, a bacteria that lives in specialized light-generating organs of certain deep sea fish. The lux gene was fused with a promoter normally associated with the naphthalene degradation pathway. Unlike firefly luciferase, these lux genes do not require an independent substrate for light production. The modified strain, P. fluorescens HK44, responds to naphthalene (or salicylate, a degradation product) by luminescing.
This research is being conducted with oversight from the Environmental Protection Agency. The regulations of EPA's Toxic Substances Control Act were triggered since the GEM is an intergeneric recombinant microbe. While the lux genes are not expected to confer a competitive advantage to the GEM or other soil microorganisms, there was concern about horizontal transfer of a second engineered gene which encodes the tetracycline resistance marker trait derived from E. coli. The EPA consent order specifies containment conditions to mitigate any potential risks.
The study facility at ORNL provides a high level of containment since it was originally designed to study uranium leaching. Experiments are conducted in steel and concrete vessels, called lysimeters, that are 8 feet in diameter and 10 feet deep. PAHs were mixed with locally-obtained, contaminant-free soil which has a high sand to clay ratio to allow water movement. The GEMs were sprayed evenly over the surface of this contaminated soil after it was placed in the lysimeter. An additional two-foot layer of clean soil capped off each vessel which was then covered. Water and soil from the experimental area are prevented from mixing with the surrounding environment; any leakage is collected and treated, if necessary, prior to discharge. As an additional precaution, test wells surrounding the facility monitor the groundwater and track contaminant plumes.
In the presence of PAH pollutants, luminescence from the engineered microbes is detected in situ by light probes placed below the soil surface during loading of the lysimeters. Some of the probes have the light-generating bacteria immobilized onto a wire mesh screen placed at the tip of an optical fiber probe (2). Other sensors are bare fiber optic cables. The light signals produced by the luminescing bacteria pass through the fibers to a photomultiplier and the data are stored directly in a computer. Data are collected continually, without disturbing the soil or removing samples to the laboratory.
The bioreporter method's threshold of sensitivity is approximately 45ppb; the response is proportional to the amount of the contaminant present (3). The method is less accurate than chemical analytical methods for determining PAH concentration in soil samples, but it provides additional unique information on bioavailability. Because a significant amount of the contaminant adsorbs to soil particles, it is important for the purpose of bioremediation to determine the amount of PAH available for biodegradation.
Initial results from the Oak Ridge study show that the GEM has a low level of fluorescent activity even though the population remains fairly steady at about 1 million per gram of soil, probably because little naphthalene remains. The investigators have found that the modified strain is useful for detecting naphthalene in the simulated spill site. The next step is to add a new mixture of PAHs to the soil along with some nutrients (nitrogen and phosphorous) which should result in a pronounced increase in degradative activity and light production. In an effort to optimize biodegradation, the level of the water table, the moisture content of the soil, and levels of various gases will be altered. In the long run, the investigators hope the work will be a "positive stimulus for further development of safe and effective utilization of GEMs in the environment."
References:
1. King, J.M.H. et al. 1990. Rapid, sensitive bioluminescent
reporter technology for naphthalene exposure and biodegradation.
Science 249:778-781.
2. Heitzler, A. et al. 1994. Optical biosensor for environmental on-line monitoring of naphthalene and salicylate bioavailability with an immobilized bioluminescent catabolic reporter bacterium. Appl. & Environ. Microbiol. 60:1487-1494.
3. Heitzler, A. et al. 1992. Specific and quantitative assessment of naphthalene and salicylate bioavailabillity by using a bioluminescent catabolic reporter bacterium. Appl. & Environ. Microbiol. 58:1839-1846.
Jan Klein
kleinja@nbiap.biochem.vt.edu
Awareness of the potential of transgenic technology has been elevated to a new level with the recent announcement that a sheep has been cloned using DNA from adult mammary tissue. One of the traditional methods of creating transgenic animals involves the manual micro-injection of foreign DNA into a fertilized single-cell embryo. This technique has become standard practice for generating mouse transgenics for use in biological and pharmaceutical research. But the technique has limitations, and never before had it been demonstrated that non-germline DNA from differentiated cells of an adult animal could be used by an embryo to direct the development of an organism. The response by the lay community has been mixed, ranging from fear to fascination, while the scientific community, although captivated, has been more predictably cautious. But how has the business community responded, and what does this new technique mean for companies working to develop commercial transgenic applications?
A partial list of companies developing transgenic animals includes:
The current issue of Strategic Developments in Biotechnology notes a collaboration between two of these companies, Chrysalis International and Taconic Corporation. The collaboration will allow the production, distribution, and marketing of transgenic rodent models to the pharmaceutical and biotechnology industries. Chrysalis holds patents on the traditional micro-injection technique described above, and the company's CEO notes that while the new cloning technique could have commercial potential for companies cloning larger animals, it won't necessarily have the same impact on companies developing transgenic rodents, which have rapid breeding cycles and for which viable production techniques are already in place (1).
