HDTenEightyP/NetNews huggingface dataset:
From: barbet@tournesol.versailles.inra.fr (Jean-Claude Barbet)
Newsgroups: bionet.genome.arabidopsis
Subject: POSTDOCTORAL POSITION
Date: 12 Oct 92 17:15:43 GMT
Distribution: bionet
Original-To: arab-gen@uk.ac.daresbury
Pp-Warning: Illegal Received field on preceding line
Original-Received: by tournesol.versailles.inra.fr, Mon, 12
                   Oct 92 18: 15:43 +0100



POSTDOCTORAL POSITION OPEN


in the "Arabidopsis Molecular Genetics" group (Group leader 
Jerome Giraudat), Institut des Sciences Vegetales (Director Adam 
Kondorosi), CNRS, Gif sur Yvette, France.

Our Institute, which is located in a multidisciplinary research 
campus of the Paris area, is composed of 5 research groups 
working on various aspects of plant molecular and cellular 
biology.

Our group is primarily studying the molecular mechanisms of 
action of the phytohormone abscisic acid: cloning and 
characterization of the abi (abscisic acid-insensitive) loci of 
Arabidopsis, and analysis of a drought adaptive response at the 
root level in Arabidopsis. In the last 6 months, we have also 
developped the characterization of Expressed Sequence Tags (EST) 
of the Arabidopsis genome: partial sequencing, and ultimately 
mapping, of cDNAs. This project is part of an ongoing integrated 
French effort which comprises of 8 different labs, and will soon 
(EEC decision pending) be part of the multinational Arabidopsis 
genome project of the EEC BIOTECH program. 

We are looking for a postdoctoral scientist which would take the 
leadership of the team working on the EST project within our 
group. Besides this responsibility, the candidate would have the 
time and the facilities to take part in one of the other ongoing 
projects, or to develop an additional project (to be discussed 
according to his personal interests), within the group.

As for the EST project, the candidate will benefit from at least 
a senior technician, one (or more) student, an automatic 
sequenator, and all necessary computer facilities.

Please contact:

Dr. Jerome Giraudat
Institut des Sciences Vegetales
CNRS
91198 Gif sur Yvette CEDEX
France

Phone: (33-1) 69 82 36 22
FAX:   (33-1) 69 82 36 95
E-mail: EARN/BITNET  GIRAUDAT@FRCITI51.BITNET
From: benoit@med.pitt.edu (Benoit Desjardins)
Newsgroups: bionet.biology.computational
Subject: information request: biomathematics / mathematical biology
Date: 7 Oct 92 15:24:43 GMT
Distribution: bionet
Organization: University of Pittsburgh
Originator: biocomp@lerkim.umiacs.umd.edu


I would like to know what are the good research centers (for
graduate training and postdocs) in biomathematics (mathematical
biology).  Can someone provide me with this information? Also, does
anyone know about the research activities of Oxford's Center for
Mathematical Biology?

                                       Thank you

                                       B. Desjardins
                                       benoit@med.pitt.edu

P.S. Please reply to "benoit@med.pitt.edu"
From: mrmike@darwin.life.uiuc.edu (Mike McCaughey)
Newsgroups: bionet.biology.computational
Subject: 3D RNA Editor wanted
Date: 8 Oct 92 01:10:02 GMT
Distribution: bionet
Organization: University of Illinois at Urbana
Originator: biocomp@lerkim.umiacs.umd.edu


Colleagues, 

   I am in search for a computer graphics 3D editing tool to esily
compose RNA and protein spatial structure models at low as well as
atomic resolution. Known structure element coordinates for e.g.
tetraloops, stacks, helices, bends, pseudoknots and for protein
zippers, fingers, sheets, a-helices etc etc should be part of a
toolbox where one can pick structure templates for the buildup.
Structures must be seen and treated with varying detail, for example
an RNA A-helix is either a simple cylinder, a carved cylinder (showing
grooves), same with bases and sugars shown as simple tiles, and with
atoms shown. Only X-ray (and sometimes NMR) data justify the latter,
but lower resolution models from other data can be very useful. I have
seen MacroModel, Insight, Quanta, and brochures for Sybyl/Biopolymer
module. The focus of these programs are either molecular dynamics or
the price is out of line. Would any readers of this know reasonably
priced programs like described, either finished or in the works?

