From owner-recombination@net.bio.net Wed May 06 23:00:00 1998 Path: biosci!biosci!not-for-mail From: SANTOSH KUMAR NANDA Newsgroups: bionet.molbio.recombination Subject: Reg: Purification of DNA/RNA Date: 7 May 1998 10:06:28 -0700 Organization: TAMU Lines: 11 Sender: daemon@net.bio.net Approved: dellaire@odyssee.net Distribution: world Message-ID: <6ispmk$gav@net.bio.net> Reply-To: nanda@medicine.tamu.edu NNTP-Posting-Host: net.bio.net Hi, I have a fragment of 66 bp in agarose gel (cut out PCR product)to be purified. Could you suggest me of a system which would yield a higher recovery as well as concentrated prep to be used for in vitro transcription. Your help is highly solicited. Thanks in advance Santosh NAnda Texas A&M University nanda@medicine.tamu.edu From owner-recombination@net.bio.net Mon May 11 23:00:00 1998 Path: biosci!biosci!not-for-mail From: BIOSCI Administrator Newsgroups: bionet.molbio.recombination Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 12 May 1998 05:50:50 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 234 Sender: daemon@net.bio.net Approved: dellaire@odyssee.net Distribution: world Message-ID: <6j9gja$755@net.bio.net> NNTP-Posting-Host: net.bio.net (LAST REVISION: 30-JUL-95) This BIOSCI "miniFAQ" is designed to answer the questions that come up the *most frequently*. The main BIOSCI FAQ (Frequently Asked Questions) is accessible on the World Wide Web at URL http://www.bio.net/. 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. C) In the body of your message put one or more of the following commands with an "end" command on the last line, e.g., subscribe methods unsubscribe methods end Do NOT put your e-mail address or other text on these lines. The server only allows you to cancel your subscription if the address on your mail header matches the address on our mailing list. Please ask for help at biosci-help@net.bio.net if your address has changed, e.g., if you know you are on the list but the server tells you that you are not a member. Users in Europe, Africa, and Central Asia who use the BIOSCI node at -------------------------------------------------------------------- computer daresbury.ac.uk (also known as dl.ac.uk): ------------------------------------------------- To subscribe and unsubscribe to/from the BIOSCI lists, you need to specify the full USENET newsgroup name with "bionet-news." prepended. The USENET newsgroup names are listed in the BIOSCI Information sheet on the Web at http://www.bio.net/. For the METHODS-AND-REAGENTS list the USENET newsgroup name is bionet.molbio.methds-reagnts, thus the appropriate commands are sub bionet-news.bionet.molbio.methds-reagnts unsub bionet-news.bionet.molbio.methds-reagnts These commands are included in a message addressed to mxt@dl.ac.uk, NOT to the newsgroup mailing addresses. As usual, include the text in the body of the message as text on the Subject: line is ignored. To unsubscribe from all the lists at the UK node, use unsub bionet-news Please note that if the address in the list is different than the one in your mail message header, you will not be able to unsubscribe by this method. If you have problems, please mail biosci@daresbury.ac.uk. 4) The BIOSCI user address and research interest directory. ----------------------------------------------------------- Please take this opportunity to add your name, address, and research interest information to the BIOSCI User Address Database if you have not already done so. You can fill out the address form directly through our Web page at URL http://www.bio.net/adrform.html. The address database is reindexed nightly for WWW access (the URL is http://www.bio.net/). If you are not directly on the Internet but can reach it by e-mail, please use our waismail server to access the user directory. waismail use is described above. You can also request a user address form by e-mail from biosci-help@net.bio.net. Please check your database entry from time-to-time to see if your address information is still up-to-date. Because of our limited personnel resources, we ask that you resubmit a *complete* form to revise your entry; we only replace complete entries and do not have resources to edit old forms. From owner-recombination@net.bio.net Mon May 18 23:00:00 1998 Path: biosci!biosci!not-for-mail From: "Emir KHATIPOV" Newsgroups: bionet.molbio.recombination Subject: Antibiotic resistance and growth rates Date: 19 May 1998 05:51:00 -0700 Organization: Agency of Industrial Science and Technology, Tsukuba Lines: 77 Sender: daemon@net.bio.net Approved: dellaire@odyssee.net Distribution: world Message-ID: <6jrv7k$f8m@net.bio.net> NNTP-Posting-Host: net.bio.net Dear Subscribers, I would like to ask your opinion on how the presence of a plasmid bearing antibiotic (AB) resistance (particularly kanamycin) genes would affect cell growth and/or productivity of transformants. The expression of kanamycin resistance, as well as kanamycin phosphorylation which is involved in the mechanism of resistance itself, do require energy and this should be a common feature that growth and productivity of a transformant cannot be properly compared to that of a wild type. The problem is that in a certain kind of experiments imply making changes to one characteristic by genetic manipulations that would expectedly cause changes in another characteristic, which is not directly related/linked to the expression of the first one. In this case, you have to make all appropriate controls, including the transformation of the wild type with a "blank" control plasmid. The obtained control transformant is then