THE ELECTRONIC EDITION OF THE
MICROBIAL GERMPLASM DATABASE NEWSLETTER
This newsletter is published quarterly.
If you would like to be placed on the regular mailing list please contact:
Dr. Larry Moore
Department of Botany and Plant Pathology
Oregon State University
Corvallis, OR 97331-2902
USA
or
Electronic mail to:
Mr. F. Joe Hanus
hanusj@bionette.ucs.orst.edu
Please indicate whether you would like to have a hard copy by US mail or an e-
mail version. Please include your e-mail address with a preferred path if you
choose.
WELCOME TO NEW READERS
We would like to welcome those of you who are new to this newsletter. For new
readers, an article is included in this newsletter that appeared in the first
issue. It is a statement of what we perceive to be 'the reason for being' for
the MICROBIAL GERMPLASM DATA NETWORK. Briefly, our purpose is to facilitate
communication between researchers who have culture collections (of any size)
that relate to the plant sciences and to establish a database that will allow
researchers an online directory of the vast diversity of germplasm that exists
in working stock collections in the US. We expect to interface internationally
with other existing networks.
We hope that you will pass this newsletter to others in your location who may
have collections or who may be interested in the development of the database.
Provide us an address and they will be on the next mailing.
In this issue we have included a short questionnaire. You could help us greatly
if you would check off the answers so that we can tailor the newsletter and the
network to your needs.
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IN THIS ISSUE
* NETWORK NEWS
DATA FIELD SELECTION UNDERWAY
AT&T GIFT TO AID DATABASE
QUESTIONNAIRE
FREE PROGRAM FOR COLLECTIONS?
*COLLECTION NOTES
PRESERVATION OF MELOIDOGYNE
PLANT PATHOGEN MAILING OK
GRANTS AVAILABLE FOR STOCK COLLECTIONS
ELECTRONIC GRANT SUBMISSION DUE SOON
*COMMUNICATION AND COMPUTERS
CONNECTING TO THE NETWORKS
NEW SOFTWARE: FOXBASE+ FOR MAC & IBM
*EVENTS
----------------------------------------------------------------------
*********NETWORK NEWS
SELECTION UNDERWAY OF DATA FIELDS FOR CULTURE COLLECTION DATABASE
Before we can proceed with the implementation of the online database we (you)
must decide which data is of high enough priority for inclusion in a national
database and yet is sufficiently general so as not to violate the individual
researcher's proprietary rights to her/his culture collection. We are presently
consulting with experts who have working culture collections which include the
categories of organisms and entities suggested for inclusion in the database.
At this time we are proposing that inquiries to individual researchers should be
at two levels: THE FIRST LEVEL will be an attempt to identify and characterize
the collections. We will include data on location of the collection,
scientist/curator and major groups of organisms accessed in the collection. THE
SECOND LEVEL will include more specific information for each of the categories
of plant-related organisms or entities an investigator chooses to include in the
database. These data, of course, will be different for each of the classes of
entities (attributes of interest to virologists would be different from those
that might be important to researchers with endo/ecto -mycorrhizae).
We will not attempt to identify each strain in each collection. Concerns for
protection of the privacy of the individual scientist, mandate that requests
for more detailed information than included in the second level of inquiry must
be directed to the individual scientist overseeing the collection.
AT&T DONATION TO PROVIDE FIRST HOME FOR MICROBIAL GERMPLASM DATABASE.
A $383,000 grant of computer equipment has been awarded to Oregon State
University for the purpose of developing biological computing capability. The
gift includes two AT&T 3b minicomputers and associated peripherals. While the
major beneficiary of the donation will be the OSU Center for Gene Research and
Biotechnology, the package will provide the computing power necessary for us to
begin the initial phases of the Microbial Germplasm Database.
Informix 4GL, an SQL (structured query language) -based database development
package has been included in the donation and will be used to implement the
database management system. Individuals will be able to access the database
either through modem by dialing in to the OSU computer center or through the
various networks that allow communication between universities (see related
article in this issue).
Decisions regarding the nature and quantity of information to be stored in the
central database are yet to be made. The proprietary nature of individual
strain data and protection of the individual researchers interests remains a
primary concern.
