From cinthiait from yahoo.com Wed Jun 4 09:34:06 2008
From: cinthiait from yahoo.com (Cinzia Pagliuca)
Date: Wed Jun 4 10:25:06 2008
Subject: [Yeast] Acid-Washed glass Beads
Message-ID: <831049.46486.qm@web51104.mail.re2.yahoo.com>
Dear all,
I would like to thank you for the nice and usefull suggestions.
Cinzia
From hannah.silver from jefferson.edu Wed Jun 4 13:36:49 2008
From: hannah.silver from jefferson.edu (Hannah R Silver)
Date: Wed Jun 4 22:02:24 2008
Subject: [Yeast] cell cycle and temp
Message-ID: <40888dc80806041136p32b63ae9p43b1afd16825d92a@mail.gmail.com>
Hello. Does anyone know if the FACS profile for asynchronous cells looks
different at 25C vs 36C? For example, do you see a higher accumulation in G1
at 25 than you would at 36?
Also has anyone else noticed the temporary arrest in G1 after galactose
addition to asynch cells growing in YPR?
--
****************************************
HR Silver
PhD Candidate
Department of Biochemistry and Molecular Biology
Thomas Jefferson University
233 South 10th Street, BLSB 231
Philadelphia, Pennsylvania 19107
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From Nastaran.Behzadnia from wacker.com Thu Jun 5 02:11:57 2008
From: Nastaran.Behzadnia from wacker.com (Behzadnia, Dr. Nastaran)
Date: Thu Jun 5 08:16:08 2008
Subject: [Yeast] vitamins
Message-ID: <7E5C53C2307F2941AE44E09C1BFD8676044FA76C@ZBGHMAIL03.servers.wacker.corp>
Dear sir or madam,
I am looking for information whether vitamin K2 and B12 are produced in
yeast. Can you please help me?
Best regards,
N. Behzadnia
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From dirk.mueller from inf.ethz.ch Thu Jun 5 13:21:53 2008
From: dirk.mueller from inf.ethz.ch (=?ISO-8859-1?Q?Dirk_M=FCller?=)
Date: Thu Jun 5 14:01:27 2008
Subject: [Yeast] cell cycle and temp (Hannah R Silver)
In-Reply-To: <200806051703.m55H3sO02033@net.bio.net>
References: <200806051703.m55H3sO02033@net.bio.net>
Message-ID: <48482EC1.8070804@inf.ethz.ch>
yeast-request@oat.bio.indiana.edu wrote:
> Send Yeast mailing list submissions to
> yeast@net.bio.net
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://www.bio.net/biomail/listinfo/yeast
> or, via email, send a message with subject or body 'help' to
> yeast-request@net.bio.net
>
> You can reach the person managing the list at
> yeast-owner@net.bio.net
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Yeast digest..."
>
>
> Today's Topics:
>
> 1. cell cycle and temp (Hannah R Silver)
> 2. vitamins (Behzadnia, Dr. Nastaran)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 4 Jun 2008 14:36:49 -0400
> From: "Hannah R Silver"
> Subject: [Yeast] cell cycle and temp
> To: yeast@magpie.bio.indiana.edu
> Message-ID:
> <40888dc80806041136p32b63ae9p43b1afd16825d92a@mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello. Does anyone know if the FACS profile for asynchronous cells looks
> different at 25C vs 36C? For example, do you see a higher accumulation in G1
> at 25 than you would at 36?
> Also has anyone else noticed the temporary arrest in G1 after galactose
> addition to asynch cells growing in YPR?
>
>
Hi Hannah,
while I have no personal experience with the temporary cell-cycle arrest
on Galactose,
the increased G1 fraction at 25?C vs. 36?C is clearly expected.
As temperature decreases your cells grow more slowly.
This slower growth is mostly attributable to cells spending more time in G1.
Since at low growth rates daughter cells take much longer than mother
cells to complete their cycles,
you will have an increased fraction of cells in G1 (mothers and
daughters) and a higher fraction of
daughter cells (many in G1) in the population. This is consistent with
your FACS results.
