TITLE: Probe v1, n1/2. Complete Issue
PUBLICATION DATE: Spring/Summer 1991
ENTRY DATE: December 1994
EXPIRATION DATE: None
UPDATE FREQUENCY: As needed
CONTACT: Plant Genome Data and Information Center
pgenome@nalusda.gov
DOCUMENT TYPE: Text
DOCUMENT SIZE: 72 K
Probe v1, n1/3. Complete Issue
Strengthening Plant Genome Research Efforts - Goal of a New USDA Program
NAL's Plant Genome Center - A New Direction for Library Services
A Look at USDA's Competitive Grants Process
Plant Genome Database - Update
Planning Underway for USDA Soybean Genome Database
Forest Tree Genome Database - Development Begins
Information Superhighway Envisioned - Legislation Pending
French Join the International Human Genome Effort
Improving Access to Standardized Biological Terminology
Libraries Link Users With Specialized Databases
Theory and Application of YAC Technology for Genome Research
Parser Available for GenBank Flat file
Genome Sequencing Conference III Set for September
Introducing Dr. Stephen Heller
Calendar of Upcoming Genome Events
Beltsville Symposium
Jerome Miksche
Director, Plant Genome Research Program
USDA
USDA's Plant Genome Research Program, established last October, will facilitate the improvement of plants--agronomic, horticultural, and forest species--by locating important genes and markers on chromosomes, determining the structure of those genes, and transferring the genes to improve performance. The end product will be superior plant varieties that more closely meet marketplace needs and niches, while creating a positive effect on the environment.
The program is a cooperative effort of USDA agencies, the Agricultural Research Service (ARS), the National Agricultural Library (NAL), the Cooperative State Research Service (CSRS), and the Forest Service (FS). ARS has the lead role in directing the program. With a budget of $14.7 million for FY 9l, the Plant Genome Research Program is managed through grants, contracts, and inter- and intra-agency fund transfers.
Grants Component
USDA's Competitive Grants Research Office, a part of CSRS, will manage the grants portion of the program in cooperation with ARS. The grants will be peer reviewed and mission oriented. Application for grant funding is open to scientists from industry, academia, and government. Multidisciplinary submissions will be given favorable consideration.
The grants portion consists of three components: l) Support will be committed to constructing broad maps that locate important genes or gene systems in crops and forest species. This will be achieved using a technology that allows scientists to determine rather broad genetic similarities and differences, initiate assignment of DNA fragments on chromosomes, and then begin the mapping process. The budgeted dollars will not be allocated on a commodity basis, but on targeted gene systems or traits of some of the commodities that yield economic gain to American agriculture. Knowledge acquired from one commodity can be transferred to another crop species.
In this phase of the program, proposals anticipated will represent the following commodities: corn, soybean, tomato, wheat, barley, rice, pine (conifers), potato, garden bean, cotton, pea, peaches, oats, sorghum, sweet potato, carrots, onions, apple, rose, sugarcane, citrus crops, and other agriculturally important species.
2) Grants will be awarded to develop more specific information on crops for which some data has already been acquired. Many of the major acreage crop species such as corn, soybean, wheat, and rice come under this category.
Scientists will determine gene construction relative to important specific traits such as yield, heat and cold tolerance, disease resistance, quality changes, drought tolerance, gene transfer, and expression. This objective is important in that it will generate results that offer products to the agricultural community. The analysis of factors in gene systems or gene families that regulate gene expression is required.
3) Progress in the Plant Genome Research Program is tied to developing new mapping and sequencing technologies. The following are examples of new technologies that need development: A new method to tag sequences, which will eliminate the need to store mapping probes, innovative applications of the polymerase-chainreaction (PCR), new methodology to identify Quantitative Trait Loci (QTL's), creative computer software designed specifically for plant gene systems, insitu hybridization technologies for plant chromosomes, methods that allow mapping of polyploid genomes, chromosomal sorting and separation technologies specifically designed for complex plant genomes, and methods to overcome obstacles for plant regeneration and transformation.
Contracts and Agency Funds
The program's contracts and agency funds portion will support informatics and technological laboratory procedures. A high priority for the Plant Genome Research Program is the management of mapping/sequencing data and biological resources produced through genome research. These results will be of value only if they are made readily available to the community.
Plans are underway to establish a centralized plant genome database system to manage the expected enormous volume of research information to be generated and the diverse biological resources. The database will be located in NAL's new Plant Genome Data and Information Center, which provides information on plant genome research to users. A standardized database management system will enable researchers to easily deposit and retrieve mapping and sequencing data. Database development will focus on four agricultural commodities: corn, wheat, soybean, and pine. Work groups organized in these areas will address user needs, define database file structures and elements, and assume responsibility for quality control on the acquired data.
An equally urgent need is to enhance current stock centers. The deposition and distribution of new biological resources such as seeds, mutants, antibodies, protein and DNA probes are important considerations for the program. A major program challenge is to establish new centers as materials accumulate.
In addition, the increased innovative technologies that will automate DNA laboratory procedures from extraction and purification through data analysis are important challenges needed to make the program effective.
USDA staff are pleased with the support demonstrated thus far for the program throughout government, industry, and academia. For more information on the program, contact Jerry Miksche on (301) 344-2029.
Joseph H. Howard
Director, National Agricultural Library
United States Department of Agriculture
When the National Agricultural Library (NAL) opened in Beltsville, Maryland, in 1967, staff then probably could not have envisioned all the technological advances in information management that would develop over the next 24 years.
But, since that time, NAL staff have worked diligently to stay abreast of the new technologies and to adapt those that most benefit users. These technological advances combined with the talents and dedication of library staff have enabled NAL to improve and expand its services to better meet the needs of users in the agricultural community.
Recently NAL opened the Plant Genome Data and Information Center (PGC), which offers a new direction for the library in archiving and in providing the public access to a national scientific database. An initiative of USDA'S Plant Genome Research Program, the Center's primary goal is to make information on plant genome research readily available to users in useful formats.
This newsletter is but one example of the varied services PGC offers. In addition, Center staff will provide information on all aspects of plant genome mapping; identify current genome mapping research; refer users to organizations or experts in the plant genome subject area; perform brief AGRICOLA (AGRICultural OnLine Access) database searches on a complimentary basis or exhaustive searches on a cost-recovery basis; furnish users with a Quick Bibliography (QB), Special Reference Brief (SRB), or user guide to literature; and assist users in accessing NAL's extensive collection.
The services of the Center are available to anyone interested in plant genomes, including scientists, breeders, educators, students, legislators, information professionals, administrators, and the general public.
Plans are underway to develop a new database that will contain plant genome data on four agricultural commodities--soybean, corn, wheat, and pine. As producer of the AGRICOLA computerized database and as the foremost agricultural library in the world, with nearly 2 million volumes and subscriptions to 26,000 periodicals, NAL is the ideal location for establishing and maintaining the database.
NAL staff anticipates that PGC will lead the way for additional centers and databases in other agriculturally related areas.
For more information on PGC, contact Susan McCarthy, coordinator for the Center, on (301) 344-3875.
