From owner-recombination@net.bio.net Sat Oct 14 23:00:00 1995 Path: biosci!biosci!not-for-mail From: biohelp@net.bio.net (BIOSCI Administrator) Newsgroups: bionet.molbio.recombination Subject: test of bionet.molbio.recombination Date: 14 Oct 1995 18:33:54 -0700 Organization: BIOSCI International Newsgroups for Biology Lines: 148 Distribution: world Message-ID: <45poe2$36@net.bio.net> NNTP-Posting-Host: net.bio.net Test of bionet.molbio.recombination; this group is not yet ready for operation. Please do not post until you see an official opening announcement herein. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net ---------------------------------------------------------------------- Information for RECOMBINATION/bionet.molbio.recombination USENET newsgroup name: bionet.molbio.recombination Status: Unmoderated One line description: Research on the recombination of DNA or RNA. Mailing list name: RECOMBINATION E-mail posting addresses: recom@net.bio.net recom@daresbury.ac.uk Discussion leaders: *Note: Area of expertise is written in brackets Graham Dellaire, e-mail: popa0206@po-box.mcgill.ca (b2xe@musicb.mcgill.ca) Department of Medicine (Div. of Exp. Medicine) McGill Univeristy, Montreal, Quebec, Canada *(Genome Accessibility, Line-1 sequences, Gene Conversion and Ectopic Int.) George Szatmari, e-mail: szat@ere.umontreal.ca Assistant Professor Departement de Microbiologie et Immunologie Universite de Montreal CP 6128 Succursale Centre-Ville Montreal, Quebec H3C 3J7 phone (514)343 5767 fax (514)343 5701 *(Site Specific Recombination Sytems) Terry Chow e-mail: MDTY@musica.mcgill.ca Associate Professor Department of Oncology Division of Radiation-Oncology McGill University Montreal General Hospital 1650 Ave. Cedar Montreal, Quebec H3G 1A4 phone (514)934 8040 ext. 4179 fax (514)934 8220 *(Mammalian Genetics/gene therapy) Dana Lasko e-mail: CZDL@musica.mcgill.ca Assistant Professor of Medicine and Human Genetics Project Director Terry Fox Molecular Oncology Group Lady Davis Institute for Medical Research 3755 Cote-Ste-Catherine Rd. Montreal, PQ Phone 340-8260 ext. 3454 (office and machine) or ext. 5251 (lab) Fax 340-7502 *(Replication and Recombination) Charter: The purpose of the RECOMBINATION newsgroup is to provide a proper forum for the discussion of issues pertaining and involving recombination of DNA or RNA, in its many forms (see _Topics of Discussion_). Primarily it should enable those researchers who work in recombination or aligned fields to communicate ideas and information, as well as, provide a chance for collaboration among national and international research groups. Topics of Discussion include: 1. Gene conversion and ectopic integration 2. Genome accessibility and nuclear/chromosome structure and recombination -Matrix attachment sites (MARS) -nucleosomes, histone 1 -recombination hotspots -fragile sites -origins of replication 3. Effect of DNA topology on recombination (Triple strand, Z-DNA, cruciform, bent etc) 4. Homologous recombination vs. nonhomologous or illegitimate -comparisons between bacterial, yeast and higher eukaryotic recombination systems (ex. fungi, mammals) 5. Models of recombination (One-end invasion, Double strand Break Repair, SSA etc) 6. Site-specific recombination systems (invertase, Cre and Flp recombinase etc) 7. Specific recombination systems in complex organisms -VDJ recombination -Antigenic variation and recombination (ex. trypanosomes, HIV, N.gonorrhea) -Yeast mating type locus 8. Transcription and recombination 9. DNA replication and recombination (ex. gene amplification (DHFR etc)) 10. Evolution of the Genome -retroposons (Line-1, Sine's), retroviruses and transposons -formation of gene clusters and comparative mapping -recombination between other repeat elements (alpha satellites, telomeres) 11. DNA repair systems and recombination (DSB and mismatch repair) -including DNA repair deficient diseases (ex. Xoderma Pigmentosum) 12. Applications of recombination -Gene therapy -Transgenics and gene transfer 13. Viral diversity through RNA recombination 14. Population genetics and recombination:i.e. as a source of allelic variation and as a measure of genetic exchange within and between populations. In addition this newsgroup provides: A forum for the exchange of information about future congresses and meetings in areas of molecular biology relating to recombination A forum for the exchange of information about textbooks, internet resources, visual materials, and computer programs. A source of quick help for last-minute troubleshooting, sources of materials, and practical advice; in areas such as -Vector design for transgene experiments -Gene transfer techniques -Animal models and cell lines -Gene therapy protocols Subscribers are welcome. Contributions within the functions outlined above are encouraged. The newsgroup is -UNMODERATED-. From owner-recombination@net.bio.net Sat Oct 14 23:00:00 1995 Path: biosci!NET.BIO.NET!biosci-help From: biosci-help@NET.BIO.NET (BIOSCI Administrator) Newsgroups: bionet.molbio.recombination Subject: test of recom@net.bio.net Date: 14 Oct 1995 18:35:40 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 2 Sender: daemon@net.bio.net Distribution: world Message-ID: Reply-To: biosci-help@net.bio.net NNTP-Posting-Host: net.bio.net test of recom@net.bio.net; please ignore. From owner-recombination@net.bio.net Sat Oct 14 23:00:00 1995 Path: biosci!agate!howland.reston.ans.net!newsfeed.internetmci.com!news.sesqui.net!oitnews.harvard.edu!cmcl2!is2.NYU.EDU!cqw4441 From: cqw4441@is2.nyu.edu (Cheukkit Wong) Newsgroups: bionet.molbio.recombination Subject: T7 RNA polymerase Date: 15 Oct 1995 00:38:10 GMT Organization: New York University Lines: 2 Message-ID: <45pl5i$mh9@cmcl2.NYU.EDU> NNTP-Posting-Host: is2.nyu.edu X-Newsreader: TIN [version 1.2 PL2] What is the allosteric promoter(s) with a high affinity for T4 RNA polymerase? From owner-recombination@net.bio.net Mon Oct 16 23:00:00 1995 Path: biosci!daresbury!not-for-mail From: BIOSCI Administrator Newsgroups: bionet.molbio.recombination Subject: test of recom@daresbury.ac.uk Date: 17 Oct 1995 01:52:13 +0100 Lines: 1 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <45uunt$c3g@mserv1.dl.ac.uk> Reply-To: biosci-help@net.bio.net Original-To: recom@dl.ac.uk test of recom@daresbury.ac.uk, please ignore. From owner-recombination@net.bio.net Mon Oct 16 23:00:00 1995 Path: biosci!biosci!not-for-mail From: biohelp@net.bio.net (BIOSCI Administrator) Newsgroups: bionet.molbio.recombination Subject: RECOMBINATION/bionet.molbio.recombination is ready! Date: 16 Oct 1995 19:59:13 -0700 Organization: BIOSCI International Newsgroups for Biology Lines: 194 Distribution: world Message-ID: <45v661$lqr@net.bio.net> NNTP-Posting-Host: net.bio.net The RECOMBINATION/bionet.molbio.recombination newsgroup is ready for operation. Please save these usage instructions for future reference!! PLEASE NOTE that many USENET sites do not allow automatic creation of new USENET groups!!! If you do not see bionet.molbio.recombination in your newsreader within another day or two, ask your news system administrator to act on our "newgroup" message to enable the group at your site. We have already done several tests and are certain that the group is currently propagating around the network. If he/she can not find the newsgroup message, have them retrieve the bionet checkgroups message from the anonymous FTP area on net.bio.net in pub/BIOSCI/doc/bionet-checkgroups-msg. This file contains the latest list of bionet USENET newsgroups and can be used to update your bionet distribution. If the newgroup did not arrive at your site, it may also be necessary for your news administrator to contact the upstream computer site providing you with your newsfeed and determine if they acted on the newgroup message. Subscribing to this group: -------------------------- IF YOU USE USENET NEWS: you need do nothing other than participate in bionet.molbio.recombination when it appears in your newsreader. Depending upon your news software, this may entail you having to answer a prompt indicating that you want to subscribe. You might also try the command "g bionet.molbio.recombination" in rn-like newsreaders. IF YOU ARE LOCATED IN EUROPE, AFRICA, OR CENTRAL ASIA: please send the word help in the body of your message to MXT@dl.ac.uk to retrieve general server usage instructions. To subscribe to the RECOMBINATION list, first be sure that you are sending mail from the address at which you wish to receive news postings, and then send the command SUB bionet-news.bionet.molbio.recombination to MXT@dl.ac.uk. This message will be automatically read by the computer and your e-mail address will be extracted from the mail header and added to the list. IF YOU ARE LOCATED IN THE AMERICAS OR THE PACIFIC RIM: log in to the computer account in which you would like to receive mail (not an account that you use infrequently) and send a mail message to the Internet address biosci-server@net.bio.net Leave the Subject: line of the message blank and enter the following line into the body of the mail message: subscribe recom This message will be automatically read by our computer and your e-mail address will be extracted from the mail header and added to the list. Canceling your subscription: ---------------------------- IF YOU ARE LOCATED IN EUROPE, AFRICA, OR CENTRAL ASIA: first be sure that you are sending mail from the address at which you signed up to receive news postings, and then send the command (in the body of your mail message) UNSUB bionet-news.bionet.molbio.recombination to MXT@dl.ac.uk. This message will be automatically read by the computer and your e-mail address will be extracted from the mail header and removed from the list. IF YOU ARE LOCATED IN THE AMERICAS OR THE PACIFIC RIM: send a message to biosci-server@net.bio.net exactly as described above for subscribing except include the text unsubscribe recom in the body of the message. Please be sure to send the message from the account whose address matches the one on the list. If your address differs, we will be notified automatically and will remove you manually from the list if we can determine what was your old address. Please contact biosci-help@net.bio.net if you have problems. IF YOU HAVE A PROBLEM: ---------------------- Please send a message to one of the following addresses depending upon your location Address Location ------- -------- biosci@daresbury.ac.uk Europe, Africa, and Central Asia biosci-help@net.bio.net Americas and the Pacific Rim and someone on the staff will help you. PLEASE DO NOT send mail to our personal e-mail addresses as this will delay a response to your request for help. How to post a message to the group: ----------------------------------- If you use news, simply post a message into bionet.molbio.recombination. Be sure to set your "distribution" to "world" or else the message might not leave your site!! To post by e-mail, mail your message to one of the following addresses