*****************************************************
* *
* *
* MICROBIAL GERMPLASM DATA NET *
* *
* VOL 2 NO 3 *
* *
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IN THIS ISSUE
MGDN REPORTS
>MGD IN ST.LOUIS.....................1
NATIONAL OUTLOOK
>SCIENTISTS EVALUATE NETS' EFFECTS...4
>ATCC WARNS OF EXPLODING AMPOULES....5
INTERNATIONAL PERSPECTIVE
>CANADA DEVELOPS BACTERIAL DISEASE
NETWORK ........................5
SPECIAL HOW-TO SECTION
>WORDPERFECT DOUBLES AS
CULTURE DATABASE..................6
DATABASES AND CATALOGS
>DATABASE OF PLANT VIROLOGISTS......13
>ATCC VIRUS CATALOGS ON DISK........15
********
The MGDN is published quarterly by the Microbial
Germplasm Database and is a publication serving
the needs and interests of researchers 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 requests 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
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.
Each collection that we are able to document is important, regardless
of size.
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. Your response will also
insure inclusion of accurate information regarding your collection in
the MGD online database and in the Microbial Germplasm Database
Catalog of Culture Collections.
Please provide a copy of this questionnaire to colleagues who
maintain culture collections. Completing this form places them on
the mailing list for this newsletter.
*******************************************
MGDN REPORTS
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MGD DISCUSSION SESSION TO BE HELD AT
ST. LOUIS APS MEETINGS
Those of you who attend the American Phytopathological Society
Meetings in St. Louis can learn more about MGD and plans for future
efforts at a special discussion session Monday night, August 19 from
7-10pm. The session will provide a great opportunity for you to con-
tribute your own ideas and queries about the network. Each partici-
pant in the Discussion Session will present a short commentary about
their particular topic and then field questions or present questions
to the audience for feedback. We expect lively discussions about all
phases of the network. The session will explore technologies that
are available now and others that are on the horizon.
PROGRAM: Larry Moore, Oregon State U., Moderator
Introduction, Larry Moore, Oregon State U.
1. "A Database of Resources in Plant Virology" Cleo D'Arcy, U. of
Illinois.
2. "A Database for Managing a Departmental Fungal Culture
Collection" Elwin Stewart (Collaborator: Joseph O'Brien), U. of
Minnesota.
3.3. "Applications of MGD in Molecular Genetics", Arun Chatterjee,
U. of Missouri.
4. "The Microbial Germplasm Database: "Using Informational Technol-
ogy to link Scientists and Conserve Germplasm", Joe Hanus, Computer
Manager for MGD, Oregon State U.
5. "Value of a Microbial Germplasm Database to Industry", Norm
Schaad, Harris-Moran Seed Co. CA.
6. "Perspectives on the Development of a Microbial Image Mediabase",
Bruce Hemming, Microbe Inotech Laboratories, St. Louis, MO.
Each speaker will make a 15 minute presentation followed by 5 minutes
for questions from the audience. There will be discussion and wrap-
up after the last speaker.
-1-
TEST VERSION OF MICROBIAL GERMPLASM DATABASE
ONLINE FROM YOUR DESKTOP PC
You can participate in testing MGD from your PC through your campus
computer, if it is connected to NSFNET. At this time we are testing
connectivity throughout the U.S. If you have difficulty logging on,
please let us know what error messages you receive, what terminal
emulation package you're using and any other relevant info.
At present, the database supports VT-100 emulation from either Mac or
MS-DOS PCs. We have been using NCSA TELNET for both the Macintosh
and MS-DOS PCs. Suitable software that provides VT-100 emulation via
telephone modem can also access the database.
Please bear in mind that we are just now getting some of the vital
functions operational and that the system is "bare-bones" and less
than user friendly. We are currently working on anonymous ftp of
records selected from the database files and online context sensitive
help menu's. Future versions of MGD will provide a much richer base
of information (references, more detail on types of accession in
collections) , a graphical user interface, and image data objects
(You'll not only be able to locate an organism, but also view
diagnostic procedures, affected plants, habitats, graphs and charts
or even, carried to extremes, your colleagues).
Logging on through NSFnet (Internet).
1. Login to your machine.
2. Type 'telnet cogar.cgrb.orst.edu' (don't type quotes)
3. Should your computer not find this name in its host table, type
'telnet 128.193.86.2' which is the ip number of this machine.
4. The computer will ask you your login name. Users of the database
should type 'germbase'. (Note this is case sensitive and must be
lower case).
5. You will be asked for a password . This will not show on the
screen as you enter. Type 'Mgd101'.
6. A welcome screen should appear, followed by a short help screen
that displays wild card characters and logical operators. This is
pitifully short at this time and will be a full set of help
instructions when we get a little farther along.
Note the * and ? wildcards. They are used just as in MD-DOS. ?
means a single occurrence of any character and * means any number
(including zero) occurrences of any character.
It takes about 15 seconds for the database program to initialize
and start up. The first screen you see is the search form. Supply
data to restrict the search using the logical operators in the help
screen by filling in the blanks (see below). The following form
would find all instances of a person whose last name begins with SMI
and who are located in the state of OH and whose Research Interest
field contains anywhere in it, the word ERWINIA.