                                          Sincerely, Niels Larsen


           E-mail niels@darwin.life.uiuc.edu   
          _____________________________________________________________________
         /                                                            ______  /
        /  Department of Microbiology    /  1611 B Lyndhurst West    /     / /
       /  University of Illinois        /  Savoy, IL 61874          /_____/ / 
      /  131 Burrill Hall              /  U.S.A.                           /
     /  407 South Goodwin Avenue      /                                   /
    /  Urbana, IL 61801, U.S.A.      /  --------------------------       /
   /                                /  --------------------------       /
  /  Phone  (217)-333-9369         /                                   /
 /  Shared FAX (217)-244-6697     /  (217)-356-5451, ans. mach.       /
/____________________________________________________________________/
Xref: sparky bionet.biology.computational:162 bionet.jobs:551
From: mrmike@geta.life.uiuc.edu (Mike McCaughey)
Newsgroups: bionet.biology.computational,bionet.jobs
Subject: Programmer Wanted
Date: 8 Oct 92 16:12:47 GMT
Followup-To: bionet.biology.computational
Distribution: bionet
Organization: University of Illinois at Urbana
Originator: biocomp@lerkim.umiacs.umd.edu



                 RESEARCH PROGRAMMER

    The Department of Microbiology, University of Illinois at
Urbana-Champaign, seeks a qualified Research Programmer for the
ribosomal database project (RDP), which functions in a world-wide
capacity to facilitate research in some of the more interesting and
important areas of biology; evolution, microbial ecology, nucleic acid
structure, taxonomy, etc.

   Duties will include work on software for the database, automated
mechanisms for exchanging information with other biological databases
and construction of useful and tools for the user community's handling
of the data.  Duties may also include part-time systems administration
of a Unix/MacIntosh network.

   Experience should include familiarity with Unix and MacIntosh
operating systems, C or Fortran, X-windows, and preferably Prolog.
Knowledge of (and interest in) biology is also highly desirable.
A B.S. or M.S. degree is required (preferably in computer science,
engineering, or in combination with biology).

   Position is full time; duration is dependent upon continuation
of funds (from NSF).  Salary is negotiable;
starting date is as soon as possible after closing date.

   Applicants should send a resume, a summary of relevant
experience, and the names and addresses (incl. electronic)
of three references to: Ms. Carolyn Corn, Administrative
Assistant, Department of Microbiology, Univerisy of Illinois,
131 Burrill Hall, 407 S. Goodwin Avenue, Urbana, IL 61801;
Phone: 217-333-1736.

   To receive full consideration, applications should be received
by November 1, 1992. Interviews may be conducted as soon as
applications are received.  However, all applications that are
received by the above date will be given equal consideration.

The University of Illinois is an Equal Opportunity/Affirmative
Action Employer.
From: barbet@tournesol.versailles.inra.fr (Jean-Claude Barbet)
Newsgroups: bionet.molbio.gdb
Subject: POSTDOCTORAL POSITION
Date: 13 Oct 92 08:27:42 GMT
Distribution: bionet
Original-To: gene-org@uk.ac.daresbury
Pp-Warning: Illegal Received field on preceding line
Original-Received: by tournesol.versailles.inra.fr, Tue, 13
                   Oct 92 09: 27:42 +0100



POSTDOCTORAL POSITION OPEN


in the "Arabidopsis Molecular Genetics" group (Group leader 
Jerome Giraudat), Institut des Sciences Vegetales (Director Adam 
Kondorosi), CNRS, Gif sur Yvette, France.

Our Institute, which is located in a multidisciplinary research 
campus of the Paris area, is composed of 5 research groups 
working on various aspects of plant molecular and cellular 
biology.