There are several papers describing this effect, e.g.
Hartwell, L.H., and M.W. Unger (1977) /J. Cell Biol./ *75*(2): 422-435.
Lord, P.G., and A.E. Wheals (1980). /J. Bact./ *142*(3): 808-818.
Cheers,
Dirk
--
________________________________________________________________________
Dr. Dirk Mueller
Institute of Computational Science
Computational Systems Biology Group
ETH Zurich
Universitaetstr. 6, CAB J71.6
CH-8092 Zurich
Switzerland
Tel. ++41-(0)44-63-2-6434
Fax. ++41-(0)44-63-2-1374
Email: dirk.mueller@inf.ethz.ch
Web: http://csb.inf.ethz.ch
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From Gael.Yvert from ens-lyon.fr Tue Jun 10 06:40:53 2008
From: Gael.Yvert from ens-lyon.fr (=?ISO-8859-1?Q?Ga=EBl_Yvert?=)
Date: Tue Jun 10 08:46:18 2008
Subject: [Yeast] plasmid with secreted alkaline phosphatase
In-Reply-To:
References:
Message-ID: <484E6845.9030808@ens-lyon.fr>
Dear All,
We are setting up a reporter system requiring secreted enzymatic
activity in cerevisiae. The plasmid YEpFLAG-1 BAP from Sigma would be
perfect but it's no longer in their catalog and my contact at Sigma said
the product is discontinued. Would anybody having this plasmid be so
kind as to send a few microliters?
Many thanks for any help you can provide.
Gael.
----------------------------------
Ga?l YVERT
LBMC CNRS UMR5239
Ecole Normale Sup?rieure de Lyon
46 All?e d'Italie
69364 LYON cedex 07, FRANCE
Ph: +33 4 72 72 87 17
Fax: +33 4 72 72 80 80
http://www.ens-lyon.fr/LBMC/gisv/
-----------------------------------
From cedric.desmet from gmail.com Tue Jun 10 09:48:59 2008
From: cedric.desmet from gmail.com (Cedric)
Date: Tue Jun 10 11:19:20 2008
Subject: [Yeast] tagging for overexpression
Message-ID: <827989df0806100748o7a7c3ee9h55c67d3859d7b4a2@mail.gmail.com>
Hello everyone,
I would like to tag a gene C-terminally with a His6HA3 tag. How do I decide
where to insert this tag (directly before the stop codon?) and how do I
design the primers for this? Is there a website or software available?
Cheers,
Cedric De Smet
Utrecht University
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From cinthiait from yahoo.com Wed Jun 11 02:34:08 2008
From: cinthiait from yahoo.com (Cinzia Pagliuca)
Date: Wed Jun 11 08:33:54 2008
Subject: [Yeast] tagging for overexpression (Cedric)
In-Reply-To: <200806101704.m5AH4qO02222@net.bio.net>
Message-ID: <26610.5451.qm@web51109.mail.re2.yahoo.com>
Hallo Cedric,
Usually I replace the stop codon with a restriction enzyme site and then insert the tag. You can find under "primer design" in the website, the software you wish and download.
Ciao,
Cinzia
--- On Tue, 6/10/08, yeast-request@oat.bio.indiana.edu wrote:
> From: yeast-request@oat.bio.indiana.edu
> Subject: Yeast Digest, Vol 37, Issue 4
> To: yeast@magpie.bio.indiana.edu
> Date: Tuesday, June 10, 2008, 7:04 PM
> Send Yeast mailing list submissions to
> yeast@net.bio.net
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://www.bio.net/biomail/listinfo/yeast
> or, via email, send a message with subject or body
> 'help' to
> yeast-request@net.bio.net
>
> You can reach the person managing the list at
> yeast-owner@net.bio.net
>
> When replying, please edit your Subject line so it is more
> specific
> than "Re: Contents of Yeast digest..."
