***************************************************** * * * * * MICROBIAL GERMPLASM DATA NET * * * * VOL 1 NO 3 * * * ***************************************************** In this issue: SPECIAL REPORT OHIO STATE'S ONLINE NEMATODE DATABASE REVIEWS OF SOFTWARE FOR CULTURE COLLECTIONS CLONES MICRO-IS NSFNET--A COMPUTER NETWORK FOR SCIENTISTS INTERNATIONAL NETWORKS AND DATABASES NCPPB OF ENGLAND ICMP OF NEW ZEALAND BDT OF BRAZIL NEW PRODUCTS ******** The MGDN is published quarterly by the Microbial Germplasm Database and is a publication serving the needs and interests of researcers who maintain research oriented 'working' culture collections. You may be placed on the mailing list for the hard copy version of this newsletter by contacting Prof. Larry Moore, Dept of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331-2902, USA. Comments regarding the electronic edition of the newsletter or to be placed on the e-mail list for future mailings should be addressed to Joe Hanus at the above address or: hanusj@bionette.cgrb.orst.edu on internet Messages may also be left for Joe Hanus on the TRF Bulletin Board (BIOSIS) 1-215-972-6759 (Philadelphia) SURVEY RESPONSES HELP TO CHARACTERIZE DATABASE Thanks to the very positive response of scientists to our surveys, we are beginning to get a clearer picture of the spectrum of collections and germplasm types which will be served by the Microbial Germplasm Database. Survey responses indicate a total thus far of 180,000 accessions. This number may represent the tip of the iceberg (see table 1). Many researchers are not yet on our mailing list and have not had an opportunity to contribute information for their collec- tions. As the questionnaires continue to come in, it appears that most of the accessions are bacterial and fungal strains (approx 89%) and the largest numbers of collections are comprised of these germplasm groups. While some collections contain thousands of accessions many of the responses are from researchers with relatively small collections (10 to 200 accessions). Table 1. ACCESSIONS IN EACH CATEGORY OF GERMPLASM COLLECTIONS ACCESSIONS FASTIDIOUS PROCARYOTES 8 771 BACTERIAL STRAINS 148 62774 FUNGI 166 94363 ENDO/ECTOMYCORRHIZAE 21 1997 PROTOZOA 0 0 ALGAE 3 11 NEMATODES 37 8337 PLASMIDS 35 2071 CLONING VECTORS 19 330 CLONED GENES, LIBRARIES 29 5489 PLANT VIRUSES 39 1607 MYCOVIRUSES 1 10 PHAGE 8 308 MONOCLONAL ANTIBODIES 1 20 ANTISERA 9 123 VIROIDS 2 2 SATELLITE NUCLEIC ACIDS 2 4 OTHER NUCLEIC ACIDS 3 65 SEQUENCED DNA, GENES 14 2362 TOTAL 180644 The second part of the survey was designed to determine (i) the extent to which researchers share their cultures with others, and (ii) if their programs are compensated in any way for this service. Most ( 280 scientists out of 308 responses) provided cultures to other scientists. Many of those who did not were dealing with virulent plant pathogens. Of the 280 who did provide cultures, 265 1 . do not charge for this courtesy. Only 18 of these receive any funding specifically for the support of their collection. One can surmise from this that those who share cultures do so at some cost to other pursuits. The open sharing of cultures in most cases is desirable from a scientific perspective. It is apparent that financial support should be provided for this activity. Ninety percent of those surveyed maintained some form of documen- tation on their collections. Forty-four percent of these do this with the aid of a computer. Most of the remainder (48% of total responses) are interested in computerization but are dissuaded by the cost and time involved. A surprisingly large proportion of the respondents to this portion of the questionnaire (39%) use telecommunication in their research with electronic mail being the dominant form of usage. This is encouraging in that it indicates a foundation of telecommunication capability among the scientists who are likely to utilize the network. IBM compatible and Macintosh (the ratio being 3:1, respectively) were the most commonly used computers. The number of responses from each state are presented in table 2. Table 2. QUESTIONNAIRE RESPONSES ORGANIZED BY STATES ALABAMA 13 ALASKA 3 ARIZONA 10 ARKANSAS 14 AMERICAN SAMOA 0 CALIFORNIA 55 CANAL ZONE 0 COLORADO 12 CONNECTICUT 5 DELAWARE 7 DISTRICT OF COLUMBIA 5 FLORIDA 42 GEORGIA 35 GUAM 2 HAWAII 16 IDAHO 11 ILLINOIS 32 INDIANA 10 IOWA 18 KANSAS 18 2 . KENTUCKY 8 LOUISIANA 23 MAINE 11 MARYLAND 53 MASSACHUSETTS 7 MICHIGAN 23 MINNESOTA 18 MISSISSIPPI 20 MISSOURI 19 MONTANA 28 NEBRASKA 10 NEVADA 6 NEW HAMPSHIRE 11 NEW JERSEY 3 NEW MEXICO 11 NEW YORK 37 NORTH CAROLINA 20 NORTH DAKOTA 16 NORTHERN MARIANA ISLANDS 0 OHIO 11 OKLAHOMA 12 OREGON 21 PENNSYLVANIA 13 PUERTO RICO 13 RHODE ISLAND 2 SOUTH CAROLINA 17 SOUTH DAKOTA 7 TENNESSEE 11 TEXAS 37 UTAH 11 VERMONT 5 VIRGINIA 24 VIRGIN ISLANDS 0 WASHINGTON 21 WEST VIRGINIA 6 WISCONSIN 23 WYOMING 10 ________________________________ CAN MGD HELP YOU FIND THE GERMPLASM YOU'VE SEARCHED FOR? The database now includes scientists specializing in almost all plant-related groups of germplasm. Many would be willing to communicate with you if you need information or expert advice regarding some group of germplasm. We can forward your requests for information or advice to an expert in the field who may be able to help you. If you need one to several strains or specimens of some organism, 3 germplasm or antisera, send a thorough description of your needs or requests, together with your phone, address or e-mail address and we will