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Subject: BIOT: various Jan 97
From: "Bergen (ioi)" <A.A.BERGEN@AMC.UVA.NL>
Date: Wed, 12 Feb 1997 13:45:42 +0100

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
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.

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
Karolinska Institute
Halsovagen 7-9
141 57 Huddinge
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
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
10098 Berlin
phone +49-30-28025681
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
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.

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
Tel: 972-8-9343687
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

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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.
(810) 551-5077-phone
(810) 551-3694 (fax)
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
(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
14) Dear colleagues,
        Does anybody know of a company doing commercial protein sequencing?
Any information is appreciated.

Dr. Rene Zimmermann
Molecular Cardiology Laboratory
Dept. of Experimental Cardiology
Benekestrasse 2
D-61231 Bad Nauheim
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

Larry Bock

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