-2-
GERMBASE SCREEN
------------------------------------------------------
Enter criteria for selection. ESC when done, DEL to abort
----------- Type Control-W for MENU HELP -----
CODE: [ ]
Last Name: [SMI* ]
First Name: [ ]
Title: [ ]
Address: [ ]
[ ]
[ ]
City: [ ] State: [OH]
Zip: [ ][ ]
Phone: [ ]
Electronic Mail: [ ]
Research Interest: [*ERWINIA* ]
[ ]
Germplasm Types: [ ]
[ ]
----------------------------------------------------
To find instances of E coli in the database enter *E COLI* in the
research interest field. Then enter ESC and all individuals who have
listed this organism in their principal research interest field will
be selected. Soon we will have a utility for you to down load
these records but for now you'll have to use the screen capture
utility from your telecommunication software. If you are using the
telnet/ftp suite of programs from Clarkson University and NCSA, you
can capture by cutting and pasting to your printer (Mac) or capturing
to a file with ALT-C (MS-DOS).
Problems? Contact hanusj@bionette.cgrb.orst.edu
or write to this newsletter with specifics.
EXCHANGE OF DNA COULD CIRCUMVENT PERMITS
FOR SHIPPING OF BACTERIAL CULTURES
Jan E. Leach, Associate Professor
Department of Plant Pathology, Kansas State University
DNA-hybridization techniques are now commonly used for diagnosis and
evolutionary comparisons between genera, species, or pathovars of
plant pathogenic bacteria. As a consequence, many of us have genomic
DNA preparations from large numbers of various bacterial groups. The
exchange of small amounts of these genomic DNA preparations between
scientists could facilitate the testing of specificity or utility of
DNA probes, because one could test probes on an increased number of
different bacteria. An additional advantage to the exchange of DNA
-3-
is that permits, which are required for the mailing of bacterial
cultures, are not required for mailing DNA. The details of the
exchanges could vary based on quantity of DNA needed for the number
of strains from which DNA is required. For example, if a large
quantity of DNA is needed (more than enough to run two or three
gels), then the bacterial strain should be requested rather than DNA.
The Microbial Germplasm Database can include a list of willing
participants and the bacterial DNA they are willing to exchange.
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NATIONAL OUTLOOK
*********************************
HANDELSMAN AND KLOPPENBURG EVALUATE
HOW SCIENTIST'S WORK WILL CHANGE
THROUGH COMPUTER NETWORKS
Drs. Jo Handelsman, a plant pathologist, and Jack Kloppenburg, Jr., a
social scientist, of University of Wisconsin and Stephen Pollak a
researcher, recently of University of Sussex have been awarded
$85,000 for a two year investigation of what they believe is the
first systematic study of computer networking on an international
scale, as well as of its potential impact on the scientific process.
Handelsman says, "The beauty of networks is that you can pull people
from a wide range of disciplines or places into a very tightly knit
community... The question is, is that going to affect the way we
interact as scientists or the way we ask questions of each other and
the way we gather information?"
The volume of information transferred through NSFnet has tripled in
the last year and is continuing to increase at the same rate. The
information being transferred is largely between universities and
scientists. The investigators will be observing responses to queries
through Microbial Strain Data Network and three other relevant
networks. Because of the anonymity of networks, Handelsman and
coworkers are asking in this study, whether the nature of the
response would be different than would be obtained, for example, by
asking the same question at a meeting.
The researchers hope their study will help them test the accuracy of
various stereotypes about who uses computers to communicate. Some
senior scientists suspect that network users tend to be young.
Others say that women scientists are more likely to speak up on a
network than in other forums. And there is a feeling among some
users that networks enrich scientific debate by attracting
"peripheral" scientists from small institutions or from developing or
Eastern European countries. Says Pollak, "Even if you're not at a
large institution, you may still be integrated into the scientific
information flow". The study may influence the way scientific
discourse is conducted over the networks and will help in structuring
new networks.
(from The Scientist Nov 12, 1990).
-4-
SAFETY NOTE FROM ATCC
Ampules containing frozen cultures can be very dangerous if they have
not been properly sealed, exploding violently after removal from
liquid nitrogen storage. Ampules are always checked for leaks before
they are placed in storage, but nevertheless, can and do explode.
The explosions, which are the result of microscopic leaks allowing
liquid N2 to enter the ampule, usually occur during thawing in water
baths before scoring.
ATCC recommends the following:
Wear full face guard and gloves
Cover the water bath while the contents are thawing
Wrap each ampule with several folds of a sterile towel or gauze
before scoring and opening
ATCC Quarterly Newsletter, May 1991
APS BULLETIN BOARD FOR COMPUTER ACCESS
American Phytopathological Society has established a computer
bulletin board (bb) that is in operation 24 hours every day. The
board can be accessed via telephone modem with any Hayes compatible
300-2400 baud modem. The bb will help APS economize since the
preliminary program for the APS Annual Meetings will not be pub-
lished in the July issue of Plant Disease but will be available to be
downloaded from the bb. The number for connecting is 612/454-7661
Phytopathology News 1991:25:62
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INTERNATIONAL PERSPECTIVE
******************************************
CANADA DEVELOPS BACTERIAL DISEASE NETWORK
Canadian research networks encompass 15 scientific disciplines. Five
involve biological projects. One of these, The Canadian Bacterial
Disease Network (CBDN) is devoted to microbiology.
