From owner-recombination@net.bio.net Wed Jun 02 10:02:00 1999 Path: biosci!biosci!not-for-mail From: "Mr Clive Delmonte" Newsgroups: bionet.molbio.recombination Subject: Recombination Complexes Date: 2 Jun 1999 04:02:54 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Approved: genestructure@yahoo.com Distribution: world Message-ID: <7j330u$5uj@net.bio.net> NNTP-Posting-Host: net.bio.net === Moderated bionet.genome.gene-structure _________________________________________________________ Do You Yahoo!? Get your free @yahoo.com address at http://mail.yahoo.com From owner-recombination@net.bio.net Thu Jun 03 06:45:00 1999 Path: biosci!biosci!not-for-mail From: "Mr Clive Delmonte" Newsgroups: bionet.molbio.recombination Subject: Recombination Complexes Date: 3 Jun 1999 00:44:59 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 120 Sender: daemon@net.bio.net Approved: genestructure@yahoo.com Distribution: world Message-ID: <7j5bpr$jh8@net.bio.net> NNTP-Posting-Host: net.bio.net May I make a belated, and rather different contribution to the recent discussion in bionet newsgroups about the nature and purpose of "junk" DNA ? There is the possibility that the purpose of "junk" DNA is to enable long lengths of like-sequence, repetitive DNA to recognise each other, which could explain why it is needed in such long lengths. (I suspect we might only call it "junk" DNA because we haven't yet agreed a secure purpose for it.) Long lengths of repetitive DNA capable of recognising the same, or closely similar, repeat sequences could assist in the formation of the "30 nm" fibre of compacted nucleosomes, and in the assembly of centromeres. In addition, prior to cell division, the pairing of like chromosomes could be facilitated before separation during mitosis or meiosis, for example. The 13 pairs of human chromosomes would each need closely similar repeat sequences (each with the other), and these would need to be rather different from the repeat sequences in the other pairs. Perhaps subscribers know the repeat sequences of all of the human chromosomes ? The unique pairing of Watson-Crick base pairs, AT with AT and GC with GC, was described first by Loewdin in 1963, as far as I am aware. These properties of DNA and others are explored and developed in detail in my two books (1,2). In a single posting it is impossible to develop the arguments, but those wishing to consider fresh aspects of the behaviour of DNA may care to view the newsgroup "bionet.biophysics" to which I am currently posting the second series of DNA Structure Puzzles intended to focus attention on the wide range of experimental data which is otherwise unexplained in the literature. The attachments to the DNA Structure Puzzles in bionet.biophsyics" include sketches of how individual base pairs can themselves form pairs, as well as a sketch of a model of DNA which facilitates such pairing. To any interested subscribers, I could send e-mail attachments of the scheme for pairing base pairs, and of the framework of the overall structure within which such pairing is facilitated. -------------------------------------------------------1 Towards a New Structural Molecular Biology, by Clive Delmonte (1991) ISBN 0 9512276 0 2 "...I find much of Delmonte's critique of other workers sound enough to raise doubt in my mind about the bulk of the classical work in this area. ...the book was an eye-opener." Prof. Steven Benner at Eidgenossische Technische Hochscule, Zurich ------------------------------------------- "...the widely accepted Watson-Crick model is inadequate to explain many important pieces of data, and in some cases defies intuitive biological and physical logic as a predictive model..I commend you on your recognition of inconsistencies in the story of DNA..you have the potential of changing molecular biology." Prof. Robert Hopkins at the School of Applied and Natural Sciences in the University of Houston at Clear Lake, Texas ---------------------------------------------- 2 Advances in AFM & STM Applied to the Nucleic Acids, by Clive Delmonte (1997) ISBN 0 9512276 2 9, Library of Congress TX 4-856-037 ----------------------------------------------- Clive Delmonte Clive Delmonte E-mail: clived@ndirect.co.uk or: clivedelmonte@c-i-delmonte.freeserve.co.uk === Moderated bionet.genome.gene-structure _________________________________________________________ Do You Yahoo!? Get your free @yahoo.com address at http://mail.yahoo.com From owner-recombination@net.bio.net Fri Jun 04 07:52:00 1999 Path: biosci!biosci!not-for-mail From: