submissions to new Mollusc Molecular News WebSite
Elizabeth Boulding
Mollusc Molecular News Volume 4 (submissions).
I am compiling information for the fourth issue of the
Mollusc Molecular News, a hard copy newsletter aimed at
researchers working with mollusc DNA or RNA. As you may
recall this newsletter was mailed by regular Canadian postal
service to laboratories around the world free of charge. If
you have lost your copy not to worry.
As of today volume 3 of the Mollusc Molecular News
will be available on the WORLD WIDE WEBB at:
http://www.uoguelph.ca/zoology/mollusc/
In addition I am compiling information for the fourth issue of
the Mollusc Molecular News which will be available Spring 1998.
This newsletter is meant to complement the bionet/USENET newsgroup
group: MOLLUSC-MOLECULAR-NEWS/bionet.molbio.molluscs.
The newsletter is most useful and most fun when all
laboratories participate. Please send your contributions
to the newsletter to my PERSONAL email address by March
1st, 1998:
boul...@uoguelph.ca.
Ideally the information for EACH SECTION should be in
a SEPARATE EMAIL MESSAGE with the subject heading of your
message indicating which section it is for. If all
contributions are submitted in the CORRECT FORMAT my
secretary can assemble the newsletter and you won't have to
wait until I have time. But if you can't figure out the
formats, send in your contributions anyway and I will edit
them for you.
Shortly after March 15th I will post a rough draft of
the newsletter on MOLLUSC-MOLECULAR-
NEWS/bionet.molbio.molluscs so you can check for your
entries for errors. To protect the privacy of the
researchers, I will not electronically post the addresses,
telephone numbers, fax numbers, and email addresses from
the Directory of Researchers section.
Please note the correct format for a section by
studying the example. Use text characters only (ascii).
Put a hard carriage return after every 80 characters or I
may not receive all of your message. Use an underline
character in front of all genus and species names so we can
convert them to italics (e.g., _Mytilus _edulis).
The sections of the newsletter are:
I) Research News
This should be informally written in a single
paragraph of 200 words or less. The focus should be on
work not yet published or in the planning stages. We will
publish exactly what you send us so you might want to use a
spell checker or have an associate read it over. Please
give the class and family of the group(s) of molluscs you
work with. Use block capitals for the surnames of the
people in your group. Do NOT give institutions or
addresses as these will be listed in the Directory of
Researchers section. For example:
BOULDING, Elizabeth G. I am interested in rapid
evolutionary change in wild populations caused by changes
in local selective pressures. The response to local
selective pressures can be constrained by gene flow from
adjacent populations. To estimate gene flow I use
restriction analysis of DNA fragments amplified with PCR.
I also use direct sequencing of PCR fragments to
investigate the molecular systematics of recently diverged
species. My laboratory is currently working on _Littorina
spp. (Gastropoda, Littorinidae) and _Dreissena spp.
(Bivalvia, Dreissenidae).
II) PCR primers
My goal is to compile about 30 pairs of PCR
primers that are useful with a wide variety of mollusc
groups. Once I have achieved this I plan to arrange for a
commercial company to synthesize a low cost kit containing
small amounts of all 30 primers. The insect molecular
group, bug...@sfu.ca, has just done this for insect mtDNA
primers. Please note that I have no association with any
company and am only after a source of inexpensive primers
for my own laboratory.
You would normally contribute to both of two separate
databases for PCR primers. The first is the "Primer
Sequence Database" which has the primer names, primer
sequences, and the original references. The second "Primer
Pairs Database" lists all pairs of primers that have been
used together, the DNA fragment they amplify, and the
species they have been used on. You can contribute a
primer that you have designed for molluscs or one that
somebody else has designed for some other phylum. In the
hypothetical examples below you can see that Banks has
contributed three primers he designed to the Primer
Sequence Database. He then has contributed three entries
to the Primer Pairs Database documenting his attempts to
amplify DNA from three species with various pairs of his
primers. In contrast Boulding has contributed two primers
designed by Kocher to the Primer Sequence Database (She
contributed them because she wasn't sure whether they were
already in the database). She then has contributed two
entries to the Primer Pairs Database about her attempts to
amplify DNA from two different species with Kocher's pair
of primers.
Submitted entries for both databases should consist of
the appropriate number of lines with a hard carriage return
after each line. Please leave a blank line for any
information that not relevant and two carriage returns
between entries.
Entries for the Primer Sequence Database should have
the following format:
1) the name used for the primer in original publication (up
to 20 characters).
2) the surname of the person who designed the primer (up to
20 characters).
3) the primer sequence (up to 80 characters). Please give
the sequences 5' to 3' leaving a space every three
nucleotides and using lower case letters (g, a, t, c, i =
inosine). For degenerate primers use parentheses with
commas between the alternative nucleotides for that
position. For example agtc(a,t) would mean a mixture of
50% agtca and 50% agtct.
4) literature citation of the original publication in the
format used by Nature, but omitting all authors names
except the surname of the first author. Use two lines of
up to 80 characters each. Leave the second line blank if
the citation fits completely on the first line.
Example begins on the following line:
12sa-L
Kocher
aaa ctg gga tta gat acc cca cta t
Kocher 1989. Proc. Natl. Acad. Sci., U.S.A. 86:6196-6200.