depending upon your location: Posting Address Location --------------- -------- recom@daresbury.ac.uk Europe, Africa, and Central Asia recom@net.bio.net Americas and the Pacific Rim and your message will be distributed automatically to everyone on the list and the USENET newsgroup. There is no editorial intervention. PLEASE DO NOT SEND SUBSCRIPTION REQUESTS TO THE POSTING ADDRESSES as you will bother everyone on the newsgroup!!! How to reply to a message on the group: --------------------------------------- If you are using a newsreader, simply use the reply or follow-up command on your newsreader (these vary from program to program) to send either private or public replies. If you are using e-mail, replies to messages that you receive will *NOT* be automatically returned to the group. This is the standard for Internet mailing lists as opposed to BITNET LISTSERVs which often send all replies back to everyone. You must be certain that your reply contains either of the two newsgroup posting addresses above in your message header if you want to share it with everyone on the group. Otherwise in most cases your reply may go back to only the original poster of the message to which you are replying. ALWAYS be certain that you examine the address on your messages before you send them!!! Once a message is sent there is no way to cancel it or bring it back!!! Some non-Internet compliant mail systems may attempt to send replies to our error-trapping address called BIOSCI-REQUEST. If yours does this, please be sure to readdress your message to recom@net.bio.net or recom@daresbury.ac.uk if you want to send it to the newsgroup. How to look at archives of the list: ------------------------------------ The BIOSCI archives and other BIOSCI information can be found on our WWW home page at URL http://www.bio.net/. Easy access from the WWW home page to our FTP/gopher area is available for information retrieval. Archives for RECOMBINATION/bionet.molbio.recombination are kept in the anonymous FTP account at net.bio.net [204.31.212.2]. Look in the directory pub/BIOSCI/RECOMBINATION for posting archives. Each file is assigned a date such as 9312 for December 1993. Please note that ours is a UNIX system and all file and directory names are case-sensitive, i.e., upper case file names are different from lower case names. You can also access these same files via Gopher if you start a gopher session using net.bio.net as your gopher server. Gopher also allows you to view the individual messages within each monthly archive file. The files are in the RECOMBINATION directory. Postings to bionet.molbio.recombination are also WAIS indexed and can be searched via either gopher or WAIS at our site. In gopher the option at net.bio.net is "Search Bionet USENET Articles" and in WAIS one should use the WAIS source biosci.src. This is a WAIS index of all BIOSCI/bionet messages including this newsgroup. Please see the BIOSCI FAQ for details. The FAQ can be requested from biosci-help@net.bio.net. Once again, if you have any administrative questions that require personal assistance, please address them to biosci-help@net.bio.net in the U.S. or biosci@daresbury.ac.uk in the UK. Best wishes for a successful newsgroup! Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net From owner-recombination@net.bio.net Tue Oct 17 23:00:00 1995 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.molbio.recombination Subject: IMPORTANT: BIOSCI miniFAQ Date: 18 Oct 1995 02:02:10 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 196 Sender: daemon@net.bio.net Distribution: world Message-ID: <199510180900.CAA27702@net.bio.net> NNTP-Posting-Host: net.bio.net This is a new "miniFAQ" 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) What to do about "spams," i.e., junk mail, ads, etc. 2) Examples of subscribing and unsubscribing to the mailing lists. 3) How to access BIOSCI/bionet newsgroup archives. 4) The BIOSCI user address and research interest directory. 1) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups) and mailing lists. The same postings are distributed on both 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 newsgroups from about 95% of the spams that are being sent to date. This means 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. Unfortunately there are easy ways for determined spammers to override the moderation mechanism. We are working on new systems to provide access to our newsgroups over the WWW. These should be available soon, probably November 1995, and will allow you to use your Web browser to look at the news postings. While this 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. 2) 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. 3) How to access BIOSCI/bionet newsgroup archives. -------------------------------------------------- Back postings of all BIOSCI/bionet newsgroups can be found on the World Wide Web at URL http://www.bio.net/. There are several searchable newsgroup indices at this site. E-mail users can search the BIOSCI archives by using our waismail e-mail server. For instructions send the message help to waismail@net.bio.net. Leave the Subject: line blank (anything entered on the Subject: line is ignored). 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-recombination@net.bio.net Tue Oct 17 23:00:00 1995 Path: biosci!ATLAS.ODYSSEE.NET!dellaire From: dellaire@ATLAS.ODYSSEE.NET (Dellaire, Graham) Newsgroups: bionet.molbio.recombination Subject: Welcome Everyone To RECOM! Date: 18 Oct 1995 13:53:35 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 121 Sender: daemon@net.bio.net Distribution: world Message-ID: <9510182049.AA20188@odyssee.net> NNTP-Posting-Host: net.bio.net ************************************************** -------------------WELCOME TO RECOM----------------------- ************************************************** I would like to take this opportunity to welcome everyone to=20 bionet.molbio.recombination=20 Hence forth referred to as simply RECOM. First of all I would like to thank everyone who has given input and support for the creation of this news group. Particularly those in in the beginning who lent their support and ideas and eventually their vote!=7F Opening comments 1. Participation is encouraged either by USENET or via e-mail=20 2. For those of you who do not have NEWS access (USENET or BITNET etc), it possible to subscribe to the list service for this news group. A) to do this for North America and the Pacific Rim send=20 to:biosci-server@net.bio.net Subject: subscribe recom B) for Europe and the United Kingdom send =20 to:MXT@dl.ac.uk Subject: SUB bionet-news.bionet.molbio.recombination Although participation via USENET is perfectly fine on its own sometimes it is much easier to receive the posts to this group directly to your e-mail.= =20 3. All suggestions for the content of our discussion are welcome. so far suggestions that may be adopted are as follows: a)Job Listing (post doc, Institution listings etc) b)Postings of concise editorials on given areas of participants expertise =09 c)Postings of abstracts from recently published works or from pre-prints where applicable d)Postings of dates and sites of upcoming meetings =09 e)Posting of brief resumes of the events of the recent meetings. f)Posting of a recombination FAQ including: -reference lists for separate topics in recombination -lists of web resources (FTP,GOPHER etc) for genetics and recombination -broad introductory sections on particular aspects of recombination to be contributed by participants in the group. -news group charter -contact information for discussion leaders -perhaps posting of addresses of institutions that work in genetics as well as key laboratories (Idealy we would like to assemble a voluntary list of researchers and there interest and addresses they can be reached at for further discussion ) Please let us know what you think. Together we can produce the type of news forum that can benefit both the novice and veteran researcher alike. The direction that the new group takes is to be decided primarily by input from the recombination community at large. SO once again Let Us Know What You= Think! =20 On behalf of myself and the other discussion leaders I wish to thank you again for all your support, Graham Dellaire PrimaryDiscussion Leader bionet.molbio.recombination e-mail:dellaire@odyssee.net ******************************************************** Graham Dellaire Snail Mail Div. of Experimental Medicine Institute du Cancer de Montreal Dept. of Medicine Louis Charles-Simard=20 McGill University 1560 Sherbrooke Street E. e-mail:dellaire@odyssee.net Montreal, Quebec, Canada or B2XE@musicb.mcgill.ca =20 ******************************************************** From owner-recombination@net.bio.net Tue Oct 17 23:00:00 1995 Path: biosci!ATLAS.ODYSSEE.NET!dellaire From: dellaire@ATLAS.ODYSSEE.NET (Dellaire, Graham) Newsgroups: bionet.molbio.recombination Subject: Revised Charter for RECOM Date: 18 Oct 1995 14:01:48 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 147 Sender: daemon@net.bio.net Distribution: world Message-ID: <9510182057.AA20573@odyssee.net> NNTP-Posting-Host: net.bio.net ******************************************************* RECOM ******************************************************* Information on RECOMBINATION/bionet.molbio.recombination USENET newsgroup name: bionet.molbio.recombination Status: Unmoderated One line description: Research on the recombination of DNA or RNA. Mailing list name: RECOMBINATION E-mail posting addresses: recom@net.bio.net recom@daresbury.ac.uk Discussion leaders: *Note: Area of expertise is written in brackets Graham Dellaire, e-mail dellaire@atlas.odyssee.net (b2xe@musicb.mcgill.ca) Department of Medicine (Div. of Exp. Medicine) McGill Univeristy, Montreal, Quebec, Canada *(Genome Accessibility, Line-1 sequences, Gene Conversion and Ectopic Int.) George Szatmari, e-mail: szat@ere.umontreal.ca Assistant Professor Departement de Microbiologie et Immunologie Universite de Montreal CP 6128 Succursale Centre-Ville Montreal, Quebec H3C 3J7 phone (514)343 5767 fax (514)343 5701 *(Site Specific Recombination Sytems) Terry Chow e-mail: MDTY@musica.mcgill.ca Associate Professor Department of Oncology Division of Radiation-Oncology McGill University Montreal General Hospital 1650 Ave. Cedar Montreal, Quebec H3G 1A4 phone (514)934 8040 ext. 4179 fax (514)934 8220 *(Mammalian Genetics/gene therapy) Dana Lasko e-mail: CZDL@musica.mcgill.ca Assistant Professor of Medicine and Human Genetics Project Director Terry Fox Molecular Oncology Group Lady Davis Institute for Medical Research 3755 Cote-Ste-Catherine Rd. Montreal, PQ Phone 340-8260 ext. 3454 (office and machine) or ext. 5251 (lab) Fax 340-7502 *(Replication and Recombination) Charter: The purpose of the RECOMBINATION newsgroup is to provide a proper forum for the discussion of issues pertaining and involving recombination of DNA or RNA, in its many forms (see _Topics of Discussion_). Primarily it should