Anne Datko, Program Director
National Research Initiative
Competitive Grants Program, CSRS, USDA
USDA has announced a National Research Initiative on Agriculture, Food, and the Environment. The need for an increased investment in competitively awarded research was identified by the National Research Council of the National Academy of Sciences and broadly endorsed by the agricultural, scientific, and users communities. In the 1990 Farm Bill, the Initiative was authorized at a full funding level of $500 million per year. The Office of Management and Budget endorsed the full funding level and is committed to reaching this level by phased growth over the next few years. For FY 1991, Congress funded the Initiative at $73 million; the President's FY 1992 budget recommends funding at the level of $125 million.
NRICGP's Role
In 1991, the National Research Initiative Competitive Grants Program (NRICGP) subsumed the previously existing USDA Competitive Research Grants Program. Further, it was announced that while the Agricultural Research Service (ARS) would be the lead agency for the USDA Plant Genome Research Project, the competitively awarded research grant component would be administered by NRICGP and funded within the Program's Plant Systems Division at a level of $11 million.
NRICGP competitively awarded research grants support research projects judged to further USDA programs. A Solicitation, which announces guidelines for each program of NRICGP, is published in the Federal Register at the beginning of each fiscal year. Proposals for such awards may be submitted by any public or private institution, or individual.
Peer Review
In general terms, peer review is used to provide the best possible scientific advice before expenditure of Federal funds. Peer review is arranged by a Program Director, a USDA scientist responsible for overseeing the review process, upholding the highest standards of conduct, and providing assistance and advice to the Panel Manager. A Panel Manager, an active researcher in the appropriate scientific community chosen each year, is responsible, in consultation with the Chief Scientist of NRICGP, for selecting panel members with appropriate scientific expertise, review experience, and breadth of knowledge.
Written reviews are also solicited from the scientific community on
an ad hoc basis. The peer review panel, chaired by the Panel
Manager, takes into account the judgement of the panel members and
the ad hoc reviews to provide advice to the NRICGP as to the
scientific merit of each proposal. The program recommendation for
funding, based on the panel ranking, is presented to the Chief
Scientist who recommends the awards.
Plant Genome Proposals
More specifically, the 1991 NRICGP Solicitation identified research in the broad area of plant genome studies as having the potential for significant impact for improving agricultural and forest productivity, and described the areas in which proposals would be accepted. In response to the Solicitation, a large number of proposals were submitted by the postmark deadline of January 28, 1991. Dr. Maureen Hanson, director of the NSF/DOE/USDA Plant Science Center at Cornell University, was named Panel Manager for the Plant Genome Program for 1991 while Dr. Anne Datko, of the NRICGP staff, served as Program Director.
The peer panel has already met to review proposals submitted; award recommendations have been made to Dr. Paul Stumpf, Chief Scientist of NRICGP. Because of joint responsibility of NRICGP and ARS, Dr. Jerome Miksche, director of the Plant Genome Research Project, was not only consulted as to panel member selection but also received the award recommendations. The grants funded are to be published in January 1992 in "Food and Agriculture Competitively Awarded Research and Education Grants" by USDA's Cooperative State Research Service.
1992 Solicitation
NRICGP anticipates publishing the 1992 Solicitation in the Federal Register early in October 1991 with postmark deadlines for proposals being earlier than in 1991. All institutions that received the 1991 Solicitation and all applicants to the program in 1991 will automatically receive a copy of the 1992 Solicitation. Other interested individuals may request the Solicitation (in September 1991) from the address below.
A vacancy announcement is expected to be issued within the next few months by NRICGP's Plant Systems Division for the position of Plant Genome Program Director. Persons interested in applying for this full-time, permanent USDA position may contact the address below for additional information.
For Solicitation information, contact the following:
Attn: 1992 Solicitation
NRICGP/CSRS/USDA
Room 323, Aerospace Building
Washington, DC 20250-2200
Phone (202) 401-5022 or FAX (202) 401-6480
For Program Director Vacancy Information, write to the following:
Attn: Dr. Rockey, Plant Systems Director
NRICGP/CSRS/USDA
Room 323, Aerospace Building
Washington, DC 20250-2200
Phone (202) 401-5114 or FAX (202) 401-6488
Douglas Bigwood
Database Manager
Plant Genome Data and Information Center
National Agricultural Library, USDA
Providing users with fast, easy access to plant genome mapping and related information is a primary goal of USDA's Plant Genome Research Program. Currently plans are underway to develop a plant genome database system at NAL's Plant Genome Data and Information Center (PGC). The Center's database manager will direct the implementation of the plant genome database, which will contain public plant genome information for four agricultural species-- maize, soybean, wheat, and loblolly pine. In addition, procedures will be implemented to ensure that the information provided is up to date.
Project Activities
Initial activities of the database project include site visits by PGC staff to several institutions also involved in developing genome information systems. Institutions visited include the National Center for Biotechnology Information at the National Library of Medicine (GenInfo Backbone), the Los Alamos National Laboratory (GenBank), the Lawrence Berkeley Laboratory (Chromosome Information System), the Welch Library at Johns Hopkins University (Genome Data Base), the Massachusetts General Hospital (Arabidopsis mapping project), and Agrigenetics (commercial breeding projects). Center staff have benefitted from the wealth of knowledge and experience provided by these groups. Hopefully, as a result of this information sharing, some of the pitfalls and problems faced by the other institutions can be avoided in the USDA project.
The Center has also been active in two CODATA projects: Biological Macromolecules (seeking to improve coordination among institutions that compile protein and DNA sequence data) and Standardized Terminology for Access to Biological Data Banks (headed by Lois Blaine, whose article appears elsewhere in the newsletter). CODATA is an interdisciplinary Scientific Committee of the International Council of Scientific Unions that seeks to improve the quality, reliability, management, and accessibility of data important to all fields of science and technology.
Interaction With Species Groups
The task of collecting and evaluating the data that will comprise the plant genome database system is the responsibility of the principal investigators for the four plant species and their advisory committees. The principal investigators are Frank Greene and Olin Anderson (wheat), David Neal (pine), Ed Coe (maize), and Randy Shoemaker (soybean). Each of the four groups will have their own database requirements. Cooperators in the project have made a concerted effort to ensure that all database-related activities are performed in a coordinated manner. The ultimate goal is to provide a master database design that is as generic as possible. If this goal is achieved--and efforts so far are encouraging--data from a number of additional species may be easily incorporated in the database in the future. Furthermore, plans are to develop an open system so USDA's database can forge data links with related data sources such as GenBank, AGRICOLA, and the Germplasm Resources Information Network (GRIN).
Future Plans
By the time this newsletter is printed, the first meeting of the PGC advisory committee will have been held. Composed of genetic and information experts, the committee is expected to be valuable in ensuring that the plant genome database is the best possible resource for users.
PGC staff are also establishing computer and communication systems. Initial development will be performed on Unix workstations using the Sybase relational database management system. These have essentially become de facto standards in the genome community. The database system's major network access will be through Internet via a T1 line.
