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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.bio.net/bionet/mm/yeast/attachments/20080604/bd9ff0b4/attachment.html 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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URL: http://www.bio.net/bionet/mm/yeast/attachments/20080605/bdf7b7be/attachment.html 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.bio.net/bionet/mm/yeast/attachments/20080605/f1050a3f/attachment.html 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.bio.net/bionet/mm/yeast/attachments/20080610/3d69bc42/attachment.html 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 -------------- > An HTML attachment was scrubbed... > URL: > http://www.bio.net/bionet/mm/yeast/attachments/20080610/3d69bc42/attachment-0001.html > > ------------------------------ > > _______________________________________________ > 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.bio.net/bionet/mm/yeast/attachments/20080611/653a2bd0/attachment.html 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.bio.net/bionet/mm/yeast/attachments/20080619/a17269f5/attachment.html 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.bio.net/bionet/mm/yeast/attachments/20080620/72b55a45/attachment.html 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