From owner-rapd@net.bio.net Fri Dec 01 22:00:00 1995 Path: biosci!ZOOLOGY.WASHINGTON.EDU!jnusser From: jnusser@ZOOLOGY.WASHINGTON.EDU (John Nusser) Newsgroups: bionet.molbio.rapd Subject: running AMOVA analyses Date: 1 Dec 1995 16:57:34 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 20 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Hello y'all- I am trying to analyze RAPD data with AMOVA, yet am having a very difficult time getting AMOVA to accept my data set. I suspect AMOVA may have a problem because some of my individual are clones. I've generated a Euclidian distance matrix and a distance matrix of absolute differences but AMOVA can't seem to read either of these matrices. I can use AMOVA to run the sample data set included with the program, but when i try to use it to analyze my data set all i get is a translation error or winamo10 general protection error, which makes very little sense to me. Can anyone who has used AMOVA successfully give me some suggestions? AMOVA is a great way to analyze RAPD data phenotypically, but it's driving me crazy. Thanks for any suggestions. Please send them to me directly and I will post a summary of responses. John Nusser jnusser@zoology.washington.edu From owner-rapd@net.bio.net Wed Dec 06 22:00:00 1995 Path: biosci!daresbury!not-for-mail From: Roland Koelliker Newsgroups: bionet.molbio.rapd Subject: High molecular RAPD bands Date: 7 Dec 1995 15:47:05 -0000 Lines: 33 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4a729p$hhk@mserv1.dl.ac.uk> X-Sender: rkoellik@patho1.ethz.ch content-length: 1039 Original-To: rapd@dl.ac.uk Hi netters I'm working on the genetic variability of meadow fescue using RAPD markers. After screening 140 primers I did find some suitable to my project but they all give me only bands smaller than 1600 bp. I do have the feeling, that my cycling conditions are not optimal. I'm using a Hybaid Omnigene Cycler (96 wells, microtubes). My protocoll is as follows:=20 Cycling conditions: 1x 94=B0/1'; 35x 35=B0/30', 72=B0/1', 94=B0/ 5''; 1x= 35=B0/30'', 72=B0/10' =09 PCR mix: Template 10ng PCR buffer 1x MgCl2 1.5mM dNTPs 0.1mM Polymerase 0.029 U/ul Primer 0.35uM (Operon 10mer) Total volume 21 ul Does anybody know how I could improve my cycling conditions to earn more bands above 1600 kb? Thanks for your help! Roland Roland Koelliker =20 Swiss Fed Inst Technol =20 Plant Sciences =20 ETH-Zentrum, LFW-C47 =20 CH-8092 Zurich =20 Tel ++41-1-632 4890 Fax ++41-1-632 1153 e-mail: koelliker@ipw.agrl.ethz.ch From owner-rapd@net.bio.net Thu Dec 07 22:00:00 1995 Path: biosci!daresbury!bioftp.unibas.ch!news.vub.ac.be!ben.vub.ac.be!wmoens From: William Moens Newsgroups: bionet.molbio.rapd Subject: Re: Myxomycetes (Slime Moulds) Date: Fri, 8 Dec 1995 11:23:27 +0000 Organization: Brussels Free Universities VUB/ULB Lines: 12 Message-ID: References: NNTP-Posting-Host: ben.vub.ac.be. Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII In-Reply-To: We published recently a paper (Journal of medical Mycology(1995) 5,133-139) validating a method for the preparation of fungal genomic DNA suitable for PCR and RAPD. This method has worked with 24 fungal genera covering about 200 species. Reprint can be obtained through Email or at W.Moens at Institute of Hygiene & Epidemiology Service of Biosafety & Biotechnology Wytsmanstreet, 14 B-1050 Brussels BELGIUM Fx: 322-6425292 Email wmoens@sbb.ihe.be From owner-rapd@net.bio.net Thu Dec 07 22:00:00 1995 Path: biosci!ZOOLOGY.WASHINGTON.EDU!jnusser From: jnusser@ZOOLOGY.WASHINGTON.EDU (John Nusser) Newsgroups: bionet.molbio.rapd Subject: AMOVA analysis - how to do, where to find Date: 8 Dec 1995 15:18:34 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 81 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Hello!- IUd like to thank everyone who answered me with their AMOVA replies; I had a lot of helpful suggestions. AMOVA was originally designed by L.Excoffier to analyze haplotype data, but it has been used by many to do a phenotypic analysis of RAPD data. The reference is: Genetics 131: 479-491, and itUs a good idea to look over before attempting an analysis. The most recent version of AMOVA (version 1.55) can be obtained via ftp from 129.194.113.13/ftp/comp or from http://anthropologie.unige.ch/ftp/comp. While older versions of AMOVA can be found on IndianaUs server, I do NOT recommend you use these versions. To analyze data with AMOVA, data must first be put into a distance matrix. To do this, I used PAUP (many propgram will work) to calculate a distance matrix from a data file such as the one below. 