From fneumann at mail.rockefeller.edu Thu Jan 4 18:38:08 2007 From: fneumann at mail.rockefeller.edu (Frank Neumann) Date: Thu, 4 Jan 2007 13:38:08 -0500 Subject: [Pombelist] (semi)-automated segmentation and measurement of fission yeast Message-ID: <200701041838.l04Ic8go004660@smtp1.rockefeller.edu> Dear "pombelist", I am currently trying to evaluate or develop solutions for (semi)-automated cell size measurements of S. pombe cells, based on transmission images (brightfield, phase or DIC). As an alternative, fluorescence images (e.g. lectin-FITC, or peripheral GFP marker) could be used. If you know any publicly available software or algorithm (preferably ImageJ or Matlab based) which segments and quantifies images in an entirely or partially automated way, could you please contact me. Thanks in advance for any suggestion, best regards, Frank ----------------------------------------- Frank Neumann The Rockefeller University Nurse laboratory, Box 5 1230 York Avenue New York, NY, 10021 USA phone: +1 212 327 84 76 fax: +1 212 327 84 70 email: fneumann at rockefeller.edu From rama at genome.stanford.edu Thu Jan 4 18:45:20 2007 From: rama at genome.stanford.edu (Rama Balakrishnan) Date: Thu, 4 Jan 2007 10:45:20 -0800 Subject: [Pombelist] (semi)-automated segmentation and measurement of fission yeast In-Reply-To: <200701041838.l04Ic8go004660@smtp1.rockefeller.edu> References: <200701041838.l04Ic8go004660@smtp1.rockefeller.edu> Message-ID: <41067C49-F401-4F40-8FA1-FF25003DA74E@genome.stanford.edu> Frank, You may want to check the Saccharomyces Cerevisiae Morphological Database(SCMD). They have developed methods to measure cell size. http://scmd.gi.k.u-tokyo.ac.jp/datamine/ Their paper in NAR- PMID: 14681423 Rama On Jan 4, 2007, at 10:38 AM, Frank Neumann wrote: > Dear "pombelist", > > I am currently trying to evaluate or develop solutions for (semi)- > automated > cell size measurements of S. pombe cells, based on transmission images > (brightfield, phase or DIC). As an alternative, fluorescence images > (e.g. > lectin-FITC, or peripheral GFP marker) could be used. > > If you know any publicly available software or algorithm > (preferably ImageJ > or Matlab based) which segments and quantifies images in an > entirely or > partially automated way, could you please contact me. > > Thanks in advance for any suggestion, best regards, Frank > > ----------------------------------------- > Frank Neumann > The Rockefeller University > Nurse laboratory, Box 5 > 1230 York Avenue > New York, NY, 10021 > USA > > phone: +1 212 327 84 76 > fax: +1 212 327 84 70 > email: fneumann at rockefeller.edu > > > _______________________________________________ > Pombelist mailing list > Pombelist at sanger.ac.uk > http://lists.sanger.ac.uk/mailman/listinfo/pombelist From huberman at buffalo.edu Thu Jan 4 19:45:55 2007 From: huberman at buffalo.edu (Joel Huberman) Date: Thu, 4 Jan 2007 14:45:55 -0500 Subject: [Pombelist] (semi)-automated segmentation and measurement of fission yeast In-Reply-To: <200701041838.l04Ic8go004660@smtp1.rockefeller.edu> References: <200701041838.l04Ic8go004660@smtp1.rockefeller.edu> Message-ID: <3BD3BD29-C469-4405-8D5B-6FAFC5912489@buffalo.edu> Dear Frank, Several years ago, I--together with students in my lab--developed some algorithms for measuring the DNA contents of S. pombe nuclei based on their DAPI staining intensities. The algorithms (for Image) required identification of nuclei in binucleate as well as mononucleate cells. Perhaps some of our algorithms would be helpful to you. Our algorithms are freely available at http:// asajj.roswellpark.org/huberman/Quant_Flu_Microscopy/ Quant_Flu_Micro.html. The text accompanying the algorithms hasn't been updated since 31 October, 1999, but the algorithms are as valid now as they were at that time. I hope this helps you. Sincerely yours, Joel Huberman ********************************* Dr. Joel A. Huberman Professor of Cellular & Molecular Biology Department of Cancer Biology Roswell Park Cancer Institute Elm & Carlton Streets Buffalo, NY 14263-0001 (716) 845-3047 Phone (716) 845-8126 FAX huberman at buffalo.edu http://asajj.roswellpark.org/huberman/jh.html ********************************* On Jan 4, 2007, at 1:38 PM, Frank Neumann wrote: > Dear "pombelist", > > I am currently trying to evaluate or develop solutions for (semi)- > automated > cell size measurements of S. pombe cells, based on transmission images > (brightfield, phase or DIC). As an alternative, fluorescence images > (e.g. > lectin-FITC, or peripheral GFP marker) could be used. > > If you know any publicly available software or algorithm > (preferably ImageJ > or Matlab based) which segments and quantifies images in an > entirely or > partially automated way, could you please contact me. > > Thanks in advance for any suggestion, best regards, Frank > > ----------------------------------------- > Frank Neumann > The Rockefeller University > Nurse laboratory, Box 5 > 1230 York Avenue > New York, NY, 10021 > USA > > phone: +1 212 327 84 76 > fax: +1 212 327 84 70 > email: fneumann at rockefeller.edu > > > _______________________________________________ > Pombelist mailing list > Pombelist at sanger.ac.uk > http://lists.sanger.ac.uk/mailman/listinfo/pombelist -------------- Attachments -------------- An HTML attachment was scrubbed... URL: From val at sanger.ac.uk Fri Jan 5 11:26:49 2007 From: val at sanger.ac.uk (Valerie Wood) Date: Fri, 05 Jan 2007 11:26:49 +0000 Subject: [Pombelist] Pombe club in Manchester/ message from Jacky Hayles Message-ID: <459E35F9.5020800@sanger.ac.uk> Dear All A number of you have not received the Manchester Pombe Club mailing so I'm sending it out again via Val's pombe list. I am going to make a new pombe club list and hopefully sort out some of these problems. So it would be very helpful to me if you could email me at the address below (just say Pombe Club) if you would like to be on the mailing list. If you are not receiving the pombe club notices it is also worth checking with your IS department to see if the message is being blocked by your firewall. Looking forward to seeing you in Manchester and sorry to those of you who have received this twice. Happy New Year Jacky Jacqueline Hayles Cell Cycle Laboratory Cancer Research UK, London Research Institute 44 Lincoln's Inn Fields London WC2A 3PX, UNITED KINGDOM Tel ::: +44 (0) 20 7269 3105 Fax ::: +44 (0) 20 7269 3258 email jacqueline.hayles at cancer.org.uk -------------- Attachments -------------- To retrieve the following attachment, use the link provided Name: pombe_2007_notice.ppt Size: 118784 bytes URL: -------------- Attachments -------------- To retrieve the following attachment, use the link provided Name: mcrpombeinfo.doc Size: 34304 bytes URL: From jerry.wu at sanger.ac.uk Fri Jan 5 14:44:52 2007 From: jerry.wu at sanger.ac.uk (Jerry Wu) Date: Fri, 5 Jan 2007 14:44:52 -0000 Subject: [Pombelist] RE: automated cell size measurements of S. pombe cells Message-ID: Hi, Frank, I have some in-house Matlab codes to cope with the fully automated cell size measurement(inc. segmentation), originally developed for MitoCheck project and IVP treatment. In addition, it is worth to looking at the CellProfiler (http://www.cellprofiler.org/), a relatively new Matlab based open source. BTW, I would optimise my code for you if you would send me one of your image samples. Cheers Jerry --- \\\|/// \\ - - // ( @ @ ) .............................oOOo-(_)-oOOo............................ "Put your hand in a hot stove for a minute, and it seems like an hour. Sit with a pretty girl for an hour, and it seems like a minute. That's relativity." - Albert Einstein. .oooO ............................... ( )-- Oooo. .............................. \ ( ( ) \_) ) / (_/ Date: Thu, 4 Jan 2007 13:38:08 -0500 From: Frank Neumann To: pombelist at sanger.ac.uk Subject: [Pombelist] (semi)-automated segmentation and measurement of fission yeast Dear "pombelist", I am currently trying to evaluate or develop solutions for (semi)-automated cell size measurements of S. pombe cells, based on transmission images (brightfield, phase or DIC). As an alternative, fluorescence images (e.g. lectin-FITC, or peripheral GFP marker) could be used. If you know any publicly available software or algorithm (preferably ImageJ or Matlab based) which segments and quantifies images in an entirely or partially automated way, could you please contact me. Thanks in advance for any suggestion, best regards, Frank ----------------------------------------- Frank Neumann The Rockefeller University Nurse laboratory, Box 5 1230 York Avenue New York, NY, 10021 USA phone: +1 212 327 84 76 fax: +1 212 327 84 70 email: fneumann at rockefeller.edu From anita.tienhaara at helsinki.fi Fri Jan 12 11:08:43 2007 From: anita.tienhaara at helsinki.fi (Anita Tienhaara) Date: Fri, 12 Jan 2007 13:08:43 +0200 Subject: [Pombelist] PYFF3 Conference in Helsinki in June Message-ID: <45A7885B.5009.A8703E3@anita.tienhaara.helsinki.fi> Dear Colleagues, We are happy to welcome You to the Conference on Physiology of Yeasts and Filamentous Fungi (PYFF3) to be held in Helsinki, 13-16th of June 2007. If you are interested to be included in our mailing list, please, email anita.tienhaara at helsinki.fi . Please, visit also the conference web site http://pyff3.vtt.fi/ . The abstract dead-line is 12th of March. The conference will take place in the heart of Helsinki at Marina Congress centre. The meeting is the3rd one in a series under the Microbial Physiology section of the European Federation of Biotechnology. The previous meetings have been highly successful and appreciated by both academic and industrial audience. The conference will cover the most recent advances in various fundamental and applied aspects of the physiology of eukaryotic microbes. The topics include e.g: genomics; nutrition, signalling and tranport; physiological regulation; metabolomics and lipidomics; protein production; and metabolite production. The importance of yeasts and filamentous fungi in biorefinery research will also be addressed. We would appreciate if you could circulate this mail amongst your students and colleagues. Please, print the PYFF3 leaflet at http://pyff3.vtt.fi/leaflet.pdf for advertisement. Thank you! Our warmest welcome to Helsinki ! Prof. Merja Penttil? and Dr. Markku Saloheimo VTT Technical Research Centre of Finland -------------- Attachments -------------- An HTML attachment was scrubbed... URL: From onigen at my.molbio.ku.dk Tue Jan 16 11:03:58 2007 From: onigen at my.molbio.ku.dk (Olaf Nielsen) Date: Tue, 16 Jan 2007 12:03:58 +0100 Subject: [Pombelist] Postdoc position in Copenhagen Message-ID: Hi all I have a vacant postoc position in my lab. Please bring the attached add to the attention of anyone you think may be interested. Many thanks Olaf * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Olaf Nielsen, Professor, Ph.D. Department of Molecular Biology University of Copenhagen Ole Maal?es Vej 5 DK-2200 Copenhagen N Denmark tel: +45 3532 2102 fax: +45 3532 2113 email: onigen at my.molbio.ku.dk http://www.imbf.ku.dk/onigen * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * -------------- Attachments -------------- To retrieve the following attachment, use the link provided Name: postdoc.pdf Size: 92645 bytes URL: From rama at genome.stanford.edu Thu Jan 18 18:13:16 2007 From: rama at genome.stanford.edu (Rama Balakrishnan) Date: Thu, 18 Jan 2007 10:13:16 -0800 Subject: [Pombelist] Fwd: Eukaryotic Genome Annotation course at TIGR References: Message-ID: Begin forwarded message: > From: "Hannick, Linda" > Date: January 18, 2007 8:19:06 AM PST > To: "Gene Ontology" , friends at genome.stanford.edu> > Subject: Eukaryotic Genome Annotation course at TIGR > > FYI: > > > Eukaryotic Genome Annotation and Analysis Course > > TIGR is offering a new three-day course in Eukaryotic Genome > Annotation and Analysis. This course will familiarize attendees > with TIGR's eukaryotic annotation methods, tools and computational > pipeline for annotation, including our manual annotation tool > Manatee . In this class you will > learn about many of the searches, tools, and processes we use to > annotate, analyze and compare eukaryotic genomes, including a > session on GO. > > This course is aimed at researchers, post-doctoral fellows, > university faculty, students and others who desire to better > understand how genes and other features of genomes are predicted, > and how to understand and make better use of the vast amount of > information flowing from genome projects. > > Upcoming Dates for the Course > > The course is offered on the following dates at TIGR?s Rockville, > MD, US Campus: > March 6-8, 2007 > June 26-28, 2007 > > Sept. 18-20, 2007 > > > Tuition of $595.00 includes all class materials and lunch each day. > > > For more information, see the website: http://www.tigr.org/ > edutraining/training/eukaryotic_annotation.shtml, or call Anna von > Arx at 301-795-7943. > > > Thanks, > > Linda > > > ~~~~~~~~~~~~~~~~~ > Linda I. Hannick, Ph.D. > Bioinformatics Analyst > The Institute for Genomic Research (TIGR) > Rockville, MD 20850 USA > ~~~~~~~~~~~~~~~~~~~ > 301-795-7857 voice > 301-838-0227 fax > ~~~~~~~~~~~~~~~~~~~ > > -------------- Attachments -------------- An HTML attachment was scrubbed... URL: From K.A.Moore at exeter.ac.uk Sun Jan 21 16:33:27 2007 From: K.A.Moore at exeter.ac.uk (Dr. Karen Moore) Date: Sun, 21 Jan 2007 16:33:27 -0000 (GMT) Subject: [Pombelist] (no subject) Message-ID: <1162.81.132.105.105.1169397207.squirrel@www.webmail.ex.ac.uk> Please check that I am on the pombelist. Thanks, Karen Dr. Karen Moore, Department of Biosciences, University of Exeter, Henry Wellcome Building for Biocatalysis Stocker Road Exeter EX4 4QD UK Phone: +44 (0)1392 262085 From wxj580 at bham.ac.uk Tue Jan 23 11:19:24 2007 From: wxj580 at bham.ac.uk (JIkai) Date: Tue, 23 Jan 2007 11:19:24 -0000 Subject: [Pombelist] Interesting Strains References: Message-ID: <004201c73ee0$565adbe0$508ebc93@adf.bham.ac.uk> Hi, I get two strains from different groups. Both of them are Leu and Ura auxotroph, but a nonessential gene was disrupted in one strain. When I culture both strains in EMM-Supplement, the gene disrupted one grows much faster than the other one. However, If they are cultured in YES, reversely, the disrupted one grows slower than the other one. Do you have the similar experience? After yeast transformation (the plasmids don't effect the cell very much, since it just contains gfp gene in pREP41), the disrupted one still grows much quicker since the colony radius could reach about 2mm in 4-5 days), but there are a lot of tiny colonies from the other strain at the same day. Moreover, it seems very hard to get larger colonies since I try to keep the plate in 30 C for ten days and the colonies sizes are no more than 2mm. But both transformants are all right since I could see obvious fluorescence in microscope. The other common thing in my transformation is that the transformants sizes are not uniform, some are good and some are very small. It is true that the sizes of colonies located in the centre of the plate are commonly less than that in the margin. Do you know how to make it better? I just very interested in this kinds of phenomenon and try to optimize my future experiment since I am fresh and haven't good experience in S. pombe. All of disscussion, speculation and suggestions are very welcome! By the way, in the 30 C fan incubater, Is it proper to use parafilm wrap the plates or not for culture the cells? Thank you very much! Cheers, Jikai Wen School of Biosciences, Birmingham University, Birmingham, UK. B15 2TT From karl.ekwall at sh.se Fri Jan 26 11:02:50 2007 From: karl.ekwall at sh.se (Karl Ekwall) Date: Fri, 26 Jan 2007 12:02:50 +0100 Subject: [Pombelist] Post-doctoral position available Message-ID: Dear all, A post-doctoral position (3 years) is now available in my laboratory to perform comparative studies of fission yeasts, worms and flies using bioinformatics as well as wet-lab approaches. The project focuses on how general controls of gene expression and genome maintenance are governed by a combination of protein-coding and non-protein-coding genes in the three groups of organisms. If you wish to apply for this position please contact me for further details (karl.ekwall at sh.se) Best regards Karl -- ******************************************************************* Dr. Karl Ekwall Associate Professor Karolinska Institutet, Dept of Biosciences & University College S?dert?rn lab web page: http://natvet.sh.se/ekwall_lab/ swedish/svensk version: http://www.novum.se/forskning_karl_ekwall.php english version: http://www.novum.se/english/forskning_karl_ekwall.php email: karl.ekwall at cbt.ki.se karl.ekwall at sh.se CONTACT DETAILS Phone: +46 8 608 4713 (office) Fax: +46 8 608 4510 Mailing address: University College S?dert?rn School of Life Sciences S-141 89 Huddinge, SWEDEN Courier Delivery adress: Alfred Nobel's All? 3 S-141 52 Huddinge, SWEDEN ******************************************************************** -------------- Attachments -------------- An HTML attachment was scrubbed... URL: From val at sanger.ac.uk Wed Jan 31 14:21:34 2007 From: val at sanger.ac.uk (Valerie Wood) Date: Wed, 31 Jan 2007 14:21:34 +0000 Subject: [Pombelist] Announcement: Move from contigs to chromosomes in GeneDB Message-ID: <45C0A5EE.1080603@sanger.ac.uk> Dear All, In order to improve data transfer and maintenance (both within and between databases) the contig data in GeneDB has been merged into 3 chromosomes and the remaining 4 gaps filled by 100 N's. Major consequences of this move: 1. Feature coordinates have changed. GeneDB now presents the new 'chromosomes' instead of the contigs. This means that the feature coordinates represented i) on the gene pages, ii) in Artemis and iii) in GBrowse have changes to the new chromosomal coordinates. 2. Public nucleotide sequence database (EMBL/GenBank/DDBJ) updates and new accession numbers. The updated chromosome entries will be resubmitted to EMBL shortly and these sequences will be assigned new accession numbers. The old accession numbers previously assigned to the individual cosmid entries will become secondary accession numbers to the new chromosome entries, and the old cosmid entries will be suppressed. The new accession numbers for the chromosome entries will be CU329670 chromosome 1 CU329671 chromosome 2 CU329672 chromosome 3 These new entries will match the current EMBL/GenBank/DDBJ chromosomes (although if you have used older data for your analysis, you may need to incorporate the changes in 6. below) 3. Contig files are deprecated. The old 'contigs' will no longer be maintained or made available for download from the ftp site. Older versions will still be available from the archive. The chromosome sequence and annotation will be available for download. 4. You can "Web publish" your own genome wide data using the GBrowse genome viewer. The transition to chromosomes instead of contigs should make it much easier for groups to upload their own annotations which are based on chromosomal data into the GBrowse genome viewer. You can upload your own list of sequence features and annotations (for example microarray tiling path data, promoters, replication origins) to GBrowse and view them in the context of the genome. Uploaded annotations will persist until you edit them or delete them. Your annotations are private and will not be seen by other individuals. If you choose to, you can publish your annotations and share them with your colleagues. The instructions for adding tracks to GBrowse are here: http://www.genedb.org/perl-gb/gbrowse/S.pombe/?help=annotation 5. Gap Status /Gap size changes The new chromosomes have gaps filled by 100 N's instead of the 1000 N's in previous Sanger versions. This is consistent with with the EMBL/GenBank/DDBJ convention for sequence gaps (the existing fission yeast chromosome sequences in EMBL, GenBank and DDBJ have 100 N's in the gaps) The fission yeast genome sequence data is still in 7 contigs (contains 4 sequence gaps). The current status and estimated gap sizes are described here: http://www.sanger.ac.uk/Projects/S_pombe/status.shtml 6. Sequence alterations Groups who have based their analysis on previous versions of the data may need to update their sequence data, or re run their analyses to take account of small sequence changes to make their data match the current assembly. All changes to the sequence since July 2003, and any future changes will be recorded here http://www.sanger.ac.uk/Projects/S_pombe/sequence_updates.shtml Let me know if you have any questions, Val -- --------------------------------------------------------------------------- Valerie Wood Tel: 01223 496909 S. pombe Genome Project Fax: 01223 494919 Wellcome Trust Sanger Institute email: val at 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 From val at sanger.ac.uk Thu Feb 1 16:18:40 2007 From: val at sanger.ac.uk (Valerie Wood) Date: Thu, 01 Feb 2007 16:18:40 +0000 Subject: [Pombelist] Move from contigs to chromosomes in GeneDB/data downloading Message-ID: <45C212E0.4010306@sanger.ac.uk> Just to clarify: Data downloaded for individual CDS/genes from GeneDB using the list download: http://www.genedb.org/genedb/idListForm.jsp?defOrg=pombe (either user defined, or as the result of a Boolean query) is exactly the same as before. The only difference you should notice is that the genomic coordinates of sequences have changed. The changes described for the downloadable data apply to raw data you can download from the ftp site from here: http://www.sanger.ac.uk/Projects/S_pombe/download.shtml Previously cosmid and contig sequences were made avaiable to download, these are now replaced by chromosomes. -- --------------------------------------------------------------------------- Valerie Wood Tel: 01223 496909 S. pombe Genome Project Fax: 01223 494919 Wellcome Trust Sanger Institute email: val at 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 From hohmann at gmm.gu.se Wed Feb 7 08:51:51 2007 From: hohmann at gmm.gu.se (Stefan Hohmann) Date: Wed, 07 Feb 2007 09:51:51 +0100 Subject: [Pombelist] yeast systems biology course Message-ID: <45C9A137.11269.AFAAD72@hohmann.gmm.gu.se> International Course in Yeast Systems Biology June 4-21, G?teborg, Sweden This is a FEBS Course (www.febs.org). This will be a three week intense hand-on course with both experimental and theoretical studies, guided by top scientists in the field. The course is intended for advanced PhD students and post-docs. For details see the attached folder and the website at www.icysb.org Deadline for application is February 28. Prof. Stefan Hohmann Department of Cell and Molecular Biology G?teborg University Box 462 SE-40530 G?teborg, Sweden (street address: Medicinaregatan 9E, SE-41390 G?teborg) Tel: +46 31 360844; Fax: +46 31 7862525 e-mail: hohmann at gmm.gu.se http://www.gmm.gu.se/groups/hohmann Yeast Systems Biology Course: http://www.icysb.org Systems Biology Conference 2008: http://www.icsb-2008.org For mails concerning journals only use the corresponding addresses: editor at current-genetics.se editor at molecular-genetics-genomics.se editor at topics-current-genetics.se -------------- Attachments -------------- An HTML attachment was scrubbed... URL: -------------- Attachments -------------- The following section of this message contains a file attachment prepared for transmission using the Internet MIME message format. If you are using Pegasus Mail, or any other MIME-compliant system, you should be able to save it or view it from within your mailer. If you cannot, please ask your system administrator for assistance. ---- File information ----------- File: ICYSB_folder_febs.pdf Date: 2 Feb 2007, 7:20 Size: 542083 bytes. Type: Unknown -------------- Attachments -------------- To retrieve the following attachment, use the link provided Name: ICYSB_folder_febs.pdf Size: 542083 bytes URL: From onigen at my.molbio.ku.dk Fri Feb 9 12:57:09 2007 From: onigen at my.molbio.ku.dk (Olaf Nielsen) Date: Fri, 09 Feb 2007 13:57:09 +0100 Subject: [Pombelist] Registration: Fourth International Fission Yeast Meeting Message-ID: Dear all, This mail just to inform you that registration for the Fourth International Fission Yeast Meeting, Copenhagen, June 11-16, is now open at www.pombe.dk Please note that the deadline for abstract submission and for registration at reduced fee is March 15. Looking forward to seeing you in Copenhagen. Best regards, Olaf Nielsen, Organizer * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Olaf Nielsen, Professor, Ph.D. Department of Molecular Biology University of Copenhagen Ole Maal?es Vej 5 DK-2200 Copenhagen N Denmark tel: +45 3532 2102 fax: +45 3532 2113 email: onigen at my.molbio.ku.dk http://www.imbf.ku.dk/onigen * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * From Jurg at sanger.ac.uk Tue Feb 13 18:13:03 2007 From: Jurg at sanger.ac.uk (Jurg Bahler) Date: Tue, 13 Feb 2007 18:13:03 -0000 Subject: [Pombelist] Course: Genome-wide approaches with fission yeast Message-ID: <0526C4B4E593154B86E6A8651913C28DB9136B@exchsrv2.internal.sanger.ac.uk> Dear All, We are organizing a Wellcome Trust Advanced Course 'Genome-wide approaches with fission yeast' from 1-7 October 2007 in Hinxton. This hands-on course is for colleagues who would like to use large-scale methods for their research. The attendance is limited to 16-18 people, and selection will be based on the applications. More details are available here: http://www.wellcome.ac.uk/doc_WTX033405.html Cheers, -Jurg --- J?rg B?hler, Ph.D. Wellcome Trust Sanger Institute Hinxton Cambridge CB10 1HH UK P: +44(0)1223-496948 F: +44(0)1223-496802 W: http://www.sanger.ac.uk/PostGenomics/S_pombe/ From anita.tienhaara at helsinki.fi Mon Feb 19 12:07:16 2007 From: anita.tienhaara at helsinki.fi (Anita Tienhaara) Date: Mon, 19 Feb 2007 14:07:16 +0200 Subject: [Pombelist] PYFF3 Conference in Helsinki in June Message-ID: <45D9AF14.17001.F88520C@anita.tienhaara.helsinki.fi> Dear Colleagues, We areveryhappy to welcome You to the Conference on PHYSIOLOGY OF YEASTS AND FILAMENTOUS FUNGI (PYFF3) to be held in Helsinki, 13-16th of June 2007.The dead-line for abstract submission, early registration and student grant applications is 10th of April.Please,REGISTER NOW and visit the conference web site athttp://pyff3.vtt.fi/ .We haveextended the abstract dead-line from that previously announced. Note thatabstracts arriving after the10th of Aprilcannot any more be considered asoral presentations. For further information,please email anita.tienhaara at helsinki.fi . The conference will take place in the heart of Helsinki at Marina Congress centre. The meeting is the3rd one in a series under the Microbial Physiology section of the European Federation of Biotechnology. The previous meetings have been highly successful and appreciated by both academic and industrial audience.The conference will cover the most recent advances in various fundamental and applied aspects of the physiology of eukaryotic microbes. The topics include e.g: genomics; nutrition, signalling and tranport; physiological regulation; metabolomics and lipidomics; protein production; and metabolite production. The importance of yeasts and filamentous fungi in biorefinery research will also be addressed. We would appreciate if you could circulate this mail amongst your students and colleagues. Please, print the PYFF3 leaflet athttp://pyff3.vtt.fi/leaflet.pdf foradvertisement. Thank you! Our warmest welcome to Helsinki ! Prof. Merja Penttil? and Dr. Markku Saloheimo VTT Technical Research Centre of Finland From geetanjali_rajyee at yahoo.com Wed Feb 21 12:57:39 2007 From: geetanjali_rajyee at yahoo.com (geetanjali sundaram) Date: Wed, 21 Feb 2007 04:57:39 -0800 (PST) Subject: [Pombelist] s.pombe nuclear extracts Message-ID: <582320.13891.qm@web52215.mail.yahoo.com> Dear pombelist members, Can anyone of you please suggest a protocol for preparation of small scale nuclear extracts from S.pombe . i shall be very grateful for you suggestions Thanks and regards geetanjali Sundaram University of Calcutta INDIA --------------------------------- Expecting? Get great news right away with email Auto-Check. Try the Yahoo! Mail Beta. -------------- Attachments -------------- An HTML attachment was scrubbed... URL: From f.hochstenbach at amc.uva.nl Wed Feb 21 13:35:09 2007 From: f.hochstenbach at amc.uva.nl (Frans Hochstenbach) Date: Wed, 21 Feb 2007 14:35:09 +0100 Subject: [Pombelist] PhD student and postdoc positions in Amsterdam Message-ID: Dear all, Ben Distel and I have two PhD positions and one postdoc position available at the University of Amsterdam, as part of an EU-funded Marie Curie Research Training Network. One PhD student will study the SH3 protein-interaction network in S. pombe, while the other will analyze the SH3 protein-interaction network in Candida albicans. The postdoc will focus on the identification of SH3 partner proteins using mass spectrometry. Please bring the attached poster to the attention of suitable candidates who maybe interested. Many thanks, Frans -- =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Frans Hochstenbach, Ph.D. Department of Medical Biochemistry Academic Medical Center, Room K1-260 University of Amsterdam Meibergdreef 15 1105 AZ AMSTERDAM The Netherlands Phone (NL:31) (20) 5665137 Fax (NL:31) (20) 6915519 Email f.hochstenbach at amc.uva.nl =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= -------------- Attachments -------------- To retrieve the following attachment, use the link provided Name: Positions_Amsterdam.pdf Size: 336711 bytes URL: From yeast2007 at meetingplanners.com.au Thu Feb 22 06:49:26 2007 From: yeast2007 at meetingplanners.com.au (Yeast 2007) Date: Thu, 22 Feb 2007 17:49:26 +1100 Subject: [Pombelist] Yeast 2007: Early Bird Registration Closes in 1 Week Message-ID: If you cannot view the html email, go to http://www.meetings.com.au/yeast/register.html XXIII International Conference on Yeast Genetics & Molecular Biology 1-6 July 2007 Melbourne, Australia Early Bird Registration Closes in 1 Week. Register by 1st Mark to Save Visit the website to register at www.yeast2007.org Don't forget to submit your abstract by 1st April 2007 http://www.yeast2007.org/program_abstracts.php Register Now and Save > http://www.yeast2007.org/register.php For more information visit www.yeast2007.org -------------- Attachments -------------- An HTML attachment was scrubbed... URL: From yeast2007 at meetingplanners.com.au Fri Feb 23 07:11:51 2007 From: yeast2007 at meetingplanners.com.au (Yeast 2007) Date: Fri, 23 Feb 2007 18:11:51 +1100 Subject: [Pombelist] Yeast 2007: Early Bird Registration Closes in 1 Week Message-ID: If you cannot view the html email, go to http://www.meetings.com.au/yeast/register.html XXIII International Conference on Yeast Genetics & Molecular Biology 1-6 July 2007 Melbourne, Australia Early Bird Registration Closes in 1 Week. Register by 1st Mark to Save Visit the website to register at www.yeast2007.org Don't forget to submit your abstract by 1st April 2007 http://www.yeast2007.org/program_abstracts.php Register Now and Save > http://www.yeast2007.org/register.php For more information visit www.yeast2007.org -------------- Attachments -------------- An HTML attachment was scrubbed... URL: From R.M.Holmes at sussex.ac.uk Fri Feb 23 14:59:46 2007 From: R.M.Holmes at sussex.ac.uk (Rosalind Holmes) Date: Fri, 23 Feb 2007 14:59:46 +0000 Subject: [Pombelist] RIKEN ORFeome Plasmids and Gateway System Vectors Message-ID: <5C23B3B3DCE6BAD9343F0013@gcpc106.gdsc.susx.ac.uk> Hello :-) Does anyone have any experience with the pDONR201 plasmids available from RIKEN? There appear to be mutations in many of the ORFs they have cloned into pDONR, but in the paper (Matsuyama et al, Nature Biotechnol. 