The director, Robert Hancock, of University of British Columbia,
asserts that the network will aim to enhance unique collaborative re-
search among its members at universities and in government and to
develop mutually beneficial links with the private sector.
The Canadian government is providing $18 million in seed money over a
4 yr period to get the network off the ground. Matching funds are
coming from the provinces where the networks are situated. The
researchers are studying the diseases of both plants, and animals,
including fish.
The details of ownership and intellectual property are now being
worked out but basically ownership will remain with the employment
-5-
center [institution] where the work is done with proportional
ownership allocated to other cooperating groups.
***********************************************
SPECIAL: HOW-TO SECTION
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WORD PROCESSOR DOUBLES AS A CULTURE COLLECTION RECORD MANAGER
THIS STEP-BY-STEP GUIDE LETS YOU
TURN WordPerfect INTO A DATABASE MANAGER
If you would like to extract order from the apparent chaos of culture
collection records kept in notebooks and on loose sheets of paper;
yet you resist spending the funds for a database management
application, try using your word processor. Most of the functions
necessary for cataloging, sorting and printing selected records can
be managed fairly simply with WordPerfect or Microsoft Word. An added
perquisite is that you don't have to learn another computer
application, just add to your knowledge of an existing one. If you
already know the rudiments of editing and moving the cursor around,
you are well up the slope of the learning curve. As examples, we'll
use WordPerfect 5.1 to develop two types of databases and allude to a
third more sophisticated form.
Typically, researchers maintain information on any or all of the
following: taxonomy (genus, species, some sub-species category such
as pathovar, biovar, race), strain designation, some kind of ID
number for this strain for this particular laboratory, host,
geographical location of isolation, media, storage location, source
(if from another laboratory), and literature citation. If you've
been keeping records on a paper form that contains details unique to
each strain, you may already have established a format for data
collection. (A field in database jargon is each attribute or
characteristic that you will store for each organism. A record is
the set of all fields for each organism. There is one record per
culture; there may be many fields per record.) Decide which fields
you want to index for each culture. You can pare it down later if
practicality precludes maintaining the full data set. The amount of
data you must store for each record will determine the complexity
required to handle it.
DATA MANAGEMENT FOR THE MINIMALIST. If you can format your
collection data into columns with one line for each culture (Fig 1) a
line-oriented database will perform adequately. While one record can
be only one line long, you can feel free to use any formatting
maneuvers to get more characters on each line. Change your font size
to 27 characters per inch (cpi) and set your margins to 0 if your
printer can accommodate that and you can get a theoretical 230
characters across an 8.5 in page. Change to landscape orientation if
your printer can print sideways. Or define a special page size to be
20 inches wide if you are not likely to ever need to print out a
-6-
report from the full database.
We'll keep it simple. Set the margins to 0.5 (SH-F8 L M). Use Elite
(12 cpi) in portrait (standard 8.5 x 11 inch page) orientation. Set
the tabs stops so that the data will be arranged in columns with ONE
tab between each field. (Fig 1)
--------------------------------------------------------------------
# GENUS SPECIES STRAIN SOURCE STORAGE
------------------------------------------------------------
1 C. pasteurianum mx123 Transylvania lyophil
2 B. japonicum usda123 Beltsville, MD fridg2
3 Cl. michiganensis x10-a6 Ann Arbor, MI fridg1
4 R. meliloti usdax-19 Corvallis, OR dmso(-80)
5 E. coli k12(956) Bill's lab fridg2
6 S. cerevisae b46 FJH's collection fridg1
7 B. japonicum usda138 Un. Wisconsin fridg1
8 R. meliloti d142 Nairobi fridg2
Fig 1. Unsorted collection data
-------------------------------------------------------------------
Set the tab stops at the beginning of the first line by first
clearing the old default tab settings (SH-F8 L T CTRL-END). Move the
cursor to the position where a tab should be and type "L". You can
with a little trial and error, figure out where stops need to be. If
this isn't quite right, you can "tune them up" by going to the tab
screen (SH-F8 L T) then placing the cursor on the errant tab stop,
then using CTRL and the left/right arrow to adjust.
Type in the table of data with one tab between fields and a hard-
return (carriage return/linefeed) at the end of each line. You've
now built a database. Save it. Save it again with another name so
that should an inadvertent keystroke wipe it out, you've still got
the original.
You'll no doubt want to sort this on several of the fields. Probably
a useful format would be to sort alphabetically first on genus. If
it's a tie, then sort on species. If that, also, is a tie then on
strain. If two cultures are the same genus,species and strain then
sort on accession number (#). We want to sort on the field numbers 2,
3, 4 and then 1 in our example.
WordPerfect could be brighter. It can't tell the headings at the top
of the page from important stuff. If we sort without telling WP
where to start, it will try to sort the headings, lines, spaces and
other trivia. To avoid this we have to select or block the portion
of the table to be sorted. Place the cursor on the first entry at
the left margin. Block the text to the end of the table (ALT-F4 HOME
HOME DOWN-ARROW). Select the sort operation (CTRL-F9) and the screen
is split with the lower half showing parameter selection areas for
sort fields and options at the bottom of the screen. If 'sort by
line' does not appear at mid-screen, select 'type' (T) and then
select 'line' (L).