compared with the wild type and with the strain obtained by transformation of the WT with the same plasmid containing a gene of interest. However, the control transformant is grown in the presence of antibiotic and this raises a question of to what extent the growth rates and expression rates of a controlled characteristic is comparable to a wild type strain (that is grown of course in the absence of an antibiotic). I hope I made myself clear. Despite the above might be enough to raise a discussion and there is possibly no need to read the following example, I would like to be more specific about details of our work. In our lab, we have a phototrophic bacterium, a wild type (WT), with phenotype A and B, where A is a pigment content and B is production of a certain chemical. The goal is to have as high expression of B as possible. Both traits are supposedly not related, but we would like to prove that A does affect B. We obtained a stable UV mutant (M) with altered A phenotype (Ax phenotype) which also has increased productivity of a chemical (Bx phenotype). However, the mutation is not yet identified. To identify the mutation we made a complementation analysis by transforming the mutant with a plasmid (_kanamycin_ resistance) containing a wild A gene that would supposedly restore only the wild phenotype A, and succeeded with a transformant (MA). Consequently, the wild B phenotype was also restored. The only thing we can do to prove that a restoration of wild B phenotype is a result of restoration of the A phenotype is to clone the control plasmid used in complementation and lacks A-genes (MControl transformant), and to compare the expression of B phenotype in MA and MControl transformants. However, we have data showing that expression of B phenotype in MControl is lower than in MA. MControl ideally should have the same level of B phenotype as the WT, but in practice, we cannot show this, possibly because of the presence of antibiotic in the medium for growth of the transformant (MControl). The expression of B phenotype in MControl is in fact ~3 times lower than in WT. To make a correct publication we have to explain why MControl does not have the same level of B as WT. The only explanation we can give for lower B in MControl is the presence of kanamycin in the medium. However, it is better to refer to publications describing the same phenomenon in some other cases. I guess it is quite a general problem, so I expect a wide response. I would like to have references showing the comparison of WT and control transformants, and evidencing that they cannot be properly compared because of the presence of antibiotic (not only kanamycin) in the medium. Moreover, such references would be much appreciated, as well as your discussion on the matter. Thank you, Emir PS. Answers by e-mail khatipov@nibh.go.jp are also welcome. Sorry for a big size of this posting, I really tried but I could not make it shorter. > > > > From owner-recombination@net.bio.net Mon May 25 23:00:00 1998 Path: biosci!biosci!not-for-mail From: "Scott Shanes" Newsgroups: bionet.molbio.recombination Subject: US-CT-SR. SCIENTIST HIGH THROUGHPUT SCREENING Date: 26 May 1998 05:33:43 -0700 Organization: ICGNetcom Lines: 28 Sender: daemon@net.bio.net Approved: dellaire@odyssee.net Distribution: world Message-ID: <6kecr7$p9b@net.bio.net> NNTP-Posting-Host: net.bio.net US-CT-SR. SCIENTIST HIGH THROUGHPUT SCREENING I am looking for a Sr. Scientist who will be responsible for overseeing the development of high throughput screening assays within the lead discovery unit. The candidate will interact with project teams from different therapeutic areas in discussions on target selection, assay design and reagent generation. This person will supervise assay development nd performance within the unit, do data analysis and reporting of results. The selected candidate will help coordinate production of reagents required for various assay options and evaluate new technologies that may be applicable to compound testing. The candidate should possess a Ph.D. degree with 5 years experience. A background in enzymology/receptor pharmacology would be a plus, broad background in different disease areas and some knowledge of chemistry is helpful. Our client is a leading pharmaceutical company with research facilities in central Connecticut and can provide excellent benefits (health insurance, dental, and vision plan, paid vacation and more). A high impact, high profile position with excellent opportunity for advancement. Please contact Scott Shanes by phone at 609-584-8733 Ext. 218, fax resume and cover letter to 609-584-9575 or E-Mail to sis@diedremoire.com. From owner-recombination@net.bio.net Sat May 30 23:00:00 1998 Path: biosci!biosci!not-for-mail From: "G. Dellaire" Newsgroups: bionet.molbio.recombination Subject: Molecular Stategies in biological evolution Date: 31 May 1998 05:44:37 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 17 Sender: daemon@net.bio.net Approved: dellaire@odyssee.net Distribution: world Message-ID: <6krjbl$18p@net.bio.net> NNTP-Posting-Host: net.bio.net From: Lynn Caporale Subject: Molecular Stategies in biological evolution I would like to draw your attention to the agenda of a meeting, entitled "Molecular Strategies in Biological Evolution", to be held at Rockefeller University June 27-29, and would appreciate it if you could share this information with others whom you think might find it of interest. Please note that there may be some fellowship $$ available. The URL is at: http://www.nyas.org/brochmsb.html Thank you, Lynn Caporale