2006; 24:841-7) they imply that they have only allowed mutations that are "supposed to be missense changes" and those in introns that are "supposed to not affect splicing". Any further information/experience with respect to this issue would be very helpful. In addition, does anyone have any experience with the Invitrogen Gateway System compatible "pDUAL" vectors they have created? Thank you in advance :-) Roz. +++++++++++++++++++++++++++++++++++++++++ Rosalind Holmes, MSci (Hons) G4.15 Genome Damage and Stability Centre, Science Park Road, University of Sussex, Falmer, Brighton, East Sussex, United Kingdom, BN1 9RQ. Email: R.M.Holmes at sussex.ac.uk Office: +44 (0)1273 67 8976 Lab: +44 (0)1273 87 7170 Fax: +44 (0)1273 67 8121 Webpage: http://www.sussex.ac.uk/gdsc/profile180072.html My Labs: http://www.sussex.ac.uk/gdsc/1-4-1.html http://www.sussex.ac.uk/gdsc/1-4-2.html From Marc_Buehler at hms.harvard.edu Fri Feb 23 15:25:20 2007 From: Marc_Buehler at hms.harvard.edu (Buehler, Marc ) Date: Fri, 23 Feb 2007 10:25:20 -0500 Subject: [Pombelist] Ura4 antibody, orotidine 5'-phosphate decarboxylase activity assay Message-ID: <34D3E13342E7144D8E1A05032097A27A086F5F94@MAILSERVER02.MED.HARVARD.EDU> Hello, is there anyone aware of an antibody which was raised against Ura4 (orotidine 5'-phosphate decarboxylase) or an enzymatic assay to test for orotidine 5'-phosphate decarboxylase activity? Marc B?hler Marc B?hler, PhD Harvard Medical School Department of Cell Biology LHRRB room 517 240 Longwood Avenue Boston, MA 02115 Tel.: 617-432-1248 Fax.:617-432-5596 -------------- Attachments -------------- An HTML attachment was scrubbed... URL: From nick.rhind at umassmed.edu Thu Mar 1 16:31:17 2007 From: nick.rhind at umassmed.edu (Nick Rhind) Date: Thu, 01 Mar 2007 11:31:17 -0500 Subject: [Pombelist] Automated annotation of the Schizosaccharomyces japonicus genome sequence Message-ID: The initial automated gene annotation of the Schizosaccharomyces japonicus genome is now available. The annotation, containing 5172 gene models, was produced using a combination of gene finding algorithms based on coding capacity, conservation and synteny with the pombe genome. The japonicus annotated assembly is available at http://www.broad.mit.edu/annotation/genome/schizosaccharomyces_japonicus.2/H ome.html The site includes information about the sequencing, assembly and annotation of the genome, along with tools for downloading genome sequences, BLASTing against the genome assembly, and searching and browsing for features of the genome. The genome was sequenced at The Broad Institute as part of the Fungal Genome Initiative, a project funded by NHGRI. The genome of Schizosaccharomyces octosporus is currently being sequenced. Once the octosporus genome is assembled and machine annotated, the annotations of two genomes will be manually edited in collaboration with the fission yeast community. Annotations will be released as they become available. Please share this release notice with anyone you think may be interested. Sincerely, Chad Nusbaum Nick Rhind From yeast2007 at meetingplanners.com.au Fri Mar 2 11:52:40 2007 From: yeast2007 at meetingplanners.com.au (Yeast 2007) Date: Fri, 02 Mar 2007 22:52:40 +1100 Subject: [Pombelist] Yeast 2007: Early Bird Registration Extended to 1 April 2007 Message-ID: Access this link If you cannot view this email properly http://www.meetings.com.au/yeast/4th.htm EARLY BIRD REGISTRATION HAS BEEN EXTENDED TO 1ST APRIL 2007 This date will coincide with the deadline for call for abstracts Don't miss out on the leaders of our industry. Some of them are featured here: Dr Paul Chambers, Australia Generating novel wine yeasts using traditional and GM approaches Theme: Yeast Biotechnology Dr Edda Kipp, Germany Modeling of Yeast Cell Stress Response Theme: Metabolism and Metabolomics Professor Susan Liebman, USA Prion-prion interactions in yeast Theme: Yeast models for human disease and ageing Professor Mitsuhiro Yanagida, Japan Metabolic aspects of the chromosome segregation and cell cycle control in fission yeast Theme: Cell growth, division and differentiation Don't miss the opportunity to be listed along side these speakers. Deadline for submission is 1 April. For more information and to register for the conference please click on the following link: www.yeast2007.org -------------- Attachments -------------- An HTML attachment was scrubbed... URL: From jvirgin at u.washington.edu Fri Mar 2 16:13:52 2007 From: jvirgin at u.washington.edu (jvirgin at u.washington.edu) Date: Fri, 2 Mar 2007 08:13:52 -0800 (PST) Subject: [Pombelist] remove from mailing list Message-ID: Please remove me from the mailing list. Thank you. Jeff Virgin jvirgin at u.washington.edu From kasano at ksu.edu Fri Mar 2 17:05:23 2007 From: kasano at ksu.edu (Katsura Asano) Date: Fri, 2 Mar 2007 11:05:23 -0600 Subject: [Pombelist] RNA and Origins of Life on April 27-28, 2007 Message-ID: <62f14a6f18aa2ddadb50554c6a058b04@ksu.edu> Dear S. pombe scientists, I am happy to announce that a mini-syposium on RNA and Origins of Life takes place on April 27 and 28 on K-state Campus. I invited Norman Pace, the exert on ribozyme RNase P, Ron Breaker, a pioneer on riboswich studeies, and Harry Noller, who is the leader of ribosome studies. I also invited Mike Russell who hypothesizes the origin of life at alkaline hydrothermal vents. I understand that most of you do not work directly on RNA, but I wish this to be informative to anybody working on gene regulation at the posttranscriptional level. I also understand that most of you are away from the mid-West area of the United States, but if you wish to coordinate your travel with another meeting during the overlapping period, I would be happiest to help you find the best flight into and the lodging within my town of Manhattan, Kansas. I noted that 2007 Experimental Biology Meeting takes place in Washington DC, right after this symposium. The registration website is ready and the processing is straightforward. http://www.phys.ksu.edu/origins/symposium.htm Best regards, Katsura Katsura Asano Associate Professor 258 Chalmers Hall Division of Biology Kansas State University Manhattan, KS 66506, USA Tel: 785-532-0116 Fax 785-532-6653 http://www.ksu.edu/biology/bio/faculty/asano/asano.htm -------------- Attachments -------------- To retrieve the following attachment, use the link provided Name: not available Size: 1451 bytes URL: -------------- Attachments -------------- To retrieve the following attachment, use the link provided Name: Sympo-letter-fin.doc Size: 420352 bytes URL: From onigen at my.molbio.ku.dk Thu Mar 8 21:09:19 2007 From: onigen at my.molbio.ku.dk (Olaf Nielsen) Date: Thu, 8 Mar 2007 22:09:19 +0100 Subject: [Pombelist] Pombe conference deadline coming up in a week Message-ID: <46FCB0B6F9F3F64D85EB1F6713FC2D0A044F5E@dkbiocs01.bioc.local> Hello everyone, I should like to remind you that the abstract submission deadline for the Fourth International Fission Yeast Meeting is now only one week ahead. March 15 is also the last day for registration at a reduced fee. Please read more details at the conference web-site: www.pombe.dk Best regards, Olaf * * * * * * * * * * * * * * * * * * * * * * * * * Olaf Nielsen, Professor, Ph.D. Department of Molecular Biology University of Copenhagen Ole Maal?es Vej 5 DK-2200 Copenhagen N Denmark tel: +45 3532 2102 fax: +45 3532 2113 email: onigen at my.molbio.ku.dk http://www.imbf.ku.dk/onigen * * * * * * * * * * * * * * * * * * * * * * * * * -------------- Attachments -------------- An HTML attachment was scrubbed... URL: From forsburg at usc.edu Fri Mar 9 16:45:43 2007 From: forsburg at usc.edu (SLForsburg) Date: Fri, 09 Mar 2007 08:45:43 -0800 Subject: [Pombelist] ade6 alleles: your help requested Message-ID: <5A848F08-E126-4618-A8A3-12EF15395BB3@usc.edu> Hi all, I am trying to update our list of ade6 alleles. Please, can you check it out at http://www-rcf.usc.edu/~forsburg/ plasmids.html#ade6mut If you have additions or corrections, let me know. Also, there is some disagreement about what the mutation in ade6-M210 really is; I've heard several versions. I'd like to try to iron that out. Cheers susan {} {} {} {} {} {} {} {} {} {} {} {} {} {} S L Forsburg PhD, Professor University of Southern California Molecular & Computational Biology Ray R Irani Hall 1050 Childs Way, MCB 201B Los Angeles, CA 90089-2910 vox: 213-740-7342 fax: 213-740-8631 forsburg at usc.edu www.pombe.net -------------- Attachments -------------- An HTML attachment was scrubbed... URL: From geetanjali_rajyee at yahoo.com Tue Mar 13 06:49:57 2007 From: geetanjali_rajyee at yahoo.com (geetanjali sundaram) Date: Mon, 12 Mar 2007 23:49:57 -0700 (PDT) Subject: [Pombelist] Cds1 antibodies Message-ID: <322976.39972.qm@web52214.mail.yahoo.com> Hi all!, Does anyone have any experience with immunoprecipitating Cds1 using human Chk2 antibodies. If so can you please me know if it works fine? Thanking all in anticipation Geetanjali Sundaram SRF INDIA --------------------------------- Don't pick lemons. See all the new 2007 cars at Yahoo! Autos. -------------- Attachments -------------- An HTML attachment was scrubbed... URL: From Jurg at sanger.ac.uk Wed Mar 21 19:52:54 2007 From: Jurg at sanger.ac.uk (Jurg Bahler) Date: Wed, 21 Mar 2007 19:52:54 -0000 Subject: [Pombelist] Postdoc Position available Message-ID: <37340E68029F5842A315DDF21075A80207604E@exchsrv2.internal.sanger.ac.uk> Dear Friends and Colleagues, Please bring the attached advert for a Postdoc Position in my lab to the attention of candidates who may be interested. Many thanks, -J?rg B?hler We use fission yeast as a model organism and apply various genome-wide approaches for systems-level analyses of gene expression regulation at multiple levels, ranging from transcription to translation. We are seeking a motivated colleague to work with us in this exciting field. You are a highly motivated and independent biologist with interests in gene expression control and regulatory processes driving cell growth and quiescence. Candidates with experience in large-scale yeast genetics and/or proteomic approaches are particularly encouraged to apply. You should also have experience or a strong interest in computational approaches. Alternatively, you have a keen interest and skills at the interface of biology and computing to apply computational and modelling approaches to integrate different microarray and other genomic data. You will be involved in uncovering new biological relationships from our large-scale datasets to provide insight into regulatory mechanisms and networks. Previous experience in microarray data mining would be an advantage. You will also provide some computer support and have the opportunity to work closely with wet-lab biologists. Specific research projects will depend on the interests and expertise of the successful candidate as well as on ongoing projects in the lab. This position is funded by Cancer Research UK and is offered on open contract. To find out more about our work please refer to: http://www.sanger.ac.uk/PostGenomics/S_pombe/ Informal enquiries can be made to J?rg B?hler: jurg at sanger.ac.uk Salaries are highly competitive and commensurate with experience. Benefits include 25 days annual leave, final salary pension scheme, optional private healthcare, permanent disability insurance, life assurance, childcare voucher scheme, on-site restaurant, caf?, gym and active sports and social scene. To apply please send a full CV including a list of publications and the names and addresses of three referees, together with a cover letter to: jurg at sanger.ac.uk by 30 April 2007. --- J?rg B?hler, Ph.D. Wellcome Trust Sanger Institute Hinxton Cambridge CB10 1HH UK P: +44(0)1223-496948 F: +44(0)1223-496802 W: http://www.sanger.ac.uk/PostGenomics/S_pombe/ -------------- Attachments -------------- To retrieve the following attachment, use the link provided Name: PostdocAdvert.pdf Size: 70218 bytes URL: From saeeda04 at yahoo.com Thu Mar 22 08:57:29 2007 From: saeeda04 at yahoo.com (saeeda) Date: Thu, 22 Mar 2007 01:57:29 -0700 (PDT) Subject: [Pombelist] Re: Pombelist Digest, Vol 21, Issue 3 Message-ID: <20070322085729.91221.qmail@web51801.mail.re2.yahoo.com> Hello, Will there be any DNA damage meetings going on? Saeeda --------------------------------- Now that's room service! Choose from over 150,000 hotels in 45,000 destinations on Yahoo! Travel to find your fit. -------------- Attachments -------------- An HTML attachment was scrubbed... URL: From akihisa at riken.jp Wed Apr 4 07:56:02 2007 From: akihisa at riken.jp (Akihisa Matsuyama) Date: Wed, 4 Apr 2007 15:56:02 +0900 Subject: [Pombelist] S. pombe Postgenome Database Server Message-ID: <3D9642A9-CBD9-434B-87DB-20BD1E90E905@riken.jp> Dear all, We are very sorry, but now our server (http://cgl.riken.go.jp/) was down because of mechanical problems. So, it is closed for repairs. But it will take some time before network restoration. If you have a request for ORFeome clones or S. pombe expression plasmids, please visit the RIKEN BioResource Center (BRC) website (http://www.brc.riken.jp/lab/dna/en/yoshidayeast_en.html). You can find the clone ID of your interest if you download the supplementary table 6 from the Nature Biotechnology website (http:// www.nature.com/nbt/journal/v24/n7/suppinfo/nbt1222_S1.html). Several Gateway-compatible vectors are also available from BRC. I thank you for your cooperation in this matter. Best regards, Matsu *** Akihisa Matsuyama, Ph.D Chemical Genetics Laboratory, RIKEN Hirosawa 2-1, Wako-shi, Saitama, 351-0198 TEL: +81-48-462-1335 FAX: +81-48-462-1336 *** From anthony.wright at sh.se Thu Apr 5 12:48:29 2007 From: anthony.wright at sh.se (Anthony Wright) Date: Thu, 5 Apr 2007 13:48:29 +0200 Subject: [Pombelist] Postdoctoral vacancy on transcription factors Message-ID: Dear colleagues Please note the attached vacancy for a Postdoctoral Research Assistant. regards Tony Postdoctoral Research Assistant Position available to study the molecular mechanisms of evolutionary adaptation. The successful applicant will form part of a multidisciplinary programme in which molecular biologists, developmental biologists and ecologists interact. The successful applicant will have excellent skills in PCR and other central molecular biology techniques. Furthermore, he/she will have an interest in multidisciplinary approaches to complex biological problems and will be able to contribute to the different biological areas within the project. The project will test whether genes encoding transcription factors are preferred targets for adaptive mutations during evolutionary diversification. Approaches in the project involve adaptation experiments in yeast as well as DNA sequence analysis of genetic polymorphisms in morphologically different fish and plant populations. Previous experience of work with transcription factors, larger-scale sequencing projects, DNA microarrays, bioinformatics and yeast molecular biology would be an advantage. It is expected that the successful applicant will have completed their PhD studies within the last 5 years. The project will be carried out at S?dert?rns H?gskola, a new University College located in Flemingsberg, 15 km south of central Stockholm. S?dert?rns H?gskola shares its campus with the Karolinska Institute, the Royal Institute of Technology and the Karolinska Hospital. The position is for a period of 2-3 years and is available immediately. For more information, contact Prof. Anthony Wright +46(0)86084708 or Ass. Prof. Mats Grahn +48(0)860847. Applications containing curriculum vitae, publication list and the names of two referees should be sent to Prof Anthony Wright at the School of Life Sciences - anthony.wright at sh.se, not later than April 30th. Anthony Wright, Ph.D. Professor of Molecular Biology School of Life Sciences, S?dert?rns University College Unit for Biological Model Systems, Department of Biosciences and Nutrition, Karolinska Institute Mailing address: School of Life Sciences S?dert?rns H?gskola S-141 89 Huddinge Sweden +46 8 6084708 Visiting address: Alfred Nobels All? 7 http://natvet.sh.se/wright_lab/ ? -------------- Attachments -------------- An HTML attachment was scrubbed... URL: -------------- Attachments -------------- To retrieve the following attachment, use the link provided Name: postdoc advert Moast?d.doc Size: 54272 bytes URL: -------------- Attachments -------------- An HTML attachment was scrubbed... URL: From akihisa at riken.jp Tue Apr 10 10:17:21 2007 From: akihisa at riken.jp (Akihisa Matsuyama) Date: Tue, 10 Apr 2007 18:17:21 +0900 Subject: [Pombelist] S. pombe ORF clones and plasmids In-Reply-To: <3D9642A9-CBD9-434B-87DB-20BD1E90E905@riken.jp> References: <3D9642A9-CBD9-434B-87DB-20BD1E90E905@riken.jp> Message-ID: <42EC241C-7050-4CC7-9065-0C3AABA89078@riken.jp> Dear all, Thank you for your interest in our S. pombe ORF clones and plasmids. We already have several inquiries about them. Actually, all clones were constructed in our study (Nat Biotech 24, 841-7). However, since it is such a job for us to send them, BRC provides these clones on our behalf. BRC is independent from our department (we are not in the RIKEN BRC archive). So, please visit the BRC website (http://www.brc.riken.jp/lab/dna/en/ yoshidayeast_en.html) and request the clone(s) of your interest according to their instructions. Guidance for clone request: http://www.brc.riken.jp/lab/dna/en/ furnish.html Thank you for your cooperation. Best regards, Matsu On 2007/04/04, at 15:56, Akihisa Matsuyama wrote: > Dear all, > > We are very sorry, but now our server (http://cgl.riken.go.jp/) was > down because of mechanical problems. > So, it is closed for repairs. But it will take some time before > network restoration. > If you have a request for ORFeome clones or S. pombe expression > plasmids, please visit the RIKEN BioResource Center (BRC) website > (http://www.brc.riken.jp/lab/dna/en/yoshidayeast_en.html). > You can find the clone ID of your interest if you download the > supplementary table 6 from the Nature Biotechnology website (http:// > www.nature.com/nbt/journal/v24/n7/suppinfo/nbt1222_S1.html). > Several Gateway-compatible vectors are also available from BRC. > I thank you for your cooperation in this matter. > > Best regards, > > Matsu > > _______________________________________________ > Pombelist mailing list > Pombelist at sanger.ac.uk > http://lists.sanger.ac.uk/mailman/listinfo/pombelist > *** Akihisa Matsuyama, Ph.D Chemical Genetics Laboratory, RIKEN Hirosawa 2-1, Wako-shi, Saitama, 351-0198 TEL: +81-48-462-1335 FAX: +81-48-462-1336 E-mail: akihisa at riken.jp *** From maraiar at exchange.nih.gov Thu Apr 12 14:56:51 2007 From: maraiar at exchange.nih.gov (Rich Maraia) Date: Thu, 12 Apr 2007 09:56:51 -0400 Subject: [Pombelist] modern mutation mapping Message-ID: >I was wondering if anyone can reccommend a modern strategy >(including use of microarrays or possibly a large scall sequencing >strategy) to map mutations in individual S. pombe mutants. Members >of my lab have isolated and characterized new mutants in RNA >processing and are about to embark on mapping them and isolating the >gene(s) responsible. > As you may know, Maitreya J Dunham , uses dense tiling arrays for mapping mutations in S. cerevisiae mutants. She has described two different approaches, a straight hybridization comparison of parent and mutant strains that reveal point mutations, and a bulk segregant analysis also using the tiling arrays. Thank you. -- Richard J. Maraia, M.D. Captain, US Public Health Service, Commissioned Corps Chief, Section on Molecular and Cell Biology Intramural Research Program 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 From clemoal at esf.org Tue Apr 17 11:14:36 2007 From: clemoal at esf.org (Corinne Wininger - Le Moal) Date: Tue, 17 Apr 2007 12:14:36 +0200 Subject: [Pombelist] Comparative Genomics of Eukaryotic Microorganisms, Spain, October 2007 Message-ID: CALL FOR APPLICATIONS Dear Sir or Madam, Please find below information on an ESF Research Conference which may be of particular interest to you: ESF-EMBO Symposium Comparative Genomics of Eukaryotic Microorganisms: Eukaryotic Genome Evolution Hotel Eden Roc, Sant Feliu de Guixols (Costa Brava), Spain 20-25 October 2007 Chaired by: Edward J. Louis (University of Nottingham, UK) & Teun Boekhout (Centraalbureau voor Schimmelcultures, NL) Europe has been at the forefront of both eukaryotic microbial genome sequencing as well as the analysis and comparison of these genomes. The first eukaryote sequenced, the budding yeast Saccharomyces cerevisiae, laid the foundation in European for the new post-genomic era where we are dealing with this wealth of information. Many of these organisms are models for particular biological processes, others are used in industry and many are pathogens of plants, animals and humans. In this conference we bring together the experts from around Europe and the rest of the world to meet and discuss with interested participants the current state of and future of comparative genomics. There will be opportunities for participants to present both short talks, as well as posters, which will be conducted interactively with plenty of time reserved for questions and discussions. In addition there will be interactive workshops on databases and bioinformatics at three sessions. Scientific programme and application form accessible on-line through www.esf.org/conferences/07239. Closing date for application (& for abstract submission): 1 August 2007. Some grants will be available for young researchers to cover the conference fee and possibly part of the travel costs. Grant requests should be made by ticking appropriate field(s) in the paragraph "Grant application" of the application form (Ctrl + Click to follow the link). ESF Contact: Mrs. Anne Blondeel-Oman (ablondeel at esf.org). Kind regards, Corinne Wininger Publicity Officer - ESF Communications Unit European Science Foundation - Communications Unit 1 quai Lezay-Marn?sia, BP 90015 67080 Strasbourg Cedex, France Phone: +33 (0)388 76 21 50 Fax: +33 (0)388 76 71 80 clemoal at esf.org www.esf.org/conferences -------------- Attachments -------------- An HTML attachment was scrubbed... URL: From onigen at my.molbio.ku.dk Tue May 15 17:33:50 2007 From: onigen at my.molbio.ku.dk (Olaf Nielsen) Date: Tue, 15 May 2007 18:33:50 +0200 Subject: [Pombelist] Fourth International Fission Yeast Meeting, Copenhagen June 11-16 Message-ID: Dear all, I am happy to inform you that the programme for the upcoming Copenhagen fission yeast meeting is now available at: http://www.pombe.dk/programme.aspx The 10 plenary sessions host 73 speakers. You can download the abstracts for all the talks from the web-site. In addition some 200 abstracts will be presented in the three poster sessions. Some of these will also be selected for an oral presentation in one of the six workshops. The number of participants has now passed 350. If you have not yet registered, this is still possible at www.pombe.dk . There is no official closing date. However, if you plan to attend, we should very much appreciate that you register before June 1. This makes planning of food, busses and party hats much easier. Thank you in advance. Hope to see you in Copenhagen! Best regards, Olaf * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Olaf Nielsen, Professor, Ph.D. Department of Molecular Biology University of Copenhagen Ole Maal?es Vej 5 DK-2200 Copenhagen N Denmark tel: +45 3532 2102 fax: +45 3532 2113 email: onigen at my.molbio.ku.dk http://www.imbf.ku.dk/onigen * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * From yeast2007 at meetingplanners.com.au Wed May 16 14:56:21 2007 From: yeast2007 at meetingplanners.com.au (Yeast 2007) Date: Wed, 16 May 2007 23:56:21 +1000 Subject: [Pombelist] Yeast 2007: Final Conference Program Now Available Message-ID: Final Conference Program Now Available The Conference program has been updated with the workshop speakers. Click on the following link to the final program http://www.yeast2007.org/files/Yeast_Program.pdf Details have been confirmed for the free event on Friday! Friday July 6 - City of Melbourne - Melbourne Conversations Cancer Treatments: How studying yeast can help World famous scientists are attending. Speakers include: Sir Gus Nossal - Emeritus Professor, Melbourne University, who will moderate the discussion Sir Paul Nurse - Nobel Laureate and President The Rockefeller University, New York, New York Dr Alex Franzusoff - Vice President of Research & Development and Founding Scientist, GlobeImmune, Louisville, Colorado Visit http://www.yeast2007.org/program.php for more details. Registration is still open Visit http://www.yeast2007.org/register.php to register now! From viladevl at mskcc.org Wed May 16 16:41:52 2007 From: viladevl at mskcc.org (Laia Viladevall) Date: Wed, 16 May 2007 11:41:52 -0400 Subject: [Pombelist] Pombe list Message-ID: viladevl at mskcc.org ===================================================================== Please note that this e-mail and any files transmitted with it may be privileged, confidential, and protected from disclosure under applicable law. If the reader of this message is not the intended recipient, or an employee