-7-
Before WordPerfect can sort or select records you must designate
which of the fields (columns) will be used for sorting or selecting.
You do this by selecting the keys (K). The cursor appears in the
first key parameter area. 'a' specifies that we want an alphanumeric
sort ( b sorts before c, 4 before 34). We want genus (field 2) to be
our first key so enter 2 in 'field' and leave 'word' set to '1' since
we want the sort to be performed on the first word of that field.
Use RT-ARROW to move to key 2. Similarly specify alphanumeric sort,
field 3 and word 1. RT-ARROW to key 3; specify 'a', '4' and '1'.
We want to use accession number as our fourth key. With an
alphanumeric sort the first character of each of two fields are com-
pared. I.e., in sorting 2 and 155, 2 is sorted after 1 (the first
character of 155) so the sorted order would be 155 then 2. For this
reason we specify a numeric sort in which the numeric values of the
fields are compared. For the forth key, specify 'numeric', field 1
and 1st word. The lower portion of the screen should look like
Fig 2.
---------------------------------------------------------------
Key Typ Field Word Key Typ Field Word Key Typ Field Word
1 a 2 1 2 a 3 1 3 a 4 1
4 n 1 1 5 6
7 8 9
Select
Action Order Type
Sort Ascending Line sort
1 Perform Action; 2 View; 3 Keys; 4 Select; 5 Action; 6 Order; 7
Type:
Fig 2. Entry of sort parameters
---------------------------------------------------------------
Now Perform the sort (P). The sorted table with the headings at the
top will replace the original on your screen (Fig 3). If something
strange happens, you now have your backup copy under a different name
to try again.
---------------------------------------------------------------
# GENUS SPECIES STRAIN SOURCE STORAGE
---------------------------------------------------
2 B. japonicum usda123 Beltsville, MD fridg2
7 B. japonicum usda138 Un. Wisconsin fridg1
5 C. pasteurianum mx123 Transylvania lyophil
3 Cl. michiganensis x10-a6 Ann Arbor, MI fridg1
1 E. coli k12(956) Bill's lab fridg2
8 R. meliloti d142 Nairobi fridg2
4 R. meliloti usdax-19 Corvallis, OR dmso(-80)
6 S. cerevisae b46 FJH's collection fridg1
Fig 3. Sorted collection info
-----------------------------------------------------------------
-8-
You can now print it as a well formatted catalog of your accessions,
save it to disk or perform any of several different operation on your
collection database.
For example, you could take this master list and select only the
cultures in fridg2. Block the table starting from the first record
in the table. Don't block the header or empty lines. Select 'sort'
(CTRL-F9). Select the 'keys' (K) option and arrow right to 'key 5'.
In the key 5 parameters area enter 'a' for alphanumeric, '6' for
field (the "STORAGE" field) and 1 for 'word'. (Fig 4) Exit with F7.
To select your records enter 'S' to set the selection criteria.
Specify key5=fridg2.
---------------------------------------------------------------------
Key Typ Field Word Key Typ Field Word Key Typ Field Word
1 a 2 1 2 a 3 1 3 a 4 1
4 n 1 1 5 a 6 1 6
7 8 9
Select key5=fridge2
Action Order Type
Sort Ascending Line sort
+(OR), *(AND), =, <>, >, <, >=, <=; Press Exit when done
Fig 4. Selection of Records
-----------------------------------------------------------------------
The result of the combined sort and select operations are a listing
of all the cultures stored in fridg2 (Fig 5).
------------------------------------------------------------------
# GENUS SPECIES STRAIN SOURCE STORAGE
-----------------------------------------------------
2 B. japonicum usda123 Beltsville, MD fridg2
1 E. coli k12(956) Bill's lab fridg2
8 R. meliloti d142 Nairobi fridg2
Fig 5. Results of combined sort and select
-------------------------------------------------------------------
You could also have used any of the logical operators at the bottom
of the screen, or included more than one key in the selection
criteria (key1=B. * key5=fridg2 will give you all the organisms with
B. as the genus abbreviation AND stored in refrigerator 2. Don't
forget the '.' in the key1 criteria because 'B' is not the same as
'B.') If you had included 'DATE TRANSFERRED as one of your fields,
you could have, by choosing suitable selection criteria, gotten a
list of all cultures requiring transfer.
Remember all the power you have with your standard WordPerfect
editing capabilities. You can use search (CTRL-F2 or SH-F2) to find
a specific word or number any where in the table. Or you can use a
global search and replace to modify a string of text anywhere in the
table. This might be useful for updating a column for DATE
-9-
TRANSFERRED. Word perfect makes it possible to copy, delete or move
columns of data so if you keep all your in-house data in one large
and rather unwieldy table. It is relatively easy, then, to copy the
file under another name and delete information in order to print an
easy-to-read subset of the data for general use.
MORE DETAIL. If you find that a comment of just a few words is not
sufficient to describe aspects of an accession and you would like to
include a paragraph of specifics about each culture -- no problem.