Other companies involved in commercial transgenics recorded slight increases in stock price following the announcement of the new cloning technique, but with the exception of one company, PPL Therapeutics, the increases were modest (2). Many of these companies are pursuing the development of genetically engineered animals that possess tissues which may be used for human transplantation, or produce high-value therapeutics (e.g., in their milk). The tepid response by Wall Street is driven by the fact that the new method is currently highly inefficient and the investment community is aware of the difference between a technique's viability and profitability. In addition to the technical hurdles inherent in moving the proof of concept to commercial application, this particular technology raises a number of ethical issues that are likely to spawn debate and possible legislation (3). This all boils down to uncertainty for investors which has limited the potential increases in market capitalization through price growth that some might have expected for transgenic companies on the heels of such a breakthrough.
PPL Therapeutics, which has exclusive rights to the new technology, did see its stock price (listed on the London Exchange) increase by over 15 percent following the announcement (2). While major hurdles exist, many agree that eventually the new cloning technique may have potential applications in a number of significant areas. PPL stands to profit in the short-term from licensing the technology and this has attracted investors. Aside from the technical challenges, how much the discovery is worth to the firm over the long-term will depend on a number of factors, not the least of which is new regulation that could spring up and potentially restrict use of the technology, limiting its ultimate commercial value.
References:
1. Langreth, R., and Waldholz, M. Scottish Feat Fuels Research of Drug Makers. The Wall Street Journal, Tuesday, February 25, 1997, pg. B1, B9.
2. King, R.T., and Naik, G. Tiny company could emerge a big winner. The Wall Street Journal, Tuesday, February 25, 1997, pg. B1, B9.
3. Seachrist, L. Cloning experiment stirs ethical pot. BioWorld Today, Tuesday, February 25, 1997, Vol. 8, No. 37, pg. 1-2.
William O. Bullock
Institute for Biotechnology Information, LLC
Research Triangle Park, NC
http://www.biotechinfo.com
For years, Information Systems for Biotechnology has maintained a searchable database of NBIAP/ISB News Report articles. The database is useful for following trends in agbiotech or tracing the history of newsworthy events, such as the development of the FLAVR-SAVR tomato or the controversy surrounding recombinant bovine somatotropin. The text-based News Report database, like many others created in the early 1990's, was searchable by keywords because hardware and software limitations made it too cumbersome to search through every word in every document. But using keywords is a subjective and haphazard way of accelerating searches for the user.
With the advent of the World Wide Web, a number of "search engines" -- programs designed to maintain an index of all words and then search through the index rapidly -- have emerged, primarily for finding web pages of interest to users. Search engines like Altavista (also used by Yahoo), Lycos , America Online's Webcrawler and some twenty others are used for incredibly fast searching of millions of web documents.
The utility of search engines became apparent to individual website administrators as the number of documents available for the web grew. Thanks to Microsoft's Pentium® processor, large- capacity disk drives and cheap RAM, use of search engine software now falls within the capability of any website system. Search engines have gone through several evolutionary advances in their short lifetime, progressing from the simplicity of exact keyword matching to thesaurus matching, which looks up words similar to the keywords. ISB has been evaluating search engines to find the right combination of speed, flexibility, and resultant display format and has chosen Excite, one of the latest generation.
Excite's retrieval technology uses advanced statistical methods to increase both recall and precision. Each document collection is analyzed for statistical correlations between terms and documents. These correlations are used to define the "concepts" which facilitate the retrieval process. Excite finds those documents that most closely map to the conceptual meaning of a query. It also uses its determination of concepts to augment and improve the ranking of the returned documents, so that the most important documents are shown to the user first, even when thousands of documents are found. (For a more complete discussion of this technology, connect to a white paper on the subject at http://www.excite.com/navigate/white_paper.html).
As the amount of information on the web grows, search engines are becoming more specialized in the subject matter they collect, like the age-specific "Yahooligans" for kids, the geographically-restricted "Lycos Sweden" or the subject-oriented "Lawcrawler". And although there are plenty of categories for agriculture and a few specific to biotechnology, perhaps someone will create an "agbiocrawler" which indexes all documents on the web dealing specifically with agbiotech. It's only a matter of time.
The ISB database contains over 1100 articles from past News Reports dating back to 1989. Connect to the ISB website (http://www.isb.vt.edu), then choose Search All ISB News Report Articles under ISB Monthly News Report. Give it a try!
Doug King
Information Systems for Biotechnology
nbiap@vt.edu
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.
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