or agent responsible for delivering this message to the intended recipient, you are hereby notified that any reading, dissemination, distribution, copying, or other use of this communication or any of its attachments is strictly prohibited. If you have received this communication in error, please notify the sender immediately by replying to this message and deleting this message, any attachments, and all copies and backups from your computer. From a.m.carr at sussex.ac.uk Mon May 21 15:50:19 2007 From: a.m.carr at sussex.ac.uk (Antony Carr) Date: Mon, 21 May 2007 15:50:19 +0100 Subject: [Pombelist] 2007 Gordon Conference Message-ID: Dear All Please find attached a flyer for the 2007 Gordon Research Conference on Genetic Toxicology. It will be held in Oxford from the 29th July to the 3rd of August. This is an opportunity to attend a Gordon conference in England and see lots of good talks on DNA repair and DNA damage responses. See: If you are not interested yourself, please post the notice on the departmental notice board. Also, we have a few bursaries for PhD students. These amount to $600 off the registration fee, and will be allocated based on poster abstracts etc. Thanks Tony Tony Carr MRC Genome Damage and Stability Centre University of Sussex Brighton, UK BN1 9RQ Tel 01273 678122 -------------- Attachments -------------- To retrieve the following attachment, use the link provided Name: GRCposter.pdf Size: 1068683 bytes URL: From helenadc at usal.es Wed May 23 11:46:01 2007 From: helenadc at usal.es (helenadc at usal.es) Date: Wed, 23 May 2007 12:46:01 +0200 (CEST) Subject: [Pombelist] Protein abundance Message-ID: <1350.141.14.25.217.1179917161.squirrel@correo.usal.es> Dear all, i would like to know if there is a database where one could find some information about the abundances (concentrations, molecule numbers)of pombe proteins (something like the YEAST GFP FUSION LOCALIZATION DATABASE for cerevisiae). If not, does anybody know about any article where i could find any values for cell-cycle/checkpoint proteins? Thank you very much, Helena D?az Cuervo PhD Student/Dpto Microbiolog?a y Gen?tica Laboratorio 5 Centro de Investigaci?n del C?ncer IBMCC (Universidad de Salamanca-CSIC) Campus Miguel de Unamuno s/n 37007 Salamanca? Espa?a From val at sanger.ac.uk Wed May 23 12:25:41 2007 From: val at sanger.ac.uk (Valerie Wood) Date: Wed, 23 May 2007 11:25:41 UT Subject: [Pombelist] Protein abundance Message-ID: An embedded and charset-unspecified text was scrubbed... Name: not available URL: From dom at genetics.med.harvard.edu Wed May 23 15:24:12 2007 From: dom at genetics.med.harvard.edu (Dom Helmlinger) Date: Wed, 23 May 2007 10:24:12 -0400 Subject: [Pombelist] Protein abundance In-Reply-To: References: Message-ID: <46544E8C.5030400@genetics.med.harvard.edu> Dear Helena, There is also the pombe GFP localizome which features relative abundance of all pombe ORFs tagged. See: http://www.nature.com/nbt/journal/v24/n7/abs/nbt1222.html. Their supplementary table 1 is an excel file with the relative protein expression levels. Best, Dom Valerie Wood wrote: > Dear Helena, > > There is a partial data set ...quantification of 1465 proteins based on predicted tryptic peptides in: > Comparative proteomic and transcriptomic profiling of the fission yeast Schizosaccharomyces pombe. Schmidt MW, Houseman A, Ivanov AR, Wolf DA > PMID: 17299416 > > Unfortunately this data is not on the database at present, but should be in the future. > See: > http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17299416 > > Val > > helenadc at usal.es wrote: > >> Dear all, >> i would like to know if there is a database where one could find some >> information about the abundances (concentrations, molecule numbers)of >> pombe proteins (something like the YEAST GFP FUSION LOCALIZATION DATABASE >> for cerevisiae). If not, does anybody know about any article where i could >> find any values for cell-cycle/checkpoint proteins? >> Thank you very much, >> >> Helena D?az Cuervo >> PhD Student/Dpto Microbiolog?a y Gen?tica Laboratorio 5 >> Centro de Investigaci?n del C?ncer >> IBMCC (Universidad de Salamanca-CSIC) >> Campus Miguel de Unamuno s/n >> 37007 Salamanca-- Espa?a >> >> _______________________________________________ >> Pombelist mailing list >> Pombelist at sanger.ac.uk >> http://lists.sanger.ac.uk/mailman/listinfo/pombelist >> > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pombelist mailing list > Pombelist at sanger.ac.uk > http://lists.sanger.ac.uk/mailman/listinfo/pombelist -- Dom Helmlinger, PhD Harvard Medical School NRB room 239 77 avenue Louis Pasteur Boston, MA 02115 tel: 001-617-432-7557 fax: 001-617-432-6506 dom at helmlinger.com http://genetics.med.harvard.edu/~winston/ -------------- Attachments -------------- An HTML attachment was scrubbed... URL: From grewals at mail.nih.gov Wed May 23 16:36:22 2007 From: grewals at mail.nih.gov (Shiv Grewal) Date: Wed, 23 May 2007 11:36:22 -0400 Subject: [Pombelist] FASEB CONFERENCE ON CHROMATIN & TRANSCRIPTION References: <748DBC2415E404498A5E3161D1B543AF080CE7DB@exchange1.faseb.org> Message-ID: <3980C368-9DA8-469F-8BF7-A8EBE85FFAC9@mail.nih.gov> Dear All Please find attached a flyer for the 2007 FASEB meeting on "Chromatin and Transcription". It will be held in Snowmass Colorado July 7-12. Please post the notice on the departmental notice board. Thanks, Shiv Grewal ? Please see the attached flyer regarding the FASEB Summer Research Conference entitled: ?Chromatin and Transcription? We hope to see you in Snowmass! For more information, please visit: http://src.faseb.org ?? -------------- Attachments -------------- An HTML attachment was scrubbed... URL: -------------- Attachments -------------- To retrieve the following attachment, use the link provided Name: image001.jpg Size: 26241 bytes URL: -------------- Attachments -------------- An HTML attachment was scrubbed... URL: -------------- Attachments -------------- To retrieve the following attachment, use the link provided Name: image001.jpg Size: 26241 bytes URL: -------------- Attachments -------------- To retrieve the following attachment, use the link provided Name: 11644 Flyer.pdf Size: 212283 bytes URL: -------------- Attachments -------------- An HTML attachment was scrubbed... URL: From Erik.Boye at rr-research.no Thu Jun 7 13:53:45 2007 From: Erik.Boye at rr-research.no (Erik Boye) Date: Thu, 7 Jun 2007 14:53:45 +0200 Subject: [Pombelist] FW: Message-ID: An International Conference on "Cellular Responses to DNA Damage in S. pombe" will be organized at Holmenkollen Park Hotel, Oslo, Norway from October 1 to 4, 2007. Confirmed speakers: * Fikret Osman * Paul Russel * Stephen Kearsey * Antony M Carr * Alan Lehman * Olaf Nielsen * A-Lien Lu * Johanne M Murray * Greg A Freyer * Mitsuhir Yanagida * Tom Kelly * Susan L Forsburg * Theresa S F Wang * Matthew C Whitby * Karl Ekwall * John Tainer See our information flyer (attached). Registration is now open at our web site: www.cmbn.no/pombe. We hope to welcome you to Oslo Ingrun Alseth, Birgit Eliassen, Erik Boye and Magnar Bj?r?s. -------------- Attachments -------------- An HTML attachment was scrubbed... URL: -------------- Attachments -------------- To retrieve the following attachment, use the link provided Name: pombeposter.pdf Size: 1755807 bytes URL: From jm593 at cam.ac.uk Thu Jun 7 17:12:01 2007 From: jm593 at cam.ac.uk (Juan Mata) Date: Thu, 07 Jun 2007 17:12:01 +0100 Subject: [Pombelist] Postgraduate/postdoctoral position available Message-ID: <46682E51.2030800@cam.ac.uk> Dear Colleagues, Please bring the attached advert for a position in my lab to the attention of candidates who may be interested. I will be available to discuss further details with potential candidates at the Fission Yeast meeting in Copenhagen. Many thanks Juan Mata Applications are invited for a position in Dr Juan Mata?s laboratory (Department of Biochemistry, University of Cambridge) to study the global role of RNA-binding proteins in fission yeast. The project will involve the use of functional genomics (including DNA microarrays), cell biological methods and bioinformatics to study posttranscriptional regulation at the genome-wide level. More information on the lab can be found at http://www.bioc.cam.ac.uk/uto/mata.html The position is funded by the Medical Research Council and can be filled at the postgraduate (Research Assistant) or postdoctoral (Research Associate) levels. Funding will be available from 1st October 2007 for a total of 23 months. Applicants should have a BSc (Research Assistant) or PhD (Research Associate) in a relevant subject, such as Genetics, Molecular Biology or Biochemistry. Direct experience with fission yeast or DNA microarrays is not required. Experience in protein or RNA biochemistry, microscopy or computational biology would be an advantage. For enquiries please email jm593 at cam.ac.uk From nimisha401 at yahoo.com Mon Jun 11 17:37:58 2007 From: nimisha401 at yahoo.com (nimisha sharma) Date: Mon, 11 Jun 2007 17:37:58 +0100 (BST) Subject: [Pombelist] S. pombe ORF clones and plasmids In-Reply-To: <42EC241C-7050-4CC7-9065-0C3AABA89078@riken.jp> Message-ID: <303176.74789.qm@web34804.mail.mud.yahoo.com> Hi everyone. Does someone have a S. pombe cDNA library? Nimisha NIMISHA SHARMA, Ph.D LECTURER, UNIVERSITY SCHOOL OF BIOTECHNOLOGY, G.G.S.INDRAPRASTHA UNIVERSITY, KASHMERE GATE, DELHI-110006 INDIA Send instant messages to your online friends http://uk.messenger.yahoo.com From hoffmacs at bc.edu Mon Jun 18 01:29:38 2007 From: hoffmacs at bc.edu (Charles Hoffman) Date: Sun, 17 Jun 2007 20:29:38 -0400 Subject: [Pombelist] Facebook group of pictures from Copenhagen Message-ID: I just created a Facebook group called: Copenhagen Pombe 2007 Everyone is welcome to join, even if you did not go to the meeting. I am hoping that people will tag pictures so we have a place to connect names to faces. Cheers, Charlie Hoffman Boston College "I'd rather be fission." From hoffmacs at bc.edu Mon Jun 18 14:42:11 2007 From: hoffmacs at bc.edu (Charles Hoffman) Date: Mon, 18 Jun 2007 09:42:11 -0400 Subject: [Pombelist] What is Facebook (and why is it saying those terrible things about me) Message-ID: Hi everyone, I hope this will serve as a primer for how to join facebook (a social network on the web) and join the Copenhagen Pombe 2007 group. Go to www.facebook.com and register. You can join as part of a network (such as a university group), but you don't have to. In the upper left side of the page, click on "Groups". In the upper right side of the next page, type in pombe and search for groups. That should bring you to the group. Everyone is free to join. You can look through pictures and "tag" people you know in it. You can also look at the members of the groups (there are 12 already) and ask people to be "friends" (thus the social network aspect), which allows them to see your facebook page. I will get messages that ask me to confirm any tagging, but I assume that people doing the tagging know what they are doing so I will try and approve everything once a day or so. Cheers, Charlie Hoffman Boston College "I'd rather be fission." From hoffmacs at bc.edu Mon Jun 18 16:18:39 2007 From: hoffmacs at bc.edu (Charles Hoffman) Date: Mon, 18 Jun 2007 11:18:39 -0400 Subject: [Pombelist] Hopefully the last message regarding facebook Message-ID: I initially loaded low resolution images last night from home due to the slow internet speed. I have now just finished uploading a complete replacement set of higher resolution images. If you have already tagged stuff, you will have to go back and do it again. Sorry. I would appreciate some feedback about some of the darker pictures from the banquet. Should I do some lightening in Photoshop or are they okay? Finally, you are all able to upload your own pictures to this group, so I look forward to seeing more pictures in the future. Cheers, Charlie Hoffman Boston College "I'd rather be fission." From akihisa at riken.jp Tue Jun 19 08:59:22 2007 From: akihisa at riken.jp (Akihisa Matsuyama) Date: Tue, 19 Jun 2007 16:59:22 +0900 Subject: [Pombelist] S. pombe Postgenome Database Server Message-ID: Dear all, As announced in the 4th International Fission Yeast Meeting, our web server was restored just before the meeting (http://cgl.riken.go.jp/). The sequences of a series of vectors (pDUAL- and pDUAL2-derivatives) distributed from the Bioresource Center, RIKEN, are also available on this website (http://cgl.riken.go.jp/gene/Plasmids.html). We are looking forward to your visit. All the best, Matsu ***** Akihisa Matsuyama, Ph.D Chemical Genetics Laboratory, RIKEN Hirosawa 2-1, Wako, Saitama, Japan, 351-0198 TEL: +81-48-462-1335 FAX: +81-48-462-1336 ***** From hoffmacs at bc.edu Wed Jun 20 16:53:16 2007 From: hoffmacs at bc.edu (Charles Hoffman) Date: Wed, 20 Jun 2007 11:53:16 -0400 Subject: [Pombelist] Photo album for the Facebook-averse Message-ID: Hi, For those of you who do not want to enter the world of Facebook, I have put up a webpage of my photos from the pombe meeting at: http://www2.bc.edu/%7Ehoffmacs/pombe2007/index.htm However, I strongly recommend that you use Facebook, because other people are adding their own pictures to that site as well. Cheers, Charlie Hoffman Boston College "I'd rather be fission." From Jurg at sanger.ac.uk Thu Jun 21 19:00:49 2007 From: Jurg at sanger.ac.uk (Jurg Bahler) Date: Thu, 21 Jun 2007 19:00:49 +0100 Subject: [Pombelist] Genome-wide approaches with fission yeast: COURSE DEADLINE 29 June Message-ID: <37340E68029F5842A315DDF21075A802208BBA@exchsrv2.internal.sanger.ac.uk> Dear All, The deadline is quickly approaching for the Wellcome Trust Advanced Course 'Genome-wide approaches with fission yeast' from 1-7 October 2007 in Hinxton, UK. We need your application by Friday 29 June. Details and links to the application form are available here: http://www.wellcome.ac.uk/doc_WTX033405.html This hands-on course is for colleagues who would like to use large-scale methods for their research. The attendance is limited to 16-18 people, and selection will be based on the applications. Cheers, -Jurg --- J?rg B?hler, Ph.D. Wellcome Trust Sanger Institute Hinxton Cambridge CB10 1HH UK P: +44(0)1223-496948 F: +44(0)1223-496802 W: http://www.sanger.ac.uk/PostGenomics/S_pombe/ -------------- Attachments -------------- To retrieve the following attachment, use the link provided Name: CourseFlyer.pdf Size: 524607 bytes URL: From belostotskyd at umkc.edu Tue Jul 3 14:28:18 2007 From: belostotskyd at umkc.edu (Belostotsky, Dmitry) Date: Tue, 3 Jul 2007 08:28:18 -0500 Subject: [Pombelist] experimental-driven systems biology position(s), any level Message-ID: <5C13F286F3DAE649BFF21749E3DEE0960466E577@KC-MSX1.kc.umkc.edu> WITH: - Dmitry Belostotsky @ University of Missouri - Kansas City [contact via belostotsky [at] umkc.edu ] ON: - protein complexes governing noncoding RNA-mediated and mRNA-level control of gene expression (using several models including pombe) WHEN: - immediately until filled WHO: - applicants well versed in RNA biology or/and microarrays, protein biochemistry, programming or/and statistics, with documented record of excellence MUST BE: - highly driven, self-motivated, ambitious, dynamic individuals. Postdoctoral fellowships eligibility helpful but not essential. Funding available through 2010. LAB: - equipped with Affymetrix and deconvolution microscopy (Deltavision) workstations and have, or have access to, HPLC, MALDI, LC-MS/MS and high end Linux cluster PUBS (selected): - Genome-wide high-resolution analysis of exosome substrates in Arabidopsis - In review (2007) - Shared factors mediate tethering of active genes to non-nascent mRNP and nuclear rim - In review (2007) - EMBO J 25:4253-4256 (2006) - Trends Plant Sci 10:347-353 (2005) - RNA 10:1200-1214 (2004) - Genetics 163:311-319 (2003) - RNA 9:1476-1490 (2003) - Curr Biol 11:1207-1214 (2001) LIVING IN KANSAS CITY: in brief, KC got everything but ocean - major cosmopolitan center of 2.5M plus people - dynamic cultural environment (e.g. see www.nelson-atkins.org) - vibrant music scene (best known for, but not limited to, jazz and blues) - fabulous food (best known for, but not limited to, its famous bbq) - dubbed ?Paris of the plains?, ranked within top 10 places to live in US. See www.cnn.com/2006/TRAVEL/DESTINATIONS/06/08/kansas.city/index.html Dmitry A. Belostotsky, Ph.D. Associate Professor Division of Molecular Biology and Biochemistry School of Biological Sciences University of Missouri Kansas City, MO 64110 From mishra at biochem.mpg.de Wed Jul 4 13:41:56 2007 From: mishra at biochem.mpg.de (Shravan Kumar Mishra) Date: Wed, 4 Jul 2007 14:41:56 +0200 Subject: [Pombelist] S. pombe two-hybrid library Message-ID: <1183552916.929af5b9ceb93@webmail.biochem.mpg.de> Dear collegues, Could someone please recommend a good source (lab/commercial) of S. pombe two-hybrid libraries? Thanks for your kind notice Shravan Shravan Kumar Mishra (PhD) Molecular Cell Biology, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsreid/Munich, D-82152 Germany Tel: +49-89-8578-3027 Fax: +49-89-8578-3022 http://www.biochem.mpg.de/jentsch/ --------------------------------------------------------------------- This message was sent using https://webmail.biochem.mpg.de If you encounter any problems please report to rz-linux at biochem.mpg.de ----- End forwarded message ----- Shravan Kumar Mishra (PhD) Molecular Cell Biology, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsreid/Munich, D-82152 Germany Tel: +49-89-8578-3027 Fax: +49-89-8578-3022 http://www.biochem.mpg.de/jentsch/ --------------------------------------------------------------------- This message was sent using https://webmail.biochem.mpg.de If you encounter any problems please report to rz-linux at biochem.mpg.de From laabmc at ibmb.csic.es Tue Jul 10 11:49:34 2007 From: laabmc at ibmb.csic.es (Lorena Aguilar) Date: Tue, 10 Jul 2007 12:49:34 +0200 Subject: [Pombelist] Anti-HA Agarose Conjugate Message-ID: <002e01c7c2e0$00b14970$8a3e050a@BMCLORENA> Dear ?pombelist?: I am trying to immunoprecipitate HA-tagged fusion proteins expressed in S. pombe to perform ChIP analysis and complex purification. I have seen the availability of at least two different Anti ?HA agarose conjugated, which correspond with mouse HA-7 and rat 3F10 monoclonal antibodies. Has anyone of you experience with these antibodys or even with another one that works well in pombe? Can you recommend one of these? Thanks in advance for any suggestion, Best wishes, Lorena Lorena Aguilar Arnal Institut de Biologia Molecular de Barcelona - CSIC Parc Cient?fic de Barcelona c/Josep Samitier 1-5 08028 Barcelona - SPAIN Tel?fon: +34934034964 e-mail: laabmc at ibmb.csic.es -------------- Attachments -------------- An HTML attachment was scrubbed... URL: From ashapurno.biswas at tuebingen.mpg.de Tue Jul 10 15:38:09 2007 From: ashapurno.biswas at tuebingen.mpg.de (Ashapurno Biswas) Date: Tue, 10 Jul 2007 16:38:09 +0200 Subject: [Pombelist] thanks Message-ID: Hello Many thanks for including my mail address in the pombelist mailing address. Regards, Ashapurno Ashapurno Biswas PhD student Friedrich-Miescher-Laboratory of the Max-Planck-Society Spemannstrasse 35 72076 Tuebingen Germany. From mishra at biochem.mpg.de Thu Jul 12 14:44:33 2007 From: mishra at biochem.mpg.de (Shravan Kumar Mishra) Date: Thu, 12 Jul 2007 15:44:33 +0200 Subject: Fwd: Re: [Pombelist] S. pombe two-hybrid library Message-ID: <1184247873.66aa659e6933c@webmail.biochem.mpg.de> ----- Forwarded message from shimoda at sci.osaka-cu.ac.jp ----- Date: Mon, 09 Jul 2007 09:27:00 +0900 From: "C. Shimoda" Reply-To: "C. Shimoda" Subject: Re: [Pombelist] S. pombe two-hybrid library To: Shravan Kumar Mishra Dear Dr. Mishra, The Yeast Genetic Resource Center of Japan (YGRC) can provide you with an S. pombe two-hybrid library. It was constructed from meiotic mRNA, but we know that it contains also mitotic cDNAs. For details see the attached file. If you want to get it, e-mail me. Please visit our website to search and request fission yeast resource. Regards, Chikashi Shimoda > Dear collegues, > Could someone please recommend a good source (lab/commercial) of S. pombe > two-hybrid libraries? > Thanks for your kind notice > Shravan > > Shravan Kumar Mishra (PhD) > > Molecular Cell Biology, > Max-Planck Institute of Biochemistry, > Am Klopferspitz 18, Martinsreid/Munich, > D-82152 Germany > Tel: +49-89-8578-3027 > Fax: +49-89-8578-3022 > http://www.biochem.mpg.de/jentsch/ > > --------------------------------------------------------------------- > This message was sent using https://webmail.biochem.mpg.de > If you encounter any problems please report to rz-linux at biochem.mpg.de > > > ----- End forwarded message ----- > > > Shravan Kumar Mishra (PhD) > > Molecular Cell Biology, > Max-Planck Institute of Biochemistry, > Am Klopferspitz 18, Martinsreid/Munich, > D-82152 Germany > Tel: +49-89-8578-3027 > Fax: +49-89-8578-3022 > http://www.biochem.mpg.de/jentsch/ > > --------------------------------------------------------------------- > This message was sent using https://webmail.biochem.mpg.de > If you encounter any problems please report to rz-linux at biochem.mpg.de > > > _______________________________________________ > Pombelist mailing list > Pombelist at sanger.ac.uk > http://lists.sanger.ac.uk/mailman/listinfo/pombelist > -------------------------------------------------- Prof. Chikashi Shimoda Head of YGRC (Fission Yeast) Department of Biology, Graduate School of Science Osaka City University Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan Tel +81 66605 2576; FAX +81 66605 3158 E-mail: shimoda at sci.osaka-cu.ac.jp National BioResource Project Japan Yeast Genetic Resource Center E-mail: nbrpombe at sci.osaka-cu.ac.jp S. pombe resource search : http://yeast.lab.nig.ac.jp/nig/english/index.html ------------------------------------------------ ----- End forwarded message ----- Shravan Kumar Mishra (PhD) Molecular Cell Biology, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsreid/Munich, D-82152 Germany Tel: +49-89-8578-3027 Fax: +49-89-8578-3022 http://www.biochem.mpg.de/jentsch/ --------------------------------------------------------------------- This message was sent using https://webmail.biochem.mpg.de If you encounter any problems please report to rz-linux at biochem.mpg.de -------------- Attachments -------------- To retrieve the following attachment, use the link provided Name: Description of libraries (Nondisclosure).xls Size: 14848 bytes URL: From val at sanger.ac.uk Tue Jul 17 13:56:02 2007 From: val at sanger.ac.uk (Valerie Wood) Date: Tue, 17 Jul 2007 13:56:02 +0100 Subject: [Pombelist] An update on ortholog resources/ Tools and tips Message-ID: <469CBC62.2040102@sanger.ac.uk> Some of the most frequent responses to the fission yeast database survey were requests for additional comparison resources to assess sequence relationships (including ortholog identification, their associated alignments and phylogenetic trees). However, ortholog identification is not trivial and there is no 'gold standard' resource. The likely future move to the Saccharomyces Genome Database (SGD) architecture would allow fission yeast to take advantage of the tools available for the budding yeast (particularly those exploiting synteny when the S. japonicus genome is published). The following resources are currently available and may be useful now: CURATED BUDDING YEAST ORTHOLOGS A manually curated list of S. pombe/S. cerevisiae orthologs covering 75% of fission yeast gene products is available. Alignments used to make orthology inferences are submitted to the Pfam protein family database. You can subscribe to the mailing list 'Yeast_orthologous_groups' to receive the curated ortholog inventory and updates as a spreadsheet. http://lists.sanger.ac.uk/mailman/listinfo/yeast_orthologous_groups/ SEARCHING CURATED ORTHOLOGS IN GENEDB You can search for curated orthologs of individual S. cerevisiae genes in GeneDB http://www.genedb.org/genedb/pombe/. You must use the S. cerevisiae systematic identifier (e.g YOR073W) and the "Full Content Search" box. EUKARYOTIC ORTHOLOGS AND ASSOCIATED GENE ONTOLOGY (GO) ANNOTATION. YOGY is a tool which uses the major orthology predictors (KOGS, OrthoMcl, Inparanoid, Homologene) to identify potential orthologs in the major model eukaryotes and allows the user to retrieve GO terms manually associated with these orthologs by curators at the Model Organism Databases. YOGY is accessible from http://www.sanger.ac.uk/PostGenomics/S_pombe/YOGY/ OR via a link from the "Database Cross-References" section of every GeneDB_Spombe gene page GENES WITH NO APPARENT ORTHOLOGS If you are working on one of the 474 gene products which have no homologs identified (357 sequence orphans, 71 published genes with no apparent homologs, 46 S. pombe specific families), the Japonicus genome at the Broad Institute may provide new insights: http://www.broad.mit.edu/annotation/genome/schizosaccharomyces_japonicus/Blast.html;jsessionid=6A016D3A95661A10AA9654198A1D4F81?sp=Stblastn It is possible that a PSI Blast search (Position-Specific Iterated BLAST) http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi?PAGE=Proteins&PROGRAM=blastp&BLAST_PROGRAMS=blastp&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on with the japonicus ortholog as a query will provide a good enough seed alignment to detect more distant orthologs which were missed by searching with the fission yeast sequence. (Note that current 'non conserved' status assignments in GeneDB have not been systematically checked against Japonicus) TREEFAM http://www.treefam.org/ Treefam is a database of phylogenetic trees and also an ortholog database. Because Treefam infers orthology using trees it can be more accurate than some of the 'Blast based' orthology prediction methods. Although developed for animal genes it tries to include S. cerevisiae and S. pombe as outgroups. With Treefam distant relationships are sometimes missed, however, the incidence of false positives is low. Treefam will become increasingly useful to assess how pombe genes are related to animal families as further families are curated. From Sophie.Martin at unil.ch Sat Aug 4 18:23:57 2007 From: Sophie.Martin at unil.ch (Sophie Martin) Date: Sat, 04 Aug 2007 13:23:57 -0400 Subject: [Pombelist] PhD/postdoctoral positions available Message-ID: <46b4b62d.2e7.62d0.1558288442@unil.ch> Dear Colleagues, Thank you for bringing the attached advert for PhD students and postdocs in my lab to the attention of candidates who may be interested. Many thanks Sophie Martin We are seeking outstanding and enthusiastic candidates to join the group of Sophie Martin at the Center for Integrative Genomics of the University of Lausanne, Switzerland. Applicants should have a Bachelor?s degree or equivalent (PhD position) or PhD degree (postdoc position) in a relevant discipline (biology, genetics, etc.) Our group studies molecular mechanisms of cell polarisation and cytosketal function, using the fission yeast, S. pombe, as a model system. Several potential projects are available, integrating live-cell imaging, genetic and biochemical experimental approaches. For more information, see http://www.unil.ch/cig/page44769.html, or contact Sophie.Martin at unil.ch The Center for Integrative Genomics is a new, dynamic institute with international and interactive research groups and world-class facilities in imaging, genomics and proteomics. The working language is English. The Center is located in Lausanne (Switzerland), a beautiful city by Lake Geneva that offers excellent opportunities for cultural and outdoor activities. Please send a CV and 2 letters of recommendation to: Sophie.Martin at unil.ch ______________________________________ Sophie Martin, PhD Center for Integrative Genomics University of Lausanne Genopode Building CH-1015 Lausanne Switzerland email: Sophie.Martin at unil.ch http://www.unil.ch/cig/page44769.html From marti5_kupiec at yahoo.com Wed Aug 8 15:07:02 2007 From: marti5_kupiec at yahoo.com (Martin Kupiec) Date: Wed, 8 Aug 2007 07:07:02 -0700 (PDT) Subject: [Pombelist] Looking for wt pombe Message-ID: <41452.95036.qm@web34307.mail.mud.yahoo.com> Dear Fission People, We are looking for wild strains of pombe for a variability study. Surprisingly, most people have just Leupold's isolates. If you happen to have one, or you know who might, would you pls send them to me? Thanks a lot! Martin Martin Kupiec Dept. of Molecular Micro & Biotech, Tel Aviv University, Ramat Aviv 69978, Israel. Phone: 972-3-640-9031 FAX: 