publish it here. Please, restrict your requests to small numbers of strains or cultures. As we are all aware, provision of strains to colleagues can become an expensive and time consuming courtesy. If you prefer to not have your name published in the newsletter let us know and we will forward responses to you. REMINDER: An APHIS permit is required at present to ship pathogenic strains interstate. ***** SPECIAL REPORT NEMANET The Ohio State University Plant Pathology Department Nematode Database System William W. Shane and Richard M. Riedel Living cultures of nematodes are essential to research and instruction in nematology and other biological sciences. Currently, there is no centralized source for nematode cultures. Collections are being maintained at a number of laboratories throughout the United States. We have established at Ohio State University the NEMANET nematode culture database. The purpose of the database is to maintain and distribute information on the availability and characteristics of living cultures of nematodes in the United States. The emphasis of the NEMANET database is on plant parasitic nematodes although information on a lesser number of non-pathogenic types is also avail- able. Funding for the development of the NEMANET system was obtained from CSRS through the efforts of Drs. Bill Mai, Richard Riedel and Jack Barnes. The NEMANET database can be accessed by computer modem at 300, 1200, 2400, and 9600 baud rates. No charge is assessed for use of the system except normal long distance telephone call costs. Database Development -- Database files and programs of the NEMANET system are maintained on the Ohio State IBM 3081-D mainframe computer. Programming was done by Executive Decisions, a Columbus- based consulting firm. Online dialogue with the user is handled by TSO PDF. The PDF (Presentation Display Facility) system allows the addition of new host and nematode names, and new locations for culture collections without reprogramming. Information is presented to the user in full screen mode rather than the more traditional line-at-a-time mode. The result is an attractive, easy-to-use system. 4 . Database Description -- Considerable work has gone into the design of the NEMANET database. The basis of the whole system is the culture record. A culture record consists of the data (scientific name, original host, geographical origin, etc.) for one living nematode culture. Information on individual cultures is displayed by the NEMANET database as two screens (Fig. 1 and 2). The database can be searched on the basis of nematode species, collection location (repository), and original host plant for the individual cultures (Fig. 3). The system is menu-driven so that problems due to typing errors are minimized. Data Entry -- New information or revisions to existing data on nematode cultures can be entered online. For large amounts of data (more than 50 culture records) it is more efficient to mail the information on a floppy disk to W. Shane or R. Riedel at Ohio State University. The system has a password security system so that users can modify only the information from their site. Accessing the NEMANET Database -- Anyone with the proper computer, modem, and communication software can access the NEMANET Database. A variety of microcomputers and software packages can be used (Table 1). The procedure for accessing the database are given in Table 2. A users manual is available free of charge by calling or writing as given above. --------------- Nematode Culture Record ----------Nemanet No. 2 Command ===> CHAIN_ (HELP,CHAIN,END,=1,=2,=3,=4) Revision Date 09/08/88 *---------------------Taxonomic Information ----------------------------* |Species APHELENCHOIDES FRAGARIAE | |Authority (RITZEMABOS, 1891) CHRISTIE | |Race BEGONIA | | | |Date Verified Verifier R. M. RIEDEL | *--------------------------Origin---------------------------------------* |Geographical Origin ASHTABULA CO., OHIO, USA | |Host (Linnean name) BEGONIA SP. | |Soil Type | |Collection OHIO ST. U. | |Collection Date 01/01/76 | |Culture Id A. FRAGARIAE B | *-------------------------Culture Information---------------------------* |Type MONOXENIC CULTURE | |Storage Conditions ALFALFA CALLUS (CVP545) (10 G AGAR, 20 G SUCROSE, | | 2 G YEAST EXTRACT IN 100 ML WATER) | |Culture Procedures ZUCKERMAN, B.M., W.F. MAI & M.B. HARRISON. 1985 | | PLANT NEMATOLOGY; LAB MANUAL. | *-----------------------------------------------------------------------* 5 . (Use the CHAIN command for the next page, for this culture) Figure 1. Example of culture record information (1st page) as displayed by the NEMANET database. ---------- Nematode Culture Record (cont.) ----------Nemanet No. 2 Command ===> CHAIN_ (HELP,CHAIN,END,=1,=2,=3,=4) *-----------------------------------------------------------------------* | | |Species APHELENCHOIDES FRAGARIAE Revision Date 09/08/88 | | | *-------------------- Pathogenicity Notes ------------------------------* |Host Range | |Damage Threshold | |Misc . PATHOG. ON ALL BEGONIA EXCEPT FIBROUS ROOT TYPE | *----------------------- Morphometric Measurements ---------------------* |Measurements FEMALE L=0.73 MM; A=45; B=11; C=13; V=66; SPEAR=10U | | MALE L=0.552-0.886 ; A=36-63;B=40-63; C=12-17U | |Date Measured ________ Chromosome No. _________ | |Misc. | *-------------------------- Order Information --------------------------* |Availability ________ Source OHIO STATE UNIVERSITY | |Contact R. M. RIEDEL Telephone (614)-292-1375 | |Address 2021 COFFEY RD., COLUMBUS, OH, USA 43210 | *-----------------------------------------------------------------------* (Use the CHAIN command for the previous page, for this culture) Figure 2. Continuation of culture record information (2nd page) as displayed by the NEMANET database. 