enable those researchers who work in recombination or aligned fields to communicate ideas and information, as well as, provide a chance for collaboration among national and international research groups. Topics of Discussion include: 1. Gene conversion and ectopic integration 2. Genome accessibility and nuclear/chromosome structure and recombination -Matrix attachment sites (MARS) -nucleosomes, histone 1 -recombination hotspots -fragile sites -origins of replication 3. Effect of DNA topology on recombination (Triple strand, Z-DNA, cruciform, bent etc) 4. Homologous recombination vs. nonhomologous or illegitimate -comparisons between bacterial, yeast and higher eukaryotic recombination systems (ex. fungi, mammals) 5. Models of recombination (One-end invasion, Double strand Break Repair, SSA etc) 6. Site-specific recombination systems (invertase, Cre and Flp recombinase etc) 7. Specific recombination systems in complex organisms -VDJ recombination -Antigenic variation and recombination (ex. trypanosomes, HIV, N.gonorrhea) -Yeast mating type locus 8. Transcription and recombination 9. DNA replication and recombination (ex. gene amplification (DHFR etc)) 10. Evolution of the Genome -retroposons (Line-1, Sine's), retroviruses and transposons -formation of gene clusters and comparative mapping -recombination between other repeat elements (alpha satellites, telomeres) 11. DNA repair systems and recombination (DSB and mismatch repair) -including DNA repair deficient diseases (ex. Xoderma Pigmentosum) 12. Applications of recombination -Gene therapy -Transgenics and gene transfer 13. Viral diversity through RNA recombination 14. Population genetics and recombination:i.e. as a source of allelic variation and as a measure of genetic exchange within and between populations. In addition this newsgroup provides: A forum for the exchange of information about future congresses and meetings in areas of molecular biology relating to recombination A forum for the exchange of information about textbooks, internet resources, visual materials, and computer programs. A source of quick help for last-minute troubleshooting, sources of materials, and practical advice; in areas such as -Vector design for transgene experiments -Gene transfer techniques -Animal models and cell lines -Gene therapy protocols Subscribers are welcome. Contributions within the functions outlined above are encouraged. The newsgroup is -UNMODERATED-. ******************************************************** Graham Dellaire Snail Mail Div. of Experimental Medicine Institute du Cancer de Montreal Dept. of Medicine Louis Charles-Simard McGill University 1560 Sherbrooke Street E. e-mail:dellaire@odyssee.net Montreal, Quebec, Canada or B2XE@musicb.mcgill.ca ******************************************************** From owner-recombination@net.bio.net Tue Oct 17 23:00:00 1995 Newsgroups: bionet.molbio.recombination Path: biosci!lhc.nlm.nih.gov!nih-csl!NewsWatcher!user From: lichten@helix.nih.gov (Michael Lichten) Subject: Abstract posting Message-ID: Sender: postman@alw.nih.gov (AMDS Postmaster) Nntp-Posting-Host: 128.231.218.92 Organization: LB/DCBDC/NCI Date: Wed, 18 Oct 1995 13:29:47 GMT Lines: 7 I would like to propose that this newsgroup be used for posting abstracts of papers submitted for publication. Anyone else have any feelings on this matter? -- Michael Lichten lichten@helix.nih.gov From owner-recombination@net.bio.net Thu Oct 19 23:00:00 1995 Path: biosci!VAXA.CIS.UWOSH.EDU!lansman From: lansman@VAXA.CIS.UWOSH.EDU (Bob Lansman) Newsgroups: bionet.molbio.recombination Subject: Alu sequences as portable regions of homology Date: 20 Oct 1995 11:37:22 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Distribution: world Message-ID: <01HWNY9PZMCI00EDPO@VAXA.CIS.UWOSH.EDU> NNTP-Posting-Host: net.bio.net At a symposium this summer, Richard Fishel, of the University of Vermont, made the statement that, in cells with fully functional mismatch repair, recombination between heterologous Alu sequence is inhibited by lack of complete homology. But, this type of recombination can occur in tumor cells, in which mutation in genes like MSH has disabled mismatch repair. Does anyone have references to work which would support these statments? Does anyone have comments regarding the general acceptance of these ideas? I have always thought that recombination between Alus in different chromosomal locations was a likely cause of chromosome rearrangements during evolution, such as the duplication of beta-like globin genes. Is this not a widely accepted model? From owner-recombination@net.bio.net Thu Oct 19 23:00:00 1995 Newsgroups: bionet.molbio.recombination Path: biosci!lhc.nlm.nih.gov!nih-csl!NewsWatcher!user From: lichten@helix.nih.gov (Michael Lichten) Subject: Re: Alu sequences as portable regions of homology Message-ID: Sender: postman@alw.nih.gov (AMDS Postmaster) Nntp-Posting-Host: 128.231.218.92 Organization: LB/DCBDC/NCI References: <01HWNY9PZMCI00EDPO@VAXA.CIS.UWOSH.EDU> Date: Fri, 20 Oct 1995 21:35:24 GMT Lines: 37 In article <01HWNY9PZMCI00EDPO@VAXA.CIS.UWOSH.EDU>, lansman@VAXA.CIS.UWOSH.EDU (Bob Lansman) wrote: > At a symposium this summer, Richard Fishel, of the University of Vermont, > made the statement that, in cells with fully functional mismatch repair, > recombination between heterologous Alu sequence is inhibited by lack of > complete homology. But, this type of recombination can occur in tumor cells, > in which mutation in genes like MSH has disabled mismatch repair. Does > anyone have references to work which would support these statments? I think Rick was running with the ball a bit. It is becoming increasingly apparent that mismatch repair functions do inhibit recombination between diverged sequences; however, the small size of Alus may preclude their efficient use for recombination irrespective of their degree of divergence. > Does > anyone have comments regarding the general acceptance of these ideas? I > have always thought that recombination between Alus in different chromosomal > locations was a likely cause of chromosome rearrangements during evolution, > such as the duplication of beta-like globin genes. Is this not a widely > accepted model? Most chromosome rearrangements examined in mammals that I know of (admittedly, biased towards those found in tumors) don't appear to occur at blocks of homology. HOWEVER, this is not to say it can't happen. In fact, John Schimenti has some very provocative evidence that ectopic gene conversion can happen at a very high frequency in the mouse male germ line. My lab has been studying ectopic recombination of this sort in Saccharomyces, and I'll post an abstract describing this work as soon as the paper is finished. -- Michael Lichten lichten@helix.nih.gov From owner-recombination@net.bio.net Thu Oct 19 23:00:00 1995 Path: biosci!ATLAS.ODYSSEE.NET!dellaire From: dellaire@ATLAS.ODYSSEE.NET (Dellaire, Graham) Newsgroups: bionet.molbio.recombination Subject: Re: RECOMBINATION/bionet.molbio.recombination is ready! Date: 20 Oct 1995 14:36:34 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 64 Sender: daemon@net.bio.net Distribution: world Message-ID: <9510202133.AA01982@odyssee.net> NNTP-Posting-Host: net.bio.net >In Article <468aog$se0@epervier.CC.UMontreal.CA>, szat@ERE.UMontreal.CA >(Szatmari George) wrote: > >[snip] > >>I'd like to start things rolling by posing a question about yeast. >>Why are yeast (notably S. cerevisiae) so recombinogenic, when >>higher eukaryotes and prokaryotes are not? Is this due to a more >>active recA-like protein (or proteins)? Or is it something >>totally different? > >Could it be that a mistake in recombination in a unicellular organism only >risks itself (the cells dies), while in a multicellular organism, a mistake >in recombination risks the entire organism (tumor - organism 10E6-10E9 cells >die)? > >Brian D. Halligan halligan@post.its.mcw.edu I think it may be inpart the fact that Yeast lacks one of the most important Histones from an accessibility point of view...H1.. It is well know that when you remove H1 you get different DNaseI parterns which indicates a change in accessibility of the DNA. Therefore DNA is going to be less compact in Yeast than in mammalian cells and more accessible to recombination and enzymes that may promote recombination (Topo I+ II, DnaseI etc.). Secondly, homologous recombination is very efficient in Yeast and not so efficient (if we can even use the word effecient in the same context as mammalian homologous recombination) in mammals. On the other hand the reverse is true. Mammalian cells are extremely efficient at illegitimate nonhomologous recombination and Yeast are pitiful in this respect. Perhaps these two differences are derived most basically from the fact that we as mammals are multicellular and yeast are not. When we have a break in our DNA our cells try to fix it as fast as possible... DNA free ends=death for most cells. In yeast this is not such a necessity if the cell dies it is only one of millions or billions in a colony and because of a quick generation time even if one cell survives from a colony with in three days you have another colony. If many of your cells die, particularly in an organ such as the liver or heart... the whole organism dies. This leads into more efficient homologous recombination in Yeast. We know that if homolgous recombination was very active in mammalian cells (to the level it is in yeast) your cells would accumulate horrible genome rearrangments in no time. This could occur by simple cross over say between histone genes or ribosomal rna's etc, never mind the 100,000 or so Line-1 sequences or ~500,000 alu's! Thus it makes sense that in mammalian cells homologous recombination is much less efficient than yeast. Now as why Yeast are more recombinogenic than bacteria... that is open as frankly I haven't the faintest idea where to begin. Graham Dellaire > ******************************************************** Graham Dellaire Snail Mail Div. of Experimental Medicine Institute du Cancer de Montreal Dept. of Medicine Louis Charles-Simard McGill University 1560 Sherbrooke Street E. e-mail:dellaire@odyssee.net Montreal, Quebec, Canada or B2XE@musicb.mcgill.ca ******************************************************** From owner-recombination@net.bio.net Thu Oct 19 23:00:00 1995 Path: biosci!ATLAS.ODYSSEE.NET!dellaire From: dellaire@ATLAS.ODYSSEE.NET (Dellaire, Graham) Newsgroups: bionet.molbio.recombination Subject: Re: Alu sequences as portable regions of homology Date: 20 Oct 1995 14:18:00 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 68 Sender: daemon@net.bio.net Distribution: world Message-ID: <9510202115.AA00970@odyssee.net> NNTP-Posting-Host: net.bio.net >At a symposium this summer, Richard Fishel, of the University of Vermont, >made the statement that, in cells with fully functional mismatch repair, >recombination between heterologous Alu sequence is inhibited by lack of >complete homology. But, this