Our group is primarily studying the molecular mechanisms of 
action of the phytohormone abscisic acid: cloning and 
characterization of the abi (abscisic acid-insensitive) loci of 
Arabidopsis, and analysis of a drought adaptive response at the 
root level in Arabidopsis. In the last 6 months, we have also 
developped the characterization of Expressed Sequence Tags (EST) 
of the Arabidopsis genome: partial sequencing, and ultimately 
mapping, of cDNAs. This project is part of an ongoing integrated 
French effort which comprises of 8 different labs, and will soon 
(EEC decision pending) be part of the multinational Arabidopsis 
genome project of the EEC BIOTECH program. 

We are looking for a postdoctoral scientist which would take the 
leadership of the team working on the EST project within our 
group. Besides this responsibility, the candidate would have the 
time and the facilities to take part in one of the other ongoing 
projects, or to develop an additional project (to be discussed 
according to his personal interests), within the group.

As for the EST project, the candidate will benefit from at least 
a senior technician, one (or more) student, an automatic 
sequenator, and all necessary computer facilities.

Please contact:

Dr. Jerome Giraudat
Institut des Sciences Vegetales
CNRS
91198 Gif sur Yvette CEDEX
France

Phone: (33-1) 69 82 36 22
FAX:   (33-1) 69 82 36 95
E-mail: EARN/BITNET  GIRAUDAT@FRCITI51.BITNET
From: bishop@MAP.MARC.USDA.GOV
Newsgroups: bionet.molbio.gdb
Subject: New Subscription
Date: 9 Oct 92 13:46:36 GMT
Distribution: bionet

Please enter my subscription to your list.
Thanks.
Michael D. Bishop
%USMARC-ARS
PO Box 166
Clay Center, NE 68933
(402)762-4367
From: wetsel_r@wums.wustl.edu
Newsgroups: bionet.molbio.methds-reagnts
Subject: RE: cross-linking
Date: 12 OCT 92 09:56:11 GMT
Organization: MIT PLASMA FUSION CENTER
NNTP-Posting-Host: msnews.wustl.edu

I've had some experience with cross-linkers.  THE best place for X-linkers,
IMHO, is Pierce Chemical Co.  They stock a large selection of them.  I'm
partial to DTSSP as it is cleavable with 2-ME, DTT, and has a rather long
reach of 11 Angstroms, if I'm not mistaken.  It's also water soluable.
I believe that you will find what you need in the Pierce Catalog.

David Haviland
haviland@kids.wustl.edu
Newsgroups: bionet.molbio.methds-reagnts
From: bchs1b@Elroy.UH.EDU (Michael Benedik)
Subject: Re: tightest promoter expression
Reply-To: bchs1b@Elroy.UH.EDU
Organization: University of Houston
Date: Tue, 13 Oct 1992 04:56:36 GMT

In article <920912.145229.eboye@pcdnr35>, eboye@radium.uio.no (Erik Boye) writes:
>
>It seems to me that you have three options:
>1. The more easily tac-like promoters used in Herman Bujard's expression
>vectors. I believe the promoter contains more operators.
>2. The arabinose promoter, which has been used to clone genes for 
>relatively toxic gene products.
>3. The lambda pL promoter, which may be the best repressed promoter of 
>the three (with excess cI857 repressor present). However, you will need
>a temperature upshift to induce transcription.

You can also use T7 in vitro where the T7 polymerase is regulated
either by lambda pL (temperature induction) or Plac (IPTG induction)
the induction serves to turn on expression of T7 polymerase and hence
results in a tightly regulated system which is quite inducible.
See recent manuscripts by Studier et al

----------------------------------------------------------------------
 Michael Benedik				INTERNET: Benedik@uh.edu
 Dept. of Biochemical & Biophysical Sciences	
 University of Houston				BITNET: Benedik@uhou
-----------------------------------------------------------------------
From: pnh@fcsparc6.ncifcrf.gov (Paul N Hengen)
Newsgroups: bionet.molbio.methds-reagnts
Subject: Re: PCR maximum length
Date: 10 Oct 92 21:05:49 GMT
Distribution: bionet
Organization: Frederick Cancer Research and Development Center

:Rich Buckholz "no association with NEB" writes:

:In their recent (Sept. 92) publication "NEB Transcript" NEB claims to 
:have extended primers over 13kb.  They don't say whether they managed to 
:isolate a fragment from that extension.