6 . ---------- Ohio State University NEMANET Database System ---------- OPTION ==> _____ 1 CULTURE -Search and Update Culture Database 2 HOST -Search and Update Host Table 3 CULTURE LOCATION -Search and Update Culture Location Table 4 NEMATODE -Search and Update Nematode Table HELP HELP -View Help Screens and Tutorial X EXIT -Terminate Nematode System Enter END command to terminate the application Figure 3. The main menu of the NEMANET database system. Table 1. Personal computer communication software known to work with the NEMANET Database. Microcomputer Software Package1 Vendor ___________________________________________________________ Apple IIe Apple Access II Apple Computer Corporation ProTERM Checkmate Technology Apple Macintosh Smartcom II Hayes Microcomputer Products Red Ryder 10 Red Ryder Enterprises MicroPhone II Software Ventures IBM & compatibles Procomm, Procomm Plus Datastorm Technologies Crosstalk XVI Digital Communication Smartcom III Hayes Microcomputer Products Relay Gold VM Personal Computing 1 Note: other software packages may also work if they support VT100 protocol. ____________________________________________________________ Table 2. Accessing the NEMANET Database at the Ohio State University 1. Dial the Ohio State University Computer via your software communications program. Choose the baud rate according to the capabilities of your modem and communications package 300 baud: (614)-292-3103 2400 baud: (614)-292-3124 1200 baud: (614)-292-3112 9600 baud: (614)-292-3196 2. When the connection has been made you should see "CONNECT XXXX" where XXXX = 300, 1200, 2400, or 9600. Hit [ENTER], i.e., the enter key, once for 300 and 1200, twice for 2400 and three times for 9600 baud. 7 . 3. You should see the following response: Welcome to the Ohio State University Network Switch. For authorized users only. Type a host name or type Help for a list of available hosts. Host Name? You should enter: FS3270 [ENTER] There will be a pause, then you should receive: "GO". Respond by hitting [ENTER]. You will then receive: Enter terminal type You should respond: VT100 [ENTER] You will receive the OSU/IRCC logo screen (full screen display) You should enter: TSO [ENTER] You should receive: USERID? You should enter: TS1946 [ENTER] You should see: PASSWORD You should enter: VHY9XJ [ENTER] You should see: UNIVERSITY ID? You should enter: 111222333 [ENTER] After a few seconds you will receive ***, after which you should hit [ENTER]. Wait until you seen the NEMANET Password Entry screen. You should respond wither with your institution's NEMANET password or, optionally, your name in the name space. You are now into the NEMANET system. The system has an extensive help facility to assist the new user. For further information contact: William W. Shane and Richard M. Riedel, Department of Plant Pathology, The Ohio State University Columbus, OH 43017 Recording your collection--Individuals or institutions that wish to add information on their nematode cultures to the NEMANET systems are encouraged to contact Drs. Richard M. Riedel or William W. Shane, Department of Plant Pathology, Ohio State University, 2021 Coffey Road, 201 Kottman Hall, Columbus, OH 43210 (614)-292-1375. In keeping with the philosophy expressed in the first issue of the Microbial Germplasm Data Net newsletter (December 1988) it is emphasized that laboratories that provide information for the database are not obligated to provide cultures or additional information. The scientist that provides the information can modify or delete the data at any time. ***** 8 . SOFTWARE REVIEWS 'CLONES' DATABASE PROGRAM AVAILABLE FOR DISTRIBUTION Dr. Hal B. Jensen of Yale University school of Medicine has developed a database management program for use in laboratories that maintain large numbers of organisms used in recombinant DNA research. The program, CLONES, is a complete stand-alone database program written specifically for organizing, storing, and accessing data for recombinant clones, recombinant libraries, bacterial strains, and plasmid and bacteriophage cloning vectors. Each recombinant clone, recombinant library, bacterial strain, or vector (either phage or plasmid) is stored in a separate record which contains items of information specific for the type of material to be documented. The database can be organized by any criteria in the records and can be specified by the user. Any number of databases can be created and merged later if desired. An individual database can contain information about any or all of these four classes of germplasm. Records are stored as variable length records to conserve space and can include five screen lines of notes on individual entries. These note fields can be searched as well. CLONES comes with an extensive on-line help facility to guide the user through data entry and retrieval and a text file that serves as an introduction to the program. Evaluation of CLONES demonstrated that it performs its tasks exceedingly well. Even though it is directed toward researchers specializing in recombinant DNA, researchers with other areas of specialization may also find the program to be a useful collection documentation tool. Its extensive use of pull-down menus and sub-menus make its use by first-time