This could be detail that is not available for all organisms, or any
descriptive or anecdotal information that is important, but that may
not be useful for sorting or selecting from the database.
WordPerfect allows you to define a paragraph-oriented database. A
paragraph (for WP database purposes) is delimited by two consecutive
hard-returns. Lines make up the paragraph and end with a single
hard-return. These may appear longer than a line on your screen.
All the information is divided into lines rather than columns with
one record per paragraph. This added freedom comes at a price since
it is more challenging to organize, sort or manipulate the data.
We can, however, use a hybrid of the line oriented and paragraph
oriented database to achieve a compromise between the relatively
free-form paragraph database and the easily organized line database.
A record can be comprised of one line which is broken into columns of
fields (like or line oriented database, above) for sorting and
selecting purposes and a second line that is a long piece of text for
descriptive material. Let's add a paragraph of textual data for each
of the cultures in our line-sort example. (Fig 6). We use an indent
on the second line for cosmetics. Each record is separated by two
hard-returns.
The first line is still highly structured. We can use this for
sorting and selection functions. The second line contains annotation
and description for the culture. Each record should contain the same
number of lines (hard-returns). Let's sort the database by genus,
species, strain and accesssion number again. First, block the text
for the sort and exclude headings, titles, lines, etc. Go to the
sort menu (CTRL-F9). If the header at mid-page doesn't say "Sort-by
Paragraph", change it by selecting the sort type by choosing 't' and
the 'p' for paragraph. You'll notice that the screen has more
features for each key than it did when we were sorting single lines.
Now we can specify which line within each record the key occurs in.
In our case, genus, species, strain and accession number all occur in
the first line with genus as the second field, species as the third
field, strain as the forth and accession number as the first. To set
this up, select keys ('k'). The cursor will be in the space for the
first key, genus. Enter a for alphanumeric sort. Enter 1 for the
first line. Enter 2 for 'second field'. Enter 1 for first word of
second field. ARROW-RT and fill in the spaces for the other three
keys similarly to the line sort we set up in the first example (Fig
7). F-7 to exit and 'p' to perform the action.
-10-
------------------------------------------------------------------
# GENUS SPECIES STRAIN SOURCE STORAGE
--------------------------------------------------
1 E. coli k12(956) Bill's lab fridg2
Used for class room demonstrations of antibiotic resistance.
This bug also carries a plasmid with no known function. Do not
store in the freezer. Can utilize gamma-emissions from
radionuclides as sole energy source.
2 B. japonicum usda123 Beltsville, MD fridg2
Produces nodules of cantaloupe size on all cultivars of soybean
3 Cl. sepedonicum x10-a6 Ann Arbor, MI fridg1
Etiological agent of Squishy Potato Syndrome (CPS).
4 R. meliloti usdax-19 Corvallis, OR dmso(-80)
Non-nodulating mutant of highly effective non-infective strain.
5 C. pasteurianum mx123 Transylvania lyophil
Isolated from nocturnal habitat of lycanthrope. Lower than
normal growth temperature. Prefers hemoglobin in medium.
6 S. cerevisae b46 FJH's collection fridg1
Produces a rich heady fragrance of aldehydes and butyric acid.
7 B. japonicum usda138 Un. Wisconsin fridg1
Contains Tn 5 insertions in nif region.
8 R. meliloti d142 Nairobi fridg2
Strain is infective, effective, defective and affective.
Fig 6. Unsorted info for paragraph sort
----------------------------------------------------------------------
----------------------------------------------------------------------
Key Typ Line Field Word Key Typ Line Field Word Key Typ Line Field Word
1 a 1 2 1 2 a 1 3 1 3 a 1 4 1
4 n 1 1 1 5 6
7 8 9
Select
Action Order Type
Sort Ascending Paragraph sort
1 Perform Action; 2 View; 3 Keys; 4 Select; 5 Action; 6 Order; 7 Type:0
--------------
Fig 7 Parameter selection for paragraph sort
------------------------------------------------------------------------
-11-
The sort is done (Fig 8).
---------------------------------------------------------------
# GENUS SPECIES STRAIN SOURCE STORAGE
------------------------------------------
2 B. japonicum usda123 Beltsville, MD fridg2
Produces nodules of cantaloupe size on all cultivars of soybean
7 B. japonicum usda138 Un. Wisconsin fridg1
Contains Tn 5 insertions in nif region.
5 C. pasteurianum mx123 Transylvania lyophil
Isolated from nocturnal habitat of lycanthrope. Lower than
normal growth temperature. Prefers hemoglobin in medium.
3 Cl. sepedonicum x10-a6 Ann Arbor, MI fridg1
Etiological agent of Squishy Potato Syndrome (CPS).
1 E. coli k12(956) Bill's lab fridg2
Used for class room demonstrations of antibiotic resistance.
This bug also carries a plasmid with no known function. Do not
store in the freezer. Can utilize gamma-emissions from
radionuclides as sole energy source.
8 R. meliloti d142 Nairobi fridg2
Strain is infective, effective, defective and affective.
4 R. meliloti usdax-19 Corvallis, OR dmso(-80)
Non-nodulating mutant of highly effective non-infective strain.