972-3-640-9407 E-mail: martin at post.tau.ac.il http://www.tau.ac.il/lifesci/departments/biotech/members/kupiec/kupiec.html ____________________________________________________________________________________ Boardwalk for $500? In 2007? Ha! Play Monopoly Here and Now (it's updated for today's economy) at Yahoo! Games. http://get.games.yahoo.com/proddesc?gamekey=monopolyherenow -------------- Attachments -------------- An HTML attachment was scrubbed... URL: From juergen.stolz at wzw.tum.de Mon Aug 20 15:07:54 2007 From: juergen.stolz at wzw.tum.de (Juergen Stolz) Date: Mon, 20 Aug 2007 16:07:54 +0200 Subject: [Pombelist] used micromanipulator Message-ID: <93A5C9CF-BB04-4C4C-9344-A8A3BE05B3D9@wzw.tum.de> Dear all, We are looking for a micromanipulator for yeast tetrad dissection. A used but functional instrument would just be fine. I have worked with Singer instruments before, but other offers are equally welcome. Thans a lot, Juergen stolz at wzw.tum.de _____________________________ Dr. J?rgen Stolz Lehrstuhl f?r Ern?hrungsphysiologie Molecular Nutrition Unit Technische Universit?t M?nchen Am Forum 5 85350 Freising-Weihenstephan -------------- Attachments -------------- An HTML attachment was scrubbed... URL: From val at sanger.ac.uk Wed Aug 22 15:16:08 2007 From: val at sanger.ac.uk (Valerie Wood) Date: Wed, 22 Aug 2007 15:16:08 +0100 Subject: [Pombelist] NEW Pfam release (Version 22) Message-ID: <46CC4528.7080101@sanger.ac.uk> This weeks update of GeneDB has uses the new Pfam release (Version 22). This provides Pfam families/domains for an additional 40 fission yeast proteins. Three of these were previously sequence orphan: SPAC144.15c Vps51/Vps67 Golgi complex component 1 (ortholog of YGL223C), still 1 subunit of this complex missing- COG7 SPAC3G6.10c Vps51/Vps67 family (ortholog of YKR020W VPS51) SPAC4G9.06c Histone chaperone domain CHZ (ortholog of YER030W CHZ1) From h.yamano at mcri.ac.uk Wed Sep 5 09:41:26 2007 From: h.yamano at mcri.ac.uk (Hiro Yamano) Date: Wed, 5 Sep 2007 09:41:26 +0100 Subject: [Pombelist] Post-doc position available Message-ID: Dear colleagues A post-doctoral position is available in my lab to work on the mechanisms of the APC/C-dependent ubiquitylation and proteolysis using fission yeast and frog egg extracts. I would be very grateful if you could post the attached advert on your notice board, and bring it to the attention of any motivated student/post-doc who may be interested in your lab or department. Many thanks, Hiro Yamano ______________________________________________________________________ This email has been scanned by the MessageLabs Email Security System. For more information please visit http://www.messagelabs.com/email ______________________________________________________________________ -------------- Attachments -------------- To retrieve the following attachment, use the link provided Name: Postdoc Ad 2007.doc Size: 377 bytes URL: -------------- Attachments -------------- To retrieve the following attachment, use the link provided Name: Postdoc Ad 2007.doc Size: 26112 bytes URL: -------------- Attachments -------------- ************************** Hiro Yamano, Ph.D. Head, Cell Cycle Control Laboratory Marie Curie Research Institute, The Chart, Oxted, Surrey RH8 0TL, UK Tel: +44 (0)1883 722306 Fax: +44 (0)1883 714375 Email: h.yamano at mcri.ac.uk http://www.mcri.ac.uk/research/cellcycle.asp From jianqiu.wu at yale.edu Thu Sep 6 19:18:38 2007 From: jianqiu.wu at yale.edu (Jian-Qiu Wu) Date: Thu, 06 Sep 2007 14:18:38 -0400 Subject: [Pombelist] New contact and postdoc position Message-ID: <20070906141838.vy26rkth7kkwg4cs@www.mail.yale.edu> Dear All, I just started a new laboratory at The Ohio State University. The below is my new address. Please see below or the attached file for postdoc positions in my lab. Thanks. Jian-Qiu Wu Assistant Professor Department of Molecular Genetics The Ohio State University Biological Sciences Building, Room 976 484 West 12th Avenue Columbus, OH 43210-1292 Phone: 614 247-6680 Email: wu.620 at osu.edu Postdoctoral Positions Funded postdoctoral positions are available immediately in Jian Qiu Wu's laboratory at Ohio State University to study the molecular mechanism of cell division in the fission yeast S. pombe using a combination of molecular, cellular, biochemical, genetic, and confocal microscopic approaches. More information can be found at http://www.osumolgen.org/faculty/index.php/profile/jianqiu_wu Highly motivated and energetic candidates with strong background in molecular biology, cell biology, or genetics are desired. Please email a cover letter, curriculum vitae, research experience and interests, reprints of publications, and names and contacts of three references to wu.620 at osu.edu. The Department of Molecular Genetics at OSU is a vigorous and highly interactive department that plays a central role in the molecular life sciences on campus. The department consists of faculty members studying important problems in molecular, cellular, and developmental biology using a variety of model organisms including plant and animal viruses, fungi, plants, worms, insects, mice and humans. Departmental faculty members participate in numerous campus-wide collaborations and focus groups such as the Cell Biology Group, the Developmental Genetics Group (http://groups.yahoo.com/group/dgmeet/), and the RNA group. The Ohio State University is the flagship institution of the state's higher education system. It is located in the state capital, Columbus, the 15th largest city in the US. Columbus and its many suburbs have been ranked as one of the country's best places to live and work. -------------- Attachments -------------- To retrieve the following attachment, use the link provided Name: Postdoctoral Position in the Wu lab.pdf Size: 52433 bytes URL: From mohan at tll.org.sg Mon Sep 10 09:25:33 2007 From: mohan at tll.org.sg (Mohan Balasubramanian) Date: Mon, 10 Sep 2007 15:25:33 +0700 Subject: [Pombelist] Asia-Pacific Regional Fission Yeast Meeting July 25-27 2008 SINGAPORE Message-ID: Dear Colleagues We plan to host a Asia-Pacific regional fission yeast meeting in July 2008 in Singapore. The dates of the meeting are July 25-27. We hope this meeting will be of interest to fission yeast researchers in the Asia-Pacific region (and elsewhere as well). We will have two special lectures to start this meeting, given by 1. Richard Losick (HARVARD) and 2. Randy Schekman (UC BERKELEY) In addition, Paul Nurse, Masayuki Yamamoto and Mitsuhiro Yanagida will attend and give talks. We plan to keep the costs low. I would appreciate knowing the extent of enthusiasm; this will allow us a better estimate of the prices. Please write to any of us listed below Best Regards Mohan Balasubramanian (mohan at tll.org.sg) Snezhana Oliferenko (snejana at tll.org.sg) and Jianhua Liu (liujh at gis.a-star.edu.sg) -- Mohan K. Balasubramanian Temasek Life Sciences Laboratory 1 Research Link The National University of Singapore Singapore 117604 Tel: 65-6872-7478: Fax: 65-6872-7007 e-mail: mohan at tll.org.sg http://www.tll.org.sg/mohan.asp -------------- Attachments -------------- An HTML attachment was scrubbed... URL: From forsburg at usc.edu Tue Oct 9 18:44:40 2007 From: forsburg at usc.edu (SLForsburg) Date: Tue, 09 Oct 2007 10:44:40 -0700 Subject: [Pombelist] Regional Pombe meeting Message-ID: North American Pombe Meeting 2008 University of Southern California, Los Angeles, 6-8 June Organizers: Nick Rhind and Susan Forsburg Webiste: http://www-rcf.usc.edu/~forsburg/pombemeeting.html Information: USCpombe at gmail.com {} {} {} {} {} {} {} {} {} {} {} {} {} {} S L Forsburg PhD, Professor University of Southern California Molecular & Computational Biology Ray R Irani Hall 1050 Childs Way, RRI 201B Los Angeles, CA 90089-2910 vox: 213-740-7342 fax: 213-740-8631 forsburg at usc.edu www.pombe.net -------------- Attachments -------------- An HTML attachment was scrubbed... URL: From vogel at mpi-cbg.de Wed Oct 10 14:08:35 2007 From: vogel at mpi-cbg.de (Sven Vogel) Date: Wed, 10 Oct 2007 15:08:35 +0200 (MEST) Subject: [Pombelist] Microtubule stabilizing drug? Message-ID: <54215.10.1.238.4.1192021715.squirrel@webmail.mpi-cbg.de> Dear all, do you know a microtubule stabilizing drug that works in S.pombe? I heard that taxol does not, yet I did not try it myself so far. If you have experience with taxol or if you know any drug that does a similar job as taxol, please let me know. I will be happy about any comments :-) Thank you Sven -- Sven Kenjiro Vogel PhD Student, Tolic-Norrelykke group Max Planck Institute of Molecular Cell Biology and Genetics Dresden Pfotenhauerstr. 108 D-01307 Dresden phone: +49-351-210-2541 fax: +49-351-210-2020 From Marc_Buehler at hms.harvard.edu Wed Oct 24 16:32:47 2007 From: Marc_Buehler at hms.harvard.edu (Buehler, Marc) Date: Wed, 24 Oct 2007 11:32:47 -0400 Subject: [Pombelist] postdoctoral position Message-ID: <34D3E13342E7144D8E1A05032097A27A0880B05F@MAILSERVER02.MED.HARVARD.EDU> Dear Colleagues, Thank you for bringing the attached advert for an open postdoc position in my lab to the attention of candidates who may be interested. Many thanks Marc B?hler Postdoctoral Position Yeast Live-Cell Imaging Applications are invited for a postdoctoral position in the group of Dr. Marc B?hler to study chromatin-dependent gene silencing mechanisms. This research aims at the elucidation of "co-transcriptional gene silencing" (CTGS) on a single-cell level (B?hler et al. 2007, Cell 129:707-721), focusing on the mechanisms linking RNA turnover to chromatin-dependent gene silencing. The project will employ genetic, biochemical, molecular biological, advanced live-cell imaging and proteomic approaches. Candidates should have extensive experience in live-cell imaging techniques. Although not required, previous experience of working with yeast is preferred. The ability to work independently is essential and applicants are expected to have a high level of organisational and communication skills and to become involved in the supervision of graduate students. The FMI, part of the Novartis Research Foundation, is an international biomedical research centre with 300 members pursuing fundamental research in Neurobiology, Cell Growth and Signalling, and Epigenetics (www.fmi.ch). A competitive salary and access to state-of-the-art research facilities will be provided. The FMI is situated in Basel, a city offering an outstanding scientific and cultural environment in the centre of Europe. Applications, including a detailed CV, the names and contact details of three referees and a summary of current and future research interests should be addressed to Dawn Hammond, Friedrich Miescher Institute, Maulbeerstrasse 66, 4058 Basel, Switzerland (dawn.hammond at fmi.ch). Marc B?hler Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 4058 Basel Switzerland -------------- Attachments -------------- An HTML attachment was scrubbed... URL: -------------- Attachments -------------- To retrieve the following attachment, use the link provided Name: Advert_FMI_Buehler.pdf Size: 14732 bytes URL: From ccc at cict.fr Thu Oct 25 07:46:13 2007 From: ccc at cict.fr (Colloque Cycle Cellulaire et Cancer (CC&C)) Date: Thu, 25 Oct 2007 08:46:13 +0200 Subject: [Pombelist] CCC2008 Message-ID: <51869DA6-26DE-4AD3-9EB9-DE3702426CCB@cict.fr> EARLY BIRDS REGISTRATION ENDS NOVEMBER 15th !.... CELL CYCLE & CANCER March 25-28, 2008 TOULOUSE (FRANCE) The objective of this international conference is to highlight the latest advances in research into the mechanisms that control the cell cycle, their alterations in cancer, and their potential utility as targets for anticancer therapies. Organisers : B. Ducommun ( Toulouse) and C. Prigent (Rennes) with the French Society of Cell Biology Scientific sessions : DNA replication, Cytoskeleton and chromosomes segregation, Mitosis, Niche-dependent cell cycle and Cancer, Genome stability, Targeting cell-cycle in cancer therapy Keynote speakers : T. Hunt (Nobel prize 2001, London), M. Barbacid (Madrid), M. Kastan (Memphis), D. Lane (Dundee) Speakers : J. Bischoff (Madrid), J. Blow (Dundee), S. Doxsey (Worcester), W. Earnshaw (Edinburgh), I. Hagan (Manchester), J. Lazo (Pittsburgh), J. Lukas (Copenhagen), J. Maller (Denver), M. Malumbres ( Madrid), M. Mechali (Montpellier), R. Medema (Utrecht), L. Meijer (Roscoff), E. Nigg (Mertinsried), M. Roberge (Vancouver), J. Roberts (Seattle), C. Sardet (Montpellier), A. Senderowicz (betshesda), M-H. Verlhac (Paris) Short communications will be selected from the abstracts. Poster sessions Additional informations available at http://ccc-2008.univ-rennes1.fr REDUCED RATE FOR EARLY BIRDS ENDS NOVEMBER 15th !.... ___________________________________ CELL CYCLE and CANCER Cycle Cellulaire et Cancer March 25th-28th, 2008 TOULOUSE - FRANCE by the French Society of Cell Biology Contact the organizer: ccc at cict.fr http://ccc-2008.univ-rennes1.fr ___________________________________ Merci de penser ? l'environnement avant d'imprimer cet e-mail -------------- Attachments -------------- An HTML attachment was scrubbed... URL: From nick.rhind at umassmed.edu Fri Oct 26 19:20:23 2007 From: nick.rhind at umassmed.edu (Nick Rhind) Date: Fri, 26 Oct 2007 14:20:23 -0400 Subject: [Pombelist] The Schizosaccharomyces octosporus genome Message-ID: The first draft of the Schizosaccharomyces octosporus genome sequence is now available. The genome was sequenced at The Broad Institute as part of the Fungal Genome Initiative, a project funded by NHGRI. The current sequence consists of 25-fold coverage by 454 sequencing. The assembled genome contains 355 contigs with an N50 of 72 kb. Early next year, we intend to add end-paired reads from genomic clones which should increase contig length and allow the contigs to be assembled into larger scaffolds. The octosporus assembly is available at http://www.broad.mit.edu/annotation/genome/schizosaccharomyces_japonicus.3 The site includes information about the S. octosporus project and assembly, along with the S. pombe and S. japonicus genomes, tools for downloading the genome sequences, BLASTing against the genome assemblies, and searching and browsing for features of the genomes. The S. octosporus genome will be automatically annotated at The Broad Institute and manually annotated in collaboration with the fission yeast community. Annotations will be released as they become available. Please share this release notice with anyone you think may be interested. Sincerely, Chad Nusbaum Nick Rhind From Simon.Labbe at USherbrooke.ca Mon Oct 29 14:10:42 2007 From: Simon.Labbe at USherbrooke.ca (Labbe Simon) Date: Mon, 29 Oct 2007 10:10:42 -0400 Subject: [Pombelist] Tenure Track position - University of Sherbrooke Canada Message-ID: STRUCTURAL BIOCHEMISTRY and BIOINFORMATICS ASSISTANT PROFESSOR The Department of Biochemistry invites applications for tenure-track positions at the Assistant Professor level starting in 2008 and 2009. The Department is composed of young scientists who are well-known for their innovation. For more details, visit http://www.usherbrooke.ca/biochimie/ . The successful candidates are expected to develop an externally funded research program in Structural biochemistry (e.g. crystallography) and Computational biology, and eventually contribute to teaching at the graduate and undergraduate levels. Curriculum vitae and description of future research goals along with the names and contact information of three references can be submitted by mail to: Comit? de recrutement D?partement de biochimie Facult? de m?decine et des sciences de la sant? Universit? de Sherbrooke 3001, 12e avenue Nord Sherbrooke (Qu?bec) J1H 5N4 Canada For further information : Simon Labb?, Ph.D. (Simon.Labbe at usherbrooke.ca) In accordance with Canadian Immigration requirements, priority will be given to Canadian citizens and permanent residents of Canada. The Universit? de Sherbrooke is committed to the principle of equity in employment and offers equal employment opportunities to qualified applicants. Simon Labb?, Ph.D. Professeur agr?g? / Associate Professor D?partement de Biochimie (Biochemistry) Facult? de m?decine Universit? de Sherbrooke 3001, 12e Avenue Nord Sherbrooke (Qu?bec) Canada J1H 5N4 Tel.: (819) 564-5281 (Secretariat) Tel.: (819) 820-6868 ext.: 15460 (Bureau / Office) Tel.: (819) 820-6868 ext.: 15461 or 15841 (Labs) Fax: (819) 564-5340 e-mail: Simon.Labbe at USherbrooke.ca Web site: http://www.med.usherbrooke.ca/labo_labbe -------------- Attachments -------------- An HTML attachment was scrubbed... URL: -------------- Attachments -------------- To retrieve the following attachment, use the link provided Name: Ad for structural biochemistry and bioinformatics person.doc Size: 33280 bytes URL: From gsmith at fhcrc.org Mon Oct 29 17:18:59 2007 From: gsmith at fhcrc.org (Gerald Smith) Date: Mon, 29 Oct 2007 10:18:59 -0700 (PDT) Subject: [Pombelist] postdoctoral position at the Hutchinson Center (Seattle) Message-ID: Postdoctoral Research Position Fred Hutchinson Cancer Research Center, Seattle A postdoctoral research position to study genetic recombination and DNA break repair is available in the lab of Gerald R. Smith in the Division of Basic Sciences at the Fred Hutchinson Cancer Research Center in Seattle. Our research uses both S. pombe and E. coli to investigate the mechanism and control of recombination. Both genetic and biochemical approaches are used. In S. pombe our research is on meiotic recombination. Emphasis is placed on the control of recombination by hotspots, meiotic DNA double-strand break (DSB) hotspots, such as M26, in S. pombe and Chi in E. coli. Additional research is on chromosome segregation in meiosis, with emphasis on the roles of chromosome pairing and recombination. For further information, see our websites: http://myprofile.cos.com/smithabc102 http://www.fhcrc.org/science/labs/gsmith/ Experience in genetics or biochemistry is required. Experience with microbes is valuable but not essential. Stipends follow the NIH guidelines for postdoctoral fellows. Starting date is flexible. The Division of Basic Sciences has approximately 30 labs pursuing research with organisms as diverse as bacteria, yeast, plants, worms, flies, fish, mice, and humans, in areas as diverse as protein structure, enzymology, evolution, development, behavior, and suspended animation. Close collaborations with the University of Washington, close by, are frequent. Seattle is outstanding for its culture and proximity to mountains and oceans for outdoor activities. Gerald R. Smith Division of Basic Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Avenue North, A1-162 P.O. Box 19024 Seattle, WA 98109-1024 United States of America Tel. 206-667-4438 FAX 206-667-6497 e-mail gsmith at fhcrc.org ______________________________________ Gerald R. Smith Fred Hutchinson Cancer Research Center 1100 Fairview Avenue North, A1-162 P.O. Box 19024 Seattle, WA 98109-1024 Tel. 206-667-4438 FAX 206-667-6497 From Janni.petersen at manchester.ac.uk Wed Oct 31 14:35:30 2007 From: Janni.petersen at manchester.ac.uk (Janni Petersen) Date: Wed, 31 Oct 2007 14:35:30 +0000 Subject: [Pombelist] Post-doc position Message-ID: Hi Would you please bring the attached to the attention of anyone that you think maybe interested. Many thanks Janni DOCTORAL RESEARCH ASSOCIATE ? YEAST CELL BIOLOGY (Environmental control over cell division and polarised growth) (Ref LS/121/07) You will join a research team investigating environmental control over cell division and polarised growth, using the fission yeast S.pombe as a model system. For more background information see Petersen, J. and Hagan, I. M. Nature. 435:507-512. 2005. Petersen and Nurse. 2007 Nature Cell Biology (advance online publications). You will focus on characterising the means by which kinase signalling regulates cytoskeletal transitions, using a wide range of contemporary molecular cell biology, biochemical and bio-imaging techniques. This position is available from 1 December 2007. The closing date for applications is 8 November 2007 ***************************************************** Janni Petersen University of Manchester Faculty of Life Sciences Michael Smith Building C.4255 Laboratory C.4223 Oxford Road Manchester M13 9PT United Kingdom Phone: 0161-275-5512 Lab: 0161-275-5107 FAX: 0161-275-5082 e-mail: Janni.Petersen at manchester.ac.uk ***************************************************** -------------- Attachments -------------- To retrieve the following attachment, use the link provided Name: DOCTORAL_RESEARCH_ASSOCIATE.doc Size: 56320 bytes URL: From M.Luetzelberger at tu-bs.de Fri Nov 2 13:56:22 2007 From: M.Luetzelberger at tu-bs.de (Martin Luetzelberger) Date: Fri, 02 Nov 2007 14:56:22 +0100 Subject: [Pombelist] Q: V5-tag in fission yeast Message-ID: <472B2C86.60101@tu-bs.de> Dear all, I'd like to ask if any of you have experience with the V5 epitope tag (KPIPNPLLGLDST) in fission yeast. We used this tag for N-terminal tagging of two essential genes. Both constructs are driven by the thiamine-repressible nmt1-8 promoter. We observe that strains within which the respective genes were exchanged with their V5-tagged version grow normally as compared to the wildtype. Thus, we have no indication that the V5 tag interferes with protein function. However, when we switch off the nmt1-8 promoter by addition of thiamine, cells arrest early. Whereas the V5-tagged strains stop growth already 10 hours after addition of thiamine, strains with an HA- or myc-tag and the same genetic background arrest only after 12-14 hours. Thus, the V5-tagged proteins appear to be short-lived and might have faster turn-over rates. Since we observed this behavior with two different proteins, we don't think that it is a gene-specific effect. Has anyone of you ever used the V5-tag in S.pombe and made similar observations? Best regards, Martin Luetzelberger Institute of Genetics Technical University of Braunschweig Spielmannstr. 7 38 106 Braunschweig Germany Phone: +49 531 391 5784 or 5796 Fax: +49 531 391 5765 Email: M.Luetzelberger at tu-bs.de From hoffmacs at bc.edu Fri Nov 2 14:09:23 2007 From: hoffmacs at bc.edu (Charles Hoffman) Date: Fri, 02 Nov 2007 10:09:23 -0400 Subject: [Pombelist] Q: V5-tag in fission yeast In-Reply-To: <472B2C86.60101@tu-bs.de> References: <472B2C86.60101@tu-bs.de> Message-ID: We have not noticed any deleterious effects of V5-tagging, however I am not sure that we have any equivalent experiment to what you are describing, which may be a more sensitive assessment of function and stability. Charlie Hoffman Boston College "I'd rather be fission." | On Fri, 02 Nov 2007 14:56:22 +0100 | Martin Luetzelberger wrote: | Dear all, | | I'd like to ask if any of you have experience with the V5 epitope tag (KPIPNPLLGLDST) in fission yeast. | We used this tag for N-terminal tagging of two essential genes. Both constructs are driven by the | thiamine-repressible nmt1-8 promoter. | We observe that strains within which the respective genes were exchanged with their V5-tagged version | grow normally as compared to the wildtype. Thus, we have no indication that the V5 tag interferes with | protein function. | However, when we switch off the nmt1-8 promoter by addition of thiamine, cells arrest | early. Whereas the V5-tagged strains stop growth already 10 hours after addition of thiamine, strains | with an HA- or myc-tag and the same genetic background arrest only after 12-14 hours. Thus, the V5-tagged | proteins appear to be short-lived and might have faster turn-over rates. Since we observed this behavior with | two different proteins, we don't think that it is a gene-specific effect. | | Has anyone of you ever used the V5-tag in S.pombe and made similar observations? | | Best regards, | | Martin Luetzelberger | | Institute of Genetics | Technical University of Braunschweig | Spielmannstr. 7 | 38 106 Braunschweig | Germany | Phone: +49 531 391 5784 or 5796 | Fax: +49 531 391 5765 | Email: M.Luetzelberger at tu-bs.de | | _______________________________________________ | Pombelist mailing list | Pombelist at sanger.ac.uk | http://lists.sanger.ac.uk/mailman/listinfo/pombelist From forsburg at usc.edu Fri Nov 2 14:28:31 2007 From: forsburg at usc.edu (SLForsburg) Date: Fri, 02 Nov 2007 07:28:31 -0700 Subject: [Pombelist] Q: V5-tag in fission yeast In-Reply-To: <472B2C86.60101@tu-bs.de> References: <472B2C86.60101@tu-bs.de> Message-ID: <7AE83148-F54E-4E8F-B65C-2E9D3EC1C901@usc.edu> We have used the tag quite a bit, at the C-terminus., without problem. We have not used it at the N-terminus. Could it be that your construct has a sequence that invokes the N-end rule and thus increases protein turnover? On Nov 2, 2007, at 6:56 AM, Martin Luetzelberger wrote: > Dear all, > > I'd like to ask if any of you have experience with the V5 epitope > tag (KPIPNPLLGLDST) in fission yeast. > We used this tag for N-terminal tagging of two essential genes. > Both constructs are driven by the > thiamine-repressible nmt1-8 promoter. > We observe that strains within which the respective genes were > exchanged with their V5-tagged version > grow normally as compared to the wildtype. Thus, we have no > indication that the V5 tag interferes with > protein function. > However, when we switch off the nmt1-8 promoter by addition of > thiamine, cells arrest > early. Whereas the V5-tagged strains stop growth already 10 hours > after addition of thiamine, strains > with an HA- or myc-tag and the same genetic background arrest only > after 12-14 hours. Thus, the V5-tagged > proteins appear to be short-lived and might have faster turn-over > rates. Since we observed this behavior with > two different proteins, we don't think that it is a gene-specific > effect. > > Has anyone of you ever used the V5-tag in S.pombe and made similar > observations? > > Best regards, > > Martin Luetzelberger > > Institute of Genetics > Technical University of Braunschweig > Spielmannstr. 7 > 38 106 Braunschweig > Germany > Phone: +49 531 391 5784 or 5796 > Fax: +49 531 391 5765 > Email: M.Luetzelberger at tu-bs.de > > _______________________________________________ > Pombelist mailing list > Pombelist at sanger.ac.uk > http://lists.sanger.ac.uk/mailman/listinfo/pombelist {} {} {} {} {} {} {} {} {} {} {} {} {} {} S L Forsburg PhD, Professor University of Southern California Molecular & Computational Biology Ray R Irani Hall 1050 Childs Way, RRI 201B Los Angeles, CA 90089-2910 vox: 213-740-7342 fax: 213-740-8631 forsburg at usc.edu www.pombe.net -------------- Attachments -------------- An HTML attachment was scrubbed... URL: From bisht at webmail.imtech.res.in Fri Nov 2 17:25:31 2007 From: bisht at webmail.imtech.res.in (Kamlesh Bisht) Date: Fri, 2 Nov 2007 22:55:31 +0530 (IST) Subject: [Pombelist] Q: V5-tag in fission yeast In-Reply-To: <7AE83148-F54E-4E8F-B65C-2E9D3EC1C901@usc.edu> References: <472B2C86.60101@tu-bs.de> <7AE83148-F54E-4E8F-B65C-2E9D3EC1C901@usc.edu> Message-ID: hello martin i am convinced with SLForsburg that v5 tag invokes N-end degradation.just because of curiosity i have submitted V5 sequence to "ProtParam tool" available at http://www.expasy.ch/tools/protparam.html. it predicts half life of any protein depending on the nature of the amino acid at the amino terminus. considering K (lys)of V5 tag is coming at N-terminal of v5 tag sequence itself is showing half time of only three minutes in yeast.means its presence at n-terminal most likely destabilise the protein of interest. Estimated half-life:of (KPIPNPLLGLDST) The N-terminal of the sequence considered is K (Lys). The estimated half-life is: 1.3 hours (mammalian reticulocytes, in vitro). 