type of recombination can occur in tumor cells, >in which mutation in genes like MSH has disabled mismatch repair. Does >anyone have references to work which would support these statments? Does >anyone have comments regarding the general acceptance of these ideas? I >have always thought that recombination between Alus in different chromosomal >locations was a likely cause of chromosome rearrangements during evolution, >such as the duplication of beta-like globin genes. Is this not a widely >accepted model? > The "Homeology" affects the migration of cross overs through homology very strongly and therefore inhibits gene conversion and shunts the recombination intermediate to another non integrative (non crossover) pathway. The result is a net drop in exchange between regions that are not 100% homologous as in Line-1 elements and Alu's. So goes the current hypotheses In my lab in (I work with Pierre Chartrand) they have done much work with Line-1 elements... there are some interesting papers by A. Belamaaza et al. and J. F.Villemure et al. that address the topic of homeology and recombination and they suggest reasons (including mismatch repair) for the apparent inhibition of cross over between regions that are homeologous. I believe both papers are in MCB (Villemure is 95 and the other is 94 or 93) If you do a medline for these authors you should find their papers easily. I will try to get the exact references if you wish but it will be Monday or later. To address the embryonic question. In the case of line-1's there is evidence that they are active as retroposons during embryogenesis. Supposedly the putative transposase found in full length Line's is transcribed in embryonic cells. Therefore you can invision integration of these elements once reverse transcribed into functional genes and disrupting them. Also in embryonic cells there is evidence that the genome is more open... ie. more genes are transcribable, more replication origins may be firing or in use (you need to rapidly duplicate cells in early development say from one cell to full blastula in 8 days) and hence probably more recombination. Just think of the DNA looping folding being cut by topoisomerases and gyrases etc to eleviate all the strain from replication and transcription and you are bound to have a stray end of DNA available for recombination. It may be that DNA mismatch system is saturated at this point (or perhaps are all DNA repair mechanisms) just by the shear number of mistakes occurring during this rapid burst of growth, and you then get stray exchanges of DNA between ALu's and line's. These exchanges do happen often enough such that quite a few hereditary disease can be ascribed to insertion of retroposable elements in functional genes. The Beta Globin locus is particularly recombinogenic and perhaps this is again (like in the embryo) linked to accessibility of the DNA because of high transcription rates and the fact that I believe there is a origin of replication linked to this locus. Graham Dellaire ******************************************************** Graham Dellaire Snail Mail Div. of Experimental Medicine Institute du Cancer de Montreal Dept. of Medicine Louis Charles-Simard McGill University 1560 Sherbrooke Street E. e-mail:dellaire@odyssee.net Montreal, Quebec, Canada or B2XE@musicb.mcgill.ca ******************************************************** From owner-recombination@net.bio.net Thu Oct 19 23:00:00 1995 Path: biosci!bdg10.niddk.nih.gov!KAYUWEW From: KAYUWEW@bdg10.niddk.nih.gov ("WAGNER, KAY-UWE") Newsgroups: bionet.molbio.recombination Subject: (none) Date: 20 Oct 1995 16:59:55 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 1 Sender: daemon@net.bio.net Distribution: world Message-ID: <308837B1@SMTP2.mm.hub.nih.gov> NNTP-Posting-Host: net.bio.net Who has antibodies for Cre recombinase? From owner-recombination@net.bio.net Thu Oct 19 23:00:00 1995 Path: biosci!agate!howland.reston.ans.net!newsfeed.internetmci.com!chi-news.cic.net!uwm.edu!post.its.mcw.edu!post!halligan From: halligan@post.its.mcw.edu (Brian Halligan) Newsgroups: bionet.molbio.recombination Subject: Re: RECOMBINATION/bionet.molbio.recombination is ready! Date: Fri, 20 Oct 95 18:46:43 GMT Organization: Department of Microbiology, Medical College of Wisconsin Lines: 20 Distribution: world Message-ID: References: <45v661$lqr@net.bio.net> <468aog$se0@epervier.CC.UMontreal.CA> NNTP-Posting-Host: d256-1.microb.mcw.edu X-Newsreader: VersaTerm Link v1.1.1 In Article <468aog$se0@epervier.CC.UMontreal.CA>, szat@ERE.UMontreal.CA (Szatmari George) wrote: [snip] >I'd like to start things rolling by posing a question about yeast. >Why are yeast (notably S. cerevisiae) so recombinogenic, when >higher eukaryotes and prokaryotes are not? Is this due to a more >active recA-like protein (or proteins)? Or is it something >totally different? Could it be that a mistake in recombination in a unicellular organism only risks itself (the cells dies), while in a multicellular organism, a mistake in recombination risks the entire organism (tumor - organism 10E6-10E9 cells die)? Brian D. Halligan halligan@post.its.mcw.edu Assistant Professor 414-456-8413 (voice) Department of Microbiology 414-266-8522 (FAX) Medical College of Wisconsin From owner-recombination@net.bio.net Fri Oct 20 23:00:00 1995 Newsgroups: bionet.molbio.recombination Path: biosci!lhc.nlm.nih.gov!nih-csl!NewsWatcher!user From: lichten@helix.nih.gov (Michael Lichten) Subject: Re: Alternative mech. to resolve Holliday junctions? Message-ID: Sender: postman@alw.nih.gov (AMDS Postmaster) Nntp-Posting-Host: 128.231.218.92 Organization: LB/DCBDC/NCI References: <468a8r$ssk@news.duke.edu> Date: Sat, 21 Oct 1995 20:03:42 GMT Lines: 24 In article <468a8r$ssk@news.duke.edu>, djt@rpiv.mc.duke.edu (Dan Tomso) wrote: > Greetings. > I'd like to collect information on alternative mechanisms for > resolving Holliday junctions. By 'alternative,' I mean mechanisms which > don't involve a specific resolvase activity. I'm working in a system > (T4) where a lot of recombination can occur even in resolvase mutants > (endo VII mutants), and I'm wondering what the mechanisms of resolution > might be. 1. Replication. Makes 2 parental and 2 recombined molecules 2. Branch migration to two nick at the same place on the appropriate strands (not very likely, huh?) 3. Branch migration to a nick in one of the crossing strands. Turns the junction into two replicating forks. 1 and 3 have pretty dire consequences for a chromosomal organism but for bacteriophage such as T4 or lambda that just need a unit lenght + a bit genome to be packaged, I think it's likely that these strategies are often used. -- Michael Lichten lichten@helix.nih.gov From owner-recombination@net.bio.net Fri Oct 20 23:00:00 1995 Path: biosci!agate!dog.ee.lbl.gov!news.cs.utah.edu!cs.utexas.edu!uunet!in2.uu.net!solaris.cc.vt.edu!news.duke.edu!rpiv.mc.duke.edu!djt From: djt@rpiv.mc.duke.edu (Dan Tomso) Newsgroups: bionet.molbio.recombination Subject: Alternative mech. to resolve Holliday junctions? Date: 20 Oct 1995 14:04:11 GMT Organization: Duke University, Durham, NC, USA Lines: 13 Message-ID: <468a8r$ssk@news.duke.edu> NNTP-Posting-Host: rpiv.mc.duke.edu X-Newsreader: TIN [version 1.2 PL2] Greetings. I'd like to collect information on alternative mechanisms for resolving Holliday junctions. By 'alternative,' I mean mechanisms which don't involve a specific resolvase activity. I'm working in a system (T4) where a lot of recombination can occur even in resolvase mutants (endo VII mutants), and I'm wondering what the mechanisms of resolution might be. I'm also curious as to just how large the readership for this newsgroup is. Hopefully, this thread will spawn some discussion and let me survey (passively) the participants at the same time. Dan Tomso From owner-recombination@net.bio.net Fri Oct 20 23:00:00 1995 Newsgroups: bionet.molbio.recombination Path: biosci!agate!howland.reston.ans.net!newsfeed.internetmci.com!uunet!in1.uu.net!nih-csl!NewsWatcher!user From: lichten@helix.nih.gov (Michael Lichten) Subject: Re: RECOMBINATION/bionet.molbio.recombination is ready! Message-ID: Sender: postman@alw.nih.gov (AMDS Postmaster) Nntp-Posting-Host: 128.231.218.92 Organization: LB/DCBDC/NCI References: <9510202133.AA01982@odyssee.net> Date: Sat, 21 Oct 1995 19:56:04 GMT Lines: 22 In article <9510202133.AA01982@odyssee.net>, dellaire@ATLAS.ODYSSEE.NET (Dellaire, Graham) wrote: > Secondly, homologous recombination is very efficient in Yeast and not so > efficient (if we can even use the word effecient in the same context as > mammalian homologous recombination) in mammals. On the other hand the > reverse is true. Mammalian cells are extremely efficient at illegitimate > nonhomologous recombination and Yeast are pitiful in this respect. Is this really true? What's the efficiency at which mammalian cells repair joints illegitimately--on a per break basis? Is it really that efficient? Let's come up with some numbers before we start speculating as to whether a single death in a colony is worse than a single death in a liver! My guess is that no one really knows what the efficiency of break repair is in mammalian cells. Transfection experiments don't count--an I think that everyone in this thread is basing their conclusions on those experiments. Give me an experiment in which the efficiency of recovery is given in terms of input molecules, please. -- Michael Lichten lichten@helix.nih.gov From owner-recombination@net.bio.net Fri Oct 20 23:00:00 1995 Path: biosci!ATLAS.ODYSSEE.NET!dellaire From: dellaire@ATLAS.ODYSSEE.NET (Dellaire, Graham) Newsgroups: bionet.molbio.recombination Subject: Re:Yeast Vs. Mammalian cells con't Date: 21 Oct 1995 15:54:20 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 116 Sender: daemon@net.bio.net Distribution: world Message-ID: <9510212251.AA06092@odyssee.net> NNTP-Posting-Host: net.bio.net >In article <9510202133.AA01982@odyssee.net>, dellaire@ATLAS.ODYSSEE.NET >(Dellaire, Graham) wrote: > >> Secondly, homologous recombination is very efficient in Yeast and not so >> efficient (if we can even use the word effecient in the same context as >> mammalian homologous recombination) in mammals. On the other hand the >> reverse is true. Mammalian cells are extremely efficient at illegitimate >> nonhomologous recombination and Yeast are pitiful in this respect. > >Is this really true? What's the efficiency at which mammalian cells >repair joints illegitimately--on a per break basis? Is it really that >efficient? Okay from personal experience homologous recombination in my hands is very inefficient in comparison to illegitimate recombination. For example using the same construct I can get one targeted event in 500,000 cells (ie. one clone after selection for a reconstituted marker) using calcium phosphate transfection with ~20 ug of DNA ( for LTA murine fibroblasts.). Now when I select for illegitimate events... I get on average ~700 to 1000 clones. Even though