daemon@net.bio.net Newsgroups: bionet.molbio.recombination Subject: Request for help regarding homology Date: 4 Jun 1999 01:52:44 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 37 Approved: genestructure@yahoo.com Distribution: world Message-ID: <7j844s$274@net.bio.net> NNTP-Posting-Host: net.bio.net I'm currently studying RecA, and I'm interested in the homology recognition part of the strand exchange process. Particularly puzzling to us right now is how homology is recognized between two DNA molecules when one of them (the one bound to RecA) is extended by 50%. There are also some topological problem I am trying to work out that seem very stubborn. If anybody reading this has an interest in or knowledge about the homology recognition phase of RecA facilitated strand exchange and wouldn't mind talking to a confused graduate student for a little while, please drop me a line. Cheers, Kevin kklap@biomath.medsch.ucla.edu === Moderated bionet.genome.gene-structure _________________________________________________________ Do You Yahoo!? Get your free @yahoo.com address at http://mail.yahoo.com From owner-recombination@net.bio.net Tue Jun 08 10:22:00 1999 Path: biosci!biosci!not-for-mail From: "Clive Delmonte" Newsgroups: bionet.molbio.recombination Subject: Re: Request for help regarding homology Date: 8 Jun 1999 04:22:19 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 92 Sender: daemon@net.bio.net Approved: genestructure@yahoo.com Distribution: world Message-ID: <7jiudb$lsk@net.bio.net> NNTP-Posting-Host: net.bio.net Kevin You raise fascinating points of wide relevance in recombination. I believe that in the literature there are the key papers and experimental observations which you need to start addressing your problem. First, and most important, Loewdin (1) described in 1963 the unique pairing of Watson-Crick base pairs, CG with CG and AT with AT, which could be essential at recognition sites prior to recombination events. If you wish, I could send you an attachment of Loewdin's diagrams (is WORD forrnat OK?). Second, Lee et al. (2) recorded under STM exactly the structure in their Figure 3b which is needed for Loewdin's base pairs to form, face to face, one duplex with another. Third, the structure found by Lee et al. was first described in the literature, as far as I am aware, from theoretical deductions, by Robert Hopkins (3, diagram (e)). I am sure Robert would be glad to discuss his work with you, and I have his e-mail address if it would help. Do let me know if you wish to discuss this with me in further detail. --------------------------------------------------------- 1 Electronic Aspects of Biochemistry, Editor: Bernard Pullman; Academic Press 1963 2 SCIENCE 244 (1989) 475 - 477 3 J theor Biol 120 (1986) 215 - 222 ---------------------------------------------------------- > Clive Delmonte > E-mail: clivedelmonte@c-i-delmonte.freeserve.co.uk > wrote in message > news:7j844s$274@net.bio.net... > > I'm currently studying RecA, and I'm interested in > > the homology recognition part of the strand > exchange > > process. Particularly puzzling to us right now is > how > > homology is recognized between two DNA molecules > when > > one of them (the one bound to RecA) is extended > by > > 50%. There are also some topological problem I am > > trying to work out that seem very stubborn. > > > > If anybody reading this has an interest in or > > knowledge about the homology recognition phase of > RecA > > facilitated strand exchange and wouldn't mind > talking > > to a confused graduate student for a little while, > > please drop me a line. > > > > Cheers, > > > > Kevin > > > > kklap@biomath.medsch.ucla.edu > > > > === Moderated bionet.genome.gene-structure _________________________________________________________ Do You Yahoo!? Get your free @yahoo.com address at http://mail.yahoo.com From owner-recombination@net.bio.net Tue Jun 08 10:24:00 1999 Path: biosci!biosci!not-for-mail From: Mark Cauchi Newsgroups: bionet.molbio.recombination Subject: Recombinant DNA Techniques Workshop Date: 8 Jun 1999 04:24:01 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 25 Sender: daemon@net.bio.net Approved: genestructure@yahoo.com Distribution: world Message-ID: <7jiugh$m1k@net.bio.net> NNTP-Posting-Host: net.bio.net The Micromon Unit at the Department of Microbiology, Monash University in Melbourne, Australia will be running its Recombinant DNA Techniques Course during the 14-19 November, 1999. This is an introductory-intermediate level course which offers a skills-based training