>
>
> Today's Topics:
>
> 1. plasmid with secreted alkaline phosphatase (Ga?l
> Yvert)
> 2. tagging for overexpression (Cedric)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 10 Jun 2008 13:40:53 +0200
> From: Ga?l Yvert
> Subject: [Yeast] plasmid with secreted alkaline phosphatase
> To: yeast@magpie.bio.indiana.edu
> Message-ID: <484E6845.9030808@ens-lyon.fr>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Dear All,
>
> We are setting up a reporter system requiring secreted
> enzymatic
> activity in cerevisiae. The plasmid YEpFLAG-1 BAP from
> Sigma would be
> perfect but it's no longer in their catalog and my
> contact at Sigma said
> the product is discontinued. Would anybody having this
> plasmid be so
> kind as to send a few microliters?
>
> Many thanks for any help you can provide.
> Gael.
>
> ----------------------------------
> Ga?l YVERT
> LBMC CNRS UMR5239
> Ecole Normale Sup?rieure de Lyon
> 46 All?e d'Italie
> 69364 LYON cedex 07, FRANCE
>
> Ph: +33 4 72 72 87 17
> Fax: +33 4 72 72 80 80
>
> http://www.ens-lyon.fr/LBMC/gisv/
> -----------------------------------
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 10 Jun 2008 16:48:59 +0200
> From: Cedric
> Subject: [Yeast] tagging for overexpression
> To: yeast@magpie.bio.indiana.edu
> Message-ID:
> <827989df0806100748o7a7c3ee9h55c67d3859d7b4a2@mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello everyone,
>
> I would like to tag a gene C-terminally with a His6HA3 tag.
> How do I decide
> where to insert this tag (directly before the stop codon?)
> and how do I
> design the primers for this? Is there a website or software
> available?
>
> Cheers,
> Cedric De Smet
> Utrecht University
> -------------- next part --------------
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> ------------------------------
>
> _______________________________________________
> Yeast mailing list
> Yeast@net.bio.net
> http://www.bio.net/biomail/listinfo/yeast
>
> End of Yeast Digest, Vol 37, Issue 4
> ************************************
From katharina.kittelmann from bio.uni-stuttgart.de Wed Jun 11 09:18:19 2008
From: katharina.kittelmann from bio.uni-stuttgart.de (Katharina Kittelmann)
Date: Wed Jun 11 09:44:03 2008
Subject: [Yeast] retinoblastoma protein
Message-ID:
Hi all,
does anybody now if there is a homologue of mammalian retinoblastoma protein
in S. pombe? I was searching the web but didn’t find anything (besides a
homologue of Rb binding protein 2).
Thank you…
Katharina
No virus found in this outgoing message.
Checked by AVG.
Version: 7.5.524 / Virus Database: 270.2.0/1495 - Release Date: 10.06.2008
17:11
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From val from sanger.ac.uk Wed Jun 11 10:48:34 2008
From: val from sanger.ac.uk (Valerie Wood)
Date: Thu Jun 12 07:47:04 2008
Subject: [Yeast] retinoblastoma protein
Message-ID:
Not that I have found,
Also no result using YOGY which presents results from some of the main ortholog predictors
http://www.sanger.ac.uk/cgi-bin/PostGenomics/S_pombe/YOGY/yogy-search.pl
and none of the conserved domains are detected in any fungi (click on the 'species icon' from the domain links below to see the species distribution)
http://pfam.sanger.ac.uk/family?acc=PF01858
http://pfam.sanger.ac.uk/family?acc=PF01858
http://pfam.sanger.ac.uk/family?acc=PF08934
However I wouldn't rule it out 100%. We still find universally conserved proteins where the similarities have been overlooked. For example only this week SPAC6F6.16c (previously orphan) was shown to be the ortholog of human TPP1 PMID:18535244
Val
>
> "Katharina Kittelmann" wrote:
> > Hi all,
> >
> > does anybody now if there is a homologue of mammalian retinoblastoma protein
> > in S. pombe? I was searching the web but didn’t find anything (besides a
> > homologue of Rb binding protein 2).
> >
> > Thank you…
> >
> > Katharina
> >
> >
> >
> >
> > No virus found in this outgoing message.