The database analysis and design is proceeding as planned. Implementation will begin in the near future.
Randy C. Shoemaker
Research Geneticist, Field Crops Research Unit
Iowa State University
Agricultural Research Service, USDA
Information on soybean genetics has, until recently, developed slowly in relation to data gathered on other major crops. However, the increased speed with which genetic data on the soybean currently is being accumulated rivals that of any other genetic system.
The importance of the soybean as a major world oilseed crop plus the increased volume of genetic information accumulating have made the soybean an important focus of the USDA Plant Genome Research Program's thrust to develop a plant genome database manage ment system. The database, to be located at the National Agricultural Library (NAL), will include information on four agricultural commodities--soybean, corn, wheat, and pine.
Soybean Conference Held
At a conference held recently in St. Louis, Missouri, over 30 participants from 14 states and Canada met to discuss developing a prototype soybean genome database. Participants provided information on the long-term needs of the project and established a priority for accomplishing the tasks required to develop a database.
The group included scientists from state and federal institutions and private industry, and representatives from the Germplasm Resource Information Network (Mark Bohning), the American Soybean Association (Keith Smith), the USDA Plant Genome Research Prog ram (Jerry Miksche), and the National Agricultural Library (Susan McCarthy). In addition, Mary Berlyn, a cooperator in the USDA program and co-developer and curator of the E. coli genetic stock center database at Yale University, provided useful input an d facilitated discussions.
Working Committees Formed
Seven committees listed below were formed during the conference to address specific concerns according to their areas of expertise. The committees will determine the probable relationships between their respective segment of the database and the other ar eas. In addition, the soybean team will examine strategies developed for other databases and genome initiatives, including those for human and bacterial genetics. The following is a list of the committees and respective chairpersons:
Disease/Pathology: Roger Boerma, University of Georgia
Phone (404) 542-0927
Germplasm: Jim Specht, University of Nebraska
Phone (402) 472-1536
Maps: Nevin Young, University of Minnesota
Phone (612) 625-2225
Metabolic Pathways: Tom Cheesebrough, South Dakota
State University
Phone (605) 688-5504
Organelles: Beth Grabau, Virginia Polytechnic
Institute and State University
Phone (703) 231-9597
Quantitative Traits
and Quality Control: Randy Shoemaker, Iowa State University
Phone (515) 294-6233
Group members have had extensive discussions with industry representatives to ensure that a maximal amount of user needs will be met. In addition, to avoid duplicated efforts, the Quantitative Traits Committee will interact closely with a similar committ ee of the maize database group. The Quality Control Committee will explore methods to maintain the integrity of the information in the database while facilitating access by its users. The soybean team also will work closely with the Germplasm Resource I nformation Network (GRIN) so that a smooth interface is established between the modified GRIN database and the developing soybean database.
If the conference was any indication, the enthusiastic "grass- roots" support shown there will assure the momentum needed to establish a comprehensive plant genome database for soybeans.
David Neale
Molecular Geneticist
Institute of Forest Genetics
U. S. Forest Service
Berkeley, California
Plans are underway by USDA's Forest Service (FS) staff to develop a prototype genome mapping database for an important forest tree species--the loblolly pine. The database project is part of USDA's Plant Genome Research Program effort to provide users with fast, easy access to plant genome data. USDA plans are to develop a plant genome database system at NAL's Plant Genome Data and Information Center, which will contain plant genome information on the loblolly pine and three additional species--corn, soybean, and wheat.
Work on the pine database project began in late May at the Institute of Forest Genetics (IFG), Pacific Southwest Research Station, in Berkeley, CA. Several goals have been identified for FY 91. First, schema must be determined for the database. Plans are to collaborate with the Human Genome Computer Science Group at the Lawrence Berkeley Lab (LBL). A computer scientist is being recruited by IFG to work with the LBL group. Two other database projects to be completed in conjunction with LBL also have been identified: (1) development of an electronic laboratory notebook for tree genome mapping and (2) image processing and analysis software for tree mapping data. In addition, IFG will collaborate with the University of Montana to develop statistical approaches and computational methods to map quantitative trait loci (QTL) in segregating tree pedigrees.
David Neale is the principal investigator for the loblolly pine database. A Forest Tree Genome Database Advisory Group will be established this summer. A workshop on the project is planned for late 1991.
Information Superhighway Envisioned--
Legislation Pending to Establish National Computer Network
Susan McCarthy
Coordinator, Plant Genome Data and Information Center
National Agricultural Library, USDA
A national superhighway for information may soon become a reality if Congress passes the proposed legislation needed to establish the National Research and Education Network (NREN)--a highcapacity, high-quality computer network that supports a broad set of applications and network services for the research and education community.
NREN would expand and upgrade the existing interconnected array of primarily scientific research networks that comprise Internet, including the nationwide NSFNET (the backbone), regional networks such as NYSERNET and SURANET, and local area networks. NSFNET, perhaps the best known of the Internet networks, allows researchers and educators to exchange up to l.5 million bits of data per second. The proposed NREN is expected to be at least a thousand times faster.
Facilitating Genome Research
Fast, high-quality networks (gigabit per second transmission rate) are needed to facilitate access to genome data. NREN would link libraries, government research laboratories, industry, and universities. The National Agricultural Library and the National Library of Medicine are cited in the proposed legislation as focal points in the information distribution networks. These libraries play vital roles in the genome programs for humans, plants, and animals.
Proposed Legislation
Senator Albert Gore, Jr. (D-TN) introduced a bill (S272) in the Senate this year to establish NREN under the High Performance Computing Act of 1991. Recently, Representative George Brown (DCA) introduced a companion bill (HR656) in the House. Legislation was first proposed by Senator Gore in 1988. Last year a revised version of the bill was unanimously passed by the Senate, but the House failed to act on the companion bill. The current Senate and House bills have been placed on the congressional calendar.
Under the proposed legislation, the National Science Foundation would provide leadership in establishing the new fiber-optic computer network in cooperation with the Department of Defense, the Department of Energy, the Department of Commerce, the National Aeronautics and Space Administration, and other agencies.
A third bill introduced this year proposes to establish a Federal High-Performance Computer Network, which would serve many of the same purposes envisioned for NREN. Senator J. Bennett Johnston (D-LA) is sponsoring the bill--the Department of Energy HighPerformance Computing Act of 1991 (S343). The Department of Energy is designated lead agency under the proposed legislation. Increased Funds and Support
A new Presidential Initiative, "Grand Challenges: HighPerformance Computing and Communications," issued by the Office of Science and Technology Policy calls for a 30 percent increase in funding for FY 1992. The funds will support high-performance computing systems, advanced software technology and algorithms, NREN, basic research, and human resources. Japan and Europe are well ahead of the United States in recognizing the need for an information infrastructure. Maintaining the United States' technological lead and competitiveness targets this critical technology for congressional action. Support of the proposed legislation will have a positive benefit for genome research programs. The supernetwork--expanded, upgraded, and connected--will maximize the benefits and technology-transfer opportunities derived from the genome projects.
