GENTECH archive 8.96-97


forwarded message from Information Systems for Biotechnology

This is a forwarded message, MIME encapsulation.


Received: from (uucp@localhost) by (8.7.5/8.7.3) with UUCP id EAA20412 for; Sat, 1 Feb 1997 04:02:15 +0100
Received: from ( [])
          by (8.8.5/8.8.5/PING-1.2C) with SMTP
	  id VAA07206 for <>; Fri, 31 Jan 1997 21:41:51 +0100
Message-Id: <>
Received: from [] by
  (SMTPD32-3.03) id A7DEB02F00E0; Fri, 31 Jan 1997 12:11:58 -0500
X-Mailer: Windows Eudora Pro Version 2.1.2
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
Precendence: bulk
From: Information Systems for Biotechnology <>
Subject: ISB News Report - February Issue
Date: Fri, 31 Jan 1997 21:41:51 +0100

                          ISB NEWS REPORT - February 1997 
                         Information Systems for Biotechnology

- 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



A new publication entitled "Global Review of Field Trials of Transgenic
Crops: 1986-1996--The First Decade of Crop Biotechnology", is available
through the International Service for the Acquisition of Agri-biotech
Applications (ISAAA).  According to Dr. Anatole Krattiger, Executive
Director of ISAAA, the report is a comprehensive review and analysis of
the 3,600 field trials from their inception in 1986 until the end of
1996.  The impact and the constraints to increased adoption of
transgenic crops as well as the future outlook for products from crop
biotechnology are discussed.  It is available free of charge and will
soon be published on the WWW.  For a copy or for more information,
contact Dr. Krattiger, Executive Director ISAAA, 260 Emerson Hall,
Cornell University, Ithaca, NY 14853, USA. Phone +1-607-255-1724,  Fax
+1-607-255-1215 or  Email


The implementation of biotechnology for California's diverse
environmental and agricultural enterprises (some 250 different crop
species) requires a different model than that used for biomedical
applications or for major acreage crops throughout the rest of the
nation.  County-based personnel, who are more closely connected to
consumers and end-users than university-based staff, must provide
leadership that facilitates teamwork and  collaborative relationships
which coordinate university and private sector-based research efforts.
One of the problems facing an individual not trained in biotechnology
but attempting to fill this role, is understanding the principles and
practices in sufficient detail to enlighten clientele making strategic
business decisions about the utility of the technology for their
particular application. Many of the educational materials developed to
date have been focused on teachers and K-12 students with an interest
in or proficiency in science and are of limited utility for the
facilitation role needed here.  

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
~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

Peggy G. Lemaux
Dept. of Plant and Microbial Biology
University of California, Berkeley


ISB is putting together a list of Institutional Biosafety Committee WWW
Homepages to add to our resource links on our Web site
(  Web searching has yielded about a dozen or so
addresses. If you are a Biosafety Officer, member of an IBC, and/or
know of an IBC homepage that is not on our starter list, please email
the address to  We are interested in IBCs that evaluate
agricultural and environmental aspects of biotechnology, as opposed to
strictly medical applications.  If your IBC does not have its own
address, please send your institution's Biosafety Office Web address
instead. Respondents will receive a free subscription to the ISB News
Report (calm down, it's free, anyway).

Doug King

A series of presentations are scheduled to explain and demonstrate the
Performance Standards for Safely Conducting Research on Genetically
Modified Fish and Shellfish. Following is a listing of dates and
locations of these presentations.

- Missouri Aquaculture Association, February 6, 1997, Jefferson City,
MO. Contact: Chuck Hicks at 573-526-6666 or Eric Hallerman at 540-231-

- World Aquaculture '97, February 20-23, Seattle, WA Biotechnology in
Aquaculture session, Friday, February 21 2:45 p.m. Anne Kapuscinski,
Eric Hallerman, and Doug King. 

- 1997 Sea Grant Extension Course in Marine Biotechnology,
Biotechnology and Aquaculture, March 13, 1997, Center for Marine
Biotechnology, Baltimore, MD.  Contact: Jonathan Kramer

- American Fisheries Society Continuing Education Workshops on
Genetics, July 30, 1997. Contact: Don Pereira at

Work has begun on the second version of the Performance Standards,
designed to conform to Windows standards. Release is expected within
the next three months.  To receive information, subscribe to the
Performance Standards listserver by sending email to saying only "subscribe fishnews [your-name]"
in the body.