*******QUESTIONNAIRE IN THIS ISSUE
This newsletter contains a questionnaire that we hope you will check off and
mail to us. We know there are many demands on your time but there is no other
way to obtain this information which will assist us in tailoring the network and
the database to your needs. While we will continue to solicit your comments and
suggestions this type of formal plea for input will not occur often. Please
attach any other comments to the questionnaire or submit them separately if you
choose. We hope to be able to bring together a summary of the information for
our next issue.
IS THERE INTEREST IN A PROGRAM FOR MANAGEMENT OF WORKING CULTURE COLLECTIONS?
Many of us have considered moving our documentation for our working culture
collections from index cards and loose leaf notebooks to a computer. The
benefits are obvious: the data can be updated quickly and an alphabetized or
ordered listing obtained almost immediately; the location of any culture could
be determined instantly; information on culture medium or last date of transfer
could be available immediately; the collection could be rapidly searched for
stains or cultures with specific biochemical, morphological, pathogenic or
genetic traits; legible labels for culture tubes could be printed. The down
side is that implementing your own database development system, even with the
relatively friendly packages available now, requires a substantial investment of
money for the initial purchase and time to learn to utilize the program.
Because of the flexibility of these extremely powerful packages a great deal of
learning time is required to devise a specific application. Most researchers do
not have this time.
We are considering the possibility of devising an application using Foxbase+ (a
database development package that is similar to dBaseIII+, see article this
newsletter) that would be dedicated for use with a working culture collection of
between a hundred and several thousand strains. We would want the package to be
extremely easy to learn (and therefore it could not be extremely flexible) but
with enough versatility to be useful in the organization of the research
oriented culture collection. We could distribute the program as either public
domain (free but copyrighted) or shareware (a small charge to defray costs but
not copy protected).
We would appreciate your input. What features do you feel are essential? What
features are desirable?
*****COLLECTION NOTES
CARRAGEENAN COATING PERMITS LONG-TERM STORAGE OF MELOIDOGYNE EGGS
Nematologists have long had a need to store root-knot nematodes for prolong
periods of time. [Ed. see last newsletter.] In an article accepted for
publication in Journal of Nematology, George Fassuliotis (USDA, ARS, U.S.
vegetable Laboratory, Charleston, SC 29414) and W.J. Connick (Southern Regional
Research Center, New Orleans, LA 70179) report success in retaining viability in
stored eggs of Meloidogyne incognita for periods of up to two years.
Fassuliotis and Connick note that hydrocolloids (specifically sodium alginate
with Ca for gelation) have been used successfully to encapsulate
sustained-release herbicides, mycoherbicides, plant embryos and entomogenous
nematodes. Though Ca-alginate gels were successful in maintaining viability of
eggs of M. incognita and Filipjevimermis leipsandra the gels exhibit extreme
syneresis. After excess water is removed the relative humidity had to be
carefully controlled to prevent desiccation and loss of viability.
Kappa carrageenan, a non-toxic hydrocolloid used as a thickener in baby food,
forms strong gels with potassium and does not exhibit the undesirable syneresis
of the alginate. These properties made it a logical choice for matrix for
storage of nematode eggs.
As described in the Journal of Nematology article, the hypochlorite-sterilized
eggs of M. incognita from lima bean (Phaeseolus limensis Macf.) root were
suspended and diluted in a carrageenan solution (2.5% Gelcarin CIC (TM)). The
solution( maintained at 28C with stirring) was added drop-wise to ) 0.3M KCl
solution. The droplets gelled on contact and formed uniform beads. After
blotting with paper toweling the beads could be stored at 15C in Ziplock (TM)
bags.
Fassuliotis and Connick determined infectivity of the stored eggs bimonthly by
inoculation of tomato (Lycopersicon esculentum) seedlings. Duplicate studies
showed viability of the carageenan stored eggs for 21 and 24 months when in both
cases failure of the incubation chambers forced termination of the experiments.
While there was a slow decline in the viability of the M. incognita after 6
months, in all cases there were ample organisms to reestablish the population.
[This is a summary of a preprint of the article accepted for publication and was
kindly provided by the authors. Ed]
PROPOSED MAIL BAN OF ETIOLOGICAL AGENTS LIKELY TO POSE NO THREAT TO SHIPPING OF
PLANT PATHOGENS
Rep. Frank McCloskey (Indiana) convened a hearing of the House Subcommittee on
Postal Personnel and Modernization to take statements on the proposed ban of
mailing of etiological agents. McCloskey's opening remarks included
acknowledgment that "banning of the mailing of etiological agents would have a
detrimental effect on standard medical research and diagnostic procedures". He
went on to say that "full enforcement of existing regulations should guarantee
public safety without jeopardizing scientific research.