Susan McCarthy
Coordinator, Plant Genome Data and Information Center
National Agricultural Library, USDA
The French government has made a major investment in bioscience research. They have established a new agency, the Groupement d'Interet Public, (GIP), which will play a lead role in coordinating genome activities in France and with other countries.
GIP Acting Director Dr. Jacques Hanoune and Acting Associate Director for Informatics Dr. Pierre Oudet are visiting the United States this summer to study the organization of genome programs and corresponding database developments for these programs. Recently, during their trip, they met with Dr. Jerome Miksche, director of the USDA Plant Genome Program, and staff of the National Agricultural Library. The visit by the GIP representatives will provide them an introduction to U.S. genome efforts and an opportunity to discuss areas for future collaboration by the two nations.
The French program will have three main scientific thrusts. The primary effort will consist of mapping and sequencing the genes expressed in man. Largely, this will be the sequencing of cDNA libraries. The program will also support high resolution mapping of identified genes to chromosome coordinates, particularly those related to genetic diseases. Model organisms will be studied to develop new and more efficient technologies and to understand gene function. The organisms under study include yeast, mouse, bacteria, and wheat.
A significant effort will involve the storage and retrieval of the mapping data, "informatics." The high volume of data generated from the mapping efforts will require two basic developments: (1) advances in adapted informatic structures--in other words, user needs assessments--and (2) programs for the acquisition and analysis of the mapping and sequencing data. Approximately 20-25 percent of program funds will support informatics.
FY 1991 will see a French investment of 50 million francs--about $10 million--in new funds. This is added to the figure of approximately 150 million francs supporting existing genome programs. The budget for next year is expected to reach 100 million francs in new funds.
Lois Blaine
Head, Bioinformatics Department
American Type Culture Collection
Rockville, Maryland
CODATA Convenes Workshop To Address Problems
Formulating a plan to improve access to standardized terminology for biological database producers and users was the goal of a workshop held May 14-16 in Nancy, France, by the CODATA Commission on Standardized Terminology for Access to Biological Data.
The workshop, jointly sponsored by the U.S. National Center for Biotechnology Information and Commission of the European Communities DG XII, was attended by representatives of the Biological Unions of the International Council of Scientific Unions (ICSU), producers of bibliographic and factual databases, and professional terminologists. This combination of participants, coming from disparate subdisciplines of biological and information science, provided an excellent blend of appropriate talents to address the multifaceted problems of terminological standardization.
A primary goal of the Commission, re-emphasized during the Nancy Workshop, is to raise the level of consciousness within the biological community of the need to communicate across disciplines. A major benefit of today's computer technology is that it provides the means to integrate data in ways that will lead to new scientific insights. Artificial intelligence, innovative programming, massive data storage capabilities, and vastly improved communication technology, will inevitably draw diverse data sources together. If data is to be integrated, exchanged, and searched efficiently, the intellectual input to make this possible must come from biologists now.
Although problems surrounding the "standardization" of nomenclature and terminology have been with us for centuries, information technology demands that we take a fresh look at these problems and devise new methods to solve them that takes full advantage of today's technological tools.
Workshop Segments
The workshop program consisted of three segments. The first segment consisted of formal presentations that provided a background and overview of the perceived problems in interdisciplinary access to biological terminology. Dr. Andrzej Elzanowski, from the Max-Planck-Institut fur Biochemie, articulately summarized the problems faced by database producers in "translating" the nomenclature and terminology used by authors who write for scientific journals into some type of "standard" that can be used for consistency of retrieval of identical concepts. During the workshop, it became apparent that authors, editors, publishers, and database producers all face a similar situation-- the lack of clear guidelines on nomenclature and taxonomy of organisms, and the terminology to describe their characteristics.
In the second segment, representatives of the Biounions, in a series of round-table discussions, presented the "state of the art" within each union regarding nomenclature and terminology standards. Broad topics covered by the union representatives included botanical and zoological nomenclature and taxonomy, biochemistry, microbiology, pharmacology, physiology, nutrition, food science, and clinical medicine. Participants discovered that the nomenclature and terminology committees of the ICSU unions face as many problems in providing standards as database producers and users do in locating standardized terminology for biological concepts. Their ability to provide wide access to standardized terminology in formats and electronic media desired by database producers is limited by the fact that almost all of their work is performed on a "volunteer basis" and is primarily designed for intradisciplinary use. Additional resources would be required to expand the work of the Biounion nomenclature and terminology committees.
During the third segment, participants heard from terminological specialists who discussed existing standards for terminology. There are general principles that must be applied when developing terminological databases, regardless of the scope and content. The Commission agreed to work with the specialists to educate biologists on the ICSU committees in the implementation of these principles. Several documents recognized by the International Standards Organization were recommended for use in the educational campaign.
Increasing Information Exchange
The workshop discussions raised the participants' awareness that the present interdisciplinary nature of many scientific activities leads to a greater need for an exchange of information within the component parts. The impact of multinational projects, such as HUGO, similarly imposes added demands for clarity and standardization of expression. The integration of international, interdisciplinary databases will require some precision in defining terminology for uniform interpretation of scientific principles.
Workshop participants agreed that the first step in providing wider access to standardized terminologic references is to expand efforts initiated by the U.S. National Library of Medicine (NLM) in establishing a "Nomenclature File" in its Directory of Biotechnology Information Resources. All agreed that the NLM file is a useful beginning, but that a broader international inventory of terminological resources and their relationships to one another is required. A steering committee composed of Commission members will be established to design procedures for developing this international terminological inventory.
"Term Bank" Needed
The ultimate goal of the Commission would be to catalyze the development of an international "Term Bank." This, of course, would have to be developed in modules and would necessitate preliminary studies to determine feasibility and user requirements. The Commission would also seek the cooperation of other international organizations such as the International Council on Scientific and Technical Information (ICSTI) and the International Federation of Scientific Editors (IFSE), both represented at the Nancy workshop. An enormous effort would be required to make such a Term Bank available to the international scientific community. While the computer and communication technology is available to link subsets of such a database, issues, including copyright, cost recovery, coordination, updating responsibilities, and funding were recognized to be potential barriers to the successful accomplishment of the goal.
A representative from the International Union Against Cancer (UICC), Dr. Leslie Sobin, aptly set to verse the precautions that must be taken by the Commission in approaching a project of this dimension:
When you're looking for the answer
how to classify all cancer,
proteins, microbes, fish and succulent legumes,
You must know a little Latin
tell a round fish from a flat one
and have memory with lots and lots of room.
But, before we start alinking
we should sit back and be thinking
on our methods, clientele and on our goal,
Lest we make a mammoth bank
rarely used and rarely thanked
just consuming funds and efforts: A BLACK HOLE.
Leslie Sobin
Members of the CODATA Commission will keep these words of wisdom in the forefront as they launch their campaign to improve access to standardized biological terminology.
For further information on the CODATA Commission on Standardized Terminology for Access to Biological Data, please contact the CODATA Secretariat, 51 bd. de Montmorency, 75016 Paris, France.