1 indicates the presence of a band, 0 the abscence of a band. The distance file will give the number of differences between individuals. Some authors will transform this matrix into a Euclidian data matrix as well. primer numbers individual1 0 1 1 1 0 0 0 1 individual2 0 1 1 0 1 0 1 1 etc The crucial step is making sure that the triagular data matrix is entered correctly. Tabs screw up the analysis, there need to be spaces before every line, and any carriage returns entered because long data matrices wrap along a few lines must be taken out. I suggest using a text editor or word processor that will show you where all the spaces and carriage returns are. The file must be saved as an ASCII text file and should look something like this: 0 1 0 2 1 0 1 9 2 0 The next step is to make your population files it should look something like this: 23 (refers to number of animals in that population) 1 3 3 1 ( the first number refers to the OTU and the second to the number of animals that shared that haplotype) Do this for each population. I saved the files as seal1.pop, seal2.pop etc Then you need to make a group file. This start out by saying 2 regions of 9 populations (so youu have 2 groups and a total of 9 populations) 1 2 3 4 5 6 7 8 9 ( this tell the program how you are going to divide the populations into groups) save this file as seal.grp You should then be ready to start the program. Some of these details will become clearer after reading the few pages of instruction that accompany the Winamova program. Apparently, AMOVA can also be used to analyze microsatellite data. I copied note from Excoffier off the server: A recent paper by Monty Slatkin (1995) has shown how to compute R_ST (a F_ST analogue) for microsatellite data. Such a statistic can be computed with AMOVA if one provides a matrix of pairwise distance between pairs of microsatellite alleles. This distance is defined as the squared difference between repeat numbers. The exact procedure on how to compute R-statistics based on several loci may be found in Michalakis and Excoffier (submitted). A copy of this manuscript is provided as a postscript file called Fst_Rst.ps on acasun1.unige.ch, directory pub/comp/win/amova Ref: Slatkin, M. (1995) A measure of population subdivision based on microsatellite allele frequencies. Genetics 139(1):457-462. Michalakis, Y. and Excoffier, L. (submitted) A generic estimation of population subdivision using distances between alleles with special interest to microsatellite loci. Genetics. Good luck. John Nusser jnusser@zoology.washington.edu From owner-rapd@net.bio.net Fri Dec 08 22:00:00 1995 Path: biosci!CS.Arizona.EDU!news.Arizona.EDU!hamblin.math.byu.edu!acs2.byu.edu!news.cuny.edu!news.sprintlink.net!newsfeed.internetmci.com!uwm.edu!reuter.cse.ogi.edu!engr.orst.edu!news.orst.edu!sslab.FSL.ORST.EDU!krutovskiik From: krutovskiik@fsl.orst.edu (Konstantin Krutovskii) Newsgroups: bionet.molbio.rapd Subject: mtDNA repeats Date: Fri, 8 Dec 1995 14:53:21 Organization: fsl.orst.edu Lines: 17 Message-ID: NNTP-Posting-Host: sslab.fsl.orst.edu X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Dear bioneters, I wonder if any regular, conservative and frequently distributed repeats or genetic elements not shorter than 15-20 bp exist in plant mitochondrial genome. I would appreciate it very much if you could help me to find any related information on this matter or recommend me papers where I can find it. Sincerely, Dr. Konstantin Krutovskii Department of Forest Science Oregon State University, FSL 077 Corvallis, OR 97331-7501, USA Phone: (503)-737-6564 (off.) or -6562 (lab.) Fax: (503)-737-1393 E-mail: krutovsk@ccmail.orst.edu or krutovskiik@fsl.orst.edu From owner-rapd@net.bio.net Fri Dec 08 22:00:00 1995 Path: biosci!PROMEGA.COM!aabdelma From: aabdelma@PROMEGA.COM Newsgroups: bionet.molbio.rapd Subject: unsubscribe Date: 9 Dec 1995 15:44:11 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 8 Sender: daemon@net.bio.net Distribution: world Message-ID: <9511098185.AA818559782@MRNA.PROMEGA.COM> NNTP-Posting-Host: net.bio.net Hi I am subcribed to this newsgroup from Egypt. I cam e to the US for a short visit. I like to unsubscribe during my stay here. My email address is mawgood@alex.eun.eg. Please let me know when you can do it. Thanks Ahmed Abdel-mawgood From owner-rapd@net.bio.net Sun Dec 10 22:00:00 1995 Path: biosci!MERCURY.UARK.EDU!DRHOADS From: DRHOADS@MERCURY.UARK.EDU ("Douglas Rhoads") Newsgroups: bionet.molbio.rapd Subject: Seek email for Naweed Naqvi Date: 11 Dec 1995 06:20:16 -0800 Organization: University of Arkansas Lines: 19 Sender: daemon@net.bio.net Distribution: world Message-ID: <2028E8655D@mercury.uark.edu> NNTP-Posting-Host: net.bio.net Sorry to bother the newsgroups but I lost my email address for Naweed Naqvi and need to contact or have this person contact me again. Please reply to drhoads@mercury.uark.edu Thanks. //========================================================\\ || Douglas Rhoads || || ||drhoads@mercury.uark.edu || Dept. of Biological Sciences|| ||drhoads@comp.uark.edu || 601 Science Engineering || ||501-575-3251 || University of Arkansas || ||FAX 501-575-4010 || Fayetteville, AR 72701 || || http://comp.uark.edu/~bioinfo/bisc.html || ==========================================================|| || My Dogma Just Got Run Over by Someone's Karma || \\========================================================// From owner-rapd@net.bio.net Mon Dec 11 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!news.dacom.co.kr!news.uoregon.edu!news.orst.edu!sslab.FSL.ORST.EDU!krutovskiik From: krutovskiik@fsl.orst.edu (Konstantin Krutovskii) Newsgroups: bionet.molbio.rapd Subject: Software to search for inverted repeats Date: Thu, 7 Dec 1995 21:19:17 Organization: fsl.orst.edu Lines: 13 Message-ID: NNTP-Posting-Host: sslab.fsl.orst.edu X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Dear Folks, Does anybody know any computer program that can search for inverted repeats of definite length in the query sequence? I would appreciate any information on this subject. Konstantin Krutovskii Department of Forest Science Oregon State University, FSL 077 Corvallis, OR 97331-7501, USA Phone: (503)-737-6564 (off.) or -6562 (lab.) Fax: (503)-737-1393 Electronic mail: krutovsk@ccmail.orst.edu or krutovskiik@fsl.orst.edu From owner-rapd@net.bio.net Tue Dec 12 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in1.uu.net!noc.near.net!das-news2.harvard.edu!fas-news.harvard.edu!fas.harvard.edu!rickles From: rickles@fas.harvard.edu (Richard Rickles) Newsgroups: bionet.molbio.rapd Subject: FENTOMOLE PROTEIN SEQUENCING Date: 13 Dec 1995 04:39:00 GMT Organization: Harvard University, Cambridge, Massachusetts Lines: 10 Message-ID: <4alld4$k20@decaxp.harvard.edu> NNTP-Posting-Host: fas.harvard.edu X-Newsreader: NN version 6.5.0 #3 (NOV) FEMTOMOLE PROTEIN SEQUENCING-Means you can identify those proteins from 2D gels and minigels! contact me at: brauer@ariad.com 617-494-0400 ex 261 for more info........ From owner-rapd@net.bio.net Tue Dec 12 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.tamu.edu!486MULLET2 From: PULANCH@bioch.tamu.edu (Paul E. Ulanch) Newsgroups: bionet.molbio.rapd Subject: Re: High molecular RAPD bands Date: Wed, 13 Dec 95 19:03:23 GMT Organization: Texas A&M University Lines: 24 Message-ID: <4an7u2$e0s@news.tamu.edu> References: <4a729p$hhk@mserv1.dl.ac.uk> NNTP-Posting-Host: 486mullet2.tamu.edu X-Newsreader: News Xpress Version 1.0 Beta #3 Roland Koelliker wrote: >Hi netters >I'm working on the genetic variability of meadow fescue using RAPD markers. >After screening 140 primers I did find some suitable to my project but they >all give me only bands smaller than 1600 bp. I do have the feeling, that my >cycling conditions are not optimal. I'm using a Hybaid Omnigene Cycler (96 >wells, microtubes). > >Does anybody know how I could improve my cycling conditions to earn more >bands above 1600 kb? > Why do you need large PCR fragments from the RAPD analysis? Is the reason just to have more possible bands therefore increasing your chances of finding a poymorphism? Paul "Goose" Ulanch Dept. Biochem/Biophys Texas A&M University College Station, TX 77843-2128 (409) 847-9379 PULANCH@bioch.tamu.edu From owner-rapd@net.bio.net Tue Dec 12 22:00:00 1995 Path: biosci!WSP1.WSPICE.COM!lab From: lab@WSP1.WSPICE.COM (Dr. Eugene Sokourenko) Newsgroups: bionet.molbio.rapd Subject: LabSEARCH Directory Date: 13 Dec 1995 09:34:44 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 32 Sender: daemon@net.bio.net Distribution: world Message-ID: <01HYR9R263HE000BOP@Acd.Tusk.Edu> NNTP-Posting-Host: net.bio.net (by way of Prakash@acd.tusk.edu) X-Sender: Prakash@acd.tusk.edu I am forwarding Information about LabSearch Directory that lists availability of reagents, probles, primers, antibodies etc from academic labs. I think it is a good idea and encourage all of you to participate. The listing is free and the copy of the directory will be freely available. --Prakash --------------------------------------------------------------------------- LabSearch International was launched by group of academic researchers from the USA and Europe in attempt to facilitate the exchange of laboratory-developed research reagents and expertise, across all biomedical fields. LabSearch will publish in hard copy and electronically a directory where investigators will be able to publicize the conditional or unconditional availability of any service or physical specimens provided by their laboratories. Alternatively, researchers may also describe materials or expertise they wish to utilize. Listings in the LabSEARCH Directory will appear in the form of short self-created abstracts which: 1) describe the material or service offered or desired; 2) provide the name and address of a contact person; and optionally, 3) define any specific interests in collaborative studies, or the cost for supply; 4) indicate relevant publications. Any number of listings are free of charge (for non-profit organizations). Access to the Directory on WWW will be unrestricted. The first issue of printed version will be distributed also free of charge to academic researchers worldwide. Deadline for abstracts submission (by e-mail or in original format) is December 28, 1995. LabSearch e-mail address: lab/wsp1.wspice.com . URL: http://www.magibox.net/~lab/search From owner-rapd@net.bio.net Fri Dec 15 22:00:00 1995 Path: biosci!AC.DAL.CA!har1 From: har1@AC.DAL.CA (Harold Robertson) Newsgroups: bionet.molbio.rapd Subject: SOFTWARE FOR WINDOWS Date: 16 Dec 1995 11:48:41 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 6 Sender: daemon@net.bio.net Distribution: world Message-ID: <199512161946.PAA00426@Snoopy.UCIS.Dal.Ca> NNTP-Posting-Host: net.bio.net Help! I am looking for software for windows or ms-dos that will line up single letter protein sequence and then shade or box or somehow set-off the identical aminoacids for a family of related proteins. Any ideas. From owner-rapd@net.bio.net Fri Dec 15 22:00:00 1995 Path: biosci!NET.BIO.NET!kristoff From: kristoff@NET.BIO.NET (Dave Kristofferson) Newsgroups: bionet.molbio.rapd Subject: *** WWW Access to BIOSCI/bionet newsgroups *** Date: 16 Dec 1995 10:41:55 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 89 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net A repost of our 12/10/95 announcement: ---------------------------------------------------------------------- Subject: *IMPORTANT* New BIOSCI WWW Service!! I am extremely pleased to announce that BIOSCI is now providing WWW access to all bionet newsgroups through its Web site at www.bio.net!!! To use this service connect to our URL http://www.bio.net and then click on the "Access the BIOSCI/bionet Newsgroups" hyperlink. David Mack, the BIOSCI systems administrator at the U.S. BIOSCI node, has done an excellent job using the hypermail program from Enterprise Integration Technologies to make both current and archived BIOSCI messages available through the World Wide Web. Hypermail converts all e-mail addresses in the messages to mailto: URLs. As long as your Web browser is correctly configured to send e-mail, you can not only read these messages, you can also send either public replies to the newsgroup posting address (present on each message To: line) or private replies to the poster (address on each message's From: line). By selecting the appropriate browser option, you may also be able to include text in your reply from the message to which you are responding. The hypermail archive message headers are threaded by default, but messages can also be displayed chronologically or sorted by author or subject line. This capability gives you, in effect, a threaded newsreader through the Web. All messages posted to the lists are still distributed by e-mail and USENET as usual. However they are now also added to the hypermail archives typically within 20 minutes of posting (a delay was added to avoid file locking problems during periods of heavy use). The new hypermail archive gives you the advantages of USENET without requiring a local news server!! You can keep your personal mail file uncluttered now by using this system instead of e-mail. If you have had problems in the past with new bionet groups not getting established in your local USENET news system, weep no more!! The latest messages will always be here at net.bio.net and all you will need is your Web browser to read and/or post to any of the newsgroups. We will also soon be offering far more WAIS indexes as you will see from browsing the new system. Our goal is to provide, in addition to our current system-wide BIOSCI index, individual indexes for each newsgroup! Although we have done extensive testing, we will not be surprised if users discover some remaining bugs in the system. Please report any problems to us at biosci-help@net.bio.net This new archive also opens up the possibility of sponsorships for individual newsgroups. If your organization is interested in helping support our work through advertising in these WWW forums, i.e., displaying your logo - broadcast ads are not allowed, please contact us at biosci-help@net.bio.net. This is one of the most exciting developments at BIOSCI in quite some time. I want to thank David Mack for all of his hard work getting this system up and running. This entailed many late nights and weekends of effort to configure our system properly. I would also like to thank David States at Washington University for calling this program to our attention several months ago. We had looked at other software for providing Web access to our services and like this one the best. Hypermail was developed by Tom Gruber for Enterprise Integration Technologies (EIT) and later rewritten in C by Kevin Hughes at EIT. It is available for free from EIT. I am also pleased to announce that we have recently developed other software here that makes newsgroup moderation very easy compared to the old methods. We continue to encourage the discussion leaders of the low-to-moderate volume newsgroups to consider moderation to protect your readers against Internet ad spams. Please contact us for details on implementing this. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net From owner-rapd@net.bio.net Sat Dec 16 22:00:00 1995 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.molbio.rapd Subject: BIOSCI miniFAQ, ver. 14-DEC-95 Date: 17 Dec 1995 02:00:25 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 199 Sender: daemon@net.bio.net Distribution: world Message-ID: <199512171000.CAA01795@net.bio.net> NNTP-Posting-Host: net.bio.net (LAST REVISION: 14-DEC-95) This BIOSCI "miniFAQ" is designed to answer the questions that come up the *most frequently*. The main BIOSCI FAQ (Frequently Asked Questions) is accessible on the World Wide Web at URL http://www.bio.net/. Contents: -------- 1) Using the WWW to access the BIOSCI/bionet newsgroups. 2) What to do about "spams," i.e., junk mail, ads, etc. 3) Examples of subscribing and unsubscribing to the mailing lists. 4) The BIOSCI user address and research interest directory. 1) Using the WWW to access the BIOSCI/bionet newsgroups. -------------------------------------------------------- As of 10 December 1995, all BIOSCI/bionet full newsgroups are accessible through the World Wide Web (WWW) at URL http://www.bio.net. One can read and reply publicly or privately to both recent postings and archived messages through one's Web browser if it is configured properly to send e-mail. Each newsgroup is equipped with its own WAIS index in addition to the master index for the entire set. The main BIOSCI home page also has access to the BIO-JOURNALS Table of Contents database WAIS index and the BIOSCI user address database described in another item further below. 2) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups), mailing lists, and a hypermail archive at URL http://www.bio.net/. The same postings are distributed on all media (except for a small number of mailing-list-only groups at net.bio.net). Unfortunately it is becoming a despicable practice on the Internet (by a few people out to make a fast buck) to do automated mass postings to thousands of newsgroups and mailing lists. These attempts to grab free advertising are refered to as "spams" in the usual, somewhat boneheaded, net terminology. USENET is more susceptible to this practice, and many spams originate on the USENET groups and then are passed on to the mailing lists. However, spammers also get lists of mailing addresses and hit these too, so neither medium is immune. What should you do personally if you get junk mail? --------------------------------------------------- Just delete it and move on without reading it further. Filing a protest is becoming increasingly useless because spammers are often disguising the addresses where the messages are sent from. Unless you really understand Internet mail systems, your attempt at protest by sending replies to the message will often end up being sent to the address of an innocent person that the spammer is victimizing. What can BIOSCI/bionet do to protect its newsgroups? ---------------------------------------------------- The only solution currently available is to moderate the newsgroup. If this newsgroup is already moderated, then you are in good shape. Moderation protects the USENET distribution from about 95% of the spams that are being sent to date and protects the mailing lists completely. Moderation means, however, that someone has to take the time to review each message before it goes out. We have set up software here that simply allows the moderator to forward to an address at net.bio.net messages that (s)he wishes to have distributed. This takes no more time than that needed to read the message and pass it on, say about 1 min. per message. Most newsgroups currently have a discussion leader who is responsible for their newsgroup. The discussions leaders and their e-mail addresses are listed in the BIOSCI Information Sheet which is available on the Web at http://www.bio.net/. If a newsgroup is being hit with too many junk postings, please contact the discussion leader for that group and see if there is interest in moderating the group. Please do not assume that by simply posting a complaint to the newsgroup itself, anyone on the BIOSCI staff will act on your complaint. With close to 100 newsgroups to run, the BIOSCI staff has to rely on the discussion leaders of each newsgroup to report problems directly to us at biosci-help@net.bio.net. We will moderate any of our newsgroups if the discussion leader tells us that the readership of the group wishes to do so and if a moderator is willing to do the work. For most BIOSCI/bionet groups, this entails only a few minutes of work each day. Moderating a newsgroup will resolve probably 95% of the junk postings on the USENET distribution. Unfortunately there are easy ways for determined spammers to override the moderation mechanism on USENET, but we can protect our e-mail subscribers from unwanted postings if the newsgroup is moderated. You can also access our newsgroups over the WWW at URL http://www.bio.net. While this Web interface will not stop spammers from trying to post to the groups, this will give you yet another way, besides using USENET news, to keep the junk out of your personal mail files. For those of you with local USENET news systems, the Web interface will also give you faster access to new newsgroups and recent postings. 