HUM-MOLGEN archive: BIOT: various Jan 97

New BIOT messages! The following are requests for help etc. regarding molecular genetic and biotechnical research and its applications. Help is requested and info shared/wanted in the following areas: 1) DGGE, 2) Factor V mutational analysis 3) a source for TNP-Ficoll and TNP-LPS, 4) non-isotopic sequencing methods, 5) SSCP-analysis, 6) a source for human gonadotropin-releasing hormone probes, 7) ideas on how to use ING1 in a science fair project, 8) how many alleles one should expect to find in 1000 bp of genomic DNA, 9) a request to collaborate on tumorigenesis in mice, 10) is it possible to perform trisomy analysis on purified genomic DNA, 11) is there a relationship between oncogenes (myc family) and brain tumors, 12) labeling of antisense oligonucleotides for in situ hybridization, 13) isolation of RNA from formalin-fixed tissue, 14) are there cDNA-libraries from uterus available, 15) is there a commercial protein sequencing facility, 16) breakdown of costs for genotyping. Arthur Bergen Edward Wilcox (BIOT editors) ************************************************************************ 1) Dear colleagues In our lab we are going to use the new D GENE System for mutation detection by DGGE (BIO-RAD). We are studying the variability of the HCV genome and treating it as if it were a quasispecies. Is there anybody who can give us suggestions on the application of this methodology for detection of sequence variation in viral RNA? Thank you in advance Elena Donadel labepvir@UX1.UNIPD.IT ************************************************************************ 2) Dear Colleagues, I am interested in the Factor V point mutation and would like a copy of the protocol used to diagnose subjects for mutations in this gene. If you have any pertinent information, please send it to me. It is very urgent. Thank you for your generous time and efforts. Sincerely, Neil ndnandi@swbel ************************************************************************ 3) I am working with immunodeficient mice using TI-1 and TI-2 antigens for the induction of an immune response. I now need TNP-Ficoll and TNP-LPS. Is there a company that sells these compounds? Sigma does not. Grateful for any advice. Lars Branden Center for BioTechnology Novum Karolinska Institute Halsovagen 7-9 141 57 Huddinge Sweden Telephone: +46(0)8-608 91 74 Fax: +46(0)8-774 55 38 E-mail: labr@thon.csb.ki.se ************************************************************************* 4) Dear colleagues: I am presently in a lab that does not utilize radioisotopes. I have been trying to sequence mtDNA after PCR amplification using cycle sequencing and silver staining with very limited success. I was wondering whether there is anyone who could help me refine my technique or advise me about other non-isotopic sequencing systems. Thanks in advance. Joseph G. Lorenz, Ph.D. Analytical Genetic Testing Center 7808 Cherry Creek S. Dr., #201 Denver, CO 80231 (303) 750-2023 (303) 750-2171 fax jlorenz@geneticid.com ************************************************************************ 5) Dear colleagues, I am currently developing a method for rapid mutation screening in the neurofibromatosis type 2 gene. Most studies use SSCP-analysis. Is this the most reliable method? I am interested in contacting anyone who works in this field. Thank You Dr.Hartmut Peters Institute of Medical Genetics Universitaetsklinikum Charite Schumannstr.20-21 10098 Berlin Fax.+49-30-28021286 phone +49-30-28025681 peters@genetik.charite.hu-berlin.de ************************************************************************ 6) Dear colleagues I am looking for the cDNA clone of human gonadotropin-releasing hormone (GnRH) for use as a probe in Northern blots. If you have this material please write to me at "gopi@biochem.iisc.ernet.in". Thank you. Y.Gopi Shanker Dept. of Biochemistry Indian Institute of Science Bangalore 560 012 INDIA ************************************************************************ 7) Dear Sir: I am doing a science fair project on the ING1 gene (a cancer suppressing gene). I am trying to develop an easily understood experiment or model for display purposes to add to my research paper. Do you have any suggestions? Perhaps I need a model of protein synthesis or how a process can be altered when the "suppressor" is missing. Thank you for any help in this matter. Melissa entzian@GJ.NET ************************************************************************ 8) I am studying the variation in olfactory receptor genes and I would like to ask a very simple question. What is the average number (and frequency) of alleles one should expect in a 1000 bp region from unrelated individuals for coding versus non-coding