Vincent Caccese, Librarian
Biological & Agricultural Sciences Reference Department
Shields Library
University of California, Davis
Some scientists, students, and others involved in research may not consider using library reference services when they need a database on molecular biology. They may fail to take advantage of a research librarian's access to non-bibliographic databases such as GenBank or NBRF-PIR. But, today, an increasing number of research libraries have access to specialized databases to better serve users. Along with those mentioned, similarly recondite databases have recently become part of reference services. One example is molecular structure searching on chemical databases, such as Chemical Abstracts, which librarians in many universities and companies have successfully mastered to benefit their users.
New Databases Created
Leading research libraries have recognized the importance of molecular biology databases to their mission. Increasingly, research libraries are not only using specialized databases but creating them as well. The National Agricultural Library (NAL) and the National Library of Medicine (NLM), for example, are updating their bibliographic files (NAL's AGRICOLA and NLM's MEDLINE) to incorporate molecular biology data while creating new databases to integrate several kinds of reference/data files (NLM's GenInfo Backbone is the most recent example).
University Library Services
Along with national libraries and special libraries in private industry, academic research libraries are important centers for genetics information. At Johns Hopkins University's Welch Medical Library, the database GDB/OMIM (Genome Data Base/Online Mendelian Inheritance in Man) has been available for some time from computers on public data lines to registered users around the country.
The Biological Sciences Library at Columbia University provides its students and faculty with access to locally mounted GenBank. While the University of California, Davis, libraries do not use dedicated equipment for such access, users can access sequence databases (such as GenBank) mounted on the campus computer via general purpose terminals in the libraries. With the additional availability of GenBank and other sequence databases via SprintNet and Internet for daily updated information, it is likely that the user population will increase.
User Assistance
Although libraries address local demands according to individual means and staffing, scientists and other users should not hesitate to ask for assistance in locating databases. Appropriate requests that do not make inordinate demands on staff or strain budgets include identifying a database, including its scope and currency; finding documentation for the database; identifying means of access and its cost; finding ancillary documentation in the scientific literature; and, if all else fails, suggesting who to call. Some libraries may also aid a new user in learning the system or in running a search. If the database requested is not available, the librarian will at least know that there is local demand for such information.
Brian M. Hauge and Howard M. Goodman
Department of Genetics, Harvard Medical School and
Department of Molecular Biology, Massachusetts General Hospital, Boston
A major challenge in plant molecular biology is isolating genes where the biochemical function of the gene product is unknown. In a variety of plant species, genes controlling a wide range of fundamental developmental and metabolic processes have been identified by mutational analysis and placed on classical genetic linkage maps. Examples include genes conferring resistance to plant pathogens, the synthesis and response to plant hormones, drought tolerance, and genes required for a variety of important developmental pathways. In most cases, while the mutant phenotype and genetic map locations are known, virtually nothing is known about the product of the gene.
Gene-Cloning Methods
There are several ways to clone genes for which the genetic locus and not the
product of the gene is known. If a gene can be tagged with a transposable
element, the gene can be cloned directly by isolating the sequences flanking
the site of insertion. The cloning of genes by transposon tagging has been
used extensively in maize. The most widely utilized and best characterized
plant transposable elements, the maize Ac and Ds elements (reviewed by
Fedoroff in Berg and Howe. 1989) are further capable of transposing in various
heterologous plants (Van Sluys et al, 1987) thereby extending the utility of
this system to plants having no well-characterized transposable element
systems. In addition to endogenous transposons, the T-DNA of Agrobacterium
tumerfaciens has also been successfully used for gene tagging (Feldmann et al,
1989).
A second alternative is to clone genes corresponding to deletion mutations using the technique of genomic subtraction (Straus and Ausubel, 1990). This method is based on the progressive enrichment for DNA fragments present in the wild type genome but absent in the mutant genome that harbors the deletion. Following multiple rounds of enrichment, the resultant fragments are amplified by PCR and cloned. The one constraint of the protocol is that the deletion must encompass a single restriction fragment which is composed entirely of non-repetitive DNA. Genomic subtraction has recently been used to clone the GA-1 gene from Arabidopsis (Sun and Ausubel, unpublished results).
Like the gene-tagging strategies, the advantage of genomic subtraction is that one has immediate access to the gene(s) of interest. A disadvantage of both approaches is that insertions or deletions in essential genes will be lethal, so phenotypes associated with "leaky" point mutations will not be detected.
Second, transposons as well as different mutagenic agents exhibit some degree of sequence specificity. Therefore, many important loci will be refractory to isolation by transposon tagging or genomic subtraction.
Chromosome-Walking Strategy
A more general approach is to clone genes by chromosome walking. This
strategy is general in the sense that the cloning of the gene is based solely
on the mutant phenotype and genetic map position. Therefore, chromosome
walking can be used to clone any gene which can be genetically identified.
The first step toward cloning the gene is to identify DNA probes residing
within one to several cM of the locus of interest. Typically this is achieved
by analyzing the meiotic segregation of restriction fragment length
polymorphisms (RFLPs). Once a linked RFLP(s) has been identified, it can be
used as the starting point to initiate a chromosome walk.
Briefly, chromosome walking entails the progressive isolation and characterization of overlapping sets of genomic clones. The overlapping clones are selected by hybridization using end-specific probes (probes generated from the extremities of the clone/contig). The walk is continued in this manner until the region spanning the intervening gap has been bridged by an overlapping set of clones. While chromosome walking is technically straight forward, in practice the procedure is extremely labor intensive and ill-suited for large projects where more than a few steps are required.
Constructing Physical Maps
Recently, interest has focused on strategies for constructing physical maps of
entire genomes. By definition, a physical map consists of a linearly ordered
set of DNA fragments encompassing the genome or region of interest. Physical
maps are of two types, macro-restriction maps and ordered clone maps. The
former consists of an ordered set of large DNA fragments generated by using
restriction enzymes whose recognition sequences are infrequently represented
in the genome (Smith et al, 1986). The macro-restriction map provides
information about the organization of DNA fragments at the level of the intact
chromosome thereby providing long-range continuity.
As the name implies, an ordered clone map consists of an overlapping collection of cloned DNA fragments. The DNA may be cloned into any one of the available vector systems--YACs, cosmids, phage, or even plasmids. Major advantages of ordered clone maps are that they are of high resolution and directly provide the clones for further study.
The immediate benefits of having a physical map are two-fold. First, the map provides ready access to any region of the genome which can be genetically identified. Given a mutation of known genetic map location, the physical map can be used to easily isolate an overlapping collection of clones encompassing the locus of interest. By eliminating the need for laborintensive steps such as chromosome walking, researchers are free to focus their efforts on the isolation and characterization of the gene of interest. Second, the physical map provides a starting point for studying global genomic organization. As an increasing number of genes are cloned and molecular biological information is accumulated, one can begin to investigate the physical linkage of cloned genes, study the organization and distribution of repetitive elements, and address questions such as how physical distance and genetic distance are correlated. In this context, the map provides the framework for cataloging and integrating molecular biological information. Ultimately, genome organization will be investigated at the nucleotide level. Clearly, physical maps are the logical substrates for genome-sequencing projects.