3) Examples of subscribing and unsubscribing to the mailing lists. ------------------------------------------------------------------ PLEASE NOTE: The BIOSCI management does NOT act on subscription/unsubscription requests that are posted improperly to the newsgroups and mailing lists. People who do this only bother everyone on the lists to no avail. Please be sure to follow the proper procedures below. Gory details are in the BIOSCI Information sheets on the Web at http://www.bio.net. Below we give an example utilizing the METHODS-AND-REAGENTS list at both of our two BIOSCI sites: Users in the Americas and Pacific Rim countries who use the BIOSCI ------------------------------------------------------------------ node at computer net.bio.net: ---------------------------- A) Determine the "listname" which is the <=8 character mail address ^^^^^^^^^^^^^ for the group. These can be found in the BIOSCI Info. Sheet. For the METHODS-AND-REAGENTS group the mailing address is methods@net.bio.net. The listname is the portion of the address to the left of the @ sign, i.e., "methods". The listname is used with the "subscribe" and "unsubscribe" commands illustrated below. B) Mail all commands in the body of a mail message addressed to biosci-server@net.bio.net. Do NOT send commands to the newsgroup posting addresses! Leave the Subject: line blank, any text on it will be ignored. C) In the body of your message put one or more of the following commands with an "end" command on the last line, e.g., subscribe methods unsubscribe methods end Do NOT put your e-mail address or other text on these lines. The server only allows you to cancel your subscription if the address on your mail header matches the address on our mailing list. Please ask for help at biosci-help@net.bio.net if your address has changed, e.g., if you know you are on the list but the server tells you that you are not a member. Users in Europe, Africa, and Central Asia who use the BIOSCI node at -------------------------------------------------------------------- computer daresbury.ac.uk (also known as dl.ac.uk): ------------------------------------------------- To subscribe and unsubscribe to/from the BIOSCI lists, you need to specify the full USENET newsgroup name with "bionet-news." prepended. The USENET newsgroup names are listed in the BIOSCI Information sheet on the Web at http://www.bio.net/. For the METHODS-AND-REAGENTS list the USENET newsgroup name is bionet.molbio.methds-reagnts, thus the appropriate commands are sub bionet-news.bionet.molbio.methds-reagnts unsub bionet-news.bionet.molbio.methds-reagnts These commands are included in a message addressed to mxt@dl.ac.uk, NOT to the newsgroup mailing addresses. As usual, include the text in the body of the message as text on the Subject: line is ignored. To unsubscribe from all the lists at the UK node, use unsub bionet-news Please note that if the address in the list is different than the one in your mail message header, you will not be able to unsubscribe by this method. If you have problems, please mail biosci@daresbury.ac.uk. 4) The BIOSCI user address and research interest directory. ----------------------------------------------------------- Please take this opportunity to add your name, address, and research interest information to the BIOSCI User Address Database if you have not already done so. You can fill out the address form directly through our Web page at URL http://www.bio.net/adrform.html. The address database is reindexed nightly for WWW access (the URL is http://www.bio.net/). If you are not directly on the Internet but can reach it by e-mail, please use our waismail server to access the user directory. waismail use is described above. You can also request a user address form by e-mail from biosci-help@net.bio.net. Please check your database entry from time-to-time to see if your address information is still up-to-date. Because of our limited personnel resources, we ask that you resubmit a *complete* form to revise your entry; we only replace complete entries and do not have resources to edit old forms. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net From owner-rapd@net.bio.net Mon Dec 18 22:00:00 1995 Path: biosci!uoguelph.ca!boulding From: boulding@uoguelph.ca (Elizabeth Boulding) Newsgroups: bionet.molbio.rapd Subject: detection of microsatellites without cloning Date: 19 Dec 1995 13:26:22 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 6 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Has anybody in this group tried using the RAMP primers to amplify random microsatellites? It is described by K.