many events are not counted because they fail to produce a selectable gene product (integrated in heterochromatin what have you) you can assume for all intents and purposese that the numbers are relative. So from my point of view in LTA's illegitimate recombination (reflected by the number of cells that have integrated a construct and produced a selectable marker) is much more efficient than homologous recombination. Three logs more efficient. I see a similar ratio with electropration. Now I do not see homology driven events if they do not result in the reconstitution of my selectable gene. So one could argue that the actual homologous recombination is higher than measured. It has not been proven that illegitimate events do not first involve some sort of homology search, in fact my current thesis project aims to shed some light on this. But on the most basic level from transfection experiments it seems that illegitimate events (as measured by integration and expression of a selectable gene) are more common than targeted events. As far as efficiency of recombination on a per break basis this would be hard to measure. It is hard to determine the amount of DNA that enters each cell in any given transfection method. For most transfection methods the mode of DNA entry into the nucleus has not been sufficiently determined. So one, you can't measure the amount of DNA your cells took up and secondly, you don't know how much of the DNA made it into the nucleus and finally, you don't know when the DNA was integrated. All of this makes it hard to calculate the number of envents per break. On top of this as discussed above you have a bias for events that produce a functional selection gene that has integrated in the genome at a site where it is expressed. > Let's come up with some numbers before we start speculating as >to whether a single death in a colony is worse than a single death in a >liver! My guess is that no one really knows what the efficiency of break >repair is in mammalian cells. Transfection experiments don't count--an I >think that everyone in this thread is basing their conclusions on those >experiments. Okay if you look at one somatic cell it may not be such a big deal at first glance. Cells die all the time particularly in the epithelia and the organism is not adversly affected. If this rearrangement leads to a tumor cell phenotype it is a different story. Secondly if you assume that a rearrangement would be able to occur in embryonic cells the death of a precursor cell (basis of fate mapping) could have severe effects on the organism. Missing limbs etc. Yeast do not have such complexities to worry about. A rearrangement in a hemopoietic myleogenic precursor (say something like the bcr/abl rearrangement) can lead to leukemias that can kill the organism regardless of whether the rest of the cells in the organism are functioning well. I think this is more clear now as to the point I was trying to make. Yeast in a colony don't have to worry about maintaining complex systems (such as organs) and the level of development in higher eukaryotes is much greater...hence there is more pressure to have cells divide correctly and maintain there genomic integrity in multicellular complex organisms. Another particularly interesting aspect to this is the number of introns..... yeast have a paucity and mammalian cells have a plethora. Perhaps this is a mechanism to minimize the damage of rearrangements in complex organisms. The more extraneous non coding material the less chance of a rearrangement ablating a gene function. > Give me an experiment in which the efficiency of recovery is >given in terms of input molecules, please. > >Michael Lichten >lichten@helix.nih.gov AS discussed above this is hard if not nearly impossible to do with current transfection protocols (sucha as CaPO4, electroporation or lipofection) as you can not be 100 percent certain of the amount of DNA that is taken up by any given cell. Microinjection may be a different story... I know in Xenopus you can inject nuclei with Linear DNA and in this way you know the number of input molecules. In Xenopus the end-end joining (illegitimate recombination) is very effecient. I am sure there must be a similar experiment with mammalian cells, if there isn't it should be simple enough to do. Graham Dellaire ******************************************************** Graham Dellaire Snail Mail Div. of Experimental Medicine Institute du Cancer de Montreal Dept. of Medicine Louis Charles-Simard McGill University 1560 Sherbrooke Street E. e-mail:dellaire@odyssee.net Montreal, Quebec, Canada or B2XE@musicb.mcgill.ca ******************************************************** From owner-recombination@net.bio.net Sat Oct 21 23:00:00 1995 Path: biosci!agate!news.ucdavis.edu!rocky.ucdavis.edu!ez020665 From: WOOKIE Newsgroups: bionet.molbio.recombination Subject: Other newsgroups like this? Date: Sat, 21 Oct 1995 20:17:00 -0700 Organization: University of California, Davis Lines: 2 Message-ID: NNTP-Posting-Host: rocky.ucdavis.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: ez020665@rocky.ucdavis.edu Does anyone know of any other newsgroups like this one? rich From owner-recombination@net.bio.net Sat Oct 21 23:00:00 1995 Path: biosci!agate!news.ucdavis.edu!boris.ucdavis.edu!fznewt From: Jeff 'Newt' Sekelsky Newsgroups: bionet.molbio.recombination Subject: Re: Alternative mech. to resolve Holliday junctions? Date: Sun, 22 Oct 1995 16:31:07 -0700 Organization: University of California, Davis Lines: 23 Message-ID: NNTP-Posting-Host: boris.ucdavis.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: fznewt@boris.ucdavis.edu In-Reply-To: <468a8r$ssk@news.duke.edu> On 20 Oct 1995, Dan Tomso wrote: > Greetings. > I'd like to collect information on alternative mechanisms for > resolving Holliday junctions. By 'alternative,' I mean mechanisms which > don't involve a specific resolvase activity. I'm working in a system > (T4) where a lot of recombination can occur even in resolvase mutants > (endo VII mutants), and I'm wondering what the mechanisms of resolution > might be. > I'm also curious as to just how large the readership for this > newsgroup is. Hopefully, this thread will spawn some discussion and let > me survey (passively) the participants at the same time. > > Dan Tomso > > For an even number of Holliday junctions (e.g. the double Holliday junction intermediate in the double-strand break repair model of recombination), Thaler, Stahl, and Stahl (1987, Genetics 116: 501) suggested that resolution can occur without resolvase by the unwinding activity of a topoisomerase. Jeff Sekelsky From owner-recombination@net.bio.net Sat Oct 21 23:00:00 1995 Path: biosci!CS.Arizona.EDU!uunet!in2.uu.net!newsflash.concordia.ca!feed.umontreal.ca!szat From: szat@ERE.UMontreal.CA (Szatmari George) Newsgroups: bionet.molbio.recombination Subject: Re: RECOMBINATION/bionet.molbio.recombination is ready! Date: 20 Oct 1995 14:12:32 GMT Organization: Universite de Montreal Lines: 15 Distribution: world Message-ID: <468aog$se0@epervier.CC.UMontreal.CA> References: <45v661$lqr@net.bio.net> NNTP-Posting-Host: alize.ere.umontreal.ca Dear readers, Thanks to all who voted "yes" to the formation of this newsgroup. I'm looking forward to many fruitful discussions about recombination. I'd like to start things rolling by posing a question about yeast. Why are yeast (notably S. cerevisiae) so recombinogenic, when higher eukaryotes and prokaryotes are not? Is this due to a more active recA-like protein (or proteins)? Or is it something totally different? George Szatmari (just a bacterial mol. biologist) Dept de microbiologie, Univ de Montreal From owner-recombination@net.bio.net Tue Oct 24 22:00:00 1995 Path: biosci!CS.Arizona.EDU!uunet!in1.uu.net!usenet.eel.ufl.edu!newsfeed.internetmci.com!howland.reston.ans.net!agate!news.duke.edu!rpiv.mc.duke.edu!djt From: djt@rpiv.mc.duke.edu (Dan Tomso) Newsgroups: bionet.molbio.recombination Subject: Re: RECOMBINATION/bionet.molbio.recombination is ready! Date: 23 Oct 1995 02:28:49 GMT Organization: Duke University, Durham, NC, USA Lines: 46 Distribution: world Message-ID: <46eul1$r92@news.duke.edu> References: <45v661$lqr@net.bio.net> <468aog$se0@epervier.CC.UMontreal.CA> NNTP-Posting-Host: rpiv.mc.duke.edu X-Newsreader: TIN [version 1.2 PL2] Greetings. I have a few comments (and questions) on this: Szatmari George (szat@ERE.UMontreal.CA) wrote: : I'd like to start things rolling by posing a question about yeast. : Why are yeast (notably S. cerevisiae) so recombinogenic, when : higher eukaryotes and prokaryotes are not? Most of the followup on this thread (which I have omitted for brevity) seems to revolve around this question: Is yeast really more recombinogenic, or do we just lack an adequate measure for meaningful comparison? It seems that transfection assays are not necessarily the best measure, since they ask for a lot of things to happen: DNA must enter the cells, find its homologue in a very large genome, and recombine in such a way as to produce a viable cell. I'm not sure what the right question to ask is, but here are some things that I am curious about: How do the frequencies of meiotic recombination events (e.g. gene conversion) compare between S. cerevisiae and, say, Drosophila? Have any experiments been done in mammalian or other euk. cells with defined substrates capable of undergoing 'internal' recombination (e.g. plasmids with 2 homologous segments). These kinds of experiments have been used extensively in yeast and bacterial sytems to measure all sorts of recombination events. You can often measure recombination directly, with a physical assay (Southern blotting). Something like this might simplify comparisons. I seem to remember seeing something like this in a recent issue of Genetics. Incidentally, I can think of a few organisms with recombination 'machinery' that is really impressive. Phage T4 (where I spend my days) shows recombination frequencies as high as 10% per 1000 bases, which means that markers as close as 5 kb assort almost independently. Another fun one is D. radiodurans, which I believe came to the attention of the field when it was cultured from a can of spoiled meat that had been (supposedly) gamma ray sterilized. I recall seeing an abstract that suggested this species can survive upwards of 150 double strand breaks. I really have no point to make with regard to these last two observations, other than to express general fascination with the mystery of recombination. Also, I suppose, I felt slighted when yeast was described as 'more recombinogenic' in an unqualified way. :) Why one organism should be more recombinogenic than another is a difficult question to address, especially without a convenient approach to 'cross-platform' experimentation. From owner-recombination@net.bio.net Thu Oct 26 22:00:00 1995 Path: biosci!agate!news.Stanford.EDU!NewsWatcher!user From: schreibr@cmgm.stanford.edu (Edgar Schreiber) Newsgroups: bionet.molbio.recombination Subject: optimization for generating recombinant Adenoviruses Followup-To: bionet.molbio.recombination Date: 26 Oct 1995 03:53:48 GMT Organization: Stanford University Lines: 7 Message-ID: NNTP-Posting-Host: tip-mp8-ncs-6.stanford.edu I would appreciate any comments and protocols that are helpful to enhance the frequency of plasmid to plasmid recombination in mammalian 293 cells for the generation of recombinant Adenoviruses. Is electroporation more "recombinogenic" than CaPO transfection ? Thank you Edgar schreibr@cmgm.stanford.edu From owner-recombination@net.bio.net Thu Oct 26 22:00:00 1995 Path: biosci!news.Stanford.EDU!agate!dog.ee.lbl.gov!news.cs.utah.edu!cs.utexas.edu!swrinde!howland.reston.ans.net!vixen.cso.uiuc.edu!newsrelay.iastate.edu!news.iastate.edu!usenet From: "Patrick S. Schnable" Newsgroups: bionet.molbio.recombination Subject: abstract from Dec Issue of The Plant Cell Date: 25 Oct 1995 14:59:42 GMT Organization: Iowa State Univ Lines: 22 Message-ID: <46ljcu$c4t@news.iastate.edu> NNTP-Posting-Host: pc2696.agron.iastate.edu Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 1.1N (Macintosh; I; 68K) X-URL: news:bionet.molbio.recombination I liked Michael Lichten's idea to post recombination abstracts here. I'll start the ball rolling with: Xu XJ, A-P Hsia, L Zhang, BJ Nikolau, PS Schnable (1995) Meiotic recombination breakpoints resolve at high rates at the 5¹ end of a maize coding sequence. Plant Cell, in press (scheduled for the December issue). Sequence analysis of recombination break points has defined a 377-bp recombination hot spot within the anthocyanin1 (a1) gene. One-fifth of all recombination events that occurred within the 140-kb a1-shrunken2 (sh2) interval resolved within this 377-bp hot spot. In yeast, meiotic double-strand breaks in chromosomal DNA are thought to initiate recombination and are generally located 5¹ of coding regions, near transcription promoter sequences. Because the a1 recombination hot spot is located within the 5¹ transcribed region of the a1 gene, the sites at which recombination events initiate and resolve appear to be different, but both appear to be regulated in relation to transcribed sequences. Although transposon insertions are known to suppress recombination and alter the ratio of crossovers to apparent gene conversions, the Mutator1 (Mu1) transposon insertion in the a1-mum2 allele does not alter the sites at which recombination events resolve. From owner-recombination@net.bio.net Thu Oct 26 22:00:00 1995 Path: biosci!dh.com!bkatz From: bkatz@dh.com (Boris Katz) Newsgroups: bionet.molbio.recombination Subject: subscribe RECOMBINATION Date: 26 Oct 1995 20:43:21 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 1 Sender: daemon@net.bio.net Distribution: world Message-ID: sibscribe RECOMBINATION Boris Katz From owner-recombination@net.bio.net Fri Oct 27 22:00:00 1995 Path: biosci!CS.Arizona.EDU!uunet!in1.uu.net!newsfeed.internetmci.com!info.ucla.edu!library.ucla.edu!agate!news.ucdavis.edu!chip.ucdavis.edu!fznewt From: Jeff 'Newt' Sekelsky Newsgroups: bionet.molbio.recombination Subject: Re: RECOMBINATION/bionet.molbio.recombination is ready! Date: Tue, 24 Oct 1995 10:48:17 -0700 Organization: University of California, Davis Lines: 29 Message-ID: NNTP-Posting-Host: chip.ucdavis.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: fznewt@chip.ucdavis.edu In-Reply-To: <46eul1$r92@news.duke.edu> On 23 Oct 1995, Dan Tomso wrote: > How do the frequencies of meiotic recombination events (e.g. gene > conversion) compare between S. cerevisiae and, say, Drosophila? > Meiotic gene conversion is rare enough in Drosophila to make it difficult to study. Nonetheless, Art Chovnick and his colleagues have done beautiful studies on conversion in the rosy (ry) gene. Chovnick determined the conversion frequencies of a number of alleles to be in the range of 1/50,000 to 1/250,000. The only reason the experiments can be done is that one can select for ry+ recombinants by adding purine to the medium. Conversion frequencies are comparable at the few other loci in which it's been measured (rudimentary, maroon-like, mei-41) which also have selections for wild-type recombinants. Exchange is probably also less frequent in Drosophila relative to yeast, measured either per chromosome, per genome, or per bp. I don't know the numbers for S. cerevisiae, but for S. pombe, the chromosomes are 940, 740, and 540 cM, corresponding to an average of 19, 15, and 11 exchanges per chromosome per meiosis. In Drosophila, each of the five major chromosome arms is about 50-60 map units (I don't why Drosophila geneticists, of all people, don't use cM as the unit), corresponding to about one exchange per arm per meiosis. Although there are regions where there seems to be more exchange per bp than expected, I'm unaware of any hot spots like those in yeast. Jeff Sekelsky From owner-recombination@net.bio.net Fri Oct 27 22:00:00 1995 Path: biosci!daresbury!hgmp.mrc.ac.uk!mraabe From: mraabe@hgmp.mrc.ac.uk (Dr. M Raabe) Newsgroups: bionet.molbio.recombination Subject: Cre expressing mice Date: 28 Oct 1995 14:42:09 GMT Organization: UK HGMP Resource Centre Lines: 14 Message-ID: <46tfg1$8om@mercury.hgmp.mrc.ac.uk> NNTP-Posting-Host: tin.hgmp.mrc.ac.uk Hi, I am interested in mice expressing the Cre recombinase under tissue-specific promoters. Does anybody have mice with Cre expressing in hepatocytes or enterocytes or testis or yolk sac? Anybody interested in a collaboration on that? Is there any commercial dealer who has already set up such strains? I would appreciate any informations. Thank you, Martin ----------------------------------------------------------------------- Martin Raabe Phone: +49-251-836293 Institute for Atherosclerosis Research FAX: +49-251-837225 University of Muenster, Germany email: mraabe at hgmp.mrc.ac.uk From owner-recombination@net.bio.net Fri Oct 27 22:00:00 1995 Path: biosci!agate!news.ucdavis.edu!library.ucla.edu!newsfeed.internetmci.com!in1.uu.net!utcsri!newsflash.concordia.ca!canopus.cc.umanitoba.ca!news From: "R.D. Gietz" Newsgroups: bionet.molbio.recombination Subject: CANADIAN PROFESSORS STRIKE FOR ACADEMIC FREEDOM Date: 26 Oct 1995 22:11:02 GMT Organization: University of Manitoba Lines: 30 Message-ID: <46p11m$9m0@canopus.cc.umanitoba.ca> NNTP-Posting-Host: gietz2.hgen.umanitoba.ca Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.12(Macintosh; I; PPC) X-URL: news:bionet.molbio.recombination On October 17, 1995 Professors at the University of Manitoba, Winnipeg, Canada, went on strike in a bid to stop their administration (fully supported by a Conservative provincial government) from destroying academic freedom at our university. This strike is not about money. UMFA (University of Manitoba Faculty Association) has already offered to accept reduced wages sufficient to meet the difficult financial circumstances. The government is demanding the right to downsize by laying off staff in any department in an arbitrary manner. The proposed changes to our contract would allow the administration to fire individual professors who are challenging conventional wisdom, academics who speak out on public issues, and faculty who criticize the administration. WE ARE A TEST CASE AND IF WE FAIL, YOUR UNIVERSITY COULD BE NEXT. PLEASE, GIVE US YOUR SUPPORT. We wish to reach concerned academics world wide. If we have intruded onto your newsgroup with an off topic message, please excuse us. For more information please consult http://www.xpressnet.com/umfa Letters of support to umfa@xpressnet.com Letters of complaint to Premier Gary Filmon FAX: 204-949-1484 (preferred) or premier@leg.gov.mb.ca From owner-recombination@net.bio.net Sat Oct 28 22:00:00 1995 Path: biosci!agate!howland.reston.ans.net!newsfeed.internetmci.com!in2.uu.net!newsflash.concordia.ca!news.mcgill.ca!news From: Graham Dellaire Newsgroups: bionet.molbio.recombination Subject: Re: optimization for generating recombinant Adenoviruses Date: 29 Oct 1995 17:39:54 GMT Organization: McGill University Computing Centre Lines: 23 Message-ID: <470e9a$5d1@sifon.cc.mcgill.ca> References: NNTP-Posting-Host: q-07.das.mcgill.ca X-Newsreader: AIR News 3.X (SPRY, Inc.) > schreibr@cmgm.stanford.edu (Edgar Schreiber) writes: > I would appreciate any comments and protocols that are helpful to enhance > the frequency of plasmid to plasmid recombination in mammalian 293 cells > for the generation of recombinant Adenoviruses. Is electroporation more > "recombinogenic" than CaPO transfection ? > Thank you > Edgar > schreibr@cmgm.stanford.edu > >>>> Dear Edgar, The main difference between Electroporation and CaPO4 precipitation is that with electroporation you get single molecules entering the nucleus rather than complexes of DNA molecules as in CaPO4. The efficiencies are atleast two logs higher for CaPO4 precipation vs. electroporation. Since this alone will increase the number of inter-plasmid recombination events this would be your best choice. Graham Dellaire Primary Discussion Leader RECOM dellaire@odyssee.net From owner-recombination@net.bio.net Sat Oct 28 22:00:00 1995 Path: biosci!news.Stanford.EDU!agate!news.duke.edu!rpiv.mc.duke.edu!djt From: djt@rpiv.mc.duke.edu (Dan Tomso) Newsgroups: bionet.molbio.recombination Subject: Thanks for help with Holliday junctions Date: 24 Oct 1995 21:00:03 GMT Organization: Duke University, Durham, NC, USA Lines: 13 Message-ID: <46jk4j$d4c@news.duke.edu> NNTP-Posting-Host: rpiv.mc.duke.edu X-Newsreader: TIN [version 1.2 PL2] Greetings. Thanks for all the responses. For the curious, my original question concerned mechanisms for resolving Holliday junctions that didn't involve specific resolvase activities. Most of the responses described mechanisms that required branch migration up to a nick (or nicks), and often involved conversion of the junction into replication forks. Topoisomerase resolution was also suggested. Is anybody aware of experiments which have specifically looked for these mechanisms? For example, synthetic lethal screens or similar approaches in resolvase-deficient backgrounds? DT From owner-recombination@net.bio.net Sun Oct 29 22:00:00 1995 Path: biosci!news.Stanford.EDU!agate!howland.reston.ans.net!newsfeed.internetmci.com!in2.uu.net!newsflash.concordia.ca!news.mcgill.ca!news From: Graham Dellaire Newsgroups: bionet.molbio.recombination Subject: WELCOME TO RECOM Date: 29 Oct 1995 17:46:44 GMT Organization: McGill University Computing Centre Lines: 298 Message-ID: <470em4$5d1@sifon.cc.mcgill.ca> NNTP-Posting-Host: q-07.das.mcgill.ca X-Newsreader: AIR News 3.X (SPRY, Inc.) *************************************************** BIONET.MOLBIO.RECOMBINATION is open FOR BUSINESS!!! *************************************************** First of all I would like to thank everyone who has given input and support for the creation of this news group. Particularly those in in the beginning who lent their support and ideas and eventually their vote! Opening comments 1.If you wish to participate via NEWS primarily you should be forewarned that the onus is upon you to ask your Institution to update their news feed and include this new group. This should be as easy as sending an e-mail to your local computing fascility or internet access provider (IAP) as the case maybe. (see below) I myself have to do this and I am the principal discussion leader! 