Laborious Process
Physical mapping of complex genomes, however, is both laborious and
computationally intensive. To illustrate the physical mapping problem,
briefly described below are the researchers' efforts to assemble a complete
physical map of the Arabidopsis thaliana genome, which will ultimately consist
of a fully overlapping collection of cloned DNA fragments encompassing the
five chromosomes.
The first stage of the mapping project involved the characterization of random cosmid clones by fingerprint analysis (Coulson et al, 1986; Hauge and Goodman, 1991). For the Arabidopsis project, approximately 20,000 random cosmid clones (~10 fold sampling redundancy) from primary libraries were fingerprinted. Using computer matching programs, the clones have been aligned into some 750 overlapping groups or contigs. The contigs encompass approximately 90-95 percent of the Arabidopsis genome (Hauge et al., 1991).
In general, some 8-10 genomic equivalents must be fingerprinted to achieve 70-95 percent coverage of the respective genome. The task of ordering the clones and aligning them with respect to the genetic map is formidable to say the least. To illustrate the magnitude of this problem, consider the maize genome, which is estimated to be 3,900,000 kb. Using random cosmid clones containing an average insert size of 40 kb, approximately a million clones would be needed for 10 genomic equivalents.
YAC Cloning Vectors
The mapping problem has been greatly simplified by the development of yeast
artificial chromosome (YAC) cloning vectors (Burke et al, 1987). The YAC
vectors allow for the routine cloning of 0.5 megabase-sized DNA fragments,
representing an improvement of at least an order of magnitude over the
previously existing techniques. The construction of YAC libraries involves
the ligation of large DNA fragments (100-1000 kb) into a vector containing
selectable markers and the functional components of a eucaryotic chromosome,
ARS elements for autonomous replication, the centromere for proper disjunction
during meiosis and mitosis, and telomeres required for the replication of
linear molecules (Murray and Szostak, 1983). The clones are transferred into
bakers yeast (S. cerevisiae) where they are replicated along with the
endogenous host chromosomes.
There are two clear advantages of the yeast-cloning system: The large size of the inserts means that fewer clones need be examined. Equally important is that YACs offer the potential to give a more random representation of clones than are obtained using conventional cloning systems.
Utility of YAC Clones
The following examples of how YAC clones are being employed for Arabidopsis
genome mapping illustrate the utility of YAC clones for genome research. Two
general approaches are being used to assemble an overlapping YAC library
covering the Arabidopsis genome. The first approach is to simply identify YAC
clones corresponding to genetically mapped DNA probes (RFLPs and cloned
genes). Presently some 380 Arabidopsis RFLP probes (Chang et al., 1988; Nam
et al, 1989; S. Hanley and H.M. Goodman, unpublished; E. Meyerowitz,
unpublished) are available for correlation of the physical map with the
classical genetic linkage map. Using the available YAC libraries (Ward and
Jen, 1990; Grill and Somerville, 1991), YAC clones corresponding to 125 RFLP
markers have been identified (Hwang et al. 1991). Based on a mean YAC insert
size of 160 kb and an average YAC contig size of 220-240, YACs of known
genetic map location encompass approximately 30,000 kb or about 30 percent of
the Arabidopsis genome (Hwang et al, 1991). Extension of this analysis to the
remaining 160 some RFLP probes should result in a collection of YAC clones
encompassing some 70 percent of the genome. Closure of the gaps can then be
achieved by either chromosome walking or by utilizing the cosmid contig map as
described below.
As an alternative strategy, the overlapping cosmid map (Hauge et al, 1991) is a powerful tool for assembling an overlapping YAC map. The linking strategy is to use the YAC clones to probe ordered arrays of cosmid clones that are representative of the contigs (Coulson et al, 1988). Cosmids within a contig are chosen so that there is minimal overlap between flanking clones, yet the clones are representative of the contigs. The cosmids are plated onto nylon membranes as ordered arrays and subsequently probed with labeled YAC clones. Using this strategy, the gaps in the contig map are closed and the YACs are aligned within the framework of the cosmid map, thereby generating an overlapping YAC map.
An advantage of this approach over traditional strategies that use endprobes to select overlapping clones is that the hybridization patterns are easily tested for a logical fit to the structure of the contig map. Linkage can, therefore, be rapidly established based largely on the results of colony hybridization. In contrast, techniques such as genome walking require laborious confirmation of each join and subsequent restriction mapping of the linking clones to determine both the direction and the extent of the walk.
Using a combination of the techniques described above, it is probable that an overlapping YAC library of the Arabidopsis genome will be completed in the near future. The overlapping YAC library will serve to facilitate the cloning of genes and will provide a minimal set of clones covering the Arabidopsis genome. Given the small genome of Arabidopsis, a representative collection of clones can be gridded at high density onto a single filter the size of a microtiter dish. These "polytene" blots (J. Sulston and A. Coulson, personal communication) can then be used to rapidly determine the chromosomal location of any new clone by simple blot hybridization.
YAC clones are likely to play an increasingly important role in future physical mapping projects. The strategies for physical mapping with YACs are essentially the same as those used for other genomic libraries (bacteriophage and cosmids). Using the existing technology, YAC clones may be fingerprinted directly and ordered into contigs (Kuspa et al, 1989). Moreover, the ability to easily generate endprobes from YACs using techniques such as inverse PCR (Ochman et al, 1988) allows for the construction of physical maps based on simple hybridization strategies.
The application of mapping strategies that use YACs should make it possible to undertake projects orders of magnitude larger than those currently underway. It remains to be determined, however, whether YACs will entirely supersede cosmid and clone maps since the smaller clones are generally required for routine procedures such as gene isolation and DNA sequencing.
References
Berg, D. E. and Howe, M. M. (1989). Mobile DNA. (American Society for
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Burke, D. T., Carle, G. F., and Olson, M. V. (1987). Cloning of large segments
of exogenous DNA into yeast by means of artificial chromosome vectors.
Science, 236, 806-812.
Chang, C., Bowman, J. L., DeJohn, A. W., Lander, E. S. and Meyerowitz, E. M.
(1988). Restriction fragment length polymorphism linkage map for Arabidopsis
thaliana. Proc. Natl. Acad. Sci. USA, 85, 6856-6860.
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Coulson, A., Waterston, R., Kiff, J., Sulston, J., and Kohara, Y. (1988).
Genome linking with yeast artificial chromosomes, Nature, 335, 184-186.
Feldman, K. A., Marks, M. D., Christianson, M. L., and Quatrano, R. S.
(1989). A dwarf mutant of Arabidopsis generated by T-DNA insertion
mutagenisis. Science, 243, 1351-1354.
Grill, E. and Somerville, C. (1991). Construction and characterization of a
yeast artificial chromosome library of Arabidopsis which is suitable for
chromosome walking. Molec. Gen. Genet., in press.
Hauge, B. M. and Goodman, H. M. (1991). Physical Mapping by Random Clone
Fingerprint Analysis. In Plant Genomes: Methods for Genetic and Physical
Mapping, T. Osborn and J.S. Beckmann eds. (Kluwer). In press.