6 S. cerevisae b46 FJH's collection fridg1
Produces a rich heady fragrance of aldehydes and butyric acid.
Fig 8. Sorted info ready to print
-----------------------------------------------------------------
Once again, don't forget the normal, search, find and replace, and
editing features found in WordPerfect. While you can't sort or
select for free text in the second, annotation line, you can search
for any word (ie. soybean) with F2 to initiate the search function.
You are not limited to only two lines in each paragraph. If you
choose, you can have a second line of fields similar to the first, as
long as each record has the same number of lines. If separated with
tabs, in a structured fashion, these data can be used as well for
sort or selection. If data is missing, put in an empty line (only a
-12-
hard-return) or empty field (just a Tab). The records need only to
be consistent.
MERGE SORT. There is a third, and vastly more sophisticated, data-
base management scheme that allows maximum versatility in formatting
of your printouts. The merge sort not only allows flexibility in
data organization, but, by setting up a template ( a primary merge
file) which designates where on a page each field will be printed,
with formatting, font sizes and characteristics, lines, underlining,
titles, etc. can print out attractive cataloging of your collection.
Further, you can make the fields and records as large as you like,
without regard for page size, and when it comes time to print, you
can select only those fields that are relevant for the type of index
or catalog you're developing. WordPerfect Merge files can have a
variety of macro commands applied to them, and with WordPerfect's
macro language, you can develop full data entry and print out
capability.
The setting up of the merge files, and the sorts and selections is a
little more complex than we can develop in this newsletter. If there
is sufficient demand for this type of information, we can make it
available in a future Newsletter feature. There is a bounty of
excellent WordPerfect Books available. One that we, at MGD have used
as a reference both in setting up the Microbial Germplasm Database,
Catalog of Culture Collections and MICROBIAL GERMPLASM DATA NET is
Using WordPerfect 5.1, published by QUE corporation.
Don't be timid about using the power already built into your word
processor as a database management tool. Many office applications
such as address lists, mailing lists and form letters incorporate
aspects of databases, so check these sections in your manuals. It
may be all the database management system you ever need. Should your
needs expand, however, its an easy move, requiring almost no data
reentry, once your information is organized, to a full fledged
database management application such as dBase, Foxpro, or Paradox.
************************************************
DATABASES AND CATALOGS
************************************************
DATABASE OF PLANT VIROLOGISTS NOW ON DISK
The Plant Virologist Specialty Program is an independent program
which contains information gathered from about 80 plant virologists
in North America by the Virology Committee of the American
Phytopathological Society. Each scientist has listed the virus
groups, commodities, and techniques with which he/she is familiar.
Also, each scientist has included a list of materials which he/she is
willing to share with colleagues. These materials include virus
isolates polyclonal antisera, monoclonal antibodies, cDNA clones,
insect vectors, and host plant seeds.
The software must have 640 kilobytes of internal RAM on a PC
compatible machine. The disk drive must be a 1.2 megabyte 5.25 inch
floppy drive, a 1.44 megabyte 3.5 inch floppy drive, or a hard drive.
-13-
A hard drive is preferred because of the large amount of data which
the program must read.
The program can be searched by one criterion (eg. a particular virus)
or by a combination of criteria eg. a particular virus and a partic-
ular host plant). The output list of names can be sent either to the
screen or to a printer. The user also can access all of the
information on any scientist included in the program. Finally,
mailing labels can be generated from the program, and the scientists'
telephone numbers, and some EMAIL and FAX numbers, also are included.
For further information or to order the Plant Virologist Specialty
Program, contact Dr. Cleora J. D'Arcy, Department of Plant Pathol-
ogy, University of Illinois, 1102 S. Goodwin Ave., Urbana, IL 61801
U.S.A. To order the program send a check or money order for $25 US
made payable to _The University of Illinois_ and state disk size.
GERMPLASM REPOSITORY PROVIDES CATALOGS
The National Clonal Germplasm Repository in Corvallis, Oregon houses
genetic resources of small fruit, hazelnuts, pears, mints, hops and
several other temperate fruit crops of lesser economic importance.
This plant germplasm is generally distributed to researchers as
clonal propagules or as seed. Informative catalogs of available
accessions are hot off the press. To receive a catalog or
information about the Germplasm Repository, contact the Curator,
National Clonal Germplasm Repository, 33447 Peoria Rd. Corvallis, OR
97333. Voice Phone (503)757-4448, FAX (503)757-4548. Please specify
crop or crops of interest when requesting catalogs.
NEW CATALOGS AVAILABLE ON DISK
The National (United Kingdom) Collection of Yeast Cultures and the
National Collection of Food Bacteria have released their latest
catalogs on disks formatted for either IBM or Macintosh. The
catalogs can be browsed or searched for specific cultures or any text
that appears in a record or group of records. Both catalogs are
available on one disk. The catalogs are available in printed form as
well and are sold individually.
NCYC & NCFB Online provides both catalogs online, as well as a
probabilistic identification program for yeast (COMPASS), a handbook
and unlimited usage for registered users.