Support for the continued mailing of etiological agents came from the Postal
Service Union who feared a reduction in Postal Service business if the ban were
to be implemented.
(the above is from an article taken from THE ATCC QUARTERLY NEWSLETTER, vol8(4).
Fall 1988.)
The ban at this time is not expected to extend to plant pathogens. In a
telephone conversation, Dr. Thomas Gavan of the American College of Pathologists
who sits on the advisory group to the Congressional Subcommittee, said that
regulation changes proposed through either the Department of Transportation or
the US Postal Service are likely to affect only those who ship materials that
are infectious to either humans or animals.
NSF SUPPORTS UPGRADES OF STOCK COLLECTIONS
NSF bulletin, GUIDELINES FOR PROPOSALS FOR SUPPORT OF LIVING ORGANISM STOCK
CENTERS (NSF 85-14) announces that the foundation is accepting proposals for the
support of stock centers "whose maintenance will preserve an essential
scientific resource at the national or international level". The proposals will
be judged on quality of the collection, uniqueness, research utilization,
national importance, type of stock center and long term commitment of the
institution to the maintenance of the collection. Proposals must provide
information regarding acquisition, documentation and utilization of the center
(cultures sent out and to whom, visiting researchers, publications).
The support is specifically for the stock centers and not for items normally
included in usual research grants such as salaries of researchers, research
supplies or specialized equipment for research. Funds are available for
NON-research technical assistance, storage and equipment, minor renovations,
expendables and supplies and publication of stock lists [could this mean
database software, printers etc.?...Ed].
Persons wishing to obtain further information should contact Dr. James Edwards,
Program Director; Biological Research Resource Program; Division of Biotic
Systems and REsources; NSF; Washington, DC 20550. Phone 202/357-7475.
NSF PREPARING TO ACCEPT PROPOSALS IN ELECTRONIC FORM
In an experimental program called EXPRES, NSF will be encouraging researchers to
submit their proposals electronically. This would mean little or no duplication
or mailing costs, transmission in minutes to NSF and then to reviewers in
minutes, cosmetic improvement because proposals would be printed on laser
printers and easier tracking of submitted proposals. Proposals will be
submitted as Postscript files (Postscript is a language for driving laser
printers) and the software for proposal submission (which is being developed by
Carnegie Mellon) should be available on most campuses in the near future. In
addition proposal templates will be available for most common document
processors. Signatures will still be required on one paper copy. If you would
like more information contact Dr. Gerald Stuck and NSF (e-mail to
gstuck@note.nsf.gov).
*****COMMUNICATION AND COMPUTERS
ACCESS: GETTING STARTED WITH TELECOMMUNICATION
GOING ON LINE. The value of a computerized database is only realized if it is
readily accessible by a large body of interested individuals. Since our goal
is to make the microbial germplasm database available to scientists throughout
the U.S. and to interface with other networks internationally we are attempting
to provide basic information to those who are linking up to computer networks.
In most academic laboratories adding the capability of telecommunication and
access to educational electronic networks is quite inexpensive and the technical
expertise to help you is readily available.
GETTING CONNECTED. For a minimal cost a microcomputer can serve as a
telecommunications terminal without losing any of its present capability. If
your need for telecommunication is not great you may find other scientists in
you location that would be willing to share the costs of adding that capability
to a single existing personal computer.
Most universities have a department specializing in computer services to assist
you in connecting your computer to the phone line or to a local area network
(LAN) on your campus. Check with them first. It is often possible to make any
needed purchases through your institution at much reduced rates. Unless you
have considerable technical background you can save money by seeking advice
either from computer specialists on your campus or from user groups since
expensive features in both software and hardware may not be essential to your
application. The advice is usually free and you can ignore it later if you
choose.