12sa-H
Kocher
gag ggt gac ggg cgg tgt gt
Kocher 1989. Proc. Natl. Acad. Sci., U.S.A. 86:6196-6200.
16SSSPC1
Banks
act cag aaa ggt tag gct tac
Tsweskison-Fullernamethanreasonable 1993. Mol. Mar. Biol.
Biotech. XX:XXX.
16SOA
Banks
ccg gcc gcc cta gcg tga ggg
Tsweskison-Fullernamethanreasonable 1993. Mol. Mar. Biol.
Biotech. XX:XXX.
16SOB
Banks
att agc ctg tta tcc ccg gcg
16SOA (Banks) 16S ribosomal gene 0.5 kb
Tsweskison-Fullernamethanreasonable 1993. Mol. Mar. Biol.
Biotech. XX:XXX.
:example ends on the previous line.
For the second database (Primer Pairs Database) please
list all pairs of primers you have used to try to amplify
DNA in molluscs. I am interested in hearing about which
pairs of primers have amplified DNA from your group of
molluscs and which pairs of primers have failed to amplify
DNA from your group of molluscs. Entries for the Primer
Pairs Database should have the following format:
1) the names and designers of two primers that you use
together (up to 80 characters).. Make sure entries for
these primers have been submitted to the first database
(Primer Sequence Database) under the same name. For
example Boulding made sure that the primers 12sa-L (Kocher)
and 12sb-H (Kocher) were both in the Primer Sequence
Database before using them below in the Primer Pairs
Database.
2) the identity and size (in kilobases) of the fragment you
tried to amplify (up to 80 characters).
3) the species (including phyla other than mollusca) whose
DNA you have tried to amplify with this pair of primers (up
to 80 characters). Please do a separate entry for every
species you tried for those primer pairs.
4) the annealing temperature (for 30 seconds?) and
extension time (at 72 oC?) you used (up to 80 characters).
5) type either SUCCESSFUL or FAILED; if reporting a failed
amplification please put in brackets the species you used
as a positive control (up to 80 characters).
6) The surname and initials of the person who tested the
primer on molluscs (up to 80 characters).
Example for Primer Pairs Database starts on the following
line:
12sa-L (Kocher) and 12sb-H (Kocher)
12S ribosomal gene 0.4 kb
_Patinopecten _yessoensis (Bivalvia, Pectenidae)
40 oC 30 s
FAILED (_Drosophila)
E.G. Boulding
12sa-L (Kocher) and 12sb-H (Kocher)
12S ribosomal gene 0.4 kb
_Littorina _sitkana (Gastropoda, Littorinidae)
44 oC 30 s
SUCCESSFUL
E.G. Boulding
16SOA (Banks) and 16SOB (Banks)
16S ribosomal gene 0.4 kb
_Crassostrea _gigas (Bivalvia, Ostreidae)
XX oC XX s
SUCCESSFUL
M. Banks
16SOA (Banks) and 16SOB (Banks)
16S ribosomal gene 0.4 kb
_Haliotis _rufescens (Gastropoda, Haliotidae)
XX oC XX s
FAILED (_Crassostrea _gigas)
M. Banks
16SOA (Banks) and 16SSSPC1 (Banks)
16S ribosomal gene 0.4 kb
_Crassostrea _sitkamea (Bivalvia, Ostreidae)
XX oC XX s
SUCCESSFUL
M. Banks
:example ends on the previous line.
III) Recent Papers
Please tell me about all papers published in
1994 or later or currently in press by you or your
colleagues that are concerned with mollusc molecular
population genetics, mollusc molecular systematics, or
contain reference to a DNA sequence from a mollusc. Please
use block capitols for authors surnames and standard
abbreviations for journal names. Do not include papers
listed in the third issue of the Mollusc Molecular
News (mailed out in May 1993) unless they were then in
press. For example:
KARL, S.A. and J.C. AVISE. 1993. PCR-based assays of
Mendelian polymorphisms from anonymous single-copy nuclear
DNA: Techniques and applications for population genetics.
Mol. Biol. Evol. 10:342-361.
IV) Directory of Researchers
This is kept in a database file which has the
following structure. Please send every field on a separate
line with a hard carriage return after each line. The
number in parentheses refers to the maximum number of
characters that can be stored in that field. Surname (15),
other names and title (15), address line 1 (30), address
line 2 (30), address line 3 (30), address line 4 (30), work
phone number with an "x" in front of your extension (20),
FAX phone number (20), email address (54), keywords
describing your past or current research with an underline
character in front of genus and species names (54). An
example using my address begins on the next line:
Boulding
Dr. Elizabeth G.
Dept. of Zoology
University of Guelph
Guelph, Ontario N1G 2W1
Canada
519 824 4120 x 4961
519 767 1656
boul...@uoguelph.ca
pop. genetics, systematics, _Littorina, _Dreissena
Incidentally if you wish to receive the email messages
from the mailing list MOLLUSC-MOLECULAR-NEWS you should
send a blank email message to biosci...@net.bio.net (if
you are in America and Pacific Rim countries) or a message
containing the word help to M...@dl.ac.uk (if you are
inEurope, Africa, and Central Asia). Do not contact me as
I am no longer able to subscribe or unsubscribe you.
best wishes,
Elizabeth Boulding.
editor, Mollusc Molecular News.