users extremely easy. Most of the program is written and compiled in C language. Those modules that are rate limiting have been compiled from assembly language. Use of B-tree structure facilitates rapid data retrieval. Dr. Jensen says that there are now several hundred users of CLONES. He indicates that there are enhancements and modifications planned for future versions that will make the program more useful for investigators with other needs. In addition to providing a more sophisticated editor for text entries, he plans to provide data compression (to reduce disk space used in storage) and data encryption as an option. Dr. Jensen is interested in 9 . hearing from researchers with other types of collections since future updates and enhancements may be directed toward a larger audience. An extremely attractive aspect of CLONES is its price. It is available from Dr. Jensen for a minimum cost of $10 to cover the cost of the disk and mailing. You may then make as many copies of the program as you choose for yourself or other researchers. Dr. Jensen is maintaining a list of individuals who have obtained copies and will notify them of updates. CLONES requires an IBM compatible pc with DOS 2.1 or later and 256k of available RAM. CLONES is described in: Jensen, Hal B. 1989. A dedicated Database Program for Cataloging Recombinant Clones and Other Laboratory Products of Molecular Biology Technology. Biocomputing 7,590-592. To obtain a copy of CLONES Send $10 to: Hal B. Jenson, M.D. Division of Infectious Diseases Department of Pediatrics, Epidemiology and Public Health, and Yale Comprehensive Cancer Center School of Medicine New Haven, Connecticut, 06510-8064 ***** MICRO-IS AVAILABLE FROM ATCC MICRO-IS, an assembly of data management software developed specifically for maintaining culture collection documentation, is now available. The software can be obtained either from ATCC Department of Bioinformatics or through Microbial Strain Data Network. MICRO-IS is not a single program, but a suite of programs based on a mainframe version that is run at NIH in Bethesda, MD. The PC version requires 448k of RAM minimum (640 is recommended) and MS/PC DOS 2.0 or later. While the programs will run with two floppy drives, a hard disk is strongly recommended by the authors for the 3 megabytes plus of information. [Ed. note: Experiences with the MICRO-IS indicate that a hard disk is a practical necessity.] The program is developed around the RKC numeric coding system for bacterial 10 . strain characteristics (Rugosa, Morrison, Krichevsky, Micah I. Colwell, Rita R..1986. Coding Microbiological Data for Computers. Springer Verlag New York) and is best suited for the collection which maintains extensive data on individual strains. Structure. Coding for individual strain characteristics is kept in a synonym file. This relates a six digit (hexadecimal) code to individual field names for strain traits. These strain traits can be defined by the user together with synonyms for them. As with most database management systems fields may be of either numeric, character or binary (logical). Numeric fields are numbers that are stored as numbers in the computer and may be used as arguments for arithmetic operations. Character fields are either alphabetic characters or numerals to be stored as character strings. Binary fields are either true, false or null (an example would be acid production from glucose. This could be recorded as '+', '-', or 'no data'). The null state eliminates ambiguity in situations which can occur when no data is available. Data Entry. Data is entered by first generating a data entry form from a Forms menu. Data can then be add/modified from this form. The data field labels are presented vertically. This allows viewing of many short fields on the screen. Data entry is horizontally scrolled through an entry window so that long fields may not be completely visible from beginning to end. Query. The Query utility searches the database and produces simple reports based on criteria selected by the user and performs simple statistics on numerical data. Search criteria can be based on binary field (yes/no/null) numeric field (based on ranges or comparisons) or character field( based on matching an entire string or a substring of characters within a field). A command processor with a built-in editor allows the user to formulate programs (more accurately scripts of query and report commands). This allows linking together complex search strategies in a reproducible file for later use. Query keywords include AND, NOT and ANY and can link binary, numeric or character fields. Reports. Reports can be sent to the screen for immediate appraisal,to a to a file for later cosmetic treatment by a word processor or graphics package or directly to a printer. Overall impression. MICRO-IS is a sophisticated approach to database management for the culture collection. It allows the cataloging of mas- sive quantities of information on individual strain characteristics. The documentation is complete but not easy reading. Don't expect to enter your culture data the same day the diskettes arrive. The demonstration program provided will give you hands-on experience (which I strongly recommend) before attempting to configure your own file system. MICRO-IS will be best utilized by collections maintaining large amounts of data on individual strains (ie carbohydrate utilization/antibiotic resistances). The program is fairly robust in that I have not been able to intentionally