Hauge, B. M., Hanley, S., Giraudat, J., and Goodman, H. M. (1991). Mapping
the Arabidopsis Genome. In Molecular Biology of Plant Development, G. Jenkins
and W. Schurch eds. In press.
Hwang, I., Kohchi, T., Hauge, B. M., Goodman, H. M., Schmidt, R., Cnops, G.,
Dean, C., Gibson, S., Iba, K., Lemieux, B. L., Danhoff, L., and Somerville,
C. (1991). Identification and map position of YAC Clones comprising one third
of the Arabidopsis genome. (submitted).
Kohara, Y., Akiyama, K., and Isono, K. (1987). The physical map of the whole
E. coli chromosome: Application of a new strategy for rapid analysis and
sorting of a large genomic library. Cell, 50, 495-508.
Kuspa, A., Vollrath, D., Cheng, Y., and Kaiser, D. (1989). Physical mapping
of the Myxococcus xanthus genome by random cloning in yeast artificial
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Murray, A. W., and Szostak, J. W. (1983). Construction of artificial
chromosomes in yeast. Nature, 305, 189-193.
Nam, H. G., Giraudat, J., den Boer, B., Moonan, F., Loos, W. D. B., Hauge, B.
M., and Goodman, H. M. (1989). Restriction fragment length polymorphism
linkage map of Arabidopsis thaliana. Plant Cell, 1, 699-705.
Ochman, H., Gerber, A. S., and Hartl, D. L. (1988). Genetic Applications of
an inverse polymerase chain reaction. Genetics, 120, 621-623.
Olson, M. V., Dutchik, J. E., Graham, M. Y., Brodeur, G. M., Helms, C., Frank,
M., MacCollin, M., Scheinman, R., and Frank, T. (1986). Random-clone strategy
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Smith, C. L., Econome, J. G., Schutt, A., Klco, S., and Cantor, C. R. (1987).
A physical map of the Escherichia coli K12 genome. Science, 236, 1448-1453.
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Robert Read and Matthew Witten
GenTools Project
University of Texas Center for High Performance Computing
A software system available from the GenTools project at the University of Texas Center for High Performance Computing may be of interest to those who need to extract information from the GenBank flat-file format.
The GenTools gbParse program parses GenBank flat-file entries and translates them into a prolog-like language. The software is expected to be useful to persons who cannot gain access to the (undoubtedly superior) relational format of GenBank implemented in the RDBMS Sybase, or to those who wish to write special programs to extract information from the feature tables.
The parser software has been written using the UNIX and Free Software Foundation tools Flex and Yacc (or Bison). A C programmer can easily adapt the source code to produce output in any other required format.
The software is now in -release. It has been tested on a Sun SPARC Station and on a VAX/VMS system. Programmers might like to see the code (grammar) that has been written even if they do not intend to use it, as it represents the most concrete description of the GenBank format, including the feature table.
Although the program translates 99 percent of the GenBank entries, the code is not trouble free, in part because it must deal with actual syntax errors in the distributed flat files. GenTools gbParse has already been used to find numerous syntax errors in the distributed flat files. The program is robust in reporting errors in particular entries.
To obtain the GenTools gbParser software, which includes documentation, send an E-mail request to "GENTOOLS@CHPC.UTEXAS.EDU" (Internet) or contact Robert Read, GenTools Project, UT-Center for High Performance Computing, Balcones Research Center, 1.154 CMS, 10100 North Burnet Road, Austin, Texas 78712.
Further information about the GenTools project may be obtained from Dr. Sarah Barron, Group Leader. GenTools Project, at the above address.Genome Sequencing Conference III Set for September
The annual Genome Sequencing Conference is an international conference devoted to discussion of the most current analyses and approaches to understanding the human genome. This year's conference will be held September 22-25 in Hilton Head, South Carolina, at the Hyatt Regency Hotel.
Innovative research by U.S., European, and Japanese groups will be presented and discussed. Presentations will detail discoveries from the human genome and model organisms, including mouse, Drosophila, C. elegans, yeast, plants, E. coli, M. capricolum, and a number of viruses. State-of-the-art technologies and new computational approaches will also be covered. Poster sessions, workshops, and discussion groups will provide a forum for researchers to present their latest data. The conference co-chairs are J. Craig Venter (NIH) and Leroy Hood (CalTech).
Registration, which includes all meals and materials, is $310 per person until August 2. After August 2, the cost is $450. Students can register for $200 (no deadline), but a letter from their thesis advisor is required. The registration fee does not cover hotel expenses, but a room-sharing program is available to reduce the cost of the rooms. Early registration is encouraged. The deadline for receipt of abstracts is August 2.
For more information, contact Susan Wallace, P.O. Box 541, Rockville, Maryland 20848, Phone (301) 480-0634, FAX (301) 480- 8588, E-mail: swallace@loglady.ninds,nih.gov.
Dr. Stephen Heller is the Informatics Project Leader for USDA's Plant Genome Research Program. Reporting directly to the Program Director, Dr. Jerry Miksche, Dr. Heller manages the informatics portion of the program, primarily activities of cooperators and NAL staff. A major activity now underway is the development of a plant genome database system, which will provide users with genome data on four plant species--wheat, pine, corn, and soybean.
Dr. Heller has been a research scientist in USDA's Agricultural Research Service (ARS) since 1985. Before assuming his current position, Dr. Heller was a member of the Systems Research Laboratory. Responsibilities included developing and coordinating agency-wide scientific database, modeling, and expert system programs; and developing a pesticide properties database and expert systems for evaluating analytical chemistry data.
From 1989-1990, on a leave of absence from ARS, Dr. Heller served as director of quality control for Scitechinform, a UK-USSR joint venture of Maxwell Communications and VINITI.
Before coming to ARS, from 1973-1983, Dr. Heller worked for the Environmental Protection Agency (EPA) as a project manager for a multi-agency, multi-organization, NIH/EPA Chemical Information System (CIS), which served over 2,200 users in 22 countries. In 1976, in recognition of his contributions to the agency, he received EPA's Gold Medal.
Dr. Heller previously served as a Senior Staff Fellow at the National Institutes of Health, from 1970-1973, and as a chemist for the U.S. Army from 1967-1969. During his career, he has served with the U.S. House Subcommittee on Health and the Environment (1979- 1980) and held the position of Lady Davis Visiting Professor of Chemistry at the Hebrew University in Jerusalem (1981).
He is an internationally well-known authority in scientific numeric and factual databases, and in chemical information. Dr. Heller is presently chairman of the IUPAC Committee on Chemical Databases and an American Chemical Society (ACS) XOMP Division Councilor. He serves on the editorial boards of various journals, including the Editorial Advisory Board for Computer Software. During the past 20 years, Dr. Heller has published over 130 papers and books, and has been the recipient of numerous fellowships and scholarships. He is a member of various professional organizations, including the ACS, IEEE, ASMS, AAAS, and Sigma Xi.