The least expensive (initially) means to connect to bulletin boards, databases
and other remote computers is by phone line through a telephone modem. This
device translates the outgoing flow of electrical pulses from your computer's
serial port to a modulated signal transmissible by phone line and then
demodulates incoming signal to regenerate the string of pulses sent by a remote
computer. You will also need telecommunication software to control the modem
and allow your computer to emulate a telecommunication terminal. Modems range
upward in price from approximately $150. Software can cost several hundred
dollars but excellent public domain or shareware software is available for free
or for a negligible registration fee. (Kermit, named after the famous frog is
free, readily available and almost universally used at most UNIX based
university computer sites). While some database and bulletin board services
accessible by phone are free or have a minimal charge (i.e. the TRF bulletin
board sponsored by BIOSIS) others have a substantial monthly charge plus an
additional pro rata charge for the time used. Data transfer is slow, usually
1200 to 2400 baud (less than 150 to 300 characters per second or about 10-20
seconds to fill the screen on a pc.) Large data files can take minutes to hours
to transfer. The economy of this option may only be apparent if long distance
charges and phone line charges become substantial.
Another option is to connect your terminal or pc to your campus computer system
by either phone line via modem or by a device analogous to the modem but much
faster and operating on dedicated cabling on a local area network (LAN). You
will first establish an account (usually free or inexpensive) on a host machine
on your campus that will handle all the protocol of connecting you to other host
machines both on your campus and at other remote locations (other universities).
Each host machine has a unique name (a mail server on the Oregon State
University campus is named beasley after the mailman in the comic strip,
Dagwood). You can then log on to your host machine with your login name and
password and use your pc to control the host machine as though it were an
extension of your pc.
GOING NATIONAL. Almost all academic institutions in the US are linked through
fiber optic networks sponsored by NSF. Campus LANS feed into regional networks
(NORTHWESTNET in the pacific northwest, BARRNET in the Bay Area surrounding San
Francisco and University Satellite Network (USAN) and dozens of others in the
US). These are linked along the national communication backbone, NSFNET. You,
through your pc and your campus computer can gain access to files or run
programs on remote computers thousands of miles away. The use of NSFNET is free
(no long-distance telephone charges) and is encouraged by most universities.
The actual protocol or routing through the network and connecting to the remote
computer is handled by software (Telnet) and is not much more complex than
placing a long distance phone call. Information transfer is extremely fast,
1.44 million bits per second under ideal circumstances though the practical
speed of data transfer is dependant on the network traffic. An actual example
would be the transfer of 263,000 characters (about 70 pages of single space
typewritten text) from Boulder, CO to Corvallis, OR in 51 sec.
The NSFNET connection would be the method of choice for accessing the germplasm
database since the cost to the user would be minimal and the speed would be
sufficient for interactive queries to the database. A hypothetical search of
the database which will reside on a computer whose host name is BIONETTE might
resemble the following: (For our purposes here we will title the program for
utilizing the MICROBIAL GERMPLASM DATABASE, "GERMBASE")
1. Log on to you host machine on your campus using your pc.
2. Use the TELNET program to route through NSFNET to bionette by typing
"TELNET bionette"
3. Log on to bionette with your name and a password.
4. Run the program by typing "GERMBASE" at the "$" prompt of bionette
5. Follow the instructions on the screen to search the areas in which you are
interested.
It will be also be possible for users who do not have access to NSFNET to dial
in to bionette long distance using a telephone modem. The responses will be
slower and the user will have a long distance charge.
FOXBASE+ MAKES VISUAL DATABASES POSSIBLE FOR CULTURE COLLECTIONS
Foxbase+, a dBase III+ look-alike, has moved into the database software market
with an extensive ad campaign and glowing reviews. The package is totally
compatible with dBase programs and data files and, Foxbase claims, it run
faster. Data files are identical in structure but index files are slightly
different purportedly effecting the speed-up. While the version for IBM
compatibles [we have received a demo and will review it next issue. Ed] has
given MS-DOS dBase some painful competition, the Foxbase+/Mac II combination is
apparently formidable. "Foxbase+/Mac runs circles around the competition"
(Computing Canada, June 9, 1988). Unique to Foxbase+ is its ability to integrate
graphics into the database. Visual databases for culture collections utilizing
picture fields would not only be possible with this system, but if reviews are
correct, could be executed with "blinding speed". The exceptional graphics
capabilities of the Mac II and its ability to control the graphics with windows
may make this combination a valuable taxonomic tool.
Reports in the COMPUTER DATABASES section of the UNIX news network, however,
indicate that the multi-user package has not received the same glorious welcome.
The LAN package apparently will not easily run background tasks (e.g. overnight
report generation) unless the program retains control of the terminal screen.
Also, more than one user may not have a single record available to them at the
same time (concurrent access) thereby limiting multi-user capability.