cause it to crash (though error messages are cryptic). MICRO-IS is still in the developmental stages since some choices on the many menus provide a mes- sage indicating that the programming of this part is not yet complete. Among the functions to be provided are file compression (apparently using one of the recent versions of pkarc utilities which have been around for 11 . a number of years as shareware) thereby reducing the storage space required for a database by a factor of 2 or more. The number of features yet to be added make becoming a registered user imperative. You will then be provided with updates and upgrades which will round out a elegant tool obviously designed by and for microbiologists. The prices as published in the current MSDN newsletter are as follows Disks/Manual $118 (US) Registration $ 45 Total $153 MSDN Secretariat Institute of Biotechnology 307 Huntingdon Road Cambridge CB3 OJX, U.K. We thank Dr. Lois Blaine of the Department of Bioinformatics, ATCC and Dr. Candace McManus, Microbial Systematics Section of National Institute of Dental Health for providing us with copies of the programs for review. ***** NEW PRODUCTS AND RELEASES FAST CHARACTERIZATION OF GRAM NEGATIVE BACTERIA Microbiologist can now characterize Gram negative microorganisms based on their metabolism of 95 different carbon substrates without the exasperation of extensive media preparation. BIOLOG'S GN MICROPLATE (TM) which was introduced a year ago characterized gram negative bacteria on the basis of redox reactions, which are carried out in 96 well plates. These are supplied ready-to-use in dry form and are rehydrated by the addition of inoculum. A redox dye such as tetrazolium violet is included in the reaction mixture. If a cell culture is capable of metabolising a particular carbon substrate, the accelerated metabolic rate results in the irreversible production of the formazan dye derivative. The result is an 8 x 12 color matrix of clear or purple wells in the plate, each of which contains a different carbon substrate. This matrix is unique to each gram- negative organism. The color reactions develop in 4 to 24 hours. BIOLOG'S MICROPLATE assay has been tested with over 300 Gram-negative bacteria including 200 non-enterics. The test kit can be obtained either with an IBM-PC based database in which the data is entered manually or with a plate reader that is part of an integrated computerized microbiology work station. The manufacturer indicates that the database will be extended to Gram-positive, yeast, anaerobes, and additional environmental and oligotrophic Gram-negative microorganisms. A free book is available from the manufacturer which describes the assay and BIOLOG'S technology together 12 . with a listing of the Gram-negative organism and their metabolic properties. Contact: Dr. B.R. Bochner Biolog 3447 Investment Blvd. Suite 2 Hayward CA 94545. ***** OPEN 'MICRO' TUBES ASEPTICALLY If you maintain large numbers of cultures in microcentrifuge tubes, you will appreciate the Cap-Lok (TM) Key supplied by ROBBINS SCIENTIFIC. The key will open most brands of 0.6ml and 1.5ml microcentrifuge tubes without coming in contact with the cap thereby eliminating contamination. The key is made of polypropylene and is autoclavable and is supplied in packs of ten. GENETIC DATABASES ON A COMPACT DISK Three major databases, GenBank, EMBL and Protein Identification Resource, are being supplied on a single CD-ROM. The 500 megabyte disk is being marketed by HITACHI AMERICA. Free literature is available from their Sales and Support department. DISPOSABLE MICRODISPENSERS Eliminate clean up problems and possible cross contamination with microliter pipets when loading gels or transferring toxic or radioactive liquids. These glass capillary pipets, which cannot be reused contain a small neutral piston separating the reusable plunger from the liquid and which is disposed of with the barrel. The microdispensers come in 10 to 100 L sizes in packs of 100 with 5 reusable plungers. Drummond Scientific Co.,500 Parkway, Box 700, Broomall, PA 19008 Information about new products is based on material supplied by the manufacturer. We cannot vouch for its accuracy nor do we endorse any product. 13 . NETWORK NEWS 'DO IT YOURSELF' LAN We have recently completed installation of an Ethernet local area network (lan) serving researchers and office staff in Cordley Hall on the Oregon State University Campus. The network allows rapid exchange of files among users, access to campus computing, text processing and printing facilities, world-wide electronic mail, access to NSFNET, Unix world wide news groups and genetic databases. This network is unique for two reasons: (i) it required the financial and administrative cooperation of four departments (Botany and Plant Pathology, Entomology, Zoology and the Center for Gene Research and Biotechnology and (ii) the network was installed at considerable saving in cost by volunteer help from faculty and students of these departments. The project was overseen by Dr. Kevin Currans, a research associate in Entomology with training in computer science and with advice from OSU Computer Services. If you are interested in technical details of this system contact Dr. Kevin Currans, Dept. of Entomology, Oregon State University, Corvallis, OR 97331. ***** NSFNET: A NATIONAL COMPUTER NETWORK TO PROMOTE INTERACTION AMONG SCIENTISTS. "Collaboration among researchers from all fields happens faster via networks than via conferences and journals. It is reasonable to expect a national research network to replace or augment printed journals with electronically distributed text, images and videos." 