-S. Wu et al. in a paper entitled "Detection of microsatellite polymorphisms without cloning" in Nucleic Acids Research 22:3257-3258. best, Elizabeth Boulding. From owner-rapd@net.bio.net Mon Dec 18 22:00:00 1995 Path: biosci!MED2.KUFM.KAGOSHIMA-U.AC.JP!masakun From: masakun@MED2.KUFM.KAGOSHIMA-U.AC.JP (MASAHISA HORIUCHI) Newsgroups: bionet.molbio.rapd Subject: (none) Date: 19 Dec 1995 00:08:00 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 2 Sender: daemon@net.bio.net Distribution: world Message-ID: <199512190731.QAA09303@med2.kufm.kagoshima-u.ac.jp> NNTP-Posting-Host: net.bio.net help From owner-rapd@net.bio.net Mon Dec 18 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!uwm.edu!lll-winken.llnl.gov!fnnews.fnal.gov!lakesis.fapesp.br!bee.uspnet.usp.br!carpa!eccastel From: eccastel@carpa.ciagri.usp.br (Elaine C. Castelhano) Newsgroups: bionet.molbio.rapd Subject: maize RAPD Date: 19 Dec 1995 12:40:53 GMT Organization: Universidade de Sao Paulo / Brasil Lines: 4 Message-ID: <4b6bsl$724@bee.uspnet.usp.br> NNTP-Posting-Host: carpa.ciagri.usp.br X-Newsreader: TIN [version 1.2 PL2] I would like to know anything about maize RAPD ( like protocols, references,...) - please help!!! I can make it work!! Thanks, Elaine. From owner-rapd@net.bio.net Mon Dec 18 22:00:00 1995 Path: biosci!uoguelph.ca!boulding From: boulding@uoguelph.ca (Elizabeth Boulding) Newsgroups: bionet.molbio.rapd Subject: postdoctoral or Ph.D. positions in Molecular Ecology Date: 19 Dec 1995 13:45:16 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 40 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net The following ad appeared in the Dec. 8/95 issue of Science: Note that positions 1 and 4 require molecular experience. FOUR POSTDOCTORAL or PH.D POSITIONS A multi-university collaborative project examining the evolutionary ecology of exotic species introductions into the Great Lakes is looking for four candidates for postdoctoral or Ph.D. studies. Four research areas are currently under investigation: 1) Zooplankton diversity: allozyme and DNA markers will be used to diagnose unrecognized species invasions and to ascertain the source locations of currently recognized exotics. Contact P.D.N. Hebert Email: phebert@uoguelph.ca, 2) Theoretical ecology: mathematical theory of biological invasions. Contact P. Yodzis Email: pyodzis@uoguelph.ca, 3) Zooplankton feeding ecology: feeding rates and prey electivities, effects of _Bythotrephes density on per capita feeding rates, and spatial distribution of this predator and its prey. Contact W.G. Sprules Email: gsprules@cyclops.erin.utoronto.ca, 4) Diffusion of exotic species: development of microsatellites for species of exotic molluscs and GIS modelling of diffusion from the source populations identified with these molecular markers. Contact E.G. Boulding Email: boulding@uoguelph.ca. Application packages should include a resume, academic transcripts, the names, telephone numbers, and Email addresses of three academic referees, and an explanation of how your background relates to the position and should be sent to: Dr. Elizabeth Boulding, Dept. of Zoology, University of Guelph, Guelph, Ontario, Canada N1G 2W1. Positions will remain open until they are filled. D.K. Padilla (U. Wisconsin, Madison) and J.E. Havel (Southwest Missouri State U.) are also collaborators on this project. The University of Guelph is committed to an employment equity program that includes special measures to achieve diversity among its faculty and staff. We therefore, particularly encourage applications from qualified aboriginal Canadians, persons with disabilities, members of visible minorities, and women. From owner-rapd@net.bio.net Mon Dec 18 22:00:00 1995 Path: biosci!ml.csiro.au!chris.bolch From: chris.bolch@ml.csiro.au (Christopher Bolch) Newsgroups: bionet.molbio.rapd Subject: Re: Rubbish porn postings response Date: 19 Dec 1995 14:45:16 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 64 Sender: daemon@net.bio.net Distribution: world Message-ID: <199512192243.JAA08537@aqueous.ml.csiro.au> NNTP-Posting-Host: net.bio.net Dear rapdnet users, I responded to the rubbish advertising free porn and sex videos. The following response came from their node administrator. As usual the initial address was bogus but fortunately the mailing server was clearly shown in the header info. Chris RESPONSE: >Date: Tue, 19 Dec 1995 10:06:35 -0500 (EST) >X-Sender: GNNAdvisor@mail.gnn.com >X-Mailer: Windows Eudora Version 2.1.1 >Mime-Version: 1.0 >To: chris.bolch@aqueous.ml.csiro.au (Christopher Bolch) >From: William >Subject: Re: Rubbish postings > >Dear Internet User, > >Thanks for reporting the unacceptable post. We'll look into it and >take the appropriate action. > >For confidentiality reasons, we cannot disclose information on >actions we've taken against our members, however, the resources >available to us include written warnings and account termination. > > >Regards, > >William >GNN Advisor Staff >Global Navigator Network > > ________________________________________ Any views, statements of intent, or comment in this letter have no official status and