You might want to get your copy quickly, though. February 1989 UnixWorld
reports "Ashton-Tate has filed a copyright infringement suit against Fox
Software Inc. and The Santa Cruz Operation, charging them with copying the
concept and the appearance of four versions of Dbase...".
*****EVENTS
MARCH '89
1-6 Molecular Evolution. Lake Tahoe, CA. UCLA Symposia on Molecular and
Cellular Biology. Contact: UCLA Symposia 103 Molecular Biology Institute,
University of California, Los Angeles, CA 90024-1378, (213) 206-6292.
6-10 Recombinant DNA Methodology. Washington, D.C. Sponsor: The Catholic
University of America. Contact: Dr. Roland Nardone, The Center for Advanced
Training, The Catholic University of America, Washington, DC 20064, (202)
635-6161.
APRIL '89
UCLA Symposia on Molecular and Cellular Biology. Contact: UCLA Symposia, 103
Molecular Biology Institute, University of California, Los Angeles, CA
90024-1378, (213) 206-6292.
1-7 Plant Gene Transfer. Park City, Utah.
3-9 Molecular and Cellular Biology of Yeasts and Filamentous Fungi. Steamboat
Springs, Colo.
MAY '89
14-19 ASM Annual Meeting (89th). New Orleans, LA. Contact: Richard A. Bray,
Meetings Dept., American Society for Microbiology, 1913 I St. NW, Washington, DC
20006
15-..19 FEMS Symposium on Microbial Surface Components and Toxins in Relation to
Pathogenesis. Jerusalem, Israel. Sponsor: Federation of European Microbiological
Societies. Contact: Prof. E. Ron, Dept. of Microbiology, Faculty of Life
Sciences, Tel Aviv University, Ramat-Aviv 69-978, Tel .Aviv, Israel.
JUNE '89
11-14 Canadian Society of Microbiologists Conference (39th Annual). Laval,
Quebec, Canada. Contact: Dr. L. Berthiaume, Chairman, Local Organizing
Committee, or Dr. M. Brown, Meetings Secretary, Canadian Society of
Microbiologists, 1611 Baseline Rd, Ottawa, Ontario K2C 0B6, Canada.
12-14 European Conference on Industrial Biotechnology (4th). Varese, Italy.
Sponsor: Associazione Farmaceutici Industria, Associazione Nazionale per le
Sviluppo delle Biotechnologie. Contact: S. Merli, Conference Secretariat,
Farmitalia-C. Erba, Via dei Gracchi, 35, 20146 Milan, Italy, tel., 02-6995-4661.
27-30 Federation of Classification Societies Meeting (2nd International).
Charlottesville, Va. Sponsor: IFCS. Contact: IFCS-89, Dept. of Mathematics,
University of Virginia, Charlottesville, VA 22903, 804) 924-4919.
JULY '89
5-7 Beijing International Conference on Biotechnology. Beijing, China. Sponsors:
Chinese Society for Microbiology, ASM, China Association for Science and
Technology, and International Union of Microbiological Societies. Contact:
Secretariat, Beijing International Conference on Biotechnology, Zhongguancun,
Hidan 100080, Beijing, China.
AUGUST '89
6-10 40th Annual AIBS Meeting - "Global Change". University of Toronto,
Ontario, Canada. Chairman: Nancy G. Dengler, Associate Professor of Botany,
University of Toronto, Ontario, Canada M5S 1A1. Tel: 416/978-3536. Contact:
Meetings Department, American Institute of Biological Sciences (AIBS) 730 11th
Street, NW, Washington, DC 20001-4584 Tel: 202/628-1500.
SEPTEMBER '89
14-17 Molecular Plant Bacteriology (5th International Fallen Leaf Lake
Conference). South Lake Tahoe, Calif. Sponsor: University of California, Davis.
Contact: Clarence Kado, Director, Fallen Leaf Lake Conference, Dept. of Plant
Pathology, University of California, Davis, CA 95616.
Q U E S T I O N N A I R E
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Copy this portion to your word processor or text editor. Reset margins to left
0 and Right 0. This questionnaire may be returned by:
e-mail to hanusj@bionette.ucs.orst.edu
OR
US MAIL to
Dr. Larry Moore, Chairperson
ESCOP Subcommittee on Microbial &
Subcellular Germplasm Collections
Department of Botany and Plant Pathology
Oregon State University
Corvallis, OR 97331-2902
SURVEY OF MICROBIOLOGICAL AND SUBCELLULAR
GERMPLASM CULTURE COLLECTIONS
NAME:
INSTITUTION:
ADDRESS:
PHONE NO.