1 In previous issues of Microbial Germplasm Data Net we have mentioned national and international communication networks, specifically NSFNET, as a means of reaching the online Microbial Germplasm Database once it is implemented. While the catalog will be available in printed form and through long distance phone lines with telephone modem, the most rapid, reliable and inexpensive way to obtain information is through this government sponsored network. NSFNET allows electronic mail and file transfers between scientists who can reach the network from their campuses (many of which are not linked) and from other Unix sites through the US. Message transfer is virtually instantaneous and can allow interaction across the nation as easily as across campus. This is an invaluable asset when you are collaborating with a scientist at a distant site and need instant feedback on manuscripts or tables of data without the aggravation of answering machines and missed calls. The cost is minimal to the user and usually consists of whatever costs are incurred in reaching the campus local area network from his/her laboratory or office. (Your computer center can help you determine what you needs are and what your on-going costs will be. If you like, contact us and we can describe how we managed the hook-up). 14 . NSF began development of a national research network in 1985 with the initiative to fund five national supercomputer centers. A need developed to provide a link between these centers and with scientists who use them. In March of 1986, NSF funded a backbone network between the five supercomputer centers. It has since expanded from its original six backbone nodes (relay sites that span the country) to 280 networks serving single sites, multiple sites on a campus or several campuses. Network traffic (transfer of messages, files and programs among scientists) continues to double every 6 months. The backbone is connected to the Mid-Level Networks, which while not totally funded by NSF were provided with seed capital and are intended to be self-supporting. NCSA (National Center for Supercomputing Applications) BARRnet (San Francisco Bay area), Northwestnet for Pacific Northwest, MERIT for Michigan and numerous others fan out from the backbone to reach the campus level. It is this campus level network that we as researchers access when we communicate with others researchers, either on campus or nationally. It is only this part of the communication network that is visible to us while the vast hierarchy of hardware and software is nearly transparent. This user interface (the campus local area network or lan) is now being developed on many campuses and will make sweeping changes in the way we communicate and store and utilize information. In 1987 most campus networks were a dial up connection with the user communicating with a host mainframe at 1200 bps (bits per second, standard telephone modem speed. Most of us now use a PC as a terminal and an increasing number of campus wide Ethernet networks (extremely fast multi-user systems) tie these pcs together and establish connection to the Mid-Level Networks. This makes possible speeds of communication many orders of magnitude greater. While most of us do not routinely need systems that operate at 2 to 3 mbs (millions of bits per second), the speed and accuracy with which files can be transferred is dazzling. A full manuscript with tables of data and graphics can be transferred in seconds from coast to coast. What does this mean to Microbial Germplasm Database? It allows almost instant access to the collection information that is to be stored online. Screen updates occur rapidly enough on a user's computer that users on the east coast querying the Microbial Germplasm database will see a form on his/her screen that is generated in Corvallis OR on our host computer. S(he) will fill in the form from the east coast, to specify the information desired and the query will be initiated. When the report from MGD is completed it will be returned to the user in a few milliseconds. The view to the user is that the entire process occurred locally. High-speed telecommunication is making teleconferencing in real time not only a possibility but an extremely cost effective way to bring together scientists from distant parts of the country for interaction and allowing "audience participation" with as observing scientists submitting questions to the experts. 15 . As biological computing becomes increasingly important we, as biologists, need to be vocal in making our needs known. We encourage you to seek help from the department on your campus that coordinates computer access. They can often advise you on suitable and surprisingly economical means to provide your laboratory with network access. You can in turn provide them with guidance in the shaping of the nature of computing services on your campus. In this way we, as biologists, will share in the benefits of this revolution in communication and information access. Taken in part from: Catlett, Charles, E. 1989. The NSFNET:Beginnings of A National Research Internet. Academic Computing Vol 3 No. 5(Jan). pp18- ***** INTERNATIONAL PERSPECTIVE The Microbial Germplasm Database has been in contact with other collections and databases world wide. We are pleased to be able to present the following reports of internationally