Prices are NCYC Catalog, 15; NCFB Catalog, 15; Floppy plus both
hardcopies, 30
Natl. Coll. Yeast Cultures | Natl. Coll. Food Bacteria
AFRC Inst. Food Research | AFRC Inst. Food Research
Colney Ln, Norwich, NR$ 7UA, UK | Shinfield, Reading, RG2
9AT, UK
-14-
PLANT VIRUSES & ANTISERA CATALOG FROM ATCC
--A WELL DONE REFERENCE ON DISKS
The sixth edition of this work edited by L.L. McDaniel and E.L.
Emerson is available now from ATCC.
The plant virus collection of ATCC dates back to 1951 when it was
established following a recommendation from a Subcommittee on Virus
Type Culture Collection of the American Phytopathological Society
(APS). Since, at that time, cultures could not be stored at ATCC,
individual researchers maintained, prepared and shipped the cultures
throughout the US. In 1967 ATCC began to collect and preserve im-
portant plant viruses with the assistance of USDA and APS. In 1970
antisera accessioning into the Plant Virus Collection began.
The Plant Virus Collection is guided by a 37 member advisory board
made up of scientists from both APS and ASV.
Scientists may recommend additions to the collection or may donate
characterized specimens. There is no charge to the scientist making
the donation unless the deposit is for patent purposes.
ATCC is experimenting with releasing catalogs on disks for use on
PC's. The release we received at MGD would be a useful reference
work for virologists. It is easy to use, full featured and will make
searching for information on strains much more efficient. Searches
can be performed with logical operators (AND, OR, EXCLUSIVE OR, NOT)
and selected records sent to your printer (configurable for a wide
range of printers).
Contact: Publications Department, ATCC
12301 Parklawn Drive, Rockville, MD 20852
VOLUME ON MYCOPLASMA INFECTIONS OF PLANTS RELEASED BY NTIS
The National Technical Information Service, Springfield, VA has re-
leased a publication, Plant Diseases: Infections by Mycoplasma-like
organisms. The book is a database of citations from March of 1978 to
March of 1990.
****************************************
COMPUTER NEWS
****************************************
ONLINE SEARCHING OF LIBRARY CATALOGS
Many university libraries are now connected to INTERNET, the national
high-speed computer network that links government, academic and some
commercial sites. Now, you can search the card catalogs of
participating libraries at other institutions, throughout the United
States. You can then request a reprint or reference through inter-
library loan. A non-trivial benefit of these connection is the
capability of finding some esoteric bit of bibliographic information
-15-
needed to complete a reference when it is not in your local library
and it's 3 am on the day of a deadline.
The major academic libraries of the country are accessible.
The list of participating libraries is quite long but can be obtained
by sending e-mail to:
LISTSERV@UNMVM
The text should contain the message, GET INTERNET LIBRARY
An ascii copy of the list will be e-mailed to you. You can use
anonymous ftp (file transfer protocol (program)) to obtain copies of
this list from two sites, NIC.CERF.NET in directory cerfnet_info and
ARIEL.UNM.EDU in directory library.
MS-DOS 5.0 READY TO GO
PC WEEK's lab test of the new release of the ubiquitous OS from
Microsoft demonstrates that for once, the software lives up to the
hype. Improved memory management, new functions, bundled utilities
and graphical shell provide a valid reason to upgrade.
Many of the utilities bought separately from Peter Norton and PC
Tools are included as part of the loosely integrated package. There
is now an undelete and an unformat as part of DOS. 'EDIT' calls up a
full screen editor (a real blessing if you've ever tried to change
your autoexec.bat file with edlin). 'LOADHIGH' and 'DEVHIGH' will
load programs and device drivers into that vast wasteland above 640K.
Part of DOS 5.0, itself is loaded high. There is also a quick FORMAT
that can reformat a 1.2 Mbyte disk in 9 seconds. If you've spent
time fumbling through the abstruse DOS manuals looking for a little
help with commands you'll appreciate the command line help. Issue a
DOS command with a /? after it and you'll get you an explanation of
the command.
The real difference is in the memory management for the 286 and up
users. The new operating system, by loading drivers, resident
programs and Windows high, can give you to up an additional 40K to
60K of space for Windows applications. This is critical to give you
the breathing room necessary to run large applications like Paradox.
In short, its an upgrade that lives up to it ads and can make
noticeable differences in the performance of your machine. from material in PC Week June 10, 1991
APPLE, IBM EXPLORE CROSS LICENSING: IS THE COLD WAR OVER?
The two computer manufacturing titans initiated summit talks to
explore sharing some technology and signing licensing agreements with
each other for portions of their software and hardware. On the table
are operating system and object oriented technology and IBM's RISC
(Reduced Instruction Set Computer) technology.
IBM is also after the license to the MAC GUI (Graphical User Inter-
face, that is still being hotly contested in court with Microsoft)
-16-
for its OS/2 2.0 and could involve some royalties or technology
trading to Apple. Further, IBM is also interested in adopting
multimedia standards supported in Apple's QuickTime. Technology
trading could result in much greater interoperability for the rest of
us and greatly facilitated networking.