ELECTRONIC MAIL ADDRESS:
FAX NUMBER:
1. How many different cultures of each group are included in your collection?
a. Single/multi-cellular elements
_____Fastidious Procaryotes
_____Bacteria
_____Fungi
_____Endo/Ecto-mycorrhizae
_____Protozoa
_____Algae
_____Nematodes
b. Subcellular elements
_____Plasmids
_____Cloning Vectors
_____Cloned genes, libraries
_____Plant viruses
_____Mycoviruses
_____Phage
_____Cloned MCA's
_____Antisera
_____Viroids
_____Satellite nucleic acids
_____Other nucleic acids
2. Is your collection centered around particular organisms or groups, Yes_____
no_____ (if yes, please specify___________________________).
3. How many sequenced DNA cultures or strains are included in your
collection?_____________(actual) (estimated)
4. What proportion of your collection do you estimate is used for :
Research_______Teaching_______Other__________
5. Do you receive funds specifically for the support of your collection?
Yes_____
No______
6. Do you provide cultures to other scientists? Yes_____ No_____ Do you
charge?
Yes_____ No_____
7. a. Do you maintain some type of documentation for each accession? Yes_____
No_____
b. If yes is the documentation in computer format? Yes_____ No_____
8. If you answered NO to 7b:
a. Are you interested in developing such a system? Yes_____ No_____
b. What are the constraints against developing a computerized system.?
____time and labor
____funding
____computer availability
____not needed
9. If you answered YES to 7b:
a. What type of computer system do you use? a.Micro____ Mini____
Mainframe
b. Which type of Micro
__Macintosh
__IBM compatible
__Radio Shack
__Apple II series
Other (please list) ______________
c. Describe briefly the program you are using to catalog your collection.
d. Is your computer used for telecommunication? Yes_____ No_____. If yes
for what purposes?
__electronic mail
__local area network (sharing of common files or equipment)
__access to bibliographic databases
__access to genetic databases
__national networks (internet, bitnet, bionet)_
__other(please specify)_______________________
10. List the specific main headings of information recorded for each accession
in your documentation for your collection.(e.g. genus, species, host,
geographical location of isolation, etc.)
11. a. Would you find a directory of research laboratories compiled from this
survey useful? Yes___No___ b. What uses would such a directory have in your
work?
12 Would you find such a directory valuable if it were available for computer
access? Yes_____ No_____
KINDLY LIST THE NAMES OF THE OTHER COLLEAGUES AT YOUR INSTITUTION WHO MAINTAIN
CULTURE COLLECTIONS OR GIVE THEM A COPY OF THIS QUESTIONNAIRE TO COMPLETE AND
RETURN.
REPRINTED FROM: MICROBIAL GERMPLASM DATA NET
DECEMBER 1988 VOLUME 1 NO. 1
PROTECTION OF A RESOURCE: THE NEED FOR THE MICROBIAL GERMPLASM DATABASE
Our collections of microorganisms and subcellular entities maintained in
research laboratories represent a diverse and valuable national resource
which has been under-appreciated and under-funded in the past. The wave of
advances in biotechnology and genetic engineering has brought to focus the
value, both in commercial applications and in basic research, of the rich
pool of genetic information that is present in these many relatively small
working research collections.
Many of these small working collections face extinction as funding for
research becomes sparse, as principal investigators retire, as
institutional research interest shift. Some of the germplasm which resides
in these collections may exist nowhere else except in these col-lections
since the environment from which the original cultures were iso-lated may
no longer exist. The World Federation of Culture Collections at the
International Congress of Culture Collections VI in College Park, MD in
November devoted a complete session to the endangered culture collection.
As yet no accurate assessment has been made of the extent and variety of
germplasm in the many collections. Our present knowledge of "who" has
"what" germplasm is at best terribly disorganized. For this reason
RESEARCHERS ARE DEVELOPING A COMPUTERIZED NETWORK TO LINK TOGETHER
SCIENTISTS who as part of their research or teaching programs maintain
working collections of microorganisms or subcellular entities which have
some relationship to plants or in vitro manipulation and culture of plant
tissue. The goal is to develop a central database accessible by all
researchers. The database will contain minimum data sets describing
individual collections. Enquiries can then be made through a distributive
network to the individual laboratory in which the culture of interest
resides. As data are accumulated in the central database we will publish a
catalog with identities, interests and general contents of individual
collections in the United States.