notable collections. THE NATIONAL [ENGLAND] COLLECTION OF PLANT PATHOGENIC BACTERIA Dr. David Stead, Curator. The NCPPB is one of the largest collections of plant pathogenic bacteria and is one of the major repositories for deposition of type strains for such bacteria. The collection is maintained by the Ministry of Agriculture, Fisheries and Food at their Central Science Laboratory in Harpenden, Hertfordshire, England. We now hold over 3000 bacterial strains and a few phage. The collection was founded in 1947 and combined Dr W. J. Dowson's collection of Type cultures. The collection was transferred to Harpenden in 1956 with R. A. Lelliott as curator. He gradually built up the collection in that it now holds strains of almost all bacteria known to cause plant diseases. Sufficient cultures are kept of each taxon to represent as fully as possible its geographical range, host range and natural variation. The major accessions are within Agrobacterium, Erwinia, Pseudomonas, Xanthomonas, Clauibacter, Curtobacterium and Rhodococcus. Almost all strains are maintained in the freeze-dried state. The NCPPB also offers a wide range of services. Strains are currently 7.50 each and there is a handling charge of 7.00 per order for UK orders 16 . and 11.00 for overseas orders. UK orders also attract VAT [value added tax]. Cultures are dispatched, lyophilised in well-packed glass ampoules. Invoices are issued at the time of despatch. Correspondence to: NCPPB, ADAS Central Science Laboratory, Hatching Green, Harpenden, Hertfordshire, AL5 2BD, UK ***** INTERNATIONAL COLLECTION OF MICRO- ORGANISMS FROM PLANTS Dr. J.M. Young, Curator INVITATION TO COLLECTORS. In the United States, as in other parts of the world, there have been unique holdings of strains of plant pathogenic bacteria. These may have been represented by a few dozen cultures. Sometimes, the collector was unaware that theirs was the most comprehensive extant collection world-wide of a particular pathogen. It was not uncommon for such collections to have been lost at completion of projects. The International Collection of Micro-organisms from Plants (ICMP) now offers all researchers free access to a repository for such collections, on an exchange basis. HISTORY AND FUNCTIONS OF THE COLLECTION. The International Collection of Micro-organisms from Plants has its origin in 1952 as the personal collection of plant pathogenic bacteria and rhizobia of D.W. Dye. It expanded as the Plant Diseases Division Culture Collection (PDDCC). Recent accessions of micro-organisms related to studies in molecular biology, food technology, and insect pathology reflect the development of the diverse interests of the Department of Scientific and Industrial Research at the Mt. Albert Research Centre in Auckland. The Collection contains cultures of the world's bacterial and fungal plant pathogens and of other micro-organisms closely associated with plants. It is intended that for each taxon, the number of isolates held shall be fully representative of its geographic and host range and of the variation within the taxon. Cultures are available for use in research and teaching, and for industrial purposes. The Collection is maintained by the Microbiology Group of the Plant Diseases Division at Mt. Albert Research Centre. Staff at the centre work to confirm the identities of strains in the Collection and to determine the virulence of plant pathogens. This on-going study is helped immeasurably by scientists in other institutes with specialized knowledge of particular pathogens, who have studied strains from the Collection in the course of research. 17 . EXCHANGE OF CULTURES. The Curator prefers to waive charges if strains that enhance the inventory of the Collection are available for exchange. Host- pathogen combinations for which there are fewer than 5 strains in the Collection are most valued. Identification to pathovar level, where appropriate, is desirable but not expected for uncommon combinations. CHARGES. Unless exchange arrangements are agreed with collections or individual workers, a graduated scale of charges is made for supply of cultures. DEPOSITION OF CULTURES. Deposition of plant pathogens or micro-organisms of research interest, only meagerly represented in the collection are welcomed. Authors of new species and pathovars of bacterial pathogens especially are asked to deposit representative strains in the ICMP. Offers of strains should be addressed to the Curator and should describe their salient characteristics. ICMP will arrange import documentation. THE CATALOG. The present catalogue (US $30 airmail delivery) was published in 1988. It is divided into two parts, one comprising bacteria, and one, fungi, includes 4400 accessions of bacteria and 2400 of fungi Correspondence: The Curator International Collection of Micro-organisms from Plants Plant Diseases Division, DSIR Mt. Albert Research Centre Private Bag Auckland, New Zealand Telephone (09) 893-660 Fax (09) 863-330 International Fax 64 9 863-330 Telex NZ 21623 ***** LATIN AMERICAN EFFORT TO PRESERVE BIOLOGICAL DIVERSITY RESULTS IN INTENSIFIED FOCUS ON ELECTRONIC COMMUNICATION AND CULTURE COLLECTIONS Out of an estimated 250,000 plant species worldwide, Latin America possesses 90,000. Half of these are indigenous to Columbia, Ecuador and Peru according to Dr. Peter Raven, director of the Missouri Botanical Gardens. By comparison, the U.S. and Canada possess about 17,000 plant species. Efforts are underway in some of the Latin American Countries to