2. For those of you who do not have NEWS access (USENET or BITNET etc), it possible to subscribe to the list service for this news group. Please refer to the relevant sections below in the document provided by BIONET. 3. All suggestions for the content of our discussion are welcome. so far suggestions that may be adopted are as follows: a)Job Listing (post doc, Institution listings etc) b)Postings of concise editorials on given areas of participants expertise c)Postings of abstracts from recently published works or from pre-prints where applicable d)Postings of dates and sites of upcoming meetings e)Posting of brief resumes of the events of the recent meetings. f)Posting of a recombination FAQ including: -reference lists for separate topics in recombination -lists of web resources (FTP,GOPHER etc) for genetics and recombination -broad introductory sections on particular aspects of recombination to be contributed by participants in the group. -news group charter -contact information for discussion leaders -perhaps posting of addresses of institutions that work in genetics as well as key laboratories (basically if you give me your address we will try to include it) Well that is all for now, thank you again for your support and hope to see you in future discussions in bionet.molbio.recombination Below is a blurb on how to subscribe and how to notify your news provider so they update their list of groups to include our recombination new group. Graham dellaire@odyssee.net ****note: please use this address for all correspondance (dellaire@odyssee.net).**** <---- Begin Included Message ----> Subject: RECOMBINATION is ready! Cc: biosci-help@net.bio.net This just went out on your newsgroup as well as bionet.announce and bionet.general. Best wishes! Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net Newsgroups: bionet.molbio.recombination Subject: RECOMBINATION/bionet.molbio.recombination is ready! Distribution: world Organization: BIOSCI International Newsgroups for Biology The RECOMBINATION/bionet.molbio.recombination newsgroup is ready for operation. Please save these usage instructions for future reference!! PLEASE NOTE that many USENET sites do not allow automatic creation of new USENET groups!!! If you do not see bionet.molbio.recombination in your newsreader within another day or two, ask your news system administrator to act on our "newgroup" message to enable the group at your site. We have already done several tests and are certain that the group is currently propagating around the network. If he/she can not find the newsgroup message, have them retrieve the bionet checkgroups message from the anonymous FTP area on net.bio.net in pub/BIOSCI/doc/bionet-checkgroups-msg. This file contains the latest list of bionet USENET newsgroups and can be used to update your bionet distribution. If the newgroup did not arrive at your site, it may also be necessary for your news administrator to contact the upstream computer site providing you with your newsfeed and determine if they acted on the newgroup message. Subscribing to this group: -------------------------- IF YOU USE USENET NEWS: you need do nothing other than participate in bionet.molbio.recombination when it appears in your newsreader. Depending upon your news software, this may entail you having to answer a prompt indicating that you want to subscribe. You might also try the command "g bionet.molbio.recombination" in rn-like newsreaders. IF YOU ARE LOCATED IN EUROPE, AFRICA, OR CENTRAL ASIA: please send the word help in the body of your message to MXT@dl.ac.uk to retrieve general server usage instructions. To subscribe to the RECOMBINATION list, first be sure that you are sending mail from the address at which you wish to receive news postings, and then send the command SUB bionet-news.bionet.molbio.recombination to MXT@dl.ac.uk. This message will be automatically read by the computer and your e-mail address will be extracted from the mail header and added to the list. IF YOU ARE LOCATED IN THE AMERICAS OR THE PACIFIC RIM: log in to the computer account in which you would like to receive mail (not an account that you use infrequently) and send a mail message to the Internet address biosci-server@net.bio.net Leave the Subject: line of the message blank and enter the following line into the body of the mail message: subscribe recom This message will be automatically read by our computer and your e-mail address will be extracted from the mail header and added to the list. Canceling your subscription: ---------------------------- IF YOU ARE LOCATED IN EUROPE, AFRICA, OR CENTRAL ASIA: first be sure that you are sending mail from the address at which you signed up to receive news postings, and then send the command (in the body of your mail message) UNSUB bionet-news.bionet.molbio.recombination to MXT@dl.ac.uk. This message will be automatically read by the computer and your e-mail address will be extracted from the mail header and removed from the list. IF YOU ARE LOCATED IN THE AMERICAS OR THE PACIFIC RIM: send a message to biosci-server@net.bio.net exactly as described above for subscribing except include the text unsubscribe recom in the body of the message. Please be sure to send the message from the account whose address matches the one on the list. If your address differs, we will be notified automatically and will remove you manually from the list if we can determine what was your old address. Please contact biosci-help@net.bio.net if you have problems. IF YOU HAVE A PROBLEM: ---------------------- Please send a message to one of the following addresses depending upon your location Address Location ------- -------- biosci@daresbury.ac.uk Europe, Africa, and Central Asia biosci-help@net.bio.net Americas and the Pacific Rim and someone on the staff will help you. PLEASE DO NOT send mail to our personal e-mail addresses as this will delay a response to your request for help. How to post a message to the group: ----------------------------------- If you use news, simply post a message into bionet.molbio.recombination. Be sure to set your "distribution" to "world" or else the message might not leave your site!! To post by e-mail, mail your message to one of the following addresses depending upon your location: Posting Address Location --------------- -------- recom@daresbury.ac.uk Europe, Africa, and Central Asia recom@net.bio.net Americas and the Pacific Rim and your message will be distributed automatically to everyone on the list and the USENET newsgroup. There is no editorial intervention. PLEASE DO NOT SEND SUBSCRIPTION REQUESTS TO THE POSTING ADDRESSES as you will bother everyone on the newsgroup!!! How to reply to a message on the group: --------------------------------------- If you are using a newsreader, simply use the reply or follow-up command on your newsreader (these vary from program to program) to send either private or public replies. If you are using e-mail, replies to messages that you receive will *NOT* be automatically returned to the group. This is the standard for Internet mailing lists as opposed to BITNET LISTSERVs which often send all replies back to everyone. You must be certain that your reply contains either of the two newsgroup posting addresses above in your message header if you want to share it with everyone on the group. Otherwise in most cases your reply may go back to only the original poster of the message to which you are replying. ALWAYS be certain that you examine the address on your messages before you send them!!! Once a message is sent there is no way to cancel it or bring it back!!! Some non-Internet compliant mail systems may attempt to send replies to our error-trapping address called BIOSCI-REQUEST. If yours does this, please be sure to readdress your message to recom@net.bio.net or recom@daresbury.ac.uk if you want to send it to the newsgroup. How to look at archives of the list: ------------------------------------ The BIOSCI archives and other BIOSCI information can be found on our WWW home page at URL http://www.bio.net/. Easy access from the WWW home page to our FTP/gopher area is available for information retrieval. Archives for RECOMBINATION/bionet.molbio.recombination are kept in the anonymous FTP account at net.bio.net [204.31.212.2]. Look in the directory pub/BIOSCI/RECOMBINATION for posting archives. Each file is assigned a date such as 9312 for December 1993. Please note that ours is a UNIX system and all file and directory names are case-sensitive, i.e., upper case file names are different from lower case names. You can also access these same files via Gopher if you start a gopher session using net.bio.net as your gopher server. Gopher also allows you to view the individual messages within each monthly archive file. The files are in the RECOMBINATION directory. Postings to bionet.molbio.recombination are also WAIS indexed and can be searched via either gopher or WAIS at our site. In gopher the option at net.bio.net is "Search Bionet USENET Articles" and in WAIS one should use the WAIS source biosci.src. This is a WAIS index of all BIOSCI/bionet messages including this newsgroup. Please see the BIOSCI FAQ for details. The FAQ can be requested from biosci-help@net.bio.net. Once again, if you have any administrative questions that require personal assistance, please address them to biosci-help@net.bio.net in the U.S. or biosci@daresbury.ac.uk in the UK. Best wishes for a successful newsgroup! Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net <---- End Included Message ----> Primary Discussion leader RECOM Graham Dellaire Faculty of Medicine McGill University Div. of Experimental Medicine e-mail:dellaire@odyssee.net From owner-recombination@net.bio.net Mon Oct 30 22:00:00 1995 Path: biosci!ATLAS.ODYSSEE.NET!dellaire From: dellaire@ATLAS.ODYSSEE.NET (Dellaire, Graham) Newsgroups: bionet.molbio.recombination Subject: CAVEAT on POSTS TO RECOM (or any other group for that matter) Date: 31 Oct 1995 15:35:08 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 61 Sender: daemon@net.bio.net Distribution: world Message-ID: <9510312332.AA15921@odyssee.net> NNTP-Posting-Host: net.bio.net ***************RECOM DISCLAIMER **************** ================================================= Although bionet does archive material posted to its groups this does not ensure protection to intellectual property (ideas, protocols, etc.) Essentially anything posted to RECOM may be considered *PUBLIC DOMAIN*. It may become prudent in the future to acknowledge contributions by particular participants in any group but it is on the initiative and judgment of each individual at this point. I would like to mention that in the beginning before there was a RECOM news group I was approached by _ Derwent Information limited_, a company involved in biomedical patents and the publisher of the GENE THERAPY news letter. They showed interest in abstracting posts from this group. If this should occur and set a precedent for publishing of bionet posts in news letters and journals, once published such posts would become bonafide intellectual property which can be protected by law. I encourage such publishing at face value... BUT definite guidelines should be drawn up and I hope that we in this group can develop at least some preliminary guidelines for those parties that wish to republish our contributions to this news group. Here are a few guideline I suggest we adopt 1. At all times parties involved must be notified in advance that there post is to be published. 