3 min (yeast, in vivo). ****************************************** Kamlesh Kumar Bisht Research Scholar Yeast Molecular Biology Group IMTECH (CSIR) CHANDIGARH INDIA 160036 contact numbers: Personal +91-09872811845 Office : +91-0172-2690004 Extn 443 ********************************************* On Fri, 2 Nov 2007, SLForsburg wrote: > We have used the tag quite a bit, at the C-terminus., without problem. We > have not used it at the N-terminus. > > Could it be that your construct has a sequence that invokes the N-end rule > and thus increases protein turnover? > > > > > On Nov 2, 2007, at 6:56 AM, Martin Luetzelberger wrote: > >> Dear all, >> >> I'd like to ask if any of you have experience with the V5 epitope tag >> (KPIPNPLLGLDST) in fission yeast. >> We used this tag for N-terminal tagging of two essential genes. Both >> constructs are driven by the >> thiamine-repressible nmt1-8 promoter. >> We observe that strains within which the respective genes were exchanged >> with their V5-tagged version >> grow normally as compared to the wildtype. Thus, we have no indication that >> the V5 tag interferes with >> protein function. >> However, when we switch off the nmt1-8 promoter by addition of thiamine, >> cells arrest >> early. Whereas the V5-tagged strains stop growth already 10 hours after >> addition of thiamine, strains >> with an HA- or myc-tag and the same genetic background arrest only after >> 12-14 hours. Thus, the V5-tagged >> proteins appear to be short-lived and might have faster turn-over rates. >> Since we observed this behavior with >> two different proteins, we don't think that it is a gene-specific effect. >> >> Has anyone of you ever used the V5-tag in S.pombe and made similar >> observations? >> >> Best regards, >> >> Martin Luetzelberger >> >> Institute of Genetics >> Technical University of Braunschweig >> Spielmannstr. 7 >> 38 106 Braunschweig >> Germany >> Phone: +49 531 391 5784 or 5796 >> Fax: +49 531 391 5765 >> Email: M.Luetzelberger at tu-bs.de >> >> _______________________________________________ >> Pombelist mailing list >> Pombelist at sanger.ac.uk >> http://lists.sanger.ac.uk/mailman/listinfo/pombelist > > > {} {} {} {} {} {} {} {} {} {} {} {} {} {} > S L Forsburg PhD, Professor > University of Southern California > Molecular & Computational Biology > Ray R Irani Hall > 1050 Childs Way, RRI 201B > Los Angeles, CA 90089-2910 > > vox: 213-740-7342 > fax: 213-740-8631 > forsburg at usc.edu > www.pombe.net > > > From ibimbsm at bio.uni-stuttgart.de Tue Nov 13 09:32:59 2007 From: ibimbsm at bio.uni-stuttgart.de (Stefan Mangold) Date: Tue, 13 Nov 2007 10:32:59 +0100 Subject: [Pombelist] scFv-fusionprotein in S.pombe Message-ID: Dear Sir or Madam, in the Department of Molecular Biology at the University of Stuttgart, I have recently started my diploma thesis with the aim to express and secrete an scFv-fusion protein in Schizosaccharomyces pombe. The project is supervised by PD Dr Christina Wege in the group of Prof. Holger Jeske. The idea for this project has arosen since we have already used S. pombe for expression of a number of plant proteins, and in a collaborating institute, the Institute of Cell Biology and Immunology, scFv-fusion proteins have been expressed either in bacteria or in animal cells. Now, we want to try to combine our systems - but do not have any experience in antibody expression in yeast-based systems at all yet. Therefore, the first step of my work is to find out about an appropriate signal sequence, which should ensure the translocation of the scFv into the lumen of the ER and its entry into the secretory pathway. We hope to get functional antibodies for different applications by this method. During my literature research, I have now found a number of interesting publications. Since, however, I was not able to find any recent report on successful antibody production in S. pombe, I like to ask you if you might have any know-how or operating experience in expression and secretion of heterologous proteins in S. pombe, or perhaps even with scFv-antibodies or scFV-fusion proteins, respectively. Or maybe you can recommend somebody else who might have this experience? Helpful tips or information would assist us greatly and maybe avoid choosing a strategy which is not likely to be successful. At the moment, my main concern is the choice of a promising signal peptide sequence, as mentioned already. If you were interested, I would appreciate giving you a report about my experience later! Sincerely yours and best regards from Stuttgart, Stefan Mangold ----------------------------------------------------------- Stefan Mangold Department of Molecular Biology and Plant Virology Institute of Biology University of Stuttgart Pfaffenwaldring 57 D-70550 Stuttgart E-mail: stefan.mangold at bio.uni-stuttgart.de From nick.rhind at umassmed.edu Thu Nov 15 16:29:14 2007 From: nick.rhind at umassmed.edu (Nick Rhind) Date: Thu, 15 Nov 2007 11:29:14 -0500 Subject: [Pombelist] Searching for octosporus genes Message-ID: Those of you looking for your favorite gene in the octosporus genome at http://www.broad.mit.edu/annotation/genome/schizosaccharomyces_japonicus.3 should be aware that the octosporus genome has not yet annotated, so there are no predicted proteins or transcripts available. Therefore, you should not use BLASTP or BLASTX, and when you use BLASTN or TBLASTN, you need to search against the genomic sequence, not the transcripts. The octosporus automated annotation will be performed after the final draft assembly is released, hopefully early next year. Nick From jejasmin at ucsd.edu Tue Nov 20 08:24:54 2007 From: jejasmin at ucsd.edu (Jean-Nicolas Jasmin) Date: Tue, 20 Nov 2007 00:24:54 -0800 Subject: [Pombelist] growth on non-fermentable substrates Message-ID: <200711192022.lAJKMbIL009561@biomail.ucsd.edu> Dear all, I am working with Sz pombe strains FY261 and FY254 and I find it difficult to grow them on a non-fermentable substrate. On 5% YE and 2% glycerol and ethanol it takes about 2 weeks to get large colonies and the colonies show very high variation in size. I have tried solid media with yeast extract (1 to 5%) and glycerol (1 to 3%) and/or ethanol (1 to 3%), plus amino acids, and I obtain about the same result. Is this normal for these genotypes? Which strain should I use to obtain better growth on non-fermentable substrates? Is there another non-fermentable susbstrate that pombe use better? Note that I have previously posted this question at yeast at net.bio.net. I have received only one answer, advising me to use 0.1% glucose in the media. I am looking for other solutions as I need to grow pombe on non-fermentable substrates to select for resistance to erythromycin and chloramphenicol (mtDNA encoded resistances). Many thanks, Jean-Nicolas EBE, Biological Sciences, UCSD From nick.rhind at umassmed.edu Mon Nov 19 21:57:03 2007 From: nick.rhind at umassmed.edu (Nick Rhind) Date: Mon, 19 Nov 2007 16:57:03 -0500 Subject: [Pombelist] growth on non-fermentable substrates In-Reply-To: <200711192022.lAJKMbIL009561@biomail.ucsd.edu> Message-ID: Hi Jean-Nicolas, A lot of information on carbon source utilization by pombe is available at NCYC and CBS I don't know the genotypes of FY261 and FY254, but I doubt that you will find any differences in carbon source utilization between different strains; the lab strains of pombe are very homogeneous. Is your purpose to grow pombe on a non-fermentable carbon source to prevent mitochondrial loss during drug selection? If so, you may not have to worry. pombe is petit negative, and so should not be able to survive without mitochondrial function, even on a fermentable carbon source. Nick -- Nick Rhind Assistant Professor Biochemistry and Molecular Pharmacology University of Massachusetts Medical School 364 Plantation Street, LRB904 Worcester MA 01605 USA 1 (508) 856-8316:vox 1 (508) 856-8358:fax www.umassmed.edu/bmp/faculty/rhind.cfm From bonnefoy at cgm.cnrs-gif.fr Tue Nov 20 13:19:49 2007 From: bonnefoy at cgm.cnrs-gif.fr (Nathalie Bonnefoy) Date: Tue, 20 Nov 2007 14:19:49 +0100 Subject: [Pombelist] growth on non-fermentable substrates In-Reply-To: <200711192022.lAJKMbIL009561@biomail.ucsd.edu> References: <200711192022.lAJKMbIL009561@biomail.ucsd.edu> Message-ID: Hi Jean-Nicolas, For sure pombe cells do not grow well on glycerol. However, they will grow much better if they are ura4+: ura4 mutants are already rather compromised for growth on glycerol. If your strains are ura4- and if this marker is not necessary for your experiment, segregate it out. We use a mixture of ethanol glycerol that helps a bit: 1% yeast extract, 0.5% casaminoacids, 3% glycerol, 3% ethanol, 40 microg/ml adenine. However S. pombe respiratory chain mutants don't grow on galactose, which can be considered as a non-fermentable carbon source like for human cells even if it's fermentable for S. cerevisiae. Thus we also use galactose as non-fermentable carbon source, our medium is 1% yeast extract, 1% bactopeptone, 0.1% glucose, 2% galactose, 20 microg/ml adenine (the peptone here comes from an old cerevisiae recipe, it could be eliminated). But you can also try galactose without the 0.1% glucose (they will be slower to start growing), or you can reduce the glucose to 0.05%. I hope this helps, if you have any other questions please feel free to write again, I can forward you a review on pombe and mitochondrial studies, best wishes, Nathalie ________________________________________________________________________________ Nathalie Bonnefoy Centre de G?n?tique Mol?culaire CNRS B?timent 26 Avenue de la Terrasse 91198 Gif-sur-Yvette cedex Tel: (33) 1 69 82 31 75 Fax: (33) 1 69 82 31 60 e-mail: bonnefoy at cgm.cnrs-gif.fr >Dear all, > >I am working with Sz pombe strains FY261 and >FY254 and I find it difficult to grow them on a >non-fermentable substrate. On 5% YE and 2% >glycerol and ethanol it takes about 2 weeks to >get large colonies and the colonies show very >high variation in size. I have tried solid media >with yeast extract (1 to 5%) and glycerol (1 to >3%) and/or ethanol (1 to 3%), plus amino acids, >and I obtain about the same result. > >Is this normal for these genotypes? > >Which strain should I use to obtain better >growth on non-fermentable substrates? > >Is there another non-fermentable susbstrate that pombe use better? > >Note that I have previously posted this question >at yeast at net.bio.net. I have received only one >answer, advising me to use 0.1% glucose in the >media. I am looking for other solutions as I >need to grow pombe on non-fermentable substrates >to select for resistance to erythromycin and >chloramphenicol (mtDNA encoded resistances). > >Many thanks, > >Jean-Nicolas >EBE, Biological Sciences, UCSD > >_______________________________________________ >Pombelist mailing list >Pombelist at sanger.ac.uk >http://lists.sanger.ac.uk/mailman/listinfo/pombelist -- ________________________________________________________________________________ From hoffmacs at bc.edu Tue Nov 20 14:42:35 2007 From: hoffmacs at bc.edu (Charles Hoffman) Date: Tue, 20 Nov 2007 09:42:35 -0500 Subject: Fwd: [pombelist] Culturing S.pombe without glucose References: Message-ID: <2E9C0345-3BE5-4AA2-B237-486645E93061@bc.edu> This seems to be a popular topic that comes up ever few years. I will simply paste a previous exchange on carbon sources. I strongly agree with Nathalie that to get reasonable growth on glycerol, you need Ura+ cells. Cheers, Charlie Hoffman Begin forwarded message: > From: "Kurt Runge, Ph.D." > Date: June 11, 2004 1:07:56 PM EDT > To: hoffmacs at bc.edu, cynthia.turcotte.1 at UMontreal.CA > Subject: Re: [pombelist] Culturing S.pombe without glucose > > I have been also growing pombe in glycerol, but we have followed > the old Gutz et al. Handbook of Genetics (c. 1974) recipes. > > Basically, growth on a non-fermentable carbon source requires the > inclusion of replacements for citric acid cycle intermediates. In > the Gutz handbook for some recipes, this replacement was 0.37% mono > sodium glutamate (which is changed to alpha keto-glutarate by B6- > mediated transamination). This approach is the yeast version to > the old, difficult-to-understand adage in your biochemistry > textbooks "fats burn in the flame of carbohydrates", but done > without glycosis. > > Being an S. cerevisiae person by training, I have grown up an h- > ade6 ura4 leu1 his7 strain in 0.67% Yeast nitrogenbase with 150 mg/ > l supplements for auxotrophies plus 3% glycerol + 0.37% mono sodium > glutamate (from a 7.4% MSG filter-sterilized stock). After 2 > weeks, cells reach about 4e7 cells/ml by hemocytometer counts, > where as 3% glucose gives 6 e7 in similar medium without MSG. > > When I have done EMM2, I only get about 1 e8 cells per ml. > However, cell survival in EMM2 is better than the above medium > (called SDC). > > > Kurt Runge > > > > > Kurt Runge, Ph.D., Associate Staff > Cleveland Clinic Foundation > Lerner Research Institute > Dept. of Molecular Biology > 9500 Euclid Avenue, NC20 > Cleveland, OH 44195 > (216) 445-9771 FAX: (216) 444-0512 > http://www.lerner.ccf.org/molecbio/runge/ > >>>> "Charles S. Hoffman" - 6/8/04 10:54 AM >>> > You can use sucrose, maltose, or raffinose for somewhat reasonable > growth. > You can also grow on gluconate, but that is basically as poor as > glycerol. > > Cheers, > > Charlie Hoffman > Boston College > "I'd rather be fission." > > --On Tuesday, June 8, 2004 10:43 AM -0400 Cynthia Turcotte > wrote: > >> Dear PombeList >> >> I would like to have some advice on the culture of S. pombe with >> other >> carbon sources than glucose or glycerol. >> >> We tried already the following conditions: >> >> Both EMM and YE media >> with 0.35% lactic acid, or 2% lactic acid + EtOH, or potassium >> acetate or >> sodium >> acetate >> with or without 0.05% glucose, in each case. >> >> The only cultures that grew contained 0.05% glucose and they could >> not be >> diluted in a media lacking glucose. Moreover, these cultures did not >> grow to saturation; they attained the same O.D. as cultures >> containing >> only 0.05% glucose. >> >> >> Any suggestion will be greatly appreciated >> >> Thank you >> >> Cynthia Turcotte >> Dr. Luis A. Rokeach's laboratory >> Universit? de Montr?al >> >> >> >> >> > -------------- Attachments -------------- An HTML attachment was scrubbed... URL: From blewettn at mail.nih.gov Tue Nov 20 14:51:52 2007 From: blewettn at mail.nih.gov (Nathan Blewett) Date: Tue, 20 Nov 2007 09:51:52 -0500 Subject: [Pombelist] growth on non-fermentable substrates Message-ID: Jean-Nicolas, Our lab routinely uses Yeast Extract -dextrose + 3% glycerol as a growth assay for S. pombe. We have a strain, yYH1 which is ura4-, leu+, carrying a suppressor tRNA, and nonsense adenine allele, this strain grows well on this media, @ 32 and 37 degrees C. We also have several deletion strains which exhibit growth defects on non-fermentable carbon, both at elevated temperature, and the standard 32 deg.C. Generally, our wt strain will come up on these plates on day 3-4. Here is a link to the Forsburg lab page, a great resource for all things Pombe: http://www-rcf.usc.edu/~forsburg/media.html We use the YES recipe (0.5%YE), and subsitute glycerol for glucose. Not sure what your strains are, they may have a phenotype in this regard? I can also tell you that I have not been able to see growth on minimal media (EMM) with only non-fermentable carbon, only rich YEGly. Regards, Nate Blewett From forsburg at usc.edu Tue Nov 20 15:16:55 2007 From: forsburg at usc.edu (SLForsburg) Date: Tue, 20 Nov 2007 07:16:55 -0800 Subject: [pombelist] Culturing S.pombe without glucose In-Reply-To: <2E9C0345-3BE5-4AA2-B237-486645E93061@bc.edu> References: <2E9C0345-3BE5-4AA2-B237-486645E93061@bc.edu> Message-ID: I will post a summary of this discussion on the media page at pombe.net . Please keep the comments coming., and Jean-Nicolas, please if you could summarize any useful omments you got that were not sent to the list, that would be helpful. GEneral note: it's really helpful for the community if the conversations include the whole list. regarding pombe.net: if you notice errors or you have additions or protocols to add to the site, please email me! North American regional meeting in Los Angeles June 6-8 2008 http://www-rcf.usc.edu/~forsburg/pombemeeting.html {} {} {} {} {} {} {} {} {} {} {} {} {} {} S L Forsburg PhD, Professor University of Southern California Molecular & Computational Biology Ray R Irani Hall 1050 Childs Way, RRI 201B Los Angeles, CA 90089-2910 vox: 213-740-7342 fax: 213-740-8631 forsburg at usc.edu www.pombe.net -------------- Attachments -------------- An HTML attachment was scrubbed... URL: From forsburg at usc.edu Wed Nov 21 17:15:08 2007 From: forsburg at usc.edu (S L Forsburg) Date: Wed, 21 Nov 2007 09:15:08 -0800 Subject: [Pombelist] pombe.org and web notes Message-ID: Hi everyone, I use the domain name pombe.net for our main pombe pages, though I also own the domain pombe.org. Since everyone uses pombe.net to visit our site, I see no reason to hold onto pombe.org My ownership will expire at the end of this month, so if anyone wants to pick up pombe.org for more pombe on the web, it will be available on Nov 30. Happy Thanksgiving! susan PS: I have summarized the recent discussion of growth on non- fermentable carbon sources at http://www-rcf.usc.edu/~forsburg/media.html#glycerol If you have other information, protocols, or suggestions for the pombe pages, please let me know. I would like to keep this as up to date and useful for the community as possible. I also rely on you to tell me about broken links, etc. we hae over 50 pages on our web site and I rely on the readers to keep it current. >>>>>>>>>>>>>>>>>>>>>>>>>>> Susan L Forsburg PhD Professor, Molecular & Computational Biology Chair, Molecular Biology Graduate Committee University of Southern California RRI 201 1050 Childs Way Los Angeles CA 90089-2910 -------------- Attachments -------------- An HTML attachment was scrubbed... URL: From marti5_kupiec at yahoo.com Mon Dec 3 15:48:42 2007 From: marti5_kupiec at yahoo.com (Martin Kupiec) Date: Mon, 3 Dec 2007 07:48:42 -0800 (PST) Subject: [Pombelist] FACS Message-ID: <533334.14499.qm@web34314.mail.mud.yahoo.com> Hi everybody! We are new to the field of FACS in pombe, and I have the following observation: After adding hydroxyurea my favorite mutant stays in G2, but slowly/surely the peak spreads to the right (to what appears as higher and higher DNA content). Somehow this "smells" like some sort of artifact, and not endoreduplication (I don't see a 2C peak turn into a 4C, rather a migration of the distribution, that also gets wider as time passes). Has anybody seen this before? It seems as if for some reason the cells accumulate higher propidium iodide content, although they are not particularly longer... Any ideas/suggestions? Thanks! Martin Kupiec Dept. of Molecular Micro & Biotech, Tel Aviv University, Ramat Aviv 69978, Israel. Phone: 972-3-640-9031 FAX: 972-3-640-9407 E-mail: martin at post.tau.ac.il http://www.tau.ac.il/lifesci/departments/biotech/members/kupiec/kupiec.html ____________________________________________________________________________________ Be a better pen pal. Text or chat with friends inside Yahoo! Mail. See how. http://overview.mail.yahoo.com/ -------------- Attachments -------------- An HTML attachment was scrubbed... URL: From ssazer at bcm.edu Mon Dec 3 16:44:29 2007 From: ssazer at bcm.edu (Shelley Sazer) Date: Mon, 3 Dec 2007 10:44:29 -0600 Subject: [Pombelist] FACS In-Reply-To: <533334.14499.qm@web34314.mail.mud.yahoo.com> References: <533334.14499.qm@web34314.mail.mud.yahoo.com> Message-ID: <9640309A-C9EC-45CC-8899-AC3C091148FD@bcm.edu> Martin, I published a paper on this very topic: Sazer S, Sherwood SW. Mitochondrial growth and DNA synthesis occur in the absence of nuclear DNA replication in fission yeast. J Cell Sci. 1990 Nov;97 ( Pt 3):509-16 Let me know if you have other questions. Shelley Dr. Shelley Sazer Associate Professor Department of Biochemistry Room BCM 375A Mail Stop BCM 125 Baylor College of Medicine 1 Baylor Plaza Houston, Texas 77030 U.S.A. e-mail: ssazer at bcm.edu phone: (713) 798-4531 FAX: (713) 796-9438 -------------- Attachments -------------- An HTML attachment was scrubbed... URL: From huberman at buffalo.edu Mon Dec 3 17:05:50 2007 From: huberman at buffalo.edu (Joel Huberman) Date: Mon, 03 Dec 2007 12:05:50 -0500 Subject: [Pombelist] FACS In-Reply-To: <533334.14499.qm@web34314.mail.mud.yahoo.com> References: <533334.14499.qm@web34314.mail.mud.yahoo.com> Message-ID: Dear Martin, What mutant are you looking at, and what concentration of HU are you using? Answers to these questions are needed in order to provide a complete response to your inquiry. Wild-type fission yeast cells accumulate with an approximately haploid (1C) DNA content when incubated in high concentrations of HU (approximately 10 mM and higher). In fact, these cells have a slightly greater than 1C DNA content, because they're really in early S phase. Early origins fire in HU, and replication forks move a few kb away from those early origins before slowing down due to dNTP depletion. Even after the forks have slowed, they continue to move slowly (in wild-type cells), and their rate of movement appears to be inversely correlated with the HU concentration. Note that when fission yeast cells enter S phase in the presence of HU, the cells are initially binucleate. Although each nucleus has a DNA content of approximately 1C, the cell has a DNA content of approximately 2C. A short time (30-50 minutes) after entry into S phase, these cells go through cytokinesis and become mononucleate, with approximately 1C DNA in each cell. It is this accumulation of mononucleate cells with approximately 1C DNA content that is most noticeable when log phase fission yeast cells are incubated with HU for long times (greater than an hour). Are you sure that the peak you're describing as 2C is truly 2C and not 1C? Whether 2C or 1C, the slow rightward progression could be a consequence of either or both of the following two factors: (i) slow ongoing nuclear and mitochondrial DNA synthesis, because HU does not completely block DNA synthesis (unlikely if your HU concentration is 20 mM or greater); or (ii) changes in cell shape and size, which in turn affect the intensity of the fluorescence signal perceived by your flow cytometer. Generally, even when the DNA content of a cell remains constant, the fluorescence signal will become larger as cell size increases. In both cases, the width of the distribution will increase with time, due to heterogeneity among cells in rate of DNA synthesis and/or rate of cell size increase. I hope this information helps you. If you would be willing to send me your flow cytometry profiles by e-mail, I could attempt to provide a more educated guess. With best wishes, Joel Huberman On Dec 3, 2007, at 10:48 AM, Martin Kupiec wrote: > Hi everybody! > We are new to the field of FACS in pombe, and I have the following > observation: After adding hydroxyurea my favorite mutant stays in > G2, but slowly/surely the peak spreads to the right (to what appears > as higher and higher DNA content). Somehow this "smells" like some > sort of artifact, and not endoreduplication (I don't see a 2C peak > turn into a 4C, rather a migration of the distribution, that also > gets wider as time passes). Has anybody seen this before? It seems > as if for some reason the cells accumulate higher propidium iodide > content, although they are not particularly longer... > Any ideas/suggestions? > Thanks! > > Martin Kupiec > Dept. of Molecular Micro & Biotech, > Tel Aviv University, > Ramat Aviv 69978, Israel. > Phone: 972-3-640-9031 > FAX: 972-3-640-9407 > E-mail: martin at post.tau.ac.il > http://www.tau.ac.il/lifesci/departments/biotech/members/kupiec/kupiec.html > > > Be a better friend, newshound, and know-it-all with Yahoo! Mobile. > Try it now._______________________________________________ > Pombelist mailing list > Pombelist at sanger.ac.uk > http://lists.sanger.ac.uk/mailman/listinfo/pombelist -------------- Attachments -------------- An HTML attachment was scrubbed... URL: From nick.rhind at umassmed.edu Mon Dec 3 21:40:52 2007 From: nick.rhind at umassmed.edu (Nick Rhind) Date: Mon, 03 Dec 2007 16:40:52 -0500 Subject: [Pombelist] FACS In-Reply-To: <533334.14499.qm@web34314.mail.mud.yahoo.com> Message-ID: Hi Martin, The rightward drift you see over time as your cells elongate in the HU arrest is most likely, as you suspect, due to the accumulation of cytoplasmic background not DNA replication and is, as Shelly points out, an old problem in pombe flow cytometry. We avoid the problem by analyzing isolated nuclei instead of whole cells. This approach is not much more difficult than the standard whole-cell prep and gives much cleaner data. Our protocol is adapted from Carlson et al. (1997) Yeast 13:1329 and can be found in Forsburg and Rhind (2006) Basic methods for fission yeast. Yeast 23(3):173 The surprising result is that your favorite mutant arrests in G2; that is not a phenotype I have ever seen before. One would expect cells to arrest in early S as ~1C. As Joel points out, cells just arresting in S will be binucleate and thus have 2C DNA content. I guess it is possible that your mutant is failing to complete cytokinesis. The isolated nuclei protocol would sort that out, as would microscopic examination of your arrested cells. Another, perhaps more likely, explanation is that you are getting enough rightward drift that at the first time point your arrested cells have already drifted over from 1C, where they should be, to 2C. Good luck, Nick From tongke at bc.edu Tue Dec 4 22:26:43 2007 From: tongke at bc.edu (Kevin Tong) Date: Tue, 04 Dec 2007 17:26:43 -0500 Subject: [Pombelist] Spot assays Message-ID: Hi everyone! I am having a little bit of a technical issue when trying to perform some spots assays using strains of S.pombe on different types of solid media (i.e. YEA, EMMG, 5FOA, etc.). I find that I am unable to make consistent circular spots on my plates. Spots on some plates will spot perfectly. Some spots on other plates will hardly spread out at all and remain very small and compact. Others will "bleed" into each other or make amoeba-like shapes. I have tried drying the plates in a variety of ways (quickly, slowly, wetter, drier), but nothing seems to work very well. Does anybody know why this is happening and what I can do to generate more consistent spots? I've noticed that different types of plates will spot differently as well. Does it have something to do with the type of media being used? Thanks in advance, Kevin .???`?.. ><((((?>`?.??.><((((?> Kevin Tong Annunziato Lab Boston College, Higgins Hall Rm. 400 140 Commonwealth Ave. Chestnut Hill, MA 02467 Lab Phone: (617) 552-3110 Fax: (617) 552-2011 .???`?.. ><((((?>`?.??.><((((?> From Alison.Pidoux at ed.ac.uk Wed Dec 5 00:00:42 2007 From: Alison.Pidoux at ed.ac.uk (Alison L Pidoux) Date: Wed, 05 Dec 2007 00:00:42 +0000 Subject: [Pombelist] Spot assays In-Reply-To: References: Message-ID: <20071205000042.c546zgt1c0g8cgkw@www.staffmail.ed.ac.uk> Dear Kevin, Different solid media do produce different spot shapes / sizes. However, the dryness of the plates is the most important thing. Freshly-poured plates are a disaster. They should be dried (we use a laminar flow hood for 30-60 min) until there is no liquid around the plate and dryness lines have begun to appear on the agar. Alternatively, leave plates out on the bench for a couple of days after pouring. Using a 48-pin 'hedge-hog' will give nice small consistent spots (probably 2-3 ul transferred). If you are pipetting with a multichannel pipettor, don't use more than 5 ul per spot. Spots will soak into the agar within a couple on minutes on a perfectly dried plate. Hope this helps. Alison Quoting Kevin Tong : > Hi everyone! > I am having a little bit of a technical issue when trying to > perform some spots assays using strains of S.pombe on different > types of solid media (i.e. YEA, EMMG, 5FOA, etc.). I find that I am > unable to make consistent circular spots on my plates. Spots on > some plates will spot perfectly. Some spots on other plates will > hardly spread out at all and remain very small and compact. Others > will "bleed" into each other or make amoeba-like shapes. I have > tried drying the plates in a variety of ways (quickly, slowly, > wetter, drier), but nothing seems to work very well. Does anybody > know why this is happening and what I can do to generate more > consistent spots? I've noticed that different types of plates will > spot differently as well. Does it have something to do with the > type of media being used? > > Thanks in advance, > Kevin > > .???`?.. ><((((?>`?.??.><((((?> > Kevin Tong > Annunziato Lab > Boston College, Higgins Hall Rm. 400 > 140 Commonwealth Ave. > Chestnut Hill, MA 02467 > Lab Phone: (617) 552-3110 > Fax: (617) 552-2011 > .???`?.. ><((((?>`?.??.><((((?