From angela_zuniga at hotmail.com Tue Jan 9 15:04:05 2007 From: angela_zuniga at hotmail.com (Angela Zuniga) Date: Mon Feb 26 12:14:30 2007 Subject: [rat-forum] RECENT DEVELOPMENTS THAT WILL MAKE 2007 A STELLAR YEAR FOR RGD USERS Message-ID: HIGHLIGHTING RECENT DEVELOPMENTS THAT WILL MAKE 2007 A STELLAR YEAR FOR RGD USERS *Weekly Data Releases - All data added obtained through manual curation and data pipelines each week is released on Saturday to ensure the most up to date information is available to users in a timely manner. *New FTP Files Weekly - FTP files are also updated on a weekly basis. *EntrezGene Synchronization - A major update of genes from EntrezGene in November added more than 15,000 new genes and pseudogenes to RGD. Weekly updates from EntrezGene continue to add new genes as well as new identifiers for Genbank, Unigene, Uniprot, KEGG, PubMed. *Increased Biological Annotations - Improvements in curation software and processes make it possible for RGD to add approximately 500 biological annotations weekly for genes, QTL and strains. Annotations include those for the Gene Ontology (function, biological process, cellular component); Mammalian Phenotype, Disease (utilizing MeSH terms) and Pathways (using RGD's Pathway Ontology). *New Disease Portals - The new Cardiovascular Disease Portal and new version of the Neurological Disease Portal create easy access to a variety of data for the disease researcher. Visit RGD Disease Portals at: http://rgd.mcw.edu/dportal/ *Sequence Annotation - The Genome Conflict Submission Form and the Genome Repair Kit on GBrowse illustrate RGD's continued commitment to the community to provide sequence annotation services. Visit RGD's Genome Repair kit at: http://rgd.mcw.edu/gbreport/gbrowser_error_conflicts.shtml -- The RGD Team http://rgd.mcw.edu/ From brodie at mcw.edu Mon Jan 15 15:43:38 2007 From: brodie at mcw.edu (Brodie, Kent) Date: Mon Feb 26 12:16:43 2007 Subject: [rat-forum] Test email Message-ID: <8F78639AC56F4143B267FE5F5A1B92C88C2222@guyton.phys.mcw.edu> This is a test email to the new rcf community forum (mailman) list. --kent --------------------------------------------------------- Kent C. Brodie - brodie@phys.mcw.edu Department of Physiology Medical College of Wisconsin (414) 456-8590 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://gray.hmgc.mcw.edu/pipermail/rat-forum/attachments/20070115/a6da0fc0/attachment.html From brodie at mcw.edu Tue Jan 16 12:01:54 2007 From: brodie at mcw.edu (Brodie, Kent) Date: Mon Feb 26 12:16:43 2007 Subject: [rat-forum] Test2 Message-ID: <8F78639AC56F4143B267FE5F5A1B92C88C2236@guyton.phys.mcw.edu> Second test after rgd DNS modification. -Kent --------------------------------------------------------- Kent C. Brodie - brodie@phys.mcw.edu Department of Physiology Medical College of Wisconsin (414) 456-8590 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://gray.hmgc.mcw.edu/pipermail/rat-forum/attachments/20070116/9c7c84d5/attachment.html From brodie at mcw.edu Tue Jan 23 15:30:53 2007 From: brodie at mcw.edu (Brodie, Kent) Date: Mon Feb 26 12:16:43 2007 Subject: [rat-forum] Introducing updated Rat Community Forum Message-ID: <8F78639AC56F4143B267FE5F5A1B92C88C22AF@guyton.phys.mcw.edu> Good day! We have been very busy updating our RGD website, with updated infrastructure changes and other improvements. Many of these are behind-the-scenes updates to help make our RGD environment more stable and better performing for our customers. This email is to announce that in addition to that, we have just completed a major overhaul of our "Rat Commuity Forum". Specifically, we have migrated from an older forum-based product known as "DCForum" to a more standard commonly-used platform, "mailman". It is very likely you're already a member of some other mailman-based distribution list, so the way this works should hopefully be familiar to many of you. Mailman is an email-based forum, which should help facilitate & generate more conversation about the many important rat-related topics out there. We have also streamlined our environment, instead of a