Dr. Heller received his B.S. degree in chemistry from the State University of New York, Stony Brook, and his Ph.D. in organic chemistry from Georgetown University in Washington, D.C.
Meetings - 1991
August 20-25: Molecular Genetics of Bacteria and Phages, Cold Spring Harbor, NY. Contact: Meetings and Course Office, Cold Spring Harbor Laboratory, Cold Spring, NY 11724.
September 2-6: 12th European Drosophila Research Conference, Mainz, Germany. Contact: Prof E. Gateef, Institute fur Genetik, Johannes Gutengerb-Universitat, postfach 3980, Mainz, FRG.
September 17-18: Genetical Society of Great Britain and British Society of Developmental Biology Joint Meeting: Insertional Mutagenesis, Lancaster, U.K. Contact: Dr. J.P.W. Young, John Innes Institute, Colney Lane, Norwich NR4 7UH, U.K.
September 22-25: Genome Sequencing Conference III, Hilton Head, SC. Contact: S. Wallace, P.O. Box 541, Rockville, MD 20848, Telephone: (301) 480-0634, FAX (301) 480-8588, E-mail swallace@loglady.ninds,nih.gov.
September 22-27: Techniques in Genome Research, Trieste, Italy. Contact: Diana Viti, ICGEB Padriciano 99, I-34012 Trieste, Italy.
September 23-25: National Symposium on Planar Chromatography: Modern Thin-Layer Chromatography, Somerset, NJ. Contact: Janet Cunningham, Barr Enterprises, Box 279, Walkerville, MD 21793, Telephone: (301) 898-3772.
September 30 - October 1: Arabidopsis thaliana and the Molecular Basis of Plant Biology, Canberra, Australia. Contact: Dr. R.E. Williamson, Plant Cell Biology Group, Research School of Biological Sciences, PO Box 475, Canberra, ACT 2601, Australia. Fax: 06-248- 9995, E-mail Williamson@rsbs0.anu.edu.au.
October 2-6: Molecular Biology of Signal Transduction in Plants, Cold Spring Harbor, NY. Contact: Meetings and Course Office, Cold Spring Harbor Laboratory, Cold Spring, NY 11724.
October 4-5: Knowledge Brokering: The Mechanics of Synthesis, St. Louis, MO. Contact: Systematics Symposium, Missouri Botanical Garden, P.O. Box 299, St. Louis, MO 63166.
October 6-8: International Biotechnology Expo & Scientific Conference, San Francisco, CA. Contact: Cartlidge & Associates, Inc., 3097 Moorpark Ave., #202, San Jose, CA 95128, Telephone: (408) 554-6644 inside CA, outside CA 1-800-882-3976, FAX: (408) 985-0660.
October 6-11: 8th International Congress of Human Genetics, Washington, DC. Contact: Administration Office, 9650 Rockville Pike, Bethesda, MD 20814.
October 6-12: Third International Congress of Plant Molecular Biology, Tucson, AZ. Contact: ISPMB, Woo Wester Conference Consultants, 2934 1/2 Beverly Glen Circle, Suite 383, Los Angeles, CA, Telephone/FAX (213) 474-5894.
October 20-23: 11th International Symposium on HPLC of Proteins, Peptides and Polynucleotides, Washington, DC. Contact: Janet Cunningham, Barr Enterprises, Box 279 Walkerville, MD 21793, Telephone: (301) 898-3772.
October 21-23: Human Genome III, San Diego, CA. Contact: Scherago Associates Inc. 1515 Broadway, Suite 1010, New York, NY 10036. Telephone: (212) 730-1050, FAX (212) 382-1921.
November 16: Genetical Society of Great Britain Meeting on Cell Cycles, London, U.K. Contact: Dr. J.P.W. Young, John Innes Institute, Colney Lane, Norwich NR4 7UH, U.K.
November 20-22: The Sixth Annual San Diego Conference on Nucleic Acids: The Leading Edge, San Diego, CA. Contact: The San Diego Section of the AACC, P.O. Box 361, Encinitas, CA 92024-9999.
January 17-24: 1992 Miami Bio/Technology Winter Symposium. Advances in Gene Technology: Feeding the World in the 21th Century, Miami Beach, FL. Contact: The 1992 Miami Bio/Technology Winter Symposium, P.O. Box 016129, Miami, FL 33101-6129. Telephone: 1-800-642-4363 or FAX 1-305-324-5665.
July 26-31: 5th International Congress on Cell Biology, Madrid, Spain. Contact: Organization Secretariat, Tilsea, Londres 39, 28028 Madrid, Spain.
August 16-21: 9th International Biotechnology Congress, Crystal City, VA. Contact: Congress Office, American Chemical Society, 1155 Sixteenth Street, N.W., Room 205, Washington, DC 20036.
Workshops and Courses
September 2-3, 9-10: Protein Techniques Workshop, Hatfield, U.K. Contact: Dr. Jim Walker, Biological Science, Hatfield Polytechnic, Hatfield, Herts AL10 9AB, U.K.
October 24 - November 7: Analysis and Genetic Manipulation of YACS, Cold Spring Harbor, NY. Contact: Meetings and Course Office, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724.
October 27 - November 5: Essential Computational Genomics for Molecular Biologists, Cold Spring Harbor, NY. Contact: Meetings and Course Office, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724.
Beltsville Symposium XVI
Photomorphogenesis in Plants: Emerging Strategies for Crop Improvement.
September 22 - 26, 1991
University of Maryland University College Conference Center
College Park, Maryland
Held jointly with the 1991 European Photomorphogenesis Symposium
PROGRAM
Sunday 9/22/91 Registration and Evening Reception
Monday a.m.Session 1. Reflections on the Early Years of
Phytochrome Research
Session 2. Phytochrome Function in the Natural Environment
p.m. Session 3. Photoperiodism
Evening Posters
Tuesday a.m. Session 4. Blue Light Photoreception, Phototropism,
and UV Photoreception
p.m. Session 5. Phytochrome Mutants and Transgenic Plants
Evening Posters
Wednesday a.m. Session 6. Phytochrome Regulated Gene Expression
p.m. Excursion
Thursday a.m. Session 7. Light Mediated Signal Transduction
p.m. Session 8. Phytochrome Structure and Properties
Session 9. Opportunities and Future Research Directions
Evening Banquet
Registration Fees
Regular (includes proceedings, reception, banquet) $175.00 Late Registration (postmarked after August 16, 1991) $225.00
Student (graduate & undergraduate; includes proceedings, reception, banquet)
$75.00
(Other meals to be purchased on a cash basis)
Symposium Co-chairmen
William J. VanDerWoude and Steven J. Britz Telephone: (301) 344-3607 Climate Stress Laboratory, USDA, ARS Fax: (301) 344-4626 Bldg. 046A, Beltsville Agricultural Research Center Telex: 7402411 CLIM 10300 Baltimore Blvd. Bitnet: wvanderwoude@umdars
Beltsville, Maryland 20705-2350
Sponsored by
Beltsville Area, Agricultural Research Service
with the cooperation of
Friends of Agricultural Research-Beltsville, Inc.