package. If you would like further information, details can be found on our web page at http://www.med.monash.edu.au/micro/department/dnacorse.htm === Moderated bionet.genome.gene-structure _________________________________________________________ Do You Yahoo!? Get your free @yahoo.com address at http://mail.yahoo.com From owner-recombination@net.bio.net Wed Jun 09 06:47:00 1999 Path: biosci!biosci!not-for-mail From: "Kevin Klapstein" Newsgroups: bionet.molbio.recombination Subject: Re: Request for help regarding homology Date: 9 Jun 1999 00:47:39 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 21 Sender: daemon@net.bio.net Approved: genestructure@yahoo.com Distribution: world Message-ID: <7jl66r$4q8@net.bio.net> NNTP-Posting-Host: net.bio.net Thanks very much for the response. I'll take a look at the references you mentioned. Cheers, Kevin Klapstein === Moderated bionet.genome.gene-structure _________________________________________________________ Do You Yahoo!? Get your free @yahoo.com address at http://mail.yahoo.com From owner-recombination@net.bio.net Tue Jun 15 07:04:00 1999 Path: biosci!biosci!not-for-mail From: BIOSCI Administrator Newsgroups: bionet.molbio.recombination Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 15 Jun 1999 01:04:19 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 403 Sender: daemon@net.bio.net Approved: genestructure@yahoo.com Distribution: world Message-ID: <7k51e3$frb@net.bio.net> NNTP-Posting-Host: net.bio.net This BIOSCI "miniFAQ" is designed to answer the questions that come up the *most frequently*. The main BIOSCI FAQ (Frequently Asked Questions) is accessible on the World Wide Web at URL http://www.bio.net/. If you can not find an answer to your question in this or other documentation, the BIOSCI technical support staff answers e-mail queries sent to biosci-help@net.bio.net We can only answer questions about the use of the newsgroups and mailing lists. We unfortunately do not have the staff to do Internet information searches or answer scientific questions. Please post those to the appropriate BIOSCI/bionet newsgroups. Contents: -------- 0) BIOSCI NEEDS YOUR SUPPORT!! 1) Using the WWW to access the BIOSCI/bionet newsgroups. 2) What to do about "spams," i.e., junk mail, ads, etc. 3) Examples of subscribing and unsubscribing to the mailing lists. 4) The BIOSCI user address and research interest directory. 0) BIOSCI NEEDS YOUR SUPPORT!! ------------------------------ BIOSCI's government funding has been expended, and we are now operating solely from advertising revenue that we have raised from our Web site at http://www.bio.net/. We need just a few minutes of your time to help us serve you. You can do two important things which will take very little time for you individually and will immensely help us continue to help you. First, please use our WWW system at http://www.bio.net/ to access the archives. You can post or reply to messages via your Web browser as described in item #1 below. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. 1) Using the WWW to access the BIOSCI/bionet newsgroups. -------------------------------------------------------- As of 10 December 1995, all BIOSCI/bionet full newsgroups are accessible through the World Wide Web (WWW) at URL http://www.bio.net. One can read and reply publicly or privately to both recent postings and archived messages through one's Web browser if it is configured properly to send e-mail. Each newsgroup is equipped with its own WAIS index. The main BIOSCI home page also has access to the BIO-JOURNALS Table of Contents database WAIS index and the BIOSCI user address database described in another item further below. 2) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups), mailing lists, and a hypermail archive at URL http://www.bio.net/. The same postings are distributed on all media (except for a small number of mailing-list-only groups at net.bio.net). Unfortunately it is becoming a despicable practice on the Internet (by a few people out to make a fast buck) to do automated mass postings to thousands of newsgroups and mailing lists. These attempts to grab free advertising are refered to as "spams" in the usual, somewhat boneheaded, net terminology. USENET is more susceptible to this practice, and many spams originate on the USENET groups and then are passed on to the mailing lists. However, spammers also get lists of mailing addresses and hit these too, so neither medium is immune. What should you do personally if you get junk mail? --------------------------------------------------- Just