Rumor has it that a group at Johns Hopkins has cloned a 20 kb DNA
fragment using PCR and "Hot-Tub" polymerase. Okay guys, C'mon,
Fess up!

Paul N. Hengen
National Cancer Institute
Frederick Cancer Research and Development Center
Frederick, Maryland 21702-1201 USA
From: cytogen@chmeds.ac.nz (Martin Kennedy)
Newsgroups: bionet.molbio.methds-reagnts
Subject: Re: Lambda libraries
Date: 14 Oct 92 10:09:36 +1200

In article <1992Oct13.100236.90319@vaxc.cc.monash.edu.au>, mic255z@vaxc.cc.monash.edu.au writes:
> Dear Netters,
> 
> I am interested in using a lambda system to do some primary cloning.
> Does anyone have any thoughts on what system is better ie., what are the
> relative merits of lambda-ZAP and lambda-DASH compared with EMBL, GEM
> or gt11 apart from obvious things like unique cloning sites.
> 
> 
> Thanks in advance,
> Helen Jost,
> Department of Microbiology,
> Monash University.


I've used lambda ZAP several times, and it works beautifully; its main advantage
is the "automatic excision" of inserts - ie, you don't have to make a lambda DNA
prep, and subclone the insert, as addition of a helper phage causes copying of
the phagemid portion of lambda ZAP which contains the multiple cloning site and
your insert.  The phagemeid is then recovered as amp resistant colonies that
contain a Bluescript "subclone"of your lambda insert.  Look at various volumes
of Methods in Enzymology for good comparisons of lambda vectors.

Cheers,

Martin
From: robert@arbo.microbiol.uwa.oz.au (Robert Coelen)
Newsgroups: bionet.molbio.methds-reagnts
Subject: re: TA Cloning kits
Date: 12 Oct 1992 03:54:38 GMT
Organization: University of Western Australia
NNTP-Posting-Host: mve.microbiol.uwa.edu.au

In article <92274.190051ETWLC@CUNYVM.BITNET> Elli Wurtzel <ETWLC@CUNYVM.BITNET> writes:
>Any recommendations?

We use the Invitrogen TA kit to good effect (i.e. it works as advertised !)

Robert Coelen
Organization: Queen's University at Kingston
Date: Mon, 5 Oct 1992 10:45:31 EDT
From: Dr. Peter T. Boag <BOAGP@QUCDN.QueensU.CA>
Newsgroups: bionet.molbio.methds-reagnts
Subject: Sequencing PCR Products - How Best?

This is a repost of a query made a week or so ago. I got some
useful replies, but the original query did not seem to hang
around long. Thanks if you have already replied, and once again
I will summarize when the responses taper off.

                                We sequence mtDNA segments amplified from
total genomic DNA, using a DS amplification followed by asymetric
amplification and SS sequencing with Sequenase. We never have a problem with
DS amplification if the primers are good, but asymetric amplification
and subsequent sequencing have always been unreliable, with a high
failure rate. Quality and quantity of SS template seems the problem
but we have tried every purification technique in the book without
consistent results (precipitation, Millipore and AMicon spin dialysis,
gel slice excision, sepharose spin column, etc.).
 We have been considering alternatives such as
       cycle sequencing, or cloning
of DS PCR product, or lambda exonuclease production of single stranded
template, etc. Any experience from the net would be much appreciated.
We are leaning towards giving cycle sequencing a serious try and would
appreciate experience with various kits available that have been tried
with PCR products. Thanks in advance, I will summarize for NET if
response dictates. - Peter Boag, Biology, Queen's University, Kingston,
Ontario, Canada.
From: afc@gnv.ifas.ufl.edu
Newsgroups: bionet.molbio.methds-reagnts
Subject: Re: Lambda libraries
Date: 13 Oct 92 10:30:16 -0500

In article <1992Oct13.100236.90319@vaxc.cc.monash.edu.au>, mic255z@vaxc.cc.monash.edu.au writes:
> Dear Netters,
> 
> I am interested in using a lambda system to do some primary cloning.
> Does anyone have any thoughts on what system is better ie., what are the
> relative merits of lambda-ZAP and lambda-DASH compared with EMBL, GEM
> or gt11 apart from obvious things like unique cloning sites.