> > Checked by AVG.
> > Version: 7.5.524 / Virus Database: 270.2.0/1495 - Release Date: 10.06.2008
> > 17:11
> >
>
From rbrem from lego.berkeley.edu Mon Jun 16 14:05:24 2008
From: rbrem from lego.berkeley.edu (Rachel Brem)
Date: Mon Jun 16 23:43:45 2008
Subject: [Yeast] Postdoc position at UC Berkeley
Message-ID:
The lab of Rachel Brem at the University of California, Berkeley seeks
outstanding candidates for postdoctoral positions in projects on systems
and network traits in yeast aging. For one position, the incumbent
postdoctoral fellow will join a project on the yeast unfolded protein
response during aging. The goal of the project is to identify genes that
mediate age-associated changes in the systems properties of this
biochemical pathway. For a second position, the incumbent will screen the
yeast regulatory network for genes with age-dependent expression patterns,
with the goal of identifying novel determinants of aging phenotypes and
lifespan.
We are a young and flourishing lab in the Department of Molecular and Cell
Biology at Berkeley. Our work draws on the wealth of scientific resources
on the Berkeley campus and in the Bay Area, and our postdoctoral fellows
benefit from an exceptional training environment in genetics, genomics,
systems biology, and applied statistics. For more information about the
lab and a list of recent publications, see
http://mcb.berkeley.edu/faculty/GEN/bremr.html.
To apply, email a description of your research interests and your CV, and
have two recommendation letters sent, to rbrem at berkeley.edu. Previous
experience with systems biology or genomics is a plus, but trainees with a
molecular biology or genetics background are encouraged to apply.
--
Rachel Brem
Assistant Professor of Genetics, Genomics and Development
University of California, Berkeley
Department of Molecular & Cell Biology
304A Stanley Hall #3220
Berkeley, CA 94720-3220
Phone: (510) 642-9640
Fax: (510) 643-9290
Email: rbrem@berkeley.edu
From jonathan.jacobs from gmail.com Thu Jun 19 12:50:05 2008
From: jonathan.jacobs from gmail.com (Jonathan Jacobs)
Date: Fri Jun 20 00:32:18 2008
Subject: [Yeast] S.pombe pREP series plasmids question...
Message-ID: <508d065a0806191050l35239ef8q255ca321453ca3d5@mail.gmail.com>
Hello! this is my first post to this listserv, so please pardon me if I am a
bit overly verbose...
I was updating my sequence files & vector maps recently for various plasmids
and I noticed something that might be of interest to anyone using the
'pREP' series vectors in S.pombe.
Watanabe T et.al. (2002)
published a report that
indicated there were a number of poly(A) bearing
RNAs without long open reading frames expressed in S.pombe (so called 'prl'
genes). One of them, prl10 (Genbank
AB084822),
is a 692-bp transcript that could produce a small 40 a.a. protein. What was
interesting to me was that prl10 sits immediately upstream of nmt1. Since
the nmt1 promoter region is used in the pREP series plasmids, thus so is
the entire prl10 gene. Whether or not the prl10 transcript is expressed from
pREP vectors is not known (to me).
So I was curious: has anyone else noticed this before? And is it known
whether or not pREP series plasmids express the prl10 transcript? And
finally, is it known if there is a phenotype associated with a prl10
deletion strain? Does anyone have a hint as to what the function of this RNA
may be?
Jonathan Jacobs, Ph.D.
NICHD / NIH
lab: (301) 402-1155
cell: (240) 447-4039
http://www.linkedin.com/in/jonathanjacobs
http://www.citeulike.org/user/jonathanjacobs
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From val from sanger.ac.uk Fri Jun 20 03:12:23 2008
From: val from sanger.ac.uk (Valerie Wood)
Date: Fri Jun 20 09:17:42 2008
Subject: [Yeast] S.pombe pREP series plasmids question...