half-dozen mixed forums, there's ONE: The Rat Community Forum. To help preserve our previous environment, former DCForum members have been automatically subscribed to this list, and all previous posts or messages have been preserved in a searchable archive. We hope you enjoy these changes. Here are the details: To send a message to the Rat Community Forum, simply send an email message to: rcf@rgd.mcw.edu. That's it. Your email will be copied to all subscribers. Replies to messages will go back to the list as well. All subscribers will get a simple monthly "membership reminder", so you don't forget that address, or forget the web page to find your subscription to change it. If traffic increases a lot, you can also do things like change your membership to a "digest" version, where daily emails are all packaged into one. The primary mailman page where you can review the list, change your subscription and all that is here: http://gray.hmgc.mcw.edu/mailman/listinfo/rcf Finally, if for some reason you wish to unsubscribe from the list, simply send an email message to rcf-request@rgd.mcw.edu with the word "unsubscribe" in the body of the message. If you want to find out all the other things you can do with your membership, send a message to that same address, only include the word "help" in the body of the email message. If you have any questions, please reply to this email and we will be happy to assist. --------------------------------------------------------- Kent C. Brodie - brodie@phys.mcw.edu Department of Physiology Medical College of Wisconsin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://gray.hmgc.mcw.edu/pipermail/rat-forum/attachments/20070123/2ff21fc3/attachment.html From akindler at uni-bonn.de Thu Jan 25 07:24:54 2007 From: akindler at uni-bonn.de (Andrea =?ISO-8859-1?Q?Kindler-R=F6hrborn?=) Date: Mon Feb 26 12:16:43 2007 Subject: [rat-forum] rat strain susceptible to thyroid carcinogenesis Message-ID: Dear list members, I start to get interested in thyroid carcinogenesis, specially in the differential incidence of thyroid tumors in men amd women. Can anybody recommend rat strains susceptible and resistant respectively to chemically induced thyroid carcinogenesis, with the susceptible strain having a differential incidence in males and females? This has previously been observed in Long Evans rats. (Mori M,Naito M, Watanabe H, Takeichi N, Dohi K, Ito A. Effects of sex difference, gonadectomy, and estrogen on N-methyl-N-nitrosourea induced rat thyroid tumors.Cancer Res. 1990 Dec 1;50(23):7662-7.) Unfortunately I cannot find out which substrain they used and where it is available. Best regards, Andrea PD Dr. Andrea Kindler-R?hrborn Institute of Neuropathology University of Bonn Medical Center 53105 Bonn Germany From rnigam at mcw.edu Thu Jan 25 12:28:29 2007 From: rnigam at mcw.edu (Nigam, Rajni) Date: Mon Feb 26 12:16:43 2007 Subject: [rat-forum] rat strain susceptible to thyroid carcinogenesis Message-ID: <1448A38A42714048B9C53E473E13CCF08262BE@davis.hmgc.mcw.edu> Dear Dr. Kindler-R?hrborn, I am in the process of contacting National Institute of Genetics in Japan and National Bio Research Project in Japan to find out the details of the Long-Evans used in the publication you have mentioned. I will get back to you as soon as I hear from them. In the mean time, could you please look at: Bosland MC, Prinsen MK, et al "Induction of skin and thyroid tumors in male rats..." Carcinogenesis. 1992 Apr;13(4):669-74. PMID: 1533574 [PubMed - indexed for MEDLINE]. They have used Wistar rats (http://ringo.brc.mcw.edu/tools/strains/strains_view.cgi?id=68018) from Central Institute for Breeding of Laboratory Animals, Zeist, The Netherlands, F344 (http://ringo.brc.mcw.edu/tools/strains/strains_view.cgi?id=737926) and SD( http://ringo.brc.mcw.edu/tools/strains/strains_view.cgi?id=737891) from Charles River for inducing thyroid tumors in male rats by MNU. Besides, I also wanted to add some data related to WKY/NHsd (http://rgd.mcw.edu/tools/strains/strains_view.cgi?id=61105) According to Baum AE, Solberg LC, et al Quantitative trait loci associated with elevated thyroid-stimulating hormone in the Wistar-Kyoto rat. Endocrinology. 