regions? Dror Sharon Department of Membrane Research and Biophysics, The Weizmann Institute of Science Rehovot 76100 ISRAEL Tel: 972-8-9343687 Fax:972-8-9344112 e-mail: bmsharon@membran1.weizmann.ac.il ************************************************************************ 9) Dear colleagues, Recently I have obtained a mouse chromosomal localization for a gene which is involved in tumorigenesis in man. Because of the presence of a previously mapped (but still uncloned) susceptibility gene in this chromosomal area, the gene is a good candidate for genes involved in susceptibility to cancer in mice. To test this gene, I am now looking to start a collaboration involving tumorigenesis in mice with a laboratory that has suitable mice. Any information on this topic will be useful. Thanking you in advance, Dominique Rocha .***. .***. .***. .***. .***. * | | | * | | | * * | | | * | | | * * | | | * | | | * * | | | * * | | | * * | | | * * | | | * * | | | * * | | | * | | | * * | | | * | | | * '***' '***' '***' '***' '***' Dominique ROCHA Centre d'Immunologie de Marseille-Luminy (CIML) Parc Scientifique de Luminy - Case 906 13288 Marseille cedex 9 - France Tel. : (33) 4 91 26 94 82 Fax : (33) 4 91 26 94 30 E-mail : rocha@ciml.univ-mrs.fr ************************************************************************ 10) Last week, a child was born and lived for about an hour. There were several severe anomalies but no diagnosis was made. Before the autopsy, liver and spleen specimens were sent to my lab for DNA extraction and banking (at the request and with permission of the parents). The liver DNA was badly degraded but the spleen DNA is excellent and we have over 600 micrograms of it. Cytogenetics was also requested but no cells grew. The attending physician suspects Trisomy 18 or 13 and would like to have a diagnosis in this case. Now that cytogenetics is not possible, does anyone know of a lab that can do trisomy analysis on a DNA specimen? It would likely require a finely tuned quantitation with chromosome specific probes, perhaps by Southern blotting with an internal control. Help would be greatly appreciated. Thanks. Dan Farkas, PhD Co-director, Molecular Probe Lab Wm. Beaumont Hosp. Royal Oak, MICHIGAN, USA (810) 551-5077-phone (810) 551-3694 (fax) dfarkas@beaumont.edu ************************************************************************ 11) Please contact us if you know of research showing any relationship between oncogenes (myc family) and brain tumors. Amin El-Nashar email : ask@intouch.com ************************************************************************ 12) We are looking for a protocol using TdT and P-33 dATP to label antisense oligonucleotides for in situ hybridization of tissue sections. Any comments on the length of tail that's desirable, the need to use cold nucleotides, etc. would be appreciated. Alexander Dobrovic, Ph. D. Chief Scientist Department of Haematology-Oncology The Queen Elizabeth Hospital Woodville, SA 5011, Australia Affiliate Senior Lecturer Department of Medicine University of Adelaide e-mail: Alex Dobrovic <adobrovic@MEDICINE.ADELAIDE.EDU.AU> Tel: 61-8-8222 6884 Fax: 61-8-8222 6046 (note new numbers as of August 1996) ************************************************************************ 13) Dear colleagues, I would appreciate receiving information about: - isolation of RNA from formalin-fixed tissue for RT-PCR and Northerns - cDNA-libraries from uterus (rabbit, rat, mouse). Is there anybody who can provide me with such a library ? Thanks very much Dr. Rene Zimmermann Max-Planck-Institute (W.G. Kerckhoff-Institute) & Kerckhoff-Clinic Dept. of Experimental Cardiology Phone: +49/6032/705-404 Benekestrasse 2 Fax: +49/6032/705-419 D-61231 Bad Nauheim e-mail:rzimmer@kerckhoff.mpg.de GERMANY *********************************************************************** 14) Dear colleagues, Does anybody know of a company doing commercial protein sequencing? Any information is appreciated. Thanks Dr. Rene Zimmermann Molecular Cardiology Laboratory Max-Planck-Institute Dept. of Experimental Cardiology Benekestrasse 2 D-61231 Bad Nauheim GERMANY Tel.: (0)6032/705-404 Fax: (0)6032/705-419 e-mail: rzimmer@kerckhoff.mpg.de *********************************************************************** 15) Can anybody give any information on the breakdown of costs for a genotyping experiment between the PCR side and the separations component (i.e. labor, materials, equipment etc.). How may genotypes does your center do, how many people are devoted fulltime to the PCR side and to the separations side. How long does each step take and how are the experiments batched. Larry Bock biobock@aol.com ************************************************************************