This Newsletter is the first of what will become a regular publication of
the Microbial Germplasm Network. Its role will be to provide a forum for
discussion of problems and issues affecting the working culture collection
and to keep you informed of progress we are making in the development of
the database and the network linking participating laboratories. The
newsletter will also act to solicit from you suggestions and criticisms
about how best to achieve these goals. We also want to present innovative
laboratory techniques, notification of upcoming events, pertinent
literature citations, software criticisms, questions or suggestions and
news items that bear upon culture collections.
A few thought about the overall philosophy:
1. You do not have to have a computer or telecommunication facility to
participate. We will have the information available not only through modem
but in published catalog form.
2. Laboratories that provide information for the databases are IN NO WAY
OBLIGATED TO PROVIDE CULTURES OR ADDITIONAL INFORMATION TO ANYONE.
3. You may delete or modify any of information which you have provided at
any time you wish. You, as the scientist, maintain control of your data.
SURVEY OF MICROBIOLOGICAL AND SUBCELLULAR
GERMPLASM CULTURE COLLECTIONS
NAME:____________________________________________
DEPT:____________________________________________
INSTITUTION:_____________________________________
ADDRESS________________________________________
CITY____________________________________ST_____
POSTAL CODE_____________ COUNTRY_______________
PHONE NO.____________________________________
ELECTRONIC MAIL ADDRESS _____________________
FAX NUMBER__________________________________
1. How many (PLEASE GIVE NUMBERS, EVEN IF THEY ARE APPROXIMATE)
different cultures of each group are included in your collection?
a. Single/multi-cellular elements
_____Fastidious Procaryotes
_____Bacteria
_____Fungi
_____Endo/Ecto-mycorrhizae
_____Protozoa
_____Algae
_____Nematodes
b. Subcellular elements
_____Plasmids
_____Cloning Vectors
_____Cloned genes, libraries
_____Plant viruses
_____Mycoviruses
_____Phage
_____Cloned MCA's
_____Antisera
_____Viroids
_____Satellite nucleic acids
_____Other nucleic acids
2. Is your collection centered around particular organisms or groups,
Yes_____ no_____ (if yes, please specify___________________________).
3. How many DNA sequences are included in your collection?_____________
4. What proportion of your collection do you estimate is used for :
Research_______ Teaching_______ Other__________
5. Do you receive funds specifically for the support of your collection?
Yes_____ No______
6. Do you provide cultures to other scientists? Yes_____ No_____
Do you charge? Yes_____ No_____
7. a. Do you maintain documentation for each accession?
Yes___No____
b. If yes is the documentation in computer format? Yes_____ No_____
8. If you answered NO to 7b:
a. Are you interested in developing such a system? Yes_____ No_____
b. What are the constraints against developing a computerized system.?
____time and labor____funding____computer availability____not needed
9. If you answered YES to 7b:
a. What type of computer system do you use?
Macintosh _____ IBM compatible_____
Radio Shack_____ Apple II series____
Mini _____ Mainframe_____Other ______________
b. Describe briefly the program you are using to catalog your
collection.
c. Is your computer used for telecommunication? Yes_____ No_____. If
yes for what purposes?
_____electronic mail _____local area network
_____bibliographic databases _____access to genetic databases
_____national networks (internet, bitnet, bionet)
_____other(please specify)_______________________
10. List the specific main headings of information recorded for each
accession in your documentation for your collection.(e.g. genus,
species, host, geographical location of isolation, etc.)
11. a. Would you find a directory of research laboratories compiled
from this survey useful? Yes_____No_______
b. What uses would such a directory have in your work?
12 Would you find such a directory valuable if it were available for
computer access? Yes_____ No_____
NOTE: _____
PLEASE RETURN THIS SURVEY TO:
Dr. Larry Moore, Chairperson
ESCOP Subcommittee on Microbial & Subcellular Germplasm
Collections
Dept. of Botany & Plant Pathology
Oregon State University
Corvallis, OR 97331-2902
OR:
e-mail to hanusj@bionette.cgrb.orst.edu