The ZAP sorts of vectors are great, since they make subcloning simple.
We have been using Promega's lambda-GEM vectors, and instead of fooling
around trying to find out how to subclone six different fragments from
each clone, we get the subclones the next day.  (This is a plug for the
general approach, not Promega in particular.)

> Primarily, I want to clone bacterial outer membrane proteins using specific
> antisera to detect recombinants, but I also want to generate lambda libraries
> to store for future (unknown) use.  Does this later the comments generated 
> by the above question?

In the dark ages of the 1970s library construction was black magic.  We
constructed libraries and replicated a successful one for years.  It
was worthwhile to plan construction to maximize the percentage of the
genome represented and to try to get as big a library as possible.  Now
that you can buy fancy vectors, packaging mix that works EVERY TIME!,
and good hosts it is really pretty easy to make a library.  Even cDNA
libraries are not that hard.  It is no longer useful to try to construct
the "perfect" library.

Figure out what fragments you want to clone, configure your library 
construction *to those fragments*, and throw it away afterwards.  You
will be ahead in the long run.  IMHO, of course.

Andrew Cockburn

> ANd finally, lambda-ZAP seems a very good system and I am leaning towards
> this.  Has anyone used this system with less than satisfactory results?
> 
> Thanks in advance,
> Helen Jost,
> Department of Microbiology,
> Monash University.
Newsgroups: bionet.molbio.methds-reagnts
From: bchs1b@Elroy.UH.EDU (Michael Benedik)
Subject: Re: Savant Pump 
Reply-To: bchs1b@Elroy.UH.EDU
Organization: University of Houston
Date: Tue, 13 Oct 1992 04:58:44 GMT

In article <MeqOnTK00YV9A2c2sR@andrew.cmu.edu>, "Anand K. Bachhawat" <ab4u+@andrew.cmu.edu> writes:
>Dear Netters,
>We're thinking of getting a Savant oil free pump for drying gels. Does
>anyone have any experience with these pumps and are they better than 
>getting the regular oil pumps with a vapour trap? I understand that
>there was a lot of discussion on this several months ago but I missed
>it. If someone would be willing to summarize some of the salient
>features that came out of those discussions that would be greatly
>appreciated. Thanks a lot, Anand Bachhawat,CMU
>

We have been using one for about a year now. They work quite well
and are trouble free. More important they are essentially maintainance
free. They don't quite pull as strong a vacuum as a good oil driven
pump, but they are just fine for drying gels. I highly recommend them.

----------------------------------------------------------------------
 Michael Benedik				INTERNET: Benedik@uh.edu
 Dept. of Biochemical & Biophysical Sciences	
 University of Houston				BITNET: Benedik@uhou
-----------------------------------------------------------------------
From: wsun@jeeves.ucsd.edu (Fiberman)
Newsgroups: bionet.molbio.methds-reagnts
Subject: expression in mammalian cells
Date: 15 Oct 92 02:03:30 GMT
Organization: University of California, San Diego

Dear Netters,

I wish to express a clone of interest in mammalian cell lines.
However, I want to be able to select for the transfected cells
so I can maintain the plasmid in the cell line indefinitely.
Which plasmids are good for this purpose?  I have HeLa, COS, and
CHO cells.  Any suggestions are welcome.