In-Reply-To: <508d065a0806191050l35239ef8q255ca321453ca3d5@mail.gmail.com>
References: <508d065a0806191050l35239ef8q255ca321453ca3d5@mail.gmail.com>
Message-ID: <485B6667.5090200@sanger.ac.uk>
Hello Jonathan,
I have prl10 mapped to the opposite strand to nmt1.
However, if you look at the high resolution transcript map, it does not
appear to be detectable.
http://www.sanger.ac.uk/cgi-bin/PostGenomics/S_pombe/pombetv/pombetv?genename=SPCC1223.02&action=genedb
Nothing is published about prl10.
Somebody else may be able to comment further.
Val
Jonathan Jacobs wrote:
> Hello! this is my first post to this listserv, so please pardon me if
> I am a bit overly verbose...
>
> I was updating my sequence files & vector maps recently for various
> plasmids and I noticed something that might be of interest to anyone
> using the 'pREP' series vectors in S.pombe.
>
> Watanabe T et.al. (2002)
> published a report that indicated there were a number of poly(A)
> bearing RNAs without long open reading frames expressed in S.pombe (so
> called 'prl' genes). One of them, prl10 (Genbank AB084822
> ),
> is a 692-bp transcript that could produce a small 40 a.a. protein.
> What was interesting to me was that prl10 sits immediately upstream of
> nmt1. Since the nmt1 promoter region is used in the pREP series
> plasmids, thus so is the entire prl10 gene. Whether or not the prl10
> transcript is expressed from pREP vectors is not known (to me).
>
> So I was curious: has anyone else noticed this before? And is it known
> whether or not pREP series plasmids express the prl10 transcript? And
> finally, is it known if there is a phenotype associated with a prl10
> deletion strain? Does anyone have a hint as to what the function of
> this RNA may be?
>
> Jonathan Jacobs, Ph.D.
> NICHD / NIH
> lab: (301) 402-1155
> cell: (240) 447-4039
>
> http://www.linkedin.com/in/jonathanjacobs
> http://www.citeulike.org/user/jonathanjacobs
> ------------------------------------------------------------------------
>
> _______________________________________________
> Yeast mailing list
> Yeast@net.bio.net
> http://www.bio.net/biomail/listinfo/yeast
--
---------------------------------------------------------------------------
Valerie Wood Tel: 01223 496909
S. pombe Genome Project Fax: 01223 494919
Wellcome Trust Sanger Institute email: val@sanger.ac.uk
Wellcome Trust Genome Campus http://www.genedb.org/genedb/pombe
Hinxton, Cambridge, CB10 1HH http://www.sanger.ac.uk/Projects/S_pombe
--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
From val from sanger.ac.uk Fri Jun 20 03:27:49 2008
From: val from sanger.ac.uk (Valerie Wood)
Date: Fri Jun 20 09:17:48 2008
Subject: [Pombelist] [Yeast] S.pombe pREP series plasmids question...
In-Reply-To: <485B6667.5090200@sanger.ac.uk>
References: <508d065a0806191050l35239ef8q255ca321453ca3d5@mail.gmail.com>
<485B6667.5090200@sanger.ac.uk>
Message-ID: <485B6A05.1020107@sanger.ac.uk>
Correction
Samuel just pointed prl10 is transcribed in YE, you can see this if you select YE to see the illumina data.
Val
Valerie Wood wrote:
>
> Hello Jonathan,
>
> I have prl10 mapped to the opposite strand to nmt1.
>
> However, if you look at the high resolution transcript map, it does
> not appear to be detectable.
> http://www.sanger.ac.uk/cgi-bin/PostGenomics/S_pombe/pombetv/pombetv?genename=SPCC1223.02&action=genedb
>
>
> Nothing is published about prl10.
> Somebody else may be able to comment further.
>
> Val
>
>
> Jonathan Jacobs wrote:
>> Hello! this is my first post to this listserv, so please pardon me if
>> I am a bit overly verbose...
>>
>> I was updating my sequence files & vector maps recently for various
>> plasmids and I noticed something that might be of interest to anyone
>> using the 'pREP' series vectors in S.pombe.