2. Any changes to there post must be approved by the party responsible for its posting. 3. Full name, date and news group must be included when a post is referenced or republished in any form Further additions/discussion to these guidelines is encouraged Graham Dellaire Primary Discussion leader RECOM dellaire@odyssee.net ******************************************************** Graham Dellaire Snail Mail Div. of Experimental Medicine Institute du Cancer de Montreal Dept. of Medicine Louis Charles-Simard McGill University 1560 Sherbrooke Street E. e-mail:dellaire@odyssee.net Montreal, Quebec, Canada or B2XE@musicb.mcgill.ca ******************************************************** From owner-recombination@net.bio.net Mon Oct 30 22:00:00 1995 Newsgroups: bionet.molbio.recombination Path: biosci!agate!howland.reston.ans.net!newsfeed.internetmci.com!in1.uu.net!nih-csl!NewsWatcher!user From: lichten@helix.nih.gov (Michael Lichten) Subject: Re: RECOMBINATION/bionet.molbio.recombination is ready! Message-ID: Sender: postman@alw.nih.gov (AMDS Postmaster) Nntp-Posting-Host: 128.231.218.92 Organization: LB/DCBDC/NCI References: <45v661$lqr@net.bio.net> <468aog$se0@epervier.CC.UMontreal.CA> <46eul1$r92@news.duke.edu> Date: Tue, 31 Oct 1995 13:21:40 GMT Lines: 20 I'd like to amplify Dan Tomso's comments, re yeast being more "recombinogenic" than us (be we mice or men). As Dan implies, the problems in making this comparison is that different assays are being used in the two organisms, and one can't tell if the different results are an artefact of the assay or reflect basic differences in mechanism. I would be curious to hear what others felt would be a good trans-species assay for recombination that might allow such a comparison. I have one suggestion: the efficiency and means of repair of a defined, induced double-strand break. Systems exist in both yeast and in mice to make a single DSB in the genome by inducing expression of a rare-cutting homing endonuclease. How yeast deals with this has been the subject of intensive study; results are just beginning to come in from transgenic mouse experiments. Anyone have any other ideas? -- Michael Lichten lichten@helix.nih.gov From owner-recombination@net.bio.net Mon Oct 30 22:00:00 1995 Path: biosci!ATLAS.ODYSSEE.NET!dellaire From: dellaire@ATLAS.ODYSSEE.NET (Dellaire, Graham) Newsgroups: bionet.molbio.recombination Subject: Abstract: Unequal homologous recombination of Human DNA on YAC Date: 31 Oct 1995 15:15:30 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 92 Sender: daemon@net.bio.net Distribution: world Message-ID: <9510312311.AA14634@odyssee.net> NNTP-Posting-Host: net.bio.net The following is an interesting abstract I found recently that looks at cross species recombination in a different manner. And for the on going thread with Dr. Lichten and Dan Tomaso I have included a rough rational for an experiment. UNEQUAL HOMOLOGOUS RECOMBINATION OF HUMAN DNA ON A YEAST ARTIFICIAL CHROMOSOME Campbell et al (1995) NAR vol 23, no 18 pp 3691-3695 ABSTRACT We examined unequal homolgous DNA recombination between human repetitive DNA elements located on a yeast artificial chromosome (YAC) and transforming plasmid molecules. A plasmid vector containing an ALU element, as well as a sequence identical to a unique site on a YAC, was introduced into yeast and double recombinant clones anallyzed. Recombination occurs between vector and YAC Alu elements sharing as little as 74% identity, The physical proximity of an Alu element to the unique DNA segment appears to play a significant role in determining the frequency with which that element serves as a recombination substrate. In addition, cross-over points of the recombination reaction are largely confined to the ends of the repetitive element. Since a similar distribution of crossover sites occurs during unequal homologous recombination in human germ and somatic tissue, we propose that similar enzymatic processes may be responsible for the events observed in our system and in human cells. This suggest that a further examination of the enzymology of unequal homologous recombination of human DNA within yeast may yield a greater understanding of the molecular events which control this process in higher eukaryotes. comment: From these experiments it seems yeast and eukaryotic recombination involving unequal cross over may be quite similar. Using this system as a base you could first clone a well studied region of human genome in YAC and carry out the same recombination targeting with the plasmid in yeast and in human cells. TO answer the DBS break repair questions in this thread (see RE: Re: RECOMBINATION/bionet.molbio.recombination is ready) which was how does DSB repair and recombination differ between Yeast and man, you could do the following. As eluded to by Dr. Lichten .... rare cutting enzymes are useful to make a single DSB in a target molecule. Place in your human cell line(by gene transfer) a gene construct containing a very rare single cutter not normally present in yeast or human cells. You clone the genomic region containing this target locus into a YAC. You then have to express your rare cutter in your yeast and human cells at the same time as you transform your "ectopic" vector. To do this just transform your yeast and human cells with two vectors one with a gene encoding your rare cutting restriction enzyme and one with your recombination substrate. Reconstruction of drug resistance genes (ex neo) or gene marker (ex green fluorescent protein) can be used for scoring recombination and to determine a frequency of recombination. Graham Dellaire Experimental Medicine McGill University P.S. If anyone tries this I would like a reprint someday (hehe) Funny enough bionet does archive all this material so as soon as I send this there is a copy somewhere. Although it can be said that anything on the net is PUBLIC DOMAIN, it may become prudent in the future to acknowledge contributions no matter where they appear. In particular I would like to mention that in the beginning before there was a RECOM news group Derwent Information limited... involved in patents and publisher of the GENE THERAPY news letter showed interest in abstracting posts from this group. This would further the idea of a precedent for intellectual property on the internet and at face value I welcome it. BUT definite guidelines should be drawn up and I hope that we in this group could discuss these. ******************************************************** Graham Dellaire Snail Mail Div. of Experimental Medicine Institute du Cancer de Montreal Dept. of Medicine Louis Charles-Simard McGill University 1560 Sherbrooke Street E. e-mail:dellaire@odyssee.net Montreal, Quebec, Canada or B2XE@musicb.mcgill.ca ******************************************************** From owner-recombination@net.bio.net Mon Oct 30 22:00:00 1995 Path: biosci!ATLAS.ODYSSEE.NET!dellaire From: dellaire@ATLAS.ODYSSEE.NET (Dellaire, Graham) Newsgroups: bionet.molbio.recombination Subject: Repost of Comments on NAR ( Campbell et al. 1995) Date: 31 Oct 1995 15:41:09 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 71 Sender: daemon@net.bio.net Distribution: world Message-ID: <9510312338.AA16320@odyssee.net> NNTP-Posting-Host: net.bio.net My E-mail client clipped my comments from the abstract and posted them under "," so I will repost them In regards to the NAR (Campbell et al 1995)abstract post here are my original comments ---------------------------------------------------------------------------- comment: From these experiments it seems yeast and eukaryotic recombination involving unequal cross over may be quite similar. Using this system as a base you could first clone a well studied region of human genome in YAC and carry out the same recombination targeting with the plasmid in yeast and in human cells. TO answer the DBS break repair questions in this thread (see RE: Re: RECOMBINATION/bionet.molbio.recombination is ready) which was how does DSB repair and recombination differ between Yeast and man, you could do the following. As eluded to by Dr. Lichten .... rare cutting enzymes are useful to make a single DSB in a target molecule. Place in your human cell line(by gene transfer) a gene construct containing a very rare single cutter not normally present in yeast or human cells. You clone the genomic region containing this target locus into a YAC. You then have to express your rare cutter in your yeast and human cells at the same time as you transform your "ectopic" vector. To do this just transform your yeast and human cells with two vectors one with a gene encoding your rare cutting restriction enzyme and one with your recombination substrate. Reconstruction of drug resistance genes (ex neo) or gene marker (ex green fluorescent protein) can be used for scoring recombination and to determine a frequency of recombination. Graham Dellaire Experimental Medicine McGill University P.S. If anyone tries this I would like a reprint someday (hehe) Funny enough bionet does archive all this material so as soon as I send this there is a copy somewhere. Although it can be said that anything on the net is PUBLIC DOMAIN, it may become prudent in the future to acknowledge contributions no matter where they appear. In particular I would like to mention that in the beginning before there was a RECOM news group Derwent Information limited... involved in patents and publisher of the GENE THERAPY news letter showed interest in abstracting posts from this group. This would further the idea of a precedent for intellectual property on the internet and at face value I welcome it. BUT definite guidelines should be drawn up and I hope that we in this group could discuss these. Graham ******************************************************** Graham Dellaire Snail Mail Div. of Experimental Medicine Institute du Cancer de Montreal Dept. of Medicine Louis Charles-Simard McGill University 1560 Sherbrooke Street E. e-mail:dellaire@odyssee.net Montreal, Quebec, Canada or B2XE@musicb.mcgill.ca ********************************************************