> > > > > > _______________________________________________ > Pombelist mailing list > Pombelist at sanger.ac.uk > http://lists.sanger.ac.uk/mailman/listinfo/pombelist > > Alison Pidoux Allshire Lab Wellcome Trust Centre for Cell Biology, Insitute of Cell Biology, The University of Edinburgh, 6.4 Swann Building Mayfield Road Edinburgh EH9 3JR -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From steven.sanders at case.edu Wed Dec 5 01:18:08 2007 From: steven.sanders at case.edu (Steven Sanders) Date: Tue, 4 Dec 2007 20:18:08 -0500 Subject: [Pombelist] Spot assays In-Reply-To: References: Message-ID: Dear Kevin, >From our experience the best way to spot pombe is to use a multichannel pipette with 5ul spots. For some unknown reason we have never been able to get consistent results with "pinners". As others have mentioned dry plates are essential. You can use a hood but we just leave the plates on the beach for at least two days after pouring. Good luck, Steven Sanders On 12/4/07, Kevin Tong wrote: > > Hi everyone! > I am having a little bit of a technical issue when trying to perform > some spots assays using strains of S.pombe on different types of solid > media (i.e. YEA, EMMG, 5FOA, etc.). I find that I am unable to make > consistent circular spots on my plates. Spots on some plates will spot > perfectly. Some spots on other plates will hardly spread out at all and > remain very small and compact. Others will "bleed" into each other or make > amoeba-like shapes. I have tried drying the plates in a variety of ways > (quickly, slowly, wetter, drier), but nothing seems to work very well. Does > anybody know why this is happening and what I can do to generate more > consistent spots? I've noticed that different types of plates will spot > differently as well. Does it have something to do with the type of media > being used? > > Thanks in advance, > Kevin > > .???`?.. ><((((?>`?.??.><((((?> > Kevin Tong > Annunziato Lab > Boston College, Higgins Hall Rm. 400 > 140 Commonwealth Ave. > Chestnut Hill, MA 02467 > Lab Phone: (617) 552-3110 > Fax: (617) 552-2011 > .???`?.. ><((((?>`?.??.><((((?> > > > > > _______________________________________________ > Pombelist mailing list > Pombelist at sanger.ac.uk > http://lists.sanger.ac.uk/mailman/listinfo/pombelist > -- Steven L. Sanders, Ph.D. Assistant Professor of Biochemistry Case Comprehensive Cancer Center Case Western Reserve University 10900 Euclid Ave. Cleveland, OH. 44106-7285 Visitors and Deliveries: Wolstein Research Bldg. 3-503 Phone: 216 235 1858 Fax: 216 368 8919 steven.sanders at case.edu http://www.case.edu/med/sanders/sanderslab/Home.html -------------- Attachments -------------- An HTML attachment was scrubbed... URL: From WXJ580 at bham.ac.uk Wed Dec 5 14:22:10 2007 From: WXJ580 at bham.ac.uk (Jikai Wen) Date: Wed, 5 Dec 2007 14:22:10 +0000 Subject: [Pombelist] FISH protocol Message-ID: <169903AA38587249812CF4B7388131DED1786D221E@mbx5> Hi Everybody, I am going to do FISH in S.pombe to check my RNA localization by four 50 nt specific probes, which have C6 amino-modification on dT and could be labelled by Cy3. I get the yeast FISH protocol from my collegue that works excellent in budding. I am wondering that what's the difference for the cell spheroplasting between fission yeast and budding yeast, simply in budding, they always use lyticase and perform it in ~10 to 15 minutes after fixation but in Nurse-lab protocol, they use zymolyase and novozyme with 90 min incubation. Does somebody have the FISH protocol in pombe? Thank you very much! Cheers, Jikai From WXJ580 at bham.ac.uk Mon Dec 10 13:28:38 2007 From: WXJ580 at bham.ac.uk (Jikai Wen) Date: Mon, 10 Dec 2007 13:28:38 +0000 Subject: [Pombelist] about FISH in S.pombe Message-ID: <169903AA38587249812CF4B7388131DED1786D2225@mbx5> Hi everybody, I am going to do FISH in S.pombe to check my RNA localization by four 50 nt specific probes, which have C6 amino-modification on dT and could be labelled by Cy3. I get the yeast FISH protocol from my collegue that works excellent in budding. I am wondering that what's the difference for the cell spheroplasting between fission yeast and budding yeast, simply in budding, they always use lyticase and zymolyase, and perform it in ~10 to 15 minutes after fixation but in Nurse-lab protocol, they use zymolyase and novozyme with 90 min incubation. Does somebody have the FISH protocol in pombe? Thank you very much! Cheers, Jikai Wen Birmingham University, Edgbaston, Birmingham, UK. B15 2TT From fneumann at mail.rockefeller.edu Thu Jan 4 18:38:08 2007 From: fneumann at mail.rockefeller.edu (Frank Neumann) Date: Thu, 4 Jan 2007 13:38:08 -0500 Subject: [Pombelist] (semi)-automated segmentation and measurement of fission yeast Message-ID: <200701041838.l04Ic8go004660@smtp1.rockefeller.edu> Dear "pombelist", I am currently trying to evaluate or develop solutions for (semi)-automated cell size measurements of S. pombe cells, based on transmission images (brightfield, phase or DIC). As an alternative, fluorescence images (e.g. lectin-FITC, or peripheral GFP marker) could be used. If you know any publicly available software or algorithm (preferably ImageJ or Matlab based) which segments and quantifies images in an entirely or partially automated way, could you please contact me. Thanks in advance for any suggestion, best regards, Frank ----------------------------------------- Frank Neumann The Rockefeller University Nurse laboratory, Box 5 1230 York Avenue New York, NY, 10021 USA phone: +1 212 327 84 76 fax: +1 212 327 84 70 email: fneumann at rockefeller.edu From rama at genome.stanford.edu Thu Jan 4 18:45:20 2007 From: rama at genome.stanford.edu (Rama Balakrishnan) Date: Thu, 4 Jan 2007 10:45:20 -0800 Subject: [Pombelist] (semi)-automated segmentation and measurement of fission yeast In-Reply-To: <200701041838.l04Ic8go004660@smtp1.rockefeller.edu> References: <200701041838.l04Ic8go004660@smtp1.rockefeller.edu> Message-ID: <41067C49-F401-4F40-8FA1-FF25003DA74E@genome.stanford.edu> Frank, You may want to check the Saccharomyces Cerevisiae Morphological Database(SCMD). They have developed methods to measure cell size. http://scmd.gi.k.u-tokyo.ac.jp/datamine/ Their paper in NAR- PMID: 14681423 Rama On Jan 4, 2007, at 10:38 AM, Frank Neumann wrote: > Dear "pombelist", > > I am currently trying to evaluate or develop solutions for (semi)- > automated > cell size measurements of S. pombe cells, based on transmission images > (brightfield, phase or DIC). As an alternative, fluorescence images > (e.g. > lectin-FITC, or peripheral GFP marker) could be used. > > If you know any publicly available software or algorithm > (preferably ImageJ > or Matlab based) which segments and quantifies images in an > entirely or > partially automated way, could you please contact me. > > Thanks in advance for any suggestion, best regards, Frank > > ----------------------------------------- > Frank Neumann > The Rockefeller University > Nurse laboratory, Box 5 > 1230 York Avenue > New York, NY, 10021 > USA > > phone: +1 212 327 84 76 > fax: +1 212 327 84 70 > email: fneumann at rockefeller.edu > > > _______________________________________________ > Pombelist mailing list > Pombelist at sanger.ac.uk > http://lists.sanger.ac.uk/mailman/listinfo/pombelist From huberman at buffalo.edu Thu Jan 4 19:45:55 2007 From: huberman at buffalo.edu (Joel Huberman) Date: Thu, 4 Jan 2007 14:45:55 -0500 Subject: [Pombelist] (semi)-automated segmentation and measurement of fission yeast In-Reply-To: <200701041838.l04Ic8go004660@smtp1.rockefeller.edu> References: <200701041838.l04Ic8go004660@smtp1.rockefeller.edu> Message-ID: <3BD3BD29-C469-4405-8D5B-6FAFC5912489@buffalo.edu> Dear Frank, Several years ago, I--together with students in my lab--developed some algorithms for measuring the DNA contents of S. pombe nuclei based on their DAPI staining intensities. The algorithms (for Image) required identification of nuclei in binucleate as well as mononucleate cells. Perhaps some of our algorithms would be helpful to you. Our algorithms are freely available at http:// asajj.roswellpark.org/huberman/Quant_Flu_Microscopy/ Quant_Flu_Micro.html. The text accompanying the algorithms hasn't been updated since 31 October, 1999, but the algorithms are as valid now as they were at that time. I hope this helps you. Sincerely yours, Joel Huberman ********************************* Dr. Joel A. Huberman Professor of Cellular & Molecular Biology Department of Cancer Biology Roswell Park Cancer Institute Elm & Carlton Streets Buffalo, NY 14263-0001 (716) 845-3047 Phone (716) 845-8126 FAX huberman at buffalo.edu http://asajj.roswellpark.org/huberman/jh.html ********************************* On Jan 4, 2007, at 1:38 PM, Frank Neumann wrote: > Dear "pombelist", > > I am currently trying to evaluate or develop solutions for (semi)- > automated > cell size measurements of S. pombe cells, based on transmission images > (brightfield, phase or DIC). As an alternative, fluorescence images > (e.g. > lectin-FITC, or peripheral GFP marker) could be used. > > If you know any publicly available software or algorithm > (preferably ImageJ > or Matlab based) which segments and quantifies images in an > entirely or > partially automated way, could you please contact me. > > Thanks in advance for any suggestion, best regards, Frank > > ----------------------------------------- > Frank Neumann > The Rockefeller University > Nurse laboratory, Box 5 > 1230 York Avenue > New York, NY, 10021 > USA > > phone: +1 212 327 84 76 > fax: +1 212 327 84 70 > email: fneumann at rockefeller.edu > > > _______________________________________________ > Pombelist mailing list > Pombelist at sanger.ac.uk > http://lists.sanger.ac.uk/mailman/listinfo/pombelist -------------- next part -------------- An HTML attachment was scrubbed... URL: From val at sanger.ac.uk Fri Jan 5 11:26:49 2007 From: val at sanger.ac.uk (Valerie Wood) Date: Fri, 05 Jan 2007 11:26:49 +0000 Subject: [Pombelist] Pombe club in Manchester/ message from Jacky Hayles Message-ID: <459E35F9.5020800@sanger.ac.uk> Dear All A number of you have not received the Manchester Pombe Club mailing so I'm sending it out again via Val's pombe list. I am going to make a new pombe club list and hopefully sort out some of these problems. So it would be very helpful to me if you could email me at the address below (just say Pombe Club) if you would like to be on the mailing list. If you are not receiving the pombe club notices it is also worth checking with your IS department to see if the message is being blocked by your firewall. Looking forward to seeing you in Manchester and sorry to those of you who have received this twice. Happy New Year Jacky Jacqueline Hayles Cell Cycle Laboratory Cancer Research UK, London Research Institute 44 Lincoln's Inn Fields London WC2A 3PX, UNITED KINGDOM Tel ::: +44 (0) 20 7269 3105 Fax ::: +44 (0) 20 7269 3258 email jacqueline.hayles at cancer.org.uk -------------- next part -------------- A non-text attachment was scrubbed... Name: pombe_2007_notice.ppt Type: application/vnd.ms-powerpoint Size: 118784 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: mcrpombeinfo.doc Type: application/msword Size: 34304 bytes Desc: not available URL: From jerry.wu at sanger.ac.uk Fri Jan 5 14:44:52 2007 From: jerry.wu at sanger.ac.uk (Jerry Wu) Date: Fri, 5 Jan 2007 14:44:52 -0000 Subject: [Pombelist] RE: automated cell size measurements of S. pombe cells Message-ID: Hi, Frank, I have some in-house Matlab codes to cope with the fully automated cell size measurement(inc. segmentation), originally developed for MitoCheck project and IVP treatment. In addition, it is worth to looking at the CellProfiler (http://www.cellprofiler.org/), a relatively new Matlab based open source. BTW, I would optimise my code for you if you would send me one of your image samples. Cheers Jerry --- \\\|/// \\ - - // ( @ @ ) .............................oOOo-(_)-oOOo............................ "Put your hand in a hot stove for a minute, and it seems like an hour. Sit with a pretty girl for an hour, and it seems like a minute. That's relativity." - Albert Einstein. .oooO ............................... ( )-- Oooo. .............................. \ ( ( ) \_) ) / (_/ Date: Thu, 4 Jan 2007 13:38:08 -0500 From: Frank Neumann To: pombelist at sanger.ac.uk Subject: [Pombelist] (semi)-automated segmentation and measurement of fission yeast Dear "pombelist", I am currently trying to evaluate or develop solutions for (semi)-automated cell size measurements of S. pombe cells, based on transmission images (brightfield, phase or DIC). As an alternative, fluorescence images (e.g. lectin-FITC, or peripheral GFP marker) could be used. If you know any publicly available software or algorithm (preferably ImageJ or Matlab based) which segments and quantifies images in an entirely or partially automated way, could you please contact me. Thanks in advance for any suggestion, best regards, Frank ----------------------------------------- Frank Neumann The Rockefeller University Nurse laboratory, Box 5 1230 York Avenue New York, NY, 10021 USA phone: +1 212 327 84 76 fax: +1 212 327 84 70 email: fneumann at rockefeller.edu From anita.tienhaara at helsinki.fi Fri Jan 12 11:08:43 2007 From: anita.tienhaara at helsinki.fi (Anita Tienhaara) Date: Fri, 12 Jan 2007 13:08:43 +0200 Subject: [Pombelist] PYFF3 Conference in Helsinki in June Message-ID: <45A7885B.5009.A8703E3@anita.tienhaara.helsinki.fi> Dear Colleagues, We are happy to welcome You to the Conference on Physiology of Yeasts and Filamentous Fungi (PYFF3) to be held in Helsinki, 13-16th of June 2007. If you are interested to be included in our mailing list, please, email anita.tienhaara at helsinki.fi . Please, visit also the conference web site http://pyff3.vtt.fi/ . The abstract dead-line is 12th of March. The conference will take place in the heart of Helsinki at Marina Congress centre. The meeting is the3rd one in a series under the Microbial Physiology section of the European Federation of Biotechnology. The previous meetings have been highly successful and appreciated by both academic and industrial audience. The conference will cover the most recent advances in various fundamental and applied aspects of the physiology of eukaryotic microbes. The topics include e.g: genomics; nutrition, signalling and tranport; physiological regulation; metabolomics and lipidomics; protein production; and metabolite production. The importance of yeasts and filamentous fungi in biorefinery research will also be addressed. We would appreciate if you could circulate this mail amongst your students and colleagues. Please, print the PYFF3 leaflet at http://pyff3.vtt.fi/leaflet.pdf for advertisement. Thank you! Our warmest welcome to Helsinki ! Prof. Merja Penttil? and Dr. Markku Saloheimo VTT Technical Research Centre of Finland -------------- next part -------------- An HTML attachment was scrubbed... URL: From onigen at my.molbio.ku.dk Tue Jan 16 11:03:58 2007 From: onigen at my.molbio.ku.dk (Olaf Nielsen) Date: Tue, 16 Jan 2007 12:03:58 +0100 Subject: [Pombelist] Postdoc position in Copenhagen Message-ID: Hi all I have a vacant postoc position in my lab. Please bring the attached add to the attention of anyone you think may be interested. Many thanks Olaf * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Olaf Nielsen, Professor, Ph.D. Department of Molecular Biology University of Copenhagen Ole Maal?es Vej 5 DK-2200 Copenhagen N Denmark tel: +45 3532 2102 fax: +45 3532 2113 email: onigen at my.molbio.ku.dk http://www.imbf.ku.dk/onigen * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * -------------- next part -------------- A non-text attachment was scrubbed... Name: postdoc.pdf Type: application/octet-stream Size: 92645 bytes Desc: not available URL: From rama at genome.stanford.edu Thu Jan 18 18:13:16 2007 From: rama at genome.stanford.edu (Rama Balakrishnan) Date: Thu, 18 Jan 2007 10:13:16 -0800 Subject: [Pombelist] Fwd: Eukaryotic Genome Annotation course at TIGR References: Message-ID: Begin forwarded message: > From: "Hannick, Linda" > Date: January 18, 2007 8:19:06 AM PST > To: "Gene Ontology" , friends at genome.stanford.edu> > Subject: Eukaryotic Genome Annotation course at TIGR > > FYI: > > > Eukaryotic Genome Annotation and Analysis Course > > TIGR is offering a new three-day course in Eukaryotic Genome > Annotation and Analysis. This course will familiarize attendees > with TIGR's eukaryotic annotation methods, tools and computational > pipeline for annotation, including our manual annotation tool > Manatee . In this class you will > learn about many of the searches, tools, and processes we use to > annotate, analyze and compare eukaryotic genomes, including a > session on GO. > > This course is aimed at researchers, post-doctoral fellows, > university faculty, students and others who desire to better > understand how genes and other features of genomes are predicted, > and how to understand and make better use of the vast amount of > information flowing from genome projects. > > Upcoming Dates for the Course > > The course is offered on the following dates at TIGR?s Rockville, > MD, US Campus: > March 6-8, 2007 > June 26-28, 2007 > > Sept. 18-20, 2007 > > > Tuition of $595.00 includes all class materials and lunch each day. > > > For more information, see the website: http://www.tigr.org/ > edutraining/training/eukaryotic_annotation.shtml, or call Anna von > Arx at 301-795-7943. > > > Thanks, > > Linda > > > ~~~~~~~~~~~~~~~~~ > Linda I. Hannick, Ph.D. > Bioinformatics Analyst > The Institute for Genomic Research (TIGR) > Rockville, MD 20850 USA > ~~~~~~~~~~~~~~~~~~~ > 301-795-7857 voice > 301-838-0227 fax > ~~~~~~~~~~~~~~~~~~~ > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From K.A.Moore at exeter.ac.uk Sun Jan 21 16:33:27 2007 From: K.A.Moore at exeter.ac.uk (Dr. Karen Moore) Date: Sun, 21 Jan 2007 16:33:27 -0000 (GMT) Subject: [Pombelist] (no subject) Message-ID: <1162.81.132.105.105.1169397207.squirrel@www.webmail.ex.ac.uk> Please check that I am on the pombelist. Thanks, Karen Dr. Karen Moore, Department of Biosciences, University of Exeter, Henry Wellcome Building for Biocatalysis Stocker Road Exeter EX4 4QD UK Phone: +44 (0)1392 262085 From wxj580 at bham.ac.uk Tue Jan 23 11:19:24 2007 From: wxj580 at bham.ac.uk (JIkai) Date: Tue, 23 Jan 2007 11:19:24 -0000 Subject: [Pombelist] Interesting Strains References: Message-ID: <004201c73ee0$565adbe0$508ebc93@adf.bham.ac.uk> Hi, I get two strains from different groups. Both of them are Leu and Ura auxotroph, but a nonessential gene was disrupted in one strain. When I culture both strains in EMM-Supplement, the gene disrupted one grows much faster than the other one. However, If they are cultured in YES, reversely, the disrupted one grows slower than the other one. Do you have the similar experience? After yeast transformation (the plasmids don't effect the cell very much, since it just contains gfp gene in pREP41), the disrupted one still grows much quicker since the colony radius could reach about 2mm in 4-5 days), but there are a lot of tiny colonies from the other strain at the same day. Moreover, it seems very hard to get larger colonies since I try to keep the plate in 30 C for ten days and the colonies sizes are no more than 2mm. But both transformants are all right since I could see obvious fluorescence in microscope. The other common thing in my transformation is that the transformants sizes are not uniform, some are good and some are very small. It is true that the sizes of colonies located in the centre of the plate are commonly less than that in the margin. Do you know how to make it better? I just very interested in this kinds of phenomenon and try to optimize my future experiment since I am fresh and haven't good experience in S. pombe. All of disscussion, speculation and suggestions are very welcome! By the way, in the 30 C fan incubater, Is it proper to use parafilm wrap the plates or not for culture the cells? Thank you very much! Cheers, Jikai Wen School of Biosciences, Birmingham University, Birmingham, UK. B15 2TT From karl.ekwall at sh.se Fri Jan 26 11:02:50 2007 From: karl.ekwall at sh.se (Karl Ekwall) Date: Fri, 26 Jan 2007 12:02:50 +0100 Subject: [Pombelist] Post-doctoral position available Message-ID: Dear all, A post-doctoral position (3 years) is now available in my laboratory to perform comparative studies of fission yeasts, worms and flies using bioinformatics as well as wet-lab approaches. The project focuses on how general controls of gene expression and genome maintenance are governed by a combination of protein-coding and non-protein-coding genes in the three groups of organisms. If you wish to apply for this position please contact me for further details (karl.ekwall at sh.se) Best regards Karl -- ******************************************************************* Dr. Karl Ekwall Associate Professor Karolinska Institutet, Dept of Biosciences & University College S?dert?rn lab web page: http://natvet.sh.se/ekwall_lab/ swedish/svensk version: http://www.novum.se/forskning_karl_ekwall.php english version: http://www.novum.se/english/forskning_karl_ekwall.php email: karl.ekwall at cbt.ki.se karl.ekwall at sh.se CONTACT DETAILS Phone: +46 8 608 4713 (office) Fax: +46 8 608 4510 Mailing address: University College S?dert?rn School of Life Sciences S-141 89 Huddinge, SWEDEN Courier Delivery adress: Alfred Nobel's All? 3 S-141 52 Huddinge, SWEDEN ******************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From val at sanger.ac.uk Wed Jan 31 14:21:34 2007 From: val at sanger.ac.uk (Valerie Wood) Date: Wed, 31 Jan 2007 14:21:34 +0000 Subject: [Pombelist] Announcement: Move from contigs to chromosomes in GeneDB Message-ID: <45C0A5EE.1080603@sanger.ac.uk> Dear All, In order to improve data transfer and maintenance (both within and between databases) the contig data in GeneDB has been merged into 3 chromosomes and the remaining 4 gaps filled by 100 N's. Major consequences of this move: 1. Feature coordinates have changed. GeneDB now presents the new 'chromosomes' instead of the contigs. This means that the feature coordinates represented i) on the gene pages, ii) in Artemis and iii) in GBrowse have changes to the new chromosomal coordinates. 2. Public nucleotide sequence database (EMBL/GenBank/DDBJ) updates and new accession numbers. The updated chromosome entries will be resubmitted to EMBL shortly and these sequences will be assigned new accession numbers. The old accession numbers previously assigned to the individual cosmid entries will become secondary accession numbers to the new chromosome entries, and the old cosmid entries will be suppressed. The new accession numbers for the chromosome entries will be CU329670 chromosome 1 CU329671 chromosome 2 CU329672 chromosome 3 These new entries will match the current EMBL/GenBank/DDBJ chromosomes (although if you have used older data for your analysis, you may need to incorporate the changes in 6. below) 3. Contig files are deprecated. The old 'contigs' will no longer be maintained or made available for download from the ftp site. Older versions will still be available from the archive. The chromosome sequence and annotation will be available for download. 4. You can "Web publish" your own genome wide data using the GBrowse genome viewer. The transition to chromosomes instead of contigs should make it much easier for groups to upload their own annotations which are based on chromosomal data into the GBrowse genome viewer. You can upload your own list of sequence features and annotations (for example microarray tiling path data, promoters, replication origins) to GBrowse and view them in the context of the genome. Uploaded annotations will persist until you edit them or delete them. Your annotations are private and will not be seen by other individuals. If you choose to, you can publish your annotations and share them with your colleagues. The instructions for adding tracks to GBrowse are here: http://www.genedb.org/perl-gb/gbrowse/S.pombe/?help=annotation 5. Gap Status /Gap size changes The new chromosomes have gaps filled by 100 N's instead of the 1000 N's in previous Sanger versions. This is consistent with with the EMBL/GenBank/DDBJ convention for sequence gaps (the existing fission yeast chromosome sequences in EMBL, GenBank and DDBJ have 100 N's in the gaps) The fission yeast genome sequence data is still in 7 contigs (contains 4 sequence gaps). The current status and estimated gap sizes are described here: http://www.sanger.ac.uk/Projects/S_pombe/status.shtml 6. Sequence alterations Groups who have based their analysis on previous versions of the data may need to update their sequence data, or re run their analyses to take account of small sequence changes to make their data match the current assembly. All changes to the sequence since July 2003, and any future changes will be recorded here http://www.sanger.ac.uk/Projects/S_pombe/sequence_updates.shtml Let me know if you have any questions, Val -- --------------------------------------------------------------------------- Valerie Wood Tel: 01223 496909 S. pombe Genome Project Fax: 01223 494919 Wellcome Trust Sanger Institute email: val at 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 From val at sanger.ac.uk Thu Feb 1 16:18:40 2007 From: val at sanger.ac.uk (Valerie Wood) Date: Thu, 01 Feb 2007 16:18:40 +0000 Subject: [Pombelist] Move from contigs to chromosomes in GeneDB/data downloading Message-ID: <45C212E0.4010306@sanger.ac.uk> Just to clarify: Data downloaded for individual CDS/genes from GeneDB using the list download: http://www.genedb.org/genedb/idListForm.jsp?defOrg=pombe (either user defined, or as the result of a Boolean query) is exactly the same as before. The only difference you should notice is that the genomic coordinates of sequences have changed. The changes described for the downloadable data apply to raw data you can download from the ftp site from here: http://www.sanger.ac.uk/Projects/S_pombe/download.shtml Previously cosmid and contig sequences were made avaiable to download, these are now replaced by chromosomes. -- --------------------------------------------------------------------------- Valerie Wood Tel: 01223 496909 S. pombe Genome Project Fax: 01223 494919 Wellcome Trust Sanger Institute email: val at 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 From hohmann at gmm.gu.se Wed Feb 7 08:51:51 2007 From: hohmann at gmm.gu.se (Stefan Hohmann) Date: Wed, 07 Feb 2007 09:51:51 +0100 Subject: [Pombelist] yeast systems biology course Message-ID: <45C9A137.11269.AFAAD72@hohmann.gmm.gu.se> International Course in Yeast Systems Biology June 4-21, G?teborg, Sweden This is a FEBS Course (www.febs.org). This will be a three week intense hand-on course with both experimental and theoretical studies, guided by top scientists in the field. The course is intended for advanced PhD students and post-docs. For details see the attached folder and the website at www.icysb.org Deadline for application is February 28. Prof. Stefan Hohmann Department of Cell and Molecular Biology G?teborg University Box 462 SE-40530 G?teborg, Sweden (street address: Medicinaregatan 9E, SE-41390 G?teborg) Tel: +46 31 360844; Fax: +46 31 7862525 e-mail: hohmann at gmm.gu.se http://www.gmm.gu.se/groups/hohmann Yeast Systems Biology Course: http://www.icysb.org Systems Biology Conference 2008: http://www.icsb-2008.org For mails concerning journals only use the corresponding addresses: editor at current-genetics.se editor at molecular-genetics-genomics.se editor at topics-current-genetics.se -------------- next part -------------- An HTML attachment was scrubbed... 