guard against the devastation of this natural wealth of plant species and the microorganisms associated with them. Dr. V.P. Canhos of Brazil's Andre Tosello Tropical Research and Technology Foundation in Campinas has 18 . launched a successful program, the Tropical Database (BDT), to catalog bacterial, plasmid, fungal strains in existing culture collections. BDT had its beginnings in 1982 with an initial survey which resulted in the National Catalogue of Microorganisms being published in 1984. This listed the holdings of nine collections having a total of almost 4,000 strains. The Brazilian Government, in 1985, set up Cirandao, a computer service, which made computerized databases available to users in general. BDT utilized this resource to place the catalog online. The database was linked to Microbial Strain Data Network and international telecommunication networks in 1987 making possible electronic mail and communication with other electronically linked strain data networks. The BDT has been instrumental in sponsoring workshops with such international experts as Dr. Micah Krichevsky (NIH), Dr. Lois Blaine (ATCC) and Ms. Barbara Kirsop president of the World Federation of Culture Collections. The workshops range from the practical aspects of collection methodology and database application in biological collections to discussions of the role of collections and their services in biotechnology. The third edition of the National Catalog of Strains is presently being prepared for publication. Future plans include the publication of a catalog of human resources listing scientists working with basic and applied microbiology. Dr. V.P. Canhos Coordenador Base de Dados e Colecao de Culturas Tropical Fundacao Tropical De Pesquisas e Tecnologia "Andre' Tosello CAMPINAS-SP-Brasil Cx.Postal 1889 Genetic Engineering News, February, 1989. Proceeding of the Sixth International Congress of Culture Collections. Oct. 30 - Nov. 4, 1988. Personal Communication ***** FEEDBACK QUESTIONNAIRE This newsletter once again contains a questionnaire that we hope you will check off and mail to us if you have not already done so. 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. Please attach any other comments to the questionnaire or submit them separately if you choose. ***** 19 . USER REVIEWS It would be helpful to other researchers who maintain culture collections if you would share your experiences with them. If you have had experience with a new product, either good or bad and feel this would be helpful to others who maintain culture collections of microbial germplasm, let us know. We would like to hear about culture products, equipment, computer software or hardware. There are shareware and public domain programs available, many of which are quite good. Let us know of your experiences. Also, it would be useful to others if you would share any unique culture or taxonomic techniques that you have found helpful in your research. If you choose you can use the pre-addressed COMMENTS AND RECOMMENDATIONS space inside the back cover. Be sure to include you name and address so that we can provide recognition for the idea. ***** CALENDAR OCTOBER '89 11-13 Workshop on Computers in Microbiology, Rockville, MD. Contact Doug Drabkowski, American Type Culture Collection, 1201 Parklawn DR. Rockville, MD 20852. 15-18 American Biological Safety Conference (32nd). New Orleans, LA. Sponsor American Biological Safety Association. Contact: Daniel Leiberman, c/o Environmental Medical Services, 20C-208, Massachusetts Institute of Technology, Cambridge, MA 02139, (617)258-5646. 15-19 Conference on Comparative and Applied Virology (6th International). Sponsors: ICVO/WHO. Contact: Dr. E. Kurstak, Dept. of Microbiology and Immunology, Faculty of Medicine, University of Montreal, P.O. Box 6128, Station A, Montreal, PQ Canada H3C 3J7, (514) 343-6285 16-20 Workshop on Recombinant DNA Technology, Rockville, MD. Contact Doug Drabkowski, American Type Culture Collection, 1201 Parklawn DR. Rockville, MD 20852. 23-27 Workshop on Recombinant DNA Technology; See above Oct 16-20 24-26 BABE '89 , International Biotechnology Expo: Strategic Oppor- tunities for the 1990s. San Mateo Expo Center. Contact: Cartlidge & Assoc., Inc., 3097 Moorpark Ave., Ste. 202, San Jose, CA 95128. (408) 554-6644. 20 . NOVEMBER '89 2-4 Southern California American Society of Microbiology. San Diego, CA. Sponsor: SCASM. Contact: SCASM Conference Concepts, P.O. Box 2029, Carlsbad, CA 92008, (619)431-0565. 14 Seminar on Biotechnolgy Information. Held at Scottish Science Library in Edinburgh, U.K. Contact: British Library, Science Reference and Information Service, 25 Southhampton Bldgs., London WC2A 1AW, U.K. Call 01-323 7470 FEBRUARY '90 12-15 Biotechnology Conference on Fermentation Technologies: Industrial Applications. Palmerston, New Zealand. Sponsor: Massey University, Biochemical Processing Centre, DSIR. Contact: Conference Director, Biotechnology Dept., Massey University, Palmerston North, New Zealand. MAY '90 13-18 ASM Annual Meeting (90th). Anaheim, CA Contact: Richard A. Bray, Meetings Dept., American Society for Microbiology, 1913 I St. NW, Washington, DC 20006 SEPTEMBER '90 6-9 Promiscuous Plasmids (6th International Fallen Leaf Lake Conference) South Lake Tahoe, Calif. Sponsor: University of California, Davis. Contact: Clarence Kado, Director, Fallen Leaf Lake Conferences, Dept. of Plant Pathology, University of California, Davis, CA 95616. 21 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