do not constitute or imply any contract with myself or my employer. ________________________________________ Christopher J. S. Bolch, Algal Ecologist/Geneticist, CSIRO Division of Fisheries, GPO Box 1538, Hobart, Tasmania, Australia, 7001. Australia PH. 002 325314 FAX 002-325000 International PH. 061-02-325314 FAX. 061-02-325000 ________________________________________ From owner-rapd@net.bio.net Tue Dec 19 22:00:00 1995 Path: biosci!ACD.TUSK.EDU!Prakash From: Prakash@ACD.TUSK.EDU Newsgroups: bionet.molbio.rapd Subject: Job at Union Camp (Princeton, NJ) Date: 20 Dec 1995 06:50:04 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 16 Sender: daemon@net.bio.net Distribution: world Message-ID: <01HZ0W2M3FVC000A58@Acd.Tusk.Edu> NNTP-Posting-Host: net.bio.net The December 15 issue of Science (p.187) carries an ad by Union Camp Co. who is looking for some one to develop a marker-aided selection program and DNA fingerprinting with their tree breeding program. Fax#(609) 844-7323 Attn: Ms. Jacki DiFranco. I thought some of you may be interested in checking this out. ---------------------------------------------------------------------- C. S. Prakash Prakash@Acd.Tusk.Edu Tuskegee University Phone (334) 727 8023 School of Agriculture Fax (334) 727 8552 Tuskegee, AL 36088-1641 ---------------------------------------------------------------------- From owner-rapd@net.bio.net Tue Dec 19 22:00:00 1995 Path: biosci!CS.Arizona.EDU!news.Arizona.EDU!hamblin.math.byu.edu!usenet From: farmerj Newsgroups: bionet.molbio.rapd Subject: complaints about non-scientific postings Date: 20 Dec 1995 18:41:45 GMT Organization: Brigham Young University Lines: 22 Message-ID: <4b9ld9$cvn@hamblin.math.byu.edu> NNTP-Posting-Host: farmerj.byu.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Windows; I; 16bit) From time to time, we have received commercial postings and pseudo-commercial postings, such as the recent one about sex videos. I have discovered, to my embarrassment, that sending a reply which complains about the posting usually causes problems for an innocent party because the return addresses are often forged. Many of these postings seem to be an attempt to injure someone by flooding their mailboxes with complaints. If you are not clever and experienced enough to track down the originator of the message, don't send any reply at all, either to rapd or to the return address on the message. It is often difficult to find the offending party. You can check to see if the news administrators are working on a particular message by checking the newsgroup news.admin.net-abuse.announce If so, you need take no further action. If not, you may wish to call the message to their attention. From owner-rapd@net.bio.net Fri Dec 29 22:00:00 1995 Path: biosci!ASRR.ARSUSDA.GOV!abartlet From: abartlet@ASRR.ARSUSDA.GOV ("Alan C. Bartlett") Newsgroups: bionet.molbio.rapd Subject: Re: software for gel documentation Date: 30 Dec 1995 10:37:05 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 20 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <30DEC95.10742941.0028.MUSIC@SDSUMUS.SDSTATE.EDU> NNTP-Posting-Host: net.bio.net I have been very happy with a program called RFLPSCAN produced by CSPI,=20 800-325-3110. This program will accept TIF files and contains a database= =20 program which allows you to search for matches of bands in the scanned=20 and analyzed images. They have been good to work with and will send you=20 detailed information if you call the number. The program is rather=20 expensive, but does a lot of the analysis for you. I have looked at the=20 program produced by Jandel (SigmaScan), but have not been impressed=20 enough to change. =FCI think SigmaScan is a little cheaper to buy and has= =20 recently been updated. I have a phone number (415-453-6700) but not an=20 800 number. Their internet address is: sales@jandel.com or=20 support@jandel.com. Good luck. Alan C. Bartlett "GENES-R-US" "ALTERATIONS AVAILABLE!^" "^some restrictions may apply:)" From owner-rapd@net.bio.net Fri Dec 29 22:00:00 1995 Path: biosci!SDSUMUS.SDSTATE.EDU!PX52 From: PX52@SDSUMUS.SDSTATE.EDU ("Thomas E. Chase") Newsgroups: bionet.molbio.rapd Subject: software for gel documentation Date: 30 Dec 1995 08:03:47 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Distribution: world Message-ID: <30DEC95.10742941.0028.MUSIC@SDSUMUS.SDSTATE.EDU> NNTP-Posting-Host: net.bio.net I'd appreciate receiving any information on software for gel documentation that runs under DOS or Windows. I have access to a flatbed scanner for scanning our polaroids and saving them as TIFs or GIFs. What I'd like to do is then be able to work with these images. Thanks for any help. -------------------------------------------------------- Thomas E. Chase px52@sdsumus.sdstate.edu South Dakota State University Office: 605-688-5550 Plant Science Department Lab: 605-688-5146 Box 2108, Brookings, SD 57007 FAX: 605-688-4024 ---------------------------------------------------------