-fm
From: cytogen@chmeds.ac.nz (Martin Kennedy)
Newsgroups: bionet.molbio.methds-reagnts
Subject: Re: BRL's cloneAmp system - any experience ?
Date: 14 Oct 92 10:03:52 +1200

In article <1bda7fINNv9@uniwa.uwa.edu.au>, robert@arbo.microbiol.uwa.oz.au (Robert Coelen) writes:
> 
> We are interested in using BRL's CloneAmp system, employing pfu
> for accurate copying. Does anyone have any experience with this method ?
> Whilst we're on the topic, what about their 3' and 5' RACE kits ?
> Any comments gratefully received, acknowledged and summarised !
> 
> 
> Robert Coelen
> Dept of Microbiology
> UWA

I can't comment on the CloneAmp system, but I know of at least two groups here
who have used without success the 3' and 5' RACE kits.  I routinely do 3' and
5' RACE (without a kit) and have no problems.  I posted the method here a while
back.

Cheers,

Martin
From: wetsel_r@wums.wustl.edu
Newsgroups: bionet.molbio.methds-reagnts
Subject: RE: Automated sequencing: opinions please!
Date: 8 Oct 92 11:58:14 GMT
Organization: MIT PLASMA FUSION CENTER
NNTP-Posting-Host: msnews.wustl.edu

Ed:

I posted a querry along this line not too long ago.  The results were
unanimous... the pharmacia machine is a good dust collector.  I must have
received 20+ replies touting the ABI 373A machine.  A fellow investigator
here has replaced his pharmacia machine with the ABI as Wash_u has about 9
machines - last I heard.  I hope this helps...

David
ADD/EDIT
haviland@kids.wustl.edu
Newsgroups: bionet.molbio.methds-reagnts
From: gchacko@magnus.acs.ohio-state.edu (George W Chacko)
Subject: Re: Method for Anchored PCR/RACE
Organization: The Ohio State University
Date: Thu, 15 Oct 1992 14:35:46 GMT

In article <1992Oct15.162328.123@chmeds.ac.nz> cytogen@chmeds.ac.nz (Martin Kennedy) writes:

> Finally, anchored PCR doesn't seem to work over regions much longer
> than about 500bp, at least in my experience. Some PCR reactions show
> a nice tight band, others a smear - 

I've gotten tight bands upto 1 Kb using a 3' RACE system. I use 2 ug
of total RNA (the quality of RNA appears to be the most critical
factor IMO). I reverse transcribe using the Pharmacia cDNA synthesis
kit adding 1ug of their supplied Not1-dT18 primer in a 15ul reaction
as described in their manual. 37C for 1 hour and I amplify 1 ul of the
RT product in a 100 ul PCR reaction. The downstream primer I use is
identical to the linker region between the dT and the Not1 site. The
upstream primer I use is message specific. I also use a touchdown PCR
protocol starting with annealing at 65C and dropping 0.5C until 53C
with a total of 40 cycles. I Elutip the PCR product and clone it into
a T-vector which we make in the lab and it seems to work. The
touchdown PCR seems to have cleaned up the smears I used to see
earlier. 

George
From: mitch@uniwa.uwa.edu.au (Michelle Waycott)
Newsgroups: bionet.molbio.methds-reagnts
Subject: fingerprinting oligo's
Date: 12 Oct 1992 18:10:50 +0800
Organization: The University of Westrn Australia
NNTP-Posting-Host: uniwa.uwa.edu.au
Summary: What are people usiing for PCR fingerprinting?
Keywords: PCR fingerprinting oligonucleotides
X-Newsreader: Tin 1.1 PL5

Hello everyone,

I am interested in finding out what people are using for PCR
fingerprinting primers.  I have some references but need the 
"practical" viewpoint on what is a good method and some primer sequences
or suggestions for making primers.  I am using RAPDs already.

Also has anyone probes for or working on mobile genetic elements in
plants (anything would be helpful in this line!).

Thanks heaps in advance

Mitch

mitch@uniwa.uwa.edu.au
From: bsh@MED.PITT.EDU (Basavaraju Shankarappa)
Newsgroups: bionet.molbio.methds-reagnts
Subject: Re:  PCR max. lenght
Date: 7 Oct 92 16:02:48 GMT
Distribution: bionet

The last I saw it, Saiki et al in a review article in Science about a
year or little bit more back, had quoted unpublished observations to
indicate the max length to be about 10 kb.  
Raj Shankarappa.
Univ of Pittsburgh