delete it and move on without reading it further. Filing a protest is becoming increasingly useless because spammers are often disguising the addresses where the messages are sent from. Unless you really understand Internet mail systems, your attempt at protest by sending replies to the message will often end up being sent to the address of an innocent person that the spammer is victimizing. What can BIOSCI/bionet do to protect its newsgroups? ---------------------------------------------------- The only solution currently available is to moderate the newsgroup. If this newsgroup is already moderated, then you are in good shape. Moderation protects the USENET distribution from about 95% of the spams that are being sent to date and protects the mailing lists completely. Moderation means, however, that someone has to take the time to review each message before it goes out. We have set up software here that simply allows the moderator to forward to an address at net.bio.net messages that (s)he wishes to have distributed. This takes no more time than that needed to read the message and pass it on, say about 1 min. per message. Most newsgroups currently have a discussion leader who is responsible for their newsgroup. The discussions leaders and their e-mail addresses are listed in the BIOSCI Information Sheet which is available on the Web at http://www.bio.net/. If a newsgroup is being hit with too many junk postings, please contact the discussion leader for that group and see if there is interest in moderating the group. Please do not assume that by simply posting a complaint to the newsgroup itself, anyone on the BIOSCI staff will act on your complaint. With close to 100 newsgroups to run, the BIOSCI staff has to rely on the discussion leaders of each newsgroup to report problems directly to us at biosci-help@net.bio.net. We will moderate any of our newsgroups if the discussion leader tells us that the readership of the group wishes to do so and if a moderator is willing to do the work. For most BIOSCI/bionet groups, this entails only a few minutes of work each day. Moderating a newsgroup will resolve probably 95% of the junk postings on the USENET distribution. Unfortunately there are easy ways for determined spammers to override the moderation mechanism on USENET, but we can protect our e-mail subscribers from unwanted postings if the newsgroup is moderated. You can also access our newsgroups over the WWW at URL http://www.bio.net. While this Web interface will not stop spammers from trying to post to the groups, this will give you yet another way, besides using USENET news, to keep the junk out of your personal mail files. For those of you with local USENET news systems, the Web interface will also give you faster access to new newsgroups and recent postings. 3) Examples of subscribing and unsubscribing to the mailing lists. ------------------------------------------------------------------ PLEASE NOTE: The BIOSCI management does NOT act on subscription/unsubscription requests that are posted improperly to the newsgroups and mailing lists. People who do this only bother everyone on the lists to no avail. Please be sure to follow the proper procedures below. Gory details are in the BIOSCI Information sheets on the Web at http://www.bio.net. Below we give an example utilizing the METHODS-AND-REAGENTS list at both of our two BIOSCI sites: Users in the Americas and Pacific Rim countries who use the BIOSCI ------------------------------------------------------------------ node at computer net.bio.net: ---------------------------- A) Determine the "listname" which is the <=8 character mail address ^^^^^^^^^^^^^ for the group. These can be found in the BIOSCI Info. Sheet. For the METHODS-AND-REAGENTS group the mailing address is methods@net.bio.net. The listname is the portion of the address to the left of the @ sign, i.e., "methods". The listname is used with the "subscribe" and "unsubscribe" commands illustrated below. B) Mail all commands in the body of a mail message addressed to biosci-server@net.bio.net. Do NOT send commands to the newsgroup posting addresses! Leave the Subject: line blank, any text on it will be ignored. 