It's not professional camaraderie that draws the two together. Many
speculate that it's a common desire to decrease the clout of
Microsoft Corp. which is a dominant influence on the software side of
both computer giants. Apple may be undergoing philosophical changes
resulting in a move away from being a primary supplier of hardware
and toward becoming a supplier of operating systems. If Apple be-
comes a vendor of operating systems, it will be positioning itself to
go head to head with Microsoft. OS/2 2.0 might be able to edge into
the Windows market for MS-DOS machines if it can capitalize on some
very Mac-like features in its Workplace Shell. While Windows and OS/2
2.0 may look alike, applications likely will not be compatible.
from material in PC WEEK June 10, June 17, June 24, 1991
IBM READIES WYSIWYG WORD PROCESSOR
IBM in one more move to diminish users dependency on Microsoft
applications has debuted it own word processor. Signature, a full
featured, 'What You See Is What You Get' application was unveiled
before heavy users at the American Newspaper Publishers Association
Convention in Las Vegas the week of June 10. Users can edit text and
graphics in WYSIWYG mode. IBM says it will be ready to ship the
third quarter of this year. PC WEEK June 17, p1
******************************
NEW PRODUCTS
******************************
ANTISERA AVAILABLE FOR APPLE MOSAIC VIRUS
AND PRUNUS NECROTIC RINGSPOT VIRUS
The ATCC has available several monoclonal antisera for detection of
ApMV and PNRV. The antisera are provided as ascitic fluid. The ApMV
is available only in 70 l amounts while the PNRV can be gotten in 70
and 1 ml amounts. Descriptions of these antisera can be found in
Phytopathology 74:367, 1984. Contact ATCC sales department.
PLASMID DRAWING SOFTWARE
The Gene Construction Kit plasmid drawing program allows manipulation
of actual DNA sequences through a graphical interface. Users can
define the thickness, pattern, shape, direction and color for each
DNA segment; automatically monitor and adjust DNA fragment ends
during cutting and pasting; plan and track complex construction pro-
jects; track the history of any given DNA segment and show
alternative views; display any generation (view) for any segment of
DNA in a construct, even multiple generations in the same construct;
cut and paste segments from one construct to another; cut and paste
linkers and adapters form lists into constructs; and many more
features. Textco, 27 Gilson Rd, West Lebanon, NH 03784.
-17-
PLEASE TAKE A FEW MINUTES TO FILL IN THIS QUESTIONNAIRE.
IT CAN BE FILLED IN WITH YOUR SYSTEM'S TEXT EDITOR AND SENT
BY REPLY E-MAIL, OR DOWNLOADED, PRINTED AND SENT BY SURFACE MAIL.
( DATA ENTRY POINTS ARE MARKED BY '>'. YOU CAN SAVE TIME
BY USING YOUR EDITOR'S 'FIND' TO JUMP FORWARD TO EACH BLANK
TO BE COMPLETED )
DATA FROM ALL COLLECTIONS ARE IMPORTANT IN
MGD, REGARDLESS OF SIZE.
addresses are:
e-mail
hanusj@bionette.cgrb.orst.edu on internet
Surface mail
F. Joe Hanus
Microbial Germplasm Database
Dept. of Botany and Plant Pathology
Oregon State University
Corvallis, OR 97331, USA
_________________________________________________________________________
MICROBIOLOGICAL AND SUBCELLULAR
GERMPLASM COLLECTIONS
NAME>
DEPT>
INSTITUTION>
ADDRESS>
CITY> STATE>
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 in your collection?
> Fastidious Procaryotes
> Bacteria
> Fungi
> Endo/Ecto-mycorrhizae
> Protozoa
> Algae
> Nematodes
> 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,
> No
> Yes (Which group?)
3. What is the principal research interest of your laboratory?
>
4. How many unique sequenced genes or DNA segments (fragments) are
included in your collection?
>
5. What proportion of your collection is used for:
> Research
> Teaching
> Other
6. Do you receive funds specifically for the support of your collection?
> Yes
> No
7. Do you provide cultures to other scientists?
> Yes
> No
Do you charge?
> Yes
> No
8. a. Do you maintain documentation for each accession?
> Yes
> No
b. In computer format?
> Yes
> No
9. If you answered NO to 8b; a. Are you interested in developing such
a system?
> Yes
> No
b. Constraints against computerizing?
> time/labor
> funding
> no computer
> not needed
10. If you answered YES to 8b:
a. Type of computer
> Macintosh
> IBM compatible
> Other (specify please)
b. What program do you use to catalog your collection?
>
c. Is your computer used for telecommunication?
> Yes
> No
If yes for what purposes?
> electronic mail
> local area network
> bibliographic/genetic databases
> national networks (internet, bitnet)
other(please specify)>
11. 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.)
>
12. a. Would you find a directory of laboratories compiled
from this survey useful?
> Yes
> No
b. If online?
> Yes
> No
c. What uses would such a directory have in your work?
>
13. PLEASE LIST NAMES OF COLLEGUES AT YOUR INSTITUTION WHO
MAINTAIN COLLECTIONS. (OR GIVE THEM A COPY OF THIS QUESTIONNAIRE)
>
>
>
>
>
>
>
14. HOW DO YOU WANT THE NEXT NEWSLETTER SENT?
e-mail>
surface mail>
If you want to receive the hardcopy by surface mail,
include a complete mailing address.
>