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Name: ICYSB_folder_febs.pdf Type: application/octet-stream Size: 542083 bytes Desc: not available URL: From onigen at my.molbio.ku.dk Fri Feb 9 12:57:09 2007 From: onigen at my.molbio.ku.dk (Olaf Nielsen) Date: Fri, 09 Feb 2007 13:57:09 +0100 Subject: [Pombelist] Registration: Fourth International Fission Yeast Meeting Message-ID: Dear all, This mail just to inform you that registration for the Fourth International Fission Yeast Meeting, Copenhagen, June 11-16, is now open at www.pombe.dk Please note that the deadline for abstract submission and for registration at reduced fee is March 15. Looking forward to seeing you in Copenhagen. Best regards, Olaf Nielsen, Organizer * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Olaf Nielsen, Professor, Ph.D. Department of Molecular Biology University of Copenhagen Ole Maal?es Vej 5 DK-2200 Copenhagen N Denmark tel: +45 3532 2102 fax: +45 3532 2113 email: onigen at my.molbio.ku.dk http://www.imbf.ku.dk/onigen * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * From Jurg at sanger.ac.uk Tue Feb 13 18:13:03 2007 From: Jurg at sanger.ac.uk (Jurg Bahler) Date: Tue, 13 Feb 2007 18:13:03 -0000 Subject: [Pombelist] Course: Genome-wide approaches with fission yeast Message-ID: <0526C4B4E593154B86E6A8651913C28DB9136B@exchsrv2.internal.sanger.ac.uk> Dear All, We are organizing a Wellcome Trust Advanced Course 'Genome-wide approaches with fission yeast' from 1-7 October 2007 in Hinxton. This hands-on course is for colleagues who would like to use large-scale methods for their research. The attendance is limited to 16-18 people, and selection will be based on the applications. More details are available here: http://www.wellcome.ac.uk/doc_WTX033405.html Cheers, -Jurg --- J?rg B?hler, Ph.D. Wellcome Trust Sanger Institute Hinxton Cambridge CB10 1HH UK P: +44(0)1223-496948 F: +44(0)1223-496802 W: http://www.sanger.ac.uk/PostGenomics/S_pombe/ From anita.tienhaara at helsinki.fi Mon Feb 19 12:07:16 2007 From: anita.tienhaara at helsinki.fi (Anita Tienhaara) Date: Mon, 19 Feb 2007 14:07:16 +0200 Subject: [Pombelist] PYFF3 Conference in Helsinki in June Message-ID: <45D9AF14.17001.F88520C@anita.tienhaara.helsinki.fi> Dear Colleagues, We areveryhappy to welcome You to the Conference on PHYSIOLOGY OF YEASTS AND FILAMENTOUS FUNGI (PYFF3) to be held in Helsinki, 13-16th of June 2007.The dead-line for abstract submission, early registration and student grant applications is 10th of April.Please,REGISTER NOW and visit the conference web site athttp://pyff3.vtt.fi/ .We haveextended the abstract dead-line from that previously announced. Note thatabstracts arriving after the10th of Aprilcannot any more be considered asoral presentations. For further information,please email anita.tienhaara at helsinki.fi . The conference will take place in the heart of Helsinki at Marina Congress centre. The meeting is the3rd one in a series under the Microbial Physiology section of the European Federation of Biotechnology. The previous meetings have been highly successful and appreciated by both academic and industrial audience.The conference will cover the most recent advances in various fundamental and applied aspects of the physiology of eukaryotic microbes. The topics include e.g: genomics; nutrition, signalling and tranport; physiological regulation; metabolomics and lipidomics; protein production; and metabolite production. The importance of yeasts and filamentous fungi in biorefinery research will also be addressed. We would appreciate if you could circulate this mail amongst your students and colleagues. Please, print the PYFF3 leaflet athttp://pyff3.vtt.fi/leaflet.pdf foradvertisement. Thank you! Our warmest welcome to Helsinki ! Prof. Merja Penttil? and Dr. Markku Saloheimo VTT Technical Research Centre of Finland From geetanjali_rajyee at yahoo.com Wed Feb 21 12:57:39 2007 From: geetanjali_rajyee at yahoo.com (geetanjali sundaram) Date: Wed, 21 Feb 2007 04:57:39 -0800 (PST) Subject: [Pombelist] s.pombe nuclear extracts Message-ID: <582320.13891.qm@web52215.mail.yahoo.com> Dear pombelist members, Can anyone of you please suggest a protocol for preparation of small scale nuclear extracts from S.pombe . i shall be very grateful for you suggestions Thanks and regards geetanjali Sundaram University of Calcutta INDIA --------------------------------- Expecting? Get great news right away with email Auto-Check. Try the Yahoo! Mail Beta. -------------- next part -------------- An HTML attachment was scrubbed... URL: From f.hochstenbach at amc.uva.nl Wed Feb 21 13:35:09 2007 From: f.hochstenbach at amc.uva.nl (Frans Hochstenbach) Date: Wed, 21 Feb 2007 14:35:09 +0100 Subject: [Pombelist] PhD student and postdoc positions in Amsterdam Message-ID: Dear all, Ben Distel and I have two PhD positions and one postdoc position available at the University of Amsterdam, as part of an EU-funded Marie Curie Research Training Network. One PhD student will study the SH3 protein-interaction network in S. pombe, while the other will analyze the SH3 protein-interaction network in Candida albicans. The postdoc will focus on the identification of SH3 partner proteins using mass spectrometry. Please bring the attached poster to the attention of suitable candidates who maybe interested. Many thanks, Frans -- =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Frans Hochstenbach, Ph.D. Department of Medical Biochemistry Academic Medical Center, Room K1-260 University of Amsterdam Meibergdreef 15 1105 AZ AMSTERDAM The Netherlands Phone (NL:31) (20) 5665137 Fax (NL:31) (20) 6915519 Email f.hochstenbach at amc.uva.nl =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= -------------- next part -------------- A non-text attachment was scrubbed... Name: Positions_Amsterdam.pdf Type: application/pdf Size: 336711 bytes Desc: not available URL: From yeast2007 at meetingplanners.com.au Thu Feb 22 06:49:26 2007 From: yeast2007 at meetingplanners.com.au (Yeast 2007) Date: Thu, 22 Feb 2007 17:49:26 +1100 Subject: [Pombelist] Yeast 2007: Early Bird Registration Closes in 1 Week Message-ID: If you cannot view the html email, go to http://www.meetings.com.au/yeast/register.html XXIII International Conference on Yeast Genetics & Molecular Biology 1-6 July 2007 Melbourne, Australia Early Bird Registration Closes in 1 Week. Register by 1st Mark to Save Visit the website to register at www.yeast2007.org Don't forget to submit your abstract by 1st April 2007 http://www.yeast2007.org/program_abstracts.php Register Now and Save > http://www.yeast2007.org/register.php For more information visit www.yeast2007.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From yeast2007 at meetingplanners.com.au Fri Feb 23 07:11:51 2007 From: yeast2007 at meetingplanners.com.au (Yeast 2007) Date: Fri, 23 Feb 2007 18:11:51 +1100 Subject: [Pombelist] Yeast 2007: Early Bird Registration Closes in 1 Week Message-ID: If you cannot view the html email, go to http://www.meetings.com.au/yeast/register.html XXIII International Conference on Yeast Genetics & Molecular Biology 1-6 July 2007 Melbourne, Australia Early Bird Registration Closes in 1 Week. Register by 1st Mark to Save Visit the website to register at www.yeast2007.org Don't forget to submit your abstract by 1st April 2007 http://www.yeast2007.org/program_abstracts.php Register Now and Save > http://www.yeast2007.org/register.php For more information visit www.yeast2007.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From R.M.Holmes at sussex.ac.uk Fri Feb 23 14:59:46 2007 From: R.M.Holmes at sussex.ac.uk (Rosalind Holmes) Date: Fri, 23 Feb 2007 14:59:46 +0000 Subject: [Pombelist] RIKEN ORFeome Plasmids and Gateway System Vectors Message-ID: <5C23B3B3DCE6BAD9343F0013@gcpc106.gdsc.susx.ac.uk> Hello :-) Does anyone have any experience with the pDONR201 plasmids available from RIKEN? There appear to be mutations in many of the ORFs they have cloned into pDONR, but in the paper (Matsuyama et al, Nature Biotechnol. 2006; 24:841-7) they imply that they have only allowed mutations that are "supposed to be missense changes" and those in introns that are "supposed to not affect splicing". Any further information/experience with respect to this issue would be very helpful. In addition, does anyone have any experience with the Invitrogen Gateway System compatible "pDUAL" vectors they have created? Thank you in advance :-) Roz. +++++++++++++++++++++++++++++++++++++++++ Rosalind Holmes, MSci (Hons) G4.15 Genome Damage and Stability Centre, Science Park Road, University of Sussex, Falmer, Brighton, East Sussex, United Kingdom, BN1 9RQ. Email: R.M.Holmes at sussex.ac.uk Office: +44 (0)1273 67 8976 Lab: +44 (0)1273 87 7170 Fax: +44 (0)1273 67 8121 Webpage: http://www.sussex.ac.uk/gdsc/profile180072.html My Labs: http://www.sussex.ac.uk/gdsc/1-4-1.html http://www.sussex.ac.uk/gdsc/1-4-2.html From Marc_Buehler at hms.harvard.edu Fri Feb 23 15:25:20 2007 From: Marc_Buehler at hms.harvard.edu (Buehler, Marc ) Date: Fri, 23 Feb 2007 10:25:20 -0500 Subject: [Pombelist] Ura4 antibody, orotidine 5'-phosphate decarboxylase activity assay Message-ID: <34D3E13342E7144D8E1A05032097A27A086F5F94@MAILSERVER02.MED.HARVARD.EDU> Hello, is there anyone aware of an antibody which was raised against Ura4 (orotidine 5'-phosphate decarboxylase) or an enzymatic assay to test for orotidine 5'-phosphate decarboxylase activity? Marc B?hler Marc B?hler, PhD Harvard Medical School Department of Cell Biology LHRRB room 517 240 Longwood Avenue Boston, MA 02115 Tel.: 617-432-1248 Fax.:617-432-5596 -------------- next part -------------- An HTML attachment was scrubbed... URL: From nick.rhind at umassmed.edu Thu Mar 1 16:31:17 2007 From: nick.rhind at umassmed.edu (Nick Rhind) Date: Thu, 01 Mar 2007 11:31:17 -0500 Subject: [Pombelist] Automated annotation of the Schizosaccharomyces japonicus genome sequence Message-ID: The initial automated gene annotation of the Schizosaccharomyces japonicus genome is now available. The annotation, containing 5172 gene models, was produced using a combination of gene finding algorithms based on coding capacity, conservation and synteny with the pombe genome. The japonicus annotated assembly is available at http://www.broad.mit.edu/annotation/genome/schizosaccharomyces_japonicus.2/H ome.html The site includes information about the sequencing, assembly and annotation of the genome, along with tools for downloading genome sequences, BLASTing against the genome assembly, and searching and browsing for features of the genome. The genome was sequenced at The Broad Institute as part of the Fungal Genome Initiative, a project funded by NHGRI. The genome of Schizosaccharomyces octosporus is currently being sequenced. Once the octosporus genome is assembled and machine annotated, the annotations of two genomes will be manually edited in collaboration with the fission yeast community. Annotations will be released as they become available. Please share this release notice with anyone you think may be interested. Sincerely, Chad Nusbaum Nick Rhind From yeast2007 at meetingplanners.com.au Fri Mar 2 11:52:40 2007 From: yeast2007 at meetingplanners.com.au (Yeast 2007) Date: Fri, 02 Mar 2007 22:52:40 +1100 Subject: [Pombelist] Yeast 2007: Early Bird Registration Extended to 1 April 2007 Message-ID: Access this link If you cannot view this email properly http://www.meetings.com.au/yeast/4th.htm EARLY BIRD REGISTRATION HAS BEEN EXTENDED TO 1ST APRIL 2007 This date will coincide with the deadline for call for abstracts Don't miss out on the leaders of our industry. Some of them are featured here: Dr Paul Chambers, Australia Generating novel wine yeasts using traditional and GM approaches Theme: Yeast Biotechnology Dr Edda Kipp, Germany Modeling of Yeast Cell Stress Response Theme: Metabolism and Metabolomics Professor Susan Liebman, USA Prion-prion interactions in yeast Theme: Yeast models for human disease and ageing Professor Mitsuhiro Yanagida, Japan Metabolic aspects of the chromosome segregation and cell cycle control in fission yeast Theme: Cell growth, division and differentiation Don't miss the opportunity to be listed along side these speakers. Deadline for submission is 1 April. For more information and to register for the conference please click on the following link: www.yeast2007.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From jvirgin at u.washington.edu Fri Mar 2 16:13:52 2007 From: jvirgin at u.washington.edu (jvirgin at u.washington.edu) Date: Fri, 2 Mar 2007 08:13:52 -0800 (PST) Subject: [Pombelist] remove from mailing list Message-ID: Please remove me from the mailing list. Thank you. Jeff Virgin jvirgin at u.washington.edu From kasano at ksu.edu Fri Mar 2 17:05:23 2007 From: kasano at ksu.edu (Katsura Asano) Date: Fri, 2 Mar 2007 11:05:23 -0600 Subject: [Pombelist] RNA and Origins of Life on April 27-28, 2007 Message-ID: <62f14a6f18aa2ddadb50554c6a058b04@ksu.edu> Dear S. pombe scientists, I am happy to announce that a mini-syposium on RNA and Origins of Life takes place on April 27 and 28 on K-state Campus. I invited Norman Pace, the exert on ribozyme RNase P, Ron Breaker, a pioneer on riboswich studeies, and Harry Noller, who is the leader of ribosome studies. I also invited Mike Russell who hypothesizes the origin of life at alkaline hydrothermal vents. I understand that most of you do not work directly on RNA, but I wish this to be informative to anybody working on gene regulation at the posttranscriptional level. I also understand that most of you are away from the mid-West area of the United States, but if you wish to coordinate your travel with another meeting during the overlapping period, I would be happiest to help you find the best flight into and the lodging within my town of Manhattan, Kansas. I noted that 2007 Experimental Biology Meeting takes place in Washington DC, right after this symposium. The registration website is ready and the processing is straightforward. http://www.phys.ksu.edu/origins/symposium.htm Best regards, Katsura Katsura Asano Associate Professor 258 Chalmers Hall Division of Biology Kansas State University Manhattan, KS 66506, USA Tel: 785-532-0116 Fax 785-532-6653 http://www.ksu.edu/biology/bio/faculty/asano/asano.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 1451 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Sympo-letter-fin.doc Type: application/msword Size: 420352 bytes Desc: not available URL: From onigen at my.molbio.ku.dk Thu Mar 8 21:09:19 2007 From: onigen at my.molbio.ku.dk (Olaf Nielsen) Date: Thu, 8 Mar 2007 22:09:19 +0100 Subject: [Pombelist] Pombe conference deadline coming up in a week Message-ID: <46FCB0B6F9F3F64D85EB1F6713FC2D0A044F5E@dkbiocs01.bioc.local> Hello everyone, I should like to remind you that the abstract submission deadline for the Fourth International Fission Yeast Meeting is now only one week ahead. March 15 is also the last day for registration at a reduced fee. Please read more details at the conference web-site: www.pombe.dk Best regards, Olaf * * * * * * * * * * * * * * * * * * * * * * * * * Olaf Nielsen, Professor, Ph.D. Department of Molecular Biology University of Copenhagen Ole Maal?es Vej 5 DK-2200 Copenhagen N Denmark tel: +45 3532 2102 fax: +45 3532 2113 email: onigen at my.molbio.ku.dk http://www.imbf.ku.dk/onigen * * * * * * * * * * * * * * * * * * * * * * * * * -------------- next part -------------- An HTML attachment was scrubbed... URL: From forsburg at usc.edu Fri Mar 9 16:45:43 2007 From: forsburg at usc.edu (SLForsburg) Date: Fri, 09 Mar 2007 08:45:43 -0800 Subject: [Pombelist] ade6 alleles: your help requested Message-ID: <5A848F08-E126-4618-A8A3-12EF15395BB3@usc.edu> Hi all, I am trying to update our list of ade6 alleles. Please, can you check it out at http://www-rcf.usc.edu/~forsburg/ plasmids.html#ade6mut If you have additions or corrections, let me know. Also, there is some disagreement about what the mutation in ade6-M210 really is; I've heard several versions. I'd like to try to iron that out. Cheers susan {} {} {} {} {} {} {} {} {} {} {} {} {} {} S L Forsburg PhD, Professor University of Southern California Molecular & Computational Biology Ray R Irani Hall 1050 Childs Way, MCB 201B Los Angeles, CA 90089-2910 vox: 213-740-7342 fax: 213-740-8631 forsburg at usc.edu www.pombe.net -------------- next part -------------- An HTML attachment was scrubbed... URL: From geetanjali_rajyee at yahoo.com Tue Mar 13 06:49:57 2007 From: geetanjali_rajyee at yahoo.com (geetanjali sundaram) Date: Mon, 12 Mar 2007 23:49:57 -0700 (PDT) Subject: [Pombelist] Cds1 antibodies Message-ID: <322976.39972.qm@web52214.mail.yahoo.com> Hi all!, Does anyone have any experience with immunoprecipitating Cds1 using human Chk2 antibodies. If so can you please me know if it works fine? Thanking all in anticipation Geetanjali Sundaram SRF INDIA --------------------------------- Don't pick lemons. See all the new 2007 cars at Yahoo! Autos. -------------- next part -------------- An HTML attachment was scrubbed... URL: From Jurg at sanger.ac.uk Wed Mar 21 19:52:54 2007 From: Jurg at sanger.ac.uk (Jurg Bahler) Date: Wed, 21 Mar 2007 19:52:54 -0000 Subject: [Pombelist] Postdoc Position available Message-ID: <37340E68029F5842A315DDF21075A80207604E@exchsrv2.internal.sanger.ac.uk> Dear Friends and Colleagues, Please bring the attached advert for a Postdoc Position in my lab to the attention of candidates who may be interested. Many thanks, -J?rg B?hler We use fission yeast as a model organism and apply various genome-wide approaches for systems-level analyses of gene expression regulation at multiple levels, ranging from transcription to translation. We are seeking a motivated colleague to work with us in this exciting field. You are a highly motivated and independent biologist with interests in gene expression control and regulatory processes driving cell growth and quiescence. Candidates with experience in large-scale yeast genetics and/or proteomic approaches are particularly encouraged to apply. You should also have experience or a strong interest in computational approaches. Alternatively, you have a keen interest and skills at the interface of biology and computing to apply computational and modelling approaches to integrate different microarray and other genomic data. You will be involved in uncovering new biological relationships from our large-scale datasets to provide insight into regulatory mechanisms and networks. Previous experience in microarray data mining would be an advantage. You will also provide some computer support and have the opportunity to work closely with wet-lab biologists. Specific research projects will depend on the interests and expertise of the successful candidate as well as on ongoing projects in the lab. This position is funded by Cancer Research UK and is offered on open contract. To find out more about our work please refer to: http://www.sanger.ac.uk/PostGenomics/S_pombe/ Informal enquiries can be made to J?rg B?hler: jurg at sanger.ac.uk Salaries are highly competitive and commensurate with experience. Benefits include 25 days annual leave, final salary pension scheme, optional private healthcare, permanent disability insurance, life assurance, childcare voucher scheme, on-site restaurant, caf?, gym and active sports and social scene. To apply please send a full CV including a list of publications and the names and addresses of three referees, together with a cover letter to: jurg at sanger.ac.uk by 30 April 2007. --- J?rg B?hler, Ph.D. Wellcome Trust Sanger Institute Hinxton Cambridge CB10 1HH UK P: +44(0)1223-496948 F: +44(0)1223-496802 W: http://www.sanger.ac.uk/PostGenomics/S_pombe/ -------------- next part -------------- A non-text attachment was scrubbed... Name: PostdocAdvert.pdf Type: application/octet-stream Size: 70218 bytes Desc: PostdocAdvert.pdf URL: From saeeda04 at yahoo.com Thu Mar 22 08:57:29 2007 From: saeeda04 at yahoo.com (saeeda) Date: Thu, 22 Mar 2007 01:57:29 -0700 (PDT) Subject: [Pombelist] Re: Pombelist Digest, Vol 21, Issue 3 Message-ID: <20070322085729.91221.qmail@web51801.mail.re2.yahoo.com> Hello, Will there be any DNA damage meetings going on? Saeeda --------------------------------- Now that's room service! Choose from over 150,000 hotels in 45,000 destinations on Yahoo! Travel to find your fit. -------------- next part -------------- An HTML attachment was scrubbed... URL: From akihisa at riken.jp Wed Apr 4 07:56:02 2007 From: akihisa at riken.jp (Akihisa Matsuyama) Date: Wed, 4 Apr 2007 15:56:02 +0900 Subject: [Pombelist] S. pombe Postgenome Database Server Message-ID: <3D9642A9-CBD9-434B-87DB-20BD1E90E905@riken.jp> Dear all, We are very sorry, but now our server (http://cgl.riken.go.jp/) was down because of mechanical problems. So, it is closed for repairs. But it will take some time before network restoration. If you have a request for ORFeome clones or S. pombe expression plasmids, please visit the RIKEN BioResource Center (BRC) website (http://www.brc.riken.jp/lab/dna/en/yoshidayeast_en.html). You can find the clone ID of your interest if you download the supplementary table 6 from the Nature Biotechnology website (http:// www.nature.com/nbt/journal/v24/n7/suppinfo/nbt1222_S1.html). Several Gateway-compatible vectors are also available from BRC. I thank you for your cooperation in this matter. Best regards, Matsu *** Akihisa Matsuyama, Ph.D Chemical Genetics Laboratory, RIKEN Hirosawa 2-1, Wako-shi, Saitama, 351-0198 TEL: +81-48-462-1335 FAX: +81-48-462-1336 *** From anthony.wright at sh.se Thu Apr 5 12:48:29 2007 From: anthony.wright at sh.se (Anthony Wright) Date: Thu, 5 Apr 2007 13:48:29 +0200 Subject: [Pombelist] Postdoctoral vacancy on transcription factors Message-ID: Dear colleagues Please note the attached vacancy for a Postdoctoral Research Assistant. regards Tony Postdoctoral Research Assistant Position available to study the molecular mechanisms of evolutionary adaptation. The successful applicant will form part of a multidisciplinary programme in which molecular biologists, developmental biologists and ecologists interact. The successful applicant will have excellent skills in PCR and other central molecular biology techniques. Furthermore, he/she will have an interest in multidisciplinary approaches to complex biological problems and will be able to contribute to the different biological areas within the project. The project will test whether genes encoding transcription factors are preferred targets for adaptive mutations during evolutionary diversification. Approaches in the project involve adaptation experiments in yeast as well as DNA sequence analysis of genetic polymorphisms in morphologically different fish and plant populations. Previous experience of work with transcription factors, larger-scale sequencing projects, DNA microarrays, bioinformatics and yeast molecular biology would be an advantage. It is expected that the successful applicant will have completed their PhD studies within the last 5 years. The project will be carried out at S?dert?rns H?gskola, a new University College located in Flemingsberg, 15 km south of central Stockholm. S?dert?rns H?gskola shares its campus with the Karolinska Institute, the Royal Institute of Technology and the Karolinska Hospital. The position is for a period of 2-3 years and is available immediately. For more information, contact Prof. Anthony Wright +46(0)86084708 or Ass. Prof. Mats Grahn +48(0)860847. Applications containing curriculum vitae, publication list and the names of two referees should be sent to Prof Anthony Wright at the School of Life Sciences - anthony.wright at sh.se, not later than April 30th. Anthony Wright, Ph.D. Professor of Molecular Biology School of Life Sciences, S?dert?rns University College Unit for Biological Model Systems, Department of Biosciences and Nutrition, Karolinska Institute Mailing address: School of Life Sciences S?dert?rns H?gskola S-141 89 Huddinge Sweden +46 8 6084708 Visiting address: Alfred Nobels All? 7 http://natvet.sh.se/wright_lab/ ? -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: postdoc advert Moast?d.doc Type: application/octet-stream Size: 54272 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From akihisa at riken.jp Tue Apr 10 10:17:21 2007 From: akihisa at riken.jp (Akihisa Matsuyama) Date: Tue, 10 Apr 2007 18:17:21 +0900 Subject: [Pombelist] S. pombe ORF clones and plasmids In-Reply-To: <3D9642A9-CBD9-434B-87DB-20BD1E90E905@riken.jp> References: <3D9642A9-CBD9-434B-87DB-20BD1E90E905@riken.jp> Message-ID: <42EC241C-7050-4CC7-9065-0C3AABA89078@riken.jp> Dear all, Thank you for your interest in our S. pombe ORF clones and plasmids. We already have several inquiries about them. Actually, all clones were constructed in our study (Nat Biotech 24, 841-7). However, since it is such a job for us to send them, BRC provides these clones on our behalf. BRC is independent from our department (we are not in the RIKEN BRC archive). So, please visit the BRC website (http://www.brc.riken.jp/lab/dna/en/ yoshidayeast_en.html) and request the clone(s) of your interest according to their instructions. Guidance for clone request: http://www.brc.riken.jp/lab/dna/en/ furnish.html Thank you for your cooperation. Best regards, Matsu On 2007/04/04, at 15:56, Akihisa Matsuyama wrote: > Dear all, > > We are very sorry, but now our server (http://cgl.riken.go.jp/) was > down because of mechanical problems. > So, it is closed for repairs. But it will take some time before > network restoration. > If you have a request for ORFeome clones or S. pombe expression > plasmids, please visit the RIKEN BioResource Center (BRC) website > (http://www.brc.riken.jp/lab/dna/en/yoshidayeast_en.html). > You can find the clone ID of your interest if you download the > supplementary table 6 from the Nature Biotechnology website (http:// > www.nature.com/nbt/journal/v24/n7/suppinfo/nbt1222_S1.html). > Several Gateway-compatible vectors are also available from BRC. > I thank you for your cooperation in this matter. > > Best regards, > > Matsu > > _______________________________________________ > Pombelist mailing list > Pombelist at sanger.ac.uk > http://lists.sanger.ac.uk/mailman/listinfo/pombelist > *** Akihisa Matsuyama, Ph.D Chemical Genetics Laboratory, RIKEN Hirosawa 2-1, Wako-shi, Saitama, 351-0198 TEL: +81-48-462-1335 FAX: +81-48-462-1336 E-mail: akihisa at riken.jp *** From maraiar at exchange.nih.gov Thu Apr 12 14:56:51 2007 From: maraiar at exchange.nih.gov (Rich Maraia) Date: Thu, 12 Apr 2007 09:56:51 -0400 Subject: [Pombelist] modern mutation mapping Message-ID: >I was wondering if anyone can reccommend a modern strategy >(including use of microarrays or possibly a large scall sequencing >strategy) to map mutations in individual S. pombe mutants. Members >of my lab have isolated and characterized new mutants in RNA >processing and are about to embark on mapping them and isolating the >gene(s) responsible. > As you may know, Maitreya J Dunham , uses dense tiling arrays for mapping mutations in S. cerevisiae mutants. She has described two different approaches, a straight hybridization comparison of parent and mutant strains that reveal point mutations, and a bulk segregant analysis also using the tiling arrays. Thank you. -- Richard J. Maraia, M.D. Captain, US Public Health Service, Commissioned Corps Chief, Section on Molecular and Cell Biology Intramural Research Program 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 From clemoal at esf.org Tue Apr 17 11:14:36 2007 From: clemoal at esf.org (Corinne Wininger - Le Moal) Date: Tue, 17 Apr 2007 12:14:36 +0200 Subject: [Pombelist] Comparative Genomics of Eukaryotic Microorganisms, Spain, October 2007 Message-ID: CALL FOR APPLICATIONS Dear Sir or Madam, Please find below information on an ESF Research Conference which may be of particular interest to you: ESF-EMBO Symposium Comparative Genomics of Eukaryotic Microorganisms: Eukaryotic Genome Evolution Hotel Eden Roc, Sant Feliu de Guixols (Costa Brava), Spain 20-25 October 2007 Chaired by: Edward J. Louis (University of Nottingham, UK) & Teun Boekhout (Centraalbureau voor Schimmelcultures, NL) Europe has been at the forefront of both eukaryotic microbial genome sequencing as well as the analysis and comparison of these genomes. The first eukaryote sequenced, the budding yeast Saccharomyces cerevisiae, laid the foundation in European for the new post-genomic era where we are dealing with this wealth of information. Many of these organisms are models for particular biological processes, others are used in industry and many are pathogens of plants, animals and humans. In this conference we bring together the experts from around Europe and the rest of the world to meet and discuss with interested participants the current state of and future of comparative genomics. There will be opportunities for participants to present both short talks, as well as posters, which will be conducted interactively with plenty of time reserved for questions and discussions. In addition there will be interactive workshops on databases and bioinformatics at three sessions. Scientific programme and application form accessible on-line through www.esf.org/conferences/07239. Closing date for application (& for abstract submission): 1 August 2007. Some grants will be available for young researchers to cover the conference fee and possibly part of the travel costs. Grant requests should be made by ticking appropriate field(s) in the paragraph "Grant application" of the application form (Ctrl + Click to follow the link). ESF Contact: Mrs. Anne Blondeel-Oman (ablondeel at esf.org). Kind regards, Corinne Wininger Publicity Officer - ESF Communications Unit European Science Foundation - Communications Unit 1 quai Lezay-Marn?sia, BP 90015 67080 Strasbourg Cedex, France Phone: +33 (0)388 76 21 50 Fax: +33 (0)388 76 71 80 clemoal at