>>
>> Watanabe T et.al. (2002)
>> published a report that
>> indicated there were a number of poly(A) bearing RNAs without long
>> open reading frames expressed in S.pombe (so called 'prl' genes). One
>> of them, prl10 (Genbank AB084822
>> ),
>> is a 692-bp transcript that could produce a small 40 a.a. protein.
>> What was interesting to me was that prl10 sits immediately upstream
>> of nmt1. Since the nmt1 promoter region is used in the pREP series
>> plasmids, thus so is the entire prl10 gene. Whether or not the prl10
>> transcript is expressed from pREP vectors is not known (to me).
>>
>> So I was curious: has anyone else noticed this before? And is it
>> known whether or not pREP series plasmids express the prl10
>> transcript? And finally, is it known if there is a phenotype
>> associated with a prl10 deletion strain? Does anyone have a hint as
>> to what the function of this RNA may be?
>>
>> Jonathan Jacobs, Ph.D.
>> NICHD / NIH
>> lab: (301) 402-1155
>> cell: (240) 447-4039
>>
>> http://www.linkedin.com/in/jonathanjacobs
>> http://www.citeulike.org/user/jonathanjacobs
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> Yeast mailing list
>> Yeast@net.bio.net
>> http://www.bio.net/biomail/listinfo/yeast
>
>
--
---------------------------------------------------------------------------
Valerie Wood Tel: 01223 496909
S. pombe Genome Project Fax: 01223 494919
Wellcome Trust Sanger Institute email: val@sanger.ac.uk
Wellcome Trust Genome Campus http://www.genedb.org/genedb/pombe
Hinxton, Cambridge, CB10 1HH http://www.sanger.ac.uk/Projects/S_pombe
--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
From jonathan.jacobs from gmail.com Fri Jun 20 06:11:36 2008
From: jonathan.jacobs from gmail.com (Jonathan Jacobs)
Date: Fri Jun 20 09:17:52 2008
Subject: [Pombelist] [Yeast] S.pombe pREP series plasmids question...
In-Reply-To: <485B6A05.1020107@sanger.ac.uk>
References: <508d065a0806191050l35239ef8q255ca321453ca3d5@mail.gmail.com>
<485B6667.5090200@sanger.ac.uk> <485B6A05.1020107@sanger.ac.uk>
Message-ID: <508d065a0806200411u1b3597bx5aa44fcd552ee75e@mail.gmail.com>
Thank you for the link! Yes, i saw that prl10 was transcribed from the
opposite strand than nmt1 - i just wasn't sure if the presence of the
complete prl10 ORF present in the pREP nmt1 promoter also carried with it
additional prl10 expression.
cheers,
Jonathan Jacobs, Ph.D.
lab: (301) 402-1155
cell: (240) 447-4039
http://www.linkedin.com/in/jonathanjacobs
http://www.citeulike.org/user/jonathanjacobs
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From maraiar from exchange.nih.gov Tue Jun 24 12:01:14 2008
From: maraiar from exchange.nih.gov (Rich Maraia)
Date: Tue Jun 24 12:34:57 2008
Subject: [Yeast] transcription extract
Message-ID:
A postdoc in my lab can not seem to get in vitro transcription to
work. Either his yeast extract is not transcriptionally competent or
his in vitro transcription assay isn't working. Is anyone making
transcriptionally competent yeast extract near the NIH in Bethesda,
MD. Potentially, my postdoc could observe during the next
preparation. Alternatively, some active extract can be sent so that
he could use it as a positive control to troubleshoot his assay.
Thank you for your consideration,
Rich Maraia
--
Richard J. Maraia, M.D.
Captain, US Public Health Service, Commissioned Corps
Chief, Section on Molecular and Cell Biology
Intramural Research Program
Eunice Kennedy Shriver National Institute of Child Health and Human Development
National Institutes of Health
31 Center Dr., Rm 2A25
Bethesda, MD 20892-2426
Phone: 301 402-3567
Fax: 301 480-6863
http://eclipse.nichd.nih.gov/nichd/Maraia/Maraialabpage.html