Doug King
Information Systems for Biotechnology


The abstracts for the grants awarded through the 1996 Biotechnology
Risk Assessment Research Grants Program are now available on the World
Wide Web at biotechrisk/biotech.htm. 
Information regarding the 1997 Solicitation for Proposals which is due
out in March of this year and will be posted to this site is also
available. ISB provides a link to this site from its Annotated List of
Web Sites.


In an effort to meet current and future user needs, the National
Agricultural Library (NAL) has announced a new collection policy which
encourages the collection of digital materials over paper and intends
to provide digital access to legacy materials through conversion
projects conducted in partnership with users and their representative
professional organizations. 

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

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 (
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

Susan McCarthy
USDA,ARS National Agricultural Library


The USAID-sponsored Agricultural Biotechnology for Sustainable
Productivity project will host a global conference, Agricultural
Biotechnology for a Better World, April 28-30, 1997, at the Asilomar
Conference Center in Pacific Grove, California.  Participants will
explore the implications for the use of agricultural biotechnology
worldwide and its role in development assistance, agribusiness and
international trade.  The conference facility is ideally suited to
encourage an open exchange of ideas.

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

For registration and fee information, contact Dean Norton, Conference
Coordinator, Michigan State University +1-517-353-2290; email



While the global effort to map and sequence the massive human genome is
cruising well on schedule, scientists are also making impressive
strides in understanding the genomes of plants and animals of
agricultural importance.  This progress in agricultural genome research
is especially admirable considering its special challenges: a large
number of organisms being studied each with unique complexities;
relatively lower funding levels and fewer number of scientists working
with any single organism when compared to the human genome project. 
When more than five hundred scientists from across the world gathered
in San Diego between January 12-16, 1997 for the Plant and Animal
Genome V Conference, the outcome was a testimony for the achievements
made in understanding the genomes of organisms that feed the world. 
While the San Diego meeting has been an annual ritual for plant genome
scientists every January for the past four years, this year s meeting
included the animal genome researchers for the first time.

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

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:// allabstracts.html.

C. S. Prakash
Center for Plant Biotechnology Research
Tuskegee University


The development of transgenic food crops to enhance production or
desirable traits presents some exciting new possibilities but also a
potential health concern related to the inadvertent expression of a
protein that causes an allergic reaction in a sensitive individual. 
The testing of transgenic plants with suspected allergens can be
straightforward using an IgE test with serum from sensitive
individuals.  However, in some cases genes cloned from sources that are
not known to be allergenic are being introduced into plants.  Thus a
valid method to test proteins for potential allergenicity is needed.  

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.

Astwood et al. 1996. Nature Biotechnology 14:1269-1273.

Eric A. Wong
Dept. of Animal and Poultry Sciences
Virginia Tech



The Institute for Biotechnology Information (IBI) maintains a database
of strategic activities related to the biotechnology industry.  For the
year 1996, IBI entered 1,368 actions into the database, ranging from
marketing and licensing agreements between companies, to regulatory
approvals and public offerings of individual companies.  IBI defines a
biotechnology action in most cases as an activity that involves an
organization working with genetic engineering or other biotechnologies
in their R&D or manufacturing activities.  (See note at end of article
for more description of the database)

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

William O. Bullock
Inst. for Biotechnology Information, LLC
Research Triangle Park, NC



Most scientists perform a periodic pilgrimage to the library or
subscribe to literature alert services to keep up with recently
published papers in their area of interest. In a rapidly advancing and
information intensive field like biotechnology, it can be a continuous
and demanding activity to keep track of papers appearing in scientific
journals. Now, thanks to the Internet, you can retrieve titles and even
abstracts of scientific papers from your desktop. The most
comprehensive and integrated database of molecular biology information
is the Entrez search system ( Although
Entrez is from the National Center for Biotechnology Information of the
National Library of Medicine (NIH), the literature related to
agricultural biotechnology is well covered. For instance, a search for
'Arabidopsis' generated 1695 citations while 'Bacillus thuringiensis'
produced 863 hits.

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
(; 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 (

C. S. Prakash

*  *  *  *  *  *  *  *  *    END    *  *  *  *  *  *  *  *  *  *  

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:

For internet access to the News Report, textfiles, and databases use
one of the following procedures.  

1. Through WWW:

2. To have the News Report automatically emailed, send an email message
   to and type subscribe newsreport [your-
   name] in the message section. 

3. Use ftp to connect to  Use "anonymous" as your
   user-id, your email address as your password.      
   Type "cd pub/nbiap".