esf.org www.esf.org/conferences -------------- next part -------------- An HTML attachment was scrubbed... URL: From onigen at my.molbio.ku.dk Tue May 15 17:33:50 2007 From: onigen at my.molbio.ku.dk (Olaf Nielsen) Date: Tue, 15 May 2007 18:33:50 +0200 Subject: [Pombelist] Fourth International Fission Yeast Meeting, Copenhagen June 11-16 Message-ID: Dear all, I am happy to inform you that the programme for the upcoming Copenhagen fission yeast meeting is now available at: http://www.pombe.dk/programme.aspx The 10 plenary sessions host 73 speakers. You can download the abstracts for all the talks from the web-site. In addition some 200 abstracts will be presented in the three poster sessions. Some of these will also be selected for an oral presentation in one of the six workshops. The number of participants has now passed 350. If you have not yet registered, this is still possible at www.pombe.dk . There is no official closing date. However, if you plan to attend, we should very much appreciate that you register before June 1. This makes planning of food, busses and party hats much easier. Thank you in advance. Hope to see you in Copenhagen! Best regards, Olaf * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Olaf Nielsen, Professor, Ph.D. Department of Molecular Biology University of Copenhagen Ole Maal?es Vej 5 DK-2200 Copenhagen N Denmark tel: +45 3532 2102 fax: +45 3532 2113 email: onigen at my.molbio.ku.dk http://www.imbf.ku.dk/onigen * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * From yeast2007 at meetingplanners.com.au Wed May 16 14:56:21 2007 From: yeast2007 at meetingplanners.com.au (Yeast 2007) Date: Wed, 16 May 2007 23:56:21 +1000 Subject: [Pombelist] Yeast 2007: Final Conference Program Now Available Message-ID: Final Conference Program Now Available The Conference program has been updated with the workshop speakers. Click on the following link to the final program http://www.yeast2007.org/files/Yeast_Program.pdf Details have been confirmed for the free event on Friday! Friday July 6 - City of Melbourne - Melbourne Conversations Cancer Treatments: How studying yeast can help World famous scientists are attending. Speakers include: Sir Gus Nossal - Emeritus Professor, Melbourne University, who will moderate the discussion Sir Paul Nurse - Nobel Laureate and President The Rockefeller University, New York, New York Dr Alex Franzusoff - Vice President of Research & Development and Founding Scientist, GlobeImmune, Louisville, Colorado Visit http://www.yeast2007.org/program.php for more details. Registration is still open Visit http://www.yeast2007.org/register.php to register now! From viladevl at mskcc.org Wed May 16 16:41:52 2007 From: viladevl at mskcc.org (Laia Viladevall) Date: Wed, 16 May 2007 11:41:52 -0400 Subject: [Pombelist] Pombe list Message-ID: viladevl at mskcc.org ===================================================================== Please note that this e-mail and any files transmitted with it may be privileged, confidential, and protected from disclosure under applicable law. If the reader of this message is not the intended recipient, or an employee or agent responsible for delivering this message to the intended recipient, you are hereby notified that any reading, dissemination, distribution, copying, or other use of this communication or any of its attachments is strictly prohibited. If you have received this communication in error, please notify the sender immediately by replying to this message and deleting this message, any attachments, and all copies and backups from your computer. From a.m.carr at sussex.ac.uk Mon May 21 15:50:19 2007 From: a.m.carr at sussex.ac.uk (Antony Carr) Date: Mon, 21 May 2007 15:50:19 +0100 Subject: [Pombelist] 2007 Gordon Conference Message-ID: Dear All Please find attached a flyer for the 2007 Gordon Research Conference on Genetic Toxicology. It will be held in Oxford from the 29th July to the 3rd of August. This is an opportunity to attend a Gordon conference in England and see lots of good talks on DNA repair and DNA damage responses. See: If you are not interested yourself, please post the notice on the departmental notice board. Also, we have a few bursaries for PhD students. These amount to $600 off the registration fee, and will be allocated based on poster abstracts etc. Thanks Tony Tony Carr MRC Genome Damage and Stability Centre University of Sussex Brighton, UK BN1 9RQ Tel 01273 678122 -------------- next part -------------- A non-text attachment was scrubbed... Name: GRCposter.pdf Type: application/pdf Size: 1068683 bytes Desc: not available URL: From helenadc at usal.es Wed May 23 11:46:01 2007 From: helenadc at usal.es (helenadc at usal.es) Date: Wed, 23 May 2007 12:46:01 +0200 (CEST) Subject: [Pombelist] Protein abundance Message-ID: <1350.141.14.25.217.1179917161.squirrel@correo.usal.es> Dear all, i would like to know if there is a database where one could find some information about the abundances (concentrations, molecule numbers)of pombe proteins (something like the YEAST GFP FUSION LOCALIZATION DATABASE for cerevisiae). If not, does anybody know about any article where i could find any values for cell-cycle/checkpoint proteins? Thank you very much, Helena D?az Cuervo PhD Student/Dpto Microbiolog?a y Gen?tica Laboratorio 5 Centro de Investigaci?n del C?ncer IBMCC (Universidad de Salamanca-CSIC) Campus Miguel de Unamuno s/n 37007 Salamanca? Espa?a From val at sanger.ac.uk Wed May 23 12:25:41 2007 From: val at sanger.ac.uk (Valerie Wood) Date: Wed, 23 May 2007 11:25:41 UT Subject: [Pombelist] Protein abundance Message-ID: An embedded and charset-unspecified text was scrubbed... Name: not available URL: From dom at genetics.med.harvard.edu Wed May 23 15:24:12 2007 From: dom at genetics.med.harvard.edu (Dom Helmlinger) Date: Wed, 23 May 2007 10:24:12 -0400 Subject: [Pombelist] Protein abundance In-Reply-To: References: Message-ID: <46544E8C.5030400@genetics.med.harvard.edu> Dear Helena, There is also the pombe GFP localizome which features relative abundance of all pombe ORFs tagged. See: http://www.nature.com/nbt/journal/v24/n7/abs/nbt1222.html. Their supplementary table 1 is an excel file with the relative protein expression levels. Best, Dom Valerie Wood wrote: > Dear Helena, > > There is a partial data set ...quantification of 1465 proteins based on predicted tryptic peptides in: > Comparative proteomic and transcriptomic profiling of the fission yeast Schizosaccharomyces pombe. Schmidt MW, Houseman A, Ivanov AR, Wolf DA > PMID: 17299416 > > Unfortunately this data is not on the database at present, but should be in the future. > See: > http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17299416 > > Val > > helenadc at usal.es wrote: > >> Dear all, >> i would like to know if there is a database where one could find some >> information about the abundances (concentrations, molecule numbers)of >> pombe proteins (something like the YEAST GFP FUSION LOCALIZATION DATABASE >> for cerevisiae). If not, does anybody know about any article where i could >> find any values for cell-cycle/checkpoint proteins? >> Thank you very much, >> >> Helena D?az Cuervo >> PhD Student/Dpto Microbiolog?a y Gen?tica Laboratorio 5 >> Centro de Investigaci?n del C?ncer >> IBMCC (Universidad de Salamanca-CSIC) >> Campus Miguel de Unamuno s/n >> 37007 Salamanca-- Espa?a >> >> _______________________________________________ >> Pombelist mailing list >> Pombelist at sanger.ac.uk >> http://lists.sanger.ac.uk/mailman/listinfo/pombelist >> > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pombelist mailing list > Pombelist at sanger.ac.uk > http://lists.sanger.ac.uk/mailman/listinfo/pombelist -- Dom Helmlinger, PhD Harvard Medical School NRB room 239 77 avenue Louis Pasteur Boston, MA 02115 tel: 001-617-432-7557 fax: 001-617-432-6506 dom at helmlinger.com http://genetics.med.harvard.edu/~winston/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From grewals at mail.nih.gov Wed May 23 16:36:22 2007 From: grewals at mail.nih.gov (Shiv Grewal) Date: Wed, 23 May 2007 11:36:22 -0400 Subject: [Pombelist] FASEB CONFERENCE ON CHROMATIN & TRANSCRIPTION References: <748DBC2415E404498A5E3161D1B543AF080CE7DB@exchange1.faseb.org> Message-ID: <3980C368-9DA8-469F-8BF7-A8EBE85FFAC9@mail.nih.gov> Dear All Please find attached a flyer for the 2007 FASEB meeting on "Chromatin and Transcription". It will be held in Snowmass Colorado July 7-12. Please post the notice on the departmental notice board. Thanks, Shiv Grewal ? Please see the attached flyer regarding the FASEB Summer Research Conference entitled: ?Chromatin and Transcription? We hope to see you in Snowmass! For more information, please visit: http://src.faseb.org ?? -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... 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Confirmed speakers: * Fikret Osman * Paul Russel * Stephen Kearsey * Antony M Carr * Alan Lehman * Olaf Nielsen * A-Lien Lu * Johanne M Murray * Greg A Freyer * Mitsuhir Yanagida * Tom Kelly * Susan L Forsburg * Theresa S F Wang * Matthew C Whitby * Karl Ekwall * John Tainer See our information flyer (attached). Registration is now open at our web site: www.cmbn.no/pombe. We hope to welcome you to Oslo Ingrun Alseth, Birgit Eliassen, Erik Boye and Magnar Bj?r?s. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: pombeposter.pdf Type: application/pdf Size: 1755807 bytes Desc: pombeposter.pdf URL: From jm593 at cam.ac.uk Thu Jun 7 17:12:01 2007 From: jm593 at cam.ac.uk (Juan Mata) Date: Thu, 07 Jun 2007 17:12:01 +0100 Subject: [Pombelist] Postgraduate/postdoctoral position available Message-ID: <46682E51.2030800@cam.ac.uk> Dear Colleagues, Please bring the attached advert for a position in my lab to the attention of candidates who may be interested. I will be available to discuss further details with potential candidates at the Fission Yeast meeting in Copenhagen. Many thanks Juan Mata Applications are invited for a position in Dr Juan Mata?s laboratory (Department of Biochemistry, University of Cambridge) to study the global role of RNA-binding proteins in fission yeast. The project will involve the use of functional genomics (including DNA microarrays), cell biological methods and bioinformatics to study posttranscriptional regulation at the genome-wide level. More information on the lab can be found at http://www.bioc.cam.ac.uk/uto/mata.html The position is funded by the Medical Research Council and can be filled at the postgraduate (Research Assistant) or postdoctoral (Research Associate) levels. Funding will be available from 1st October 2007 for a total of 23 months. Applicants should have a BSc (Research Assistant) or PhD (Research Associate) in a relevant subject, such as Genetics, Molecular Biology or Biochemistry. Direct experience with fission yeast or DNA microarrays is not required. Experience in protein or RNA biochemistry, microscopy or computational biology would be an advantage. For enquiries please email jm593 at cam.ac.uk From nimisha401 at yahoo.com Mon Jun 11 17:37:58 2007 From: nimisha401 at yahoo.com (nimisha sharma) Date: Mon, 11 Jun 2007 17:37:58 +0100 (BST) Subject: [Pombelist] S. pombe ORF clones and plasmids In-Reply-To: <42EC241C-7050-4CC7-9065-0C3AABA89078@riken.jp> Message-ID: <303176.74789.qm@web34804.mail.mud.yahoo.com> Hi everyone. Does someone have a S. pombe cDNA library? Nimisha NIMISHA SHARMA, Ph.D LECTURER, UNIVERSITY SCHOOL OF BIOTECHNOLOGY, G.G.S.INDRAPRASTHA UNIVERSITY, KASHMERE GATE, DELHI-110006 INDIA Send instant messages to your online friends http://uk.messenger.yahoo.com From hoffmacs at bc.edu Mon Jun 18 01:29:38 2007 From: hoffmacs at bc.edu (Charles Hoffman) Date: Sun, 17 Jun 2007 20:29:38 -0400 Subject: [Pombelist] Facebook group of pictures from Copenhagen Message-ID: I just created a Facebook group called: Copenhagen Pombe 2007 Everyone is welcome to join, even if you did not go to the meeting. I am hoping that people will tag pictures so we have a place to connect names to faces. Cheers, Charlie Hoffman Boston College "I'd rather be fission." From hoffmacs at bc.edu Mon Jun 18 14:42:11 2007 From: hoffmacs at bc.edu (Charles Hoffman) Date: Mon, 18 Jun 2007 09:42:11 -0400 Subject: [Pombelist] What is Facebook (and why is it saying those terrible things about me) Message-ID: Hi everyone, I hope this will serve as a primer for how to join facebook (a social network on the web) and join the Copenhagen Pombe 2007 group. Go to www.facebook.com and register. You can join as part of a network (such as a university group), but you don't have to. In the upper left side of the page, click on "Groups". In the upper right side of the next page, type in pombe and search for groups. That should bring you to the group. Everyone is free to join. You can look through pictures and "tag" people you know in it. You can also look at the members of the groups (there are 12 already) and ask people to be "friends" (thus the social network aspect), which allows them to see your facebook page. I will get messages that ask me to confirm any tagging, but I assume that people doing the tagging know what they are doing so I will try and approve everything once a day or so. Cheers, Charlie Hoffman Boston College "I'd rather be fission." From hoffmacs at bc.edu Mon Jun 18 16:18:39 2007 From: hoffmacs at bc.edu (Charles Hoffman) Date: Mon, 18 Jun 2007 11:18:39 -0400 Subject: [Pombelist] Hopefully the last message regarding facebook Message-ID: I initially loaded low resolution images last night from home due to the slow internet speed. I have now just finished uploading a complete replacement set of higher resolution images. If you have already tagged stuff, you will have to go back and do it again. Sorry. I would appreciate some feedback about some of the darker pictures from the banquet. Should I do some lightening in Photoshop or are they okay? Finally, you are all able to upload your own pictures to this group, so I look forward to seeing more pictures in the future. Cheers, Charlie Hoffman Boston College "I'd rather be fission." From akihisa at riken.jp Tue Jun 19 08:59:22 2007 From: akihisa at riken.jp (Akihisa Matsuyama) Date: Tue, 19 Jun 2007 16:59:22 +0900 Subject: [Pombelist] S. pombe Postgenome Database Server Message-ID: Dear all, As announced in the 4th International Fission Yeast Meeting, our web server was restored just before the meeting (http://cgl.riken.go.jp/). The sequences of a series of vectors (pDUAL- and pDUAL2-derivatives) distributed from the Bioresource Center, RIKEN, are also available on this website (http://cgl.riken.go.jp/gene/Plasmids.html). We are looking forward to your visit. All the best, Matsu ***** Akihisa Matsuyama, Ph.D Chemical Genetics Laboratory, RIKEN Hirosawa 2-1, Wako, Saitama, Japan, 351-0198 TEL: +81-48-462-1335 FAX: +81-48-462-1336 ***** From hoffmacs at bc.edu Wed Jun 20 16:53:16 2007 From: hoffmacs at bc.edu (Charles Hoffman) Date: Wed, 20 Jun 2007 11:53:16 -0400 Subject: [Pombelist] Photo album for the Facebook-averse Message-ID: Hi, For those of you who do not want to enter the world of Facebook, I have put up a webpage of my photos from the pombe meeting at: http://www2.bc.edu/%7Ehoffmacs/pombe2007/index.htm However, I strongly recommend that you use Facebook, because other people are adding their own pictures to that site as well. Cheers, Charlie Hoffman Boston College "I'd rather be fission." From Jurg at sanger.ac.uk Thu Jun 21 19:00:49 2007 From: Jurg at sanger.ac.uk (Jurg Bahler) Date: Thu, 21 Jun 2007 19:00:49 +0100 Subject: [Pombelist] Genome-wide approaches with fission yeast: COURSE DEADLINE 29 June Message-ID: <37340E68029F5842A315DDF21075A802208BBA@exchsrv2.internal.sanger.ac.uk> Dear All, The deadline is quickly approaching for the Wellcome Trust Advanced Course 'Genome-wide approaches with fission yeast' from 1-7 October 2007 in Hinxton, UK. We need your application by Friday 29 June. Details and links to the application form are available here: http://www.wellcome.ac.uk/doc_WTX033405.html This hands-on course is for colleagues who would like to use large-scale methods for their research. The attendance is limited to 16-18 people, and selection will be based on the applications. Cheers, -Jurg --- J?rg B?hler, Ph.D. Wellcome Trust Sanger Institute Hinxton Cambridge CB10 1HH UK P: +44(0)1223-496948 F: +44(0)1223-496802 W: http://www.sanger.ac.uk/PostGenomics/S_pombe/ -------------- next part -------------- A non-text attachment was scrubbed... Name: CourseFlyer.pdf Type: application/octet-stream Size: 524607 bytes Desc: CourseFlyer.pdf URL: From belostotskyd at umkc.edu Tue Jul 3 14:28:18 2007 From: belostotskyd at umkc.edu (Belostotsky, Dmitry) Date: Tue, 3 Jul 2007 08:28:18 -0500 Subject: [Pombelist] experimental-driven systems biology position(s), any level Message-ID: <5C13F286F3DAE649BFF21749E3DEE0960466E577@KC-MSX1.kc.umkc.edu> WITH: - Dmitry Belostotsky @ University of Missouri - Kansas City [contact via belostotsky [at] umkc.edu ] ON: - protein complexes governing noncoding RNA-mediated and mRNA-level control of gene expression (using several models including pombe) WHEN: - immediately until filled WHO: - applicants well versed in RNA biology or/and microarrays, protein biochemistry, programming or/and statistics, with documented record of excellence MUST BE: - highly driven, self-motivated, ambitious, dynamic individuals. Postdoctoral fellowships eligibility helpful but not essential. Funding available through 2010. LAB: - equipped with Affymetrix and deconvolution microscopy (Deltavision) workstations and have, or have access to, HPLC, MALDI, LC-MS/MS and high end Linux cluster PUBS (selected): - Genome-wide high-resolution analysis of exosome substrates in Arabidopsis - In review (2007) - Shared factors mediate tethering of active genes to non-nascent mRNP and nuclear rim - In review (2007) - EMBO J 25:4253-4256 (2006) - Trends Plant Sci 10:347-353 (2005) - RNA 10:1200-1214 (2004) - Genetics 163:311-319 (2003) - RNA 9:1476-1490 (2003) - Curr Biol 11:1207-1214 (2001) LIVING IN KANSAS CITY: in brief, KC got everything but ocean - major cosmopolitan center of 2.5M plus people - dynamic cultural environment (e.g. see www.nelson-atkins.org) - vibrant music scene (best known for, but not limited to, jazz and blues) - fabulous food (best known for, but not limited to, its famous bbq) - dubbed ?Paris of the plains?, ranked within top 10 places to live in US. See www.cnn.com/2006/TRAVEL/DESTINATIONS/06/08/kansas.city/index.html Dmitry A. Belostotsky, Ph.D. Associate Professor Division of Molecular Biology and Biochemistry School of Biological Sciences University of Missouri Kansas City, MO 64110 From mishra at biochem.mpg.de Wed Jul 4 13:41:56 2007 From: mishra at biochem.mpg.de (Shravan Kumar Mishra) Date: Wed, 4 Jul 2007 14:41:56 +0200 Subject: [Pombelist] S. pombe two-hybrid library Message-ID: <1183552916.929af5b9ceb93@webmail.biochem.mpg.de> Dear collegues, Could someone please recommend a good source (lab/commercial) of S. pombe two-hybrid libraries? Thanks for your kind notice Shravan Shravan Kumar Mishra (PhD) Molecular Cell Biology, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsreid/Munich, D-82152 Germany Tel: +49-89-8578-3027 Fax: +49-89-8578-3022 http://www.biochem.mpg.de/jentsch/ --------------------------------------------------------------------- This message was sent using https://webmail.biochem.mpg.de If you encounter any problems please report to rz-linux at biochem.mpg.de ----- End forwarded message ----- Shravan Kumar Mishra (PhD) Molecular Cell Biology, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsreid/Munich, D-82152 Germany Tel: +49-89-8578-3027 Fax: +49-89-8578-3022 http://www.biochem.mpg.de/jentsch/ --------------------------------------------------------------------- This message was sent using https://webmail.biochem.mpg.de If you encounter any problems please report to rz-linux at biochem.mpg.de From laabmc at ibmb.csic.es Tue Jul 10 11:49:34 2007 From: laabmc at ibmb.csic.es (Lorena Aguilar) Date: Tue, 10 Jul 2007 12:49:34 +0200 Subject: [Pombelist] Anti-HA Agarose Conjugate Message-ID: <002e01c7c2e0$00b14970$8a3e050a@BMCLORENA> Dear ?pombelist?: I am trying to immunoprecipitate HA-tagged fusion proteins expressed in S. pombe to perform ChIP analysis and complex purification. I have seen the availability of at least two different Anti ?HA agarose conjugated, which correspond with mouse HA-7 and rat 3F10 monoclonal antibodies. Has anyone of you experience with these antibodys or even with another one that works well in pombe? Can you recommend one of these? Thanks in advance for any suggestion, Best wishes, Lorena Lorena Aguilar Arnal Institut de Biologia Molecular de Barcelona - CSIC Parc Cient?fic de Barcelona c/Josep Samitier 1-5 08028 Barcelona - SPAIN Tel?fon: +34934034964 e-mail: laabmc at ibmb.csic.es -------------- next part -------------- An HTML attachment was scrubbed... URL: From ashapurno.biswas at tuebingen.mpg.de Tue Jul 10 15:38:09 2007 From: ashapurno.biswas at tuebingen.mpg.de (Ashapurno Biswas) Date: Tue, 10 Jul 2007 16:38:09 +0200 Subject: [Pombelist] thanks Message-ID: Hello Many thanks for including my mail address in the pombelist mailing address. Regards, Ashapurno Ashapurno Biswas PhD student Friedrich-Miescher-Laboratory of the Max-Planck-Society Spemannstrasse 35 72076 Tuebingen Germany. From mishra at biochem.mpg.de Thu Jul 12 14:44:33 2007 From: mishra at biochem.mpg.de (Shravan Kumar Mishra) Date: Thu, 12 Jul 2007 15:44:33 +0200 Subject: Fwd: Re: [Pombelist] S. pombe two-hybrid library Message-ID: <1184247873.66aa659e6933c@webmail.biochem.mpg.de> ----- Forwarded message from shimoda at sci.osaka-cu.ac.jp ----- Date: Mon, 09 Jul 2007 09:27:00 +0900 From: "C. Shimoda" Reply-To: "C. Shimoda" Subject: Re: [Pombelist] S. pombe two-hybrid library To: Shravan Kumar Mishra Dear Dr. Mishra, The Yeast Genetic Resource Center of Japan (YGRC) can provide you with an S. pombe two-hybrid library. It was constructed from meiotic mRNA, but we know that it contains also mitotic cDNAs. For details see the attached file. If you want to get it, e-mail me. Please visit our website to search and request fission yeast resource. Regards, Chikashi Shimoda > Dear collegues, > Could someone please recommend a good source (lab/commercial) of S. pombe > two-hybrid libraries? > Thanks for your kind notice > Shravan > > Shravan Kumar Mishra (PhD) > > Molecular Cell Biology, > Max-Planck Institute of Biochemistry, > Am Klopferspitz 18, Martinsreid/Munich, > D-82152 Germany > Tel: +49-89-8578-3027 > Fax: +49-89-8578-3022 > http://www.biochem.mpg.de/jentsch/ > > --------------------------------------------------------------------- > This message was sent using https://webmail.biochem.mpg.de > If you encounter any problems please report to rz-linux at biochem.mpg.de > > > ----- End forwarded message ----- > > > Shravan Kumar Mishra (PhD) > > Molecular Cell Biology, > Max-Planck Institute of Biochemistry, > Am Klopferspitz 18, Martinsreid/Munich, > D-82152 Germany > Tel: +49-89-8578-3027 > Fax: +49-89-8578-3022 > http://www.biochem.mpg.de/jentsch/ > > --------------------------------------------------------------------- > This message was sent using https://webmail.biochem.mpg.de > If you encounter any problems please report to rz-linux at biochem.mpg.de > > > _______________________________________________ > Pombelist mailing list > Pombelist at sanger.ac.uk > http://lists.sanger.ac.uk/mailman/listinfo/pombelist > -------------------------------------------------- Prof. Chikashi Shimoda Head of YGRC (Fission Yeast) Department of Biology, Graduate School of Science Osaka City University Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan Tel +81 66605 2576; FAX +81 66605 3158 E-mail: shimoda at sci.osaka-cu.ac.jp National BioResource Project Japan Yeast Genetic Resource Center E-mail: nbrpombe at sci.osaka-cu.ac.jp S. pombe resource search : http://yeast.lab.nig.ac.jp/nig/english/index.html ------------------------------------------------ ----- End forwarded message ----- Shravan Kumar Mishra (PhD) Molecular Cell Biology, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsreid/Munich, D-82152 Germany Tel: +49-89-8578-3027 Fax: +49-89-8578-3022 http://www.biochem.mpg.de/jentsch/ --------------------------------------------------------------------- This message was sent using https://webmail.biochem.mpg.de If you encounter any problems please report to rz-linux at biochem.mpg.de -------------- next part -------------- A non-text attachment was scrubbed... Name: Description of libraries (Nondisclosure).xls Type: application/octet-stream Size: 14848 bytes Desc: not available URL: From val at sanger.ac.uk Tue Jul 17 13:56:02 2007 From: val at sanger.ac.uk (Valerie Wood) Date: Tue, 17 Jul 2007 13:56:02 +0100 Subject: [Pombelist] An update on ortholog resources/ Tools and tips Message-ID: <469CBC62.2040102@sanger.ac.uk> Some of the most frequent responses to the fission yeast database survey were requests for additional comparison resources to assess sequence relationships (including ortholog identification, their associated alignments and phylogenetic trees). However, ortholog identification is not trivial and there is no 'gold standard' resource. The likely future move to the Saccharomyces Genome Database (SGD) architecture would allow fission yeast to take advantage of the tools available for the budding yeast (particularly those exploiting synteny when the S. japonicus genome is published). The following resources are currently available and may be useful now: CURATED BUDDING YEAST ORTHOLOGS A manually curated list of S. pombe/S. cerevisiae orthologs covering 75% of fission yeast gene products is available. Alignments used to make orthology inferences are submitted to the Pfam protein family database. You can subscribe to the mailing list 'Yeast_orthologous_groups' to receive the curated ortholog inventory and updates as a spreadsheet. http://lists.sanger.ac.uk/mailman/listinfo/yeast_orthologous_groups/ SEARCHING CURATED ORTHOLOGS IN GENEDB You can search for curated orthologs of individual S. cerevisiae genes in GeneDB http://www.genedb.org/genedb/pombe/. You must use the S. cerevisiae systematic identifier (e.g YOR073W) and the "Full Content Search" box. EUKARYOTIC ORTHOLOGS AND ASSOCIATED GENE ONTOLOGY (GO) ANNOTATION. YOGY is a tool which uses the major orthology predictors (KOGS, OrthoMcl, Inparanoid, Homologene) to identify potential orthologs in the major model eukaryotes and allows the user to retrieve GO terms manually associated with these orthologs by curators at the Model Organism Databases. YOGY is accessible from http://www.sanger.ac.uk/PostGenomics/S_pombe/YOGY/ OR via a link from the "Database Cross-References" section of every GeneDB_Spombe gene page GENES WITH NO APPARENT ORTHOLOGS If you are working on one of the 474 gene products which have no homologs identified (357 sequence orphans, 71 published genes with no apparent homologs, 46 S. pombe specific families), the Japonicus genome at the Broad Institute may provide new insights: http://www.broad.mit.edu/annotation/genome/schizosaccharomyces_japonicus/Blast.html;jsessionid=6A016D3A95661A10AA9654198A1D4F81?sp=Stblastn It is possible that a PSI Blast search (Position-Specific Iterated BLAST) http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi?PAGE=Proteins&PROGRAM=blastp&BLAST_PROGRAMS=blastp&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on with the japonicus ortholog as a query will provide a good enough seed alignment to detect more distant orthologs which were missed by searching with the fission yeast sequence. (Note that current 'non conserved' status assignments in GeneDB have not been systematically checked against Japonicus) TREEFAM http://www.treefam.org/ Treefam is a database of phylogenetic trees and also an ortholog database. Because Treefam infers orthology using trees it can be more accurate than some of the 'Blast based' orthology prediction methods. Although developed for animal genes it tries to include S. cerevisiae and S. pombe as outgroups. With Treefam distant relationships are sometimes missed, however, the incidence of false positives is low. Treefam will become increasingly useful to assess how pombe genes are related to animal families as further families are curated. From Sophie.Martin at unil.ch Sat Aug 4 18:23:57 2007 From: Sophie.Martin at unil.ch (Sophie Martin) Date: Sat, 04 Aug 2007 13:23:57 -0400 Subject: [Pombelist] PhD/postdoctoral positions available Message-ID: <46b4b62d.2e7.62d