2005 Feb;146(2):870-8. Epub 2004 Oct 28. PMID: 15514085 [PubMed - indexed for MEDLINE]. WKY/Hsd have elevated serum thyroid-stimulating hormone but normal serum T4 level. We have records of another inbred substrain of LE, LE/BluGill (http://rgd.mcw.edu/tools/strains/strains_view.cgi?id=631163) Dr. Gillette has been using this strain to determine the integrative mechanisms in the brain's circadian clock. This substrain is well phenotyped and genotyped by our PGA group (http://pga.mcw.edu/) but unfortunately they have not done any investigation in your field of interest. You can contact Dr. Gillette if you need any further information. Another few options we have are LE/Han (http://rgd.mcw.edu/tools/strains/strains_view.cgi?id=737942) from Zentralinstitut fur Versuchstierzucht, Hannover, Germany and LE/Mol ( http://pga.mcw.edu/) from Denmark. Please let me know if you have any further questions, Regards, Rajni Rajni Nigam Scientific Curator Rat Genome Database (http://www.rgd.mcw.edu) Medical College of Wisconsin 8701 Watertown Plank Road Milwaukee, WI 53226 Phone: (414) 456 7508 Fax: (414) 456 6595 email: rnigam@mcw.edu email: RNigam@hmgc.mcw.edu -----Original Message----- From: rcf-bounces@rgd.mcw.edu [mailto:rcf-bounces@rgd.mcw.edu] On Behalf Of Andrea Kindler-R?hrborn Sent: Thursday, January 25, 2007 7:25 AM To: rcf@rgd.mcw.edu Subject: [rat-forum] rat strain susceptible to thyroid carcinogenesis Dear list members, I start to get interested in thyroid carcinogenesis, specially in the differential incidence of thyroid tumors in men amd women. Can anybody recommend rat strains susceptible and resistant respectively to chemically induced thyroid carcinogenesis, with the susceptible strain having a differential incidence in males and females? This has previously been observed in Long Evans rats. (Mori M,Naito M, Watanabe H, Takeichi N, Dohi K, Ito A. Effects of sex difference, gonadectomy, and estrogen on N-methyl-N-nitrosourea induced rat thyroid tumors.Cancer Res. 1990 Dec 1;50(23):7662-7.) Unfortunately I cannot find out which substrain they used and where it is available. Best regards, Andrea PD Dr. Andrea Kindler-R?hrborn Institute of Neuropathology University of Bonn Medical Center 53105 Bonn Germany _______________________________________________ rcf mailing list rcf@rgd.mcw.edu http://gray.hmgc.mcw.edu/mailman/listinfo/rcf From newfedra at yahoo.com Thu Jan 25 14:50:37 2007 From: newfedra at yahoo.com (Human) Date: Mon Feb 26 12:16:44 2007 Subject: [rat-forum] rat strain susceptible to thyroid carcinogenesis In-Reply-To: <1448A38A42714048B9C53E473E13CCF08262BE@davis.hmgc.mcw.edu> Message-ID: <418357.25204.qm@web35308.mail.mud.yahoo.com> Hi. I have found a very good tool that help me in my work: www.DNAbaser.com ______________________ What is DNA Baser? An easy to use software package providing fast DNA sequence assembly, contig editing, and rapid detection of mutations in DNA sequences. We have created a fast assembly engine with a range of features that greatly speeds the process of sequence assembly and mutation analysis. DNA BASER provides automated end trimming (clipping) so there is no need to manually trim the low quality bases from the ends of the trace files before contig assembly. This saves considerable time, especially when assembling many DNA sequences. DNA BASER offers a smart navigation system that takes you to the location of each sequence ambiguity (mutation) with only a single click. Our proprietary sequencing error correction algorithm provides further timesavings. The truly user-friendly interface makes DNA Baser the best choice for DNA contig assembly. For more details, see the DNA BASER Features page. 490$ --- "Nigam, Rajni" wrote: > Dear Dr. Kindler-R?hrborn, > > I am in the process of contacting National Institute of Genetics in Japan and National Bio > Research Project in Japan to find out the details of the Long-Evans used in the publication you > have mentioned. I will get back to you as soon as I hear from them. > > In the mean time, could you please look at: Bosland MC, Prinsen MK, et al "Induction of skin and > thyroid tumors in male rats..." Carcinogenesis. 