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For the METHODS-AND-REAGENTS list the USENET newsgroup name is bionet.molbio.methds-reagnts, thus the appropriate commands are sub bionet-news.bionet.molbio.methds-reagnts unsub bionet-news.bionet.molbio.methds-reagnts These commands are included in a message addressed to mxt@dl.ac.uk, NOT to the newsgroup mailing addresses. As usual, include the text in the body of the message as text on the Subject: line is ignored. To unsubscribe from all the lists at the UK node, use unsub bionet-news Please note that if the address in the list is different than the one in your mail message header, you will not be able to unsubscribe by this method. If you have problems, please mail biosci@daresbury.ac.uk. 4) The BIOSCI user address and research interest directory. ----------------------------------------------------------- Please take this opportunity to add your name, address, and research interest information to the BIOSCI User Address Database if you have not already done so. You can fill out the address form directly through our Web page at URL http://www.bio.net/adrform.html. The address database is reindexed nightly for WWW access (the URL is http://www.bio.net/). If you are not directly on the Internet but can reach it by e-mail, please use our waismail server to access the user directory. waismail use is described above. You can also request a user address form by e-mail from biosci-help@net.bio.net. Please check your database entry from time-to-time to see if your address information is still up-to-date. Because of our limited personnel resources, we ask that you resubmit a *complete* form to revise your entry; we only replace complete entries and do not have resources to edit old forms. === Moderated bionet.genome.gene-structure _________________________________________________________ Do You Yahoo!? Get your free @yahoo.com address at http://mail.yahoo.com From owner-recombination@net.bio.net Sun Jun 20 06:46:00 1999 Path: biosci!biosci!not-for-mail From: Cindy Gresham Newsgroups: bionet.molbio.recombination Subject: Questions re science illustration Date: 20 Jun 1999 00:46:31 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 69 Sender: daemon@net.bio.net Approved: genestructure@yahoo.com Distribution: world Message-ID: <7ki68n$7tm@net.bio.net> NNTP-Posting-Host: net.bio.net I am a freelance graphic designer hoping to switch my focus to science illustration, and have just completed a BSc in biology. I am just beginning my research into who uses science illustrators and for what type of projects, so I thought it wouldn't hurt to just broadcast these questions in a few newsgroups. Any responses to any of my questions will be very much appreciated. 1. Have any of the participants in this newgroup ever been involved in the production of a biology textbook? If so... a. How much specific instructions were the illustrators given about the content of the illustrations? b. How much did the publisher or author rely on the illustrator's own knowedge of the subject? c. Are authors involved in the selection of illustrators, or do the publishers usually do the selection? 2. Do any of the participants in this newsgroup ever work with illustrators to enhance a slide presentation or an article? If so... a. How do you go about selecting an illustrator for projects such as this? b. Is there someone else who would do the selecting for you? c. Would you do a search on the internet for science illustrators? d. Would it be helpful to receive a sample of an illustrator's work in the mail to keep on hand? I am very grateful to anyone who can offer any advice or insights. And, naturally, I am happy to send some samples of my work to any one who is interested! Best regards, Cindy Gresham Houston, TX === Moderated bionet.genome.gene-structure _________________________________________________________ Do You Yahoo!? Get your free @yahoo.com address at http://mail.yahoo.com From owner-recombination@net.bio.net Sun Jun 20 06:47:00 1999 Path: biosci!biosci!not-for-mail From: "Andrew M Smith" Newsgroups: bionet.molbio.recombination Subject: Searchable Conference Database Date: 20 Jun 1999 00:47:18 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 27 Sender: daemon@net.bio.net Approved: genestructure@yahoo.com Distribution: world Message-ID: <7ki6a6$82n@net.bio.net> NNTP-Posting-Host: net.bio.net If you want to find out about upcoming events in your discipline, come to www.selectscience.net If you are organising a meeting, please drop me a line (andrew@selectscience.net) so I can add your event to our database. I'm looking forward to hearing from you, Andrew Smith (andrew@selectscience.net) Editor, www.selectscience.net === Moderated bionet.genome.gene-structure _________________________________________________________ Do You Yahoo!? Get your free @yahoo.com address at http://mail.yahoo.com