1992 Apr;13(4):669-74. PMID: 1533574 [PubMed - > indexed for MEDLINE]. They have used Wistar rats > (http://ringo.brc.mcw.edu/tools/strains/strains_view.cgi?id=68018) from Central Institute for > Breeding of Laboratory Animals, Zeist, The Netherlands, F344 > (http://ringo.brc.mcw.edu/tools/strains/strains_view.cgi?id=737926) and SD( > http://ringo.brc.mcw.edu/tools/strains/strains_view.cgi?id=737891) from Charles River for > inducing thyroid tumors in male rats by MNU. > > Besides, I also wanted to add some data related to WKY/NHsd > (http://rgd.mcw.edu/tools/strains/strains_view.cgi?id=61105) According to Baum AE, Solberg LC, > et al Quantitative trait loci associated with elevated thyroid-stimulating hormone in the > Wistar-Kyoto rat. Endocrinology. 2005 Feb;146(2):870-8. Epub 2004 Oct 28. > PMID: 15514085 [PubMed - indexed for MEDLINE]. WKY/Hsd have elevated serum thyroid-stimulating > hormone but normal serum T4 level. > > We have records of another inbred substrain of LE, LE/BluGill > (http://rgd.mcw.edu/tools/strains/strains_view.cgi?id=631163) Dr. Gillette has been using this > strain to determine the integrative mechanisms in the brain's circadian clock. > This substrain is well phenotyped and genotyped by our PGA group (http://pga.mcw.edu/) but > unfortunately they have not done any investigation in your field of interest. You can contact > Dr. Gillette if you need any further information. > > Another few options we have are LE/Han > (http://rgd.mcw.edu/tools/strains/strains_view.cgi?id=737942) from Zentralinstitut fur > Versuchstierzucht, Hannover, Germany and LE/Mol ( http://pga.mcw.edu/) from Denmark. > > Please let me know if you have any further questions, > > Regards, > > Rajni > > Rajni Nigam > Scientific Curator > Rat Genome Database > (http://www.rgd.mcw.edu) > Medical College of Wisconsin > 8701 Watertown Plank Road > Milwaukee, WI 53226 > > Phone: (414) 456 7508 > Fax: (414) 456 6595 > email: rnigam@mcw.edu > email: RNigam@hmgc.mcw.edu > > > > > -----Original Message----- > From: rcf-bounces@rgd.mcw.edu [mailto:rcf-bounces@rgd.mcw.edu] On Behalf Of Andrea > Kindler-R?hrborn > Sent: Thursday, January 25, 2007 7:25 AM > To: rcf@rgd.mcw.edu > Subject: [rat-forum] rat strain susceptible to thyroid carcinogenesis > > Dear list members, > I start to get interested in thyroid carcinogenesis, specially in the differential incidence of > thyroid tumors in men amd women. > Can anybody recommend rat strains susceptible and resistant respectively to chemically induced > thyroid carcinogenesis, with the susceptible strain having a differential incidence in males and > females? This has previously been observed in Long Evans rats. (Mori M,Naito M, Watanabe H, > Takeichi N, Dohi K, Ito A. Effects of sex difference, gonadectomy, and estrogen on > N-methyl-N-nitrosourea induced rat thyroid tumors.Cancer Res. 1990 Dec 1;50(23):7662-7.) > Unfortunately I cannot find out which substrain they used and where it is available. > Best regards, Andrea > > PD Dr. Andrea Kindler-R?hrborn > > Institute of Neuropathology > > University of Bonn Medical Center > > 53105 Bonn > > Germany > > _______________________________________________ > rcf mailing list > rcf@rgd.mcw.edu > http://gray.hmgc.mcw.edu/mailman/listinfo/rcf > _______________________________________________ > rcf mailing list > rcf@rgd.mcw.edu > http://gray.hmgc.mcw.edu/mailman/listinfo/rcf > If I choose Christianity then the Islamic will say I'm a pagan. If I choose Islamic then the Buddhist will say I'm a pagan. If I chose Buddhism then the Jewish will say I'm pagan. If I choose no God then everybody will say I'm pagan. Please, can I be free? Can you NOT tell me how I should live MY life? ____________________________________________________________________________________ Finding fabulous fares is fun. Let Yahoo! FareChase search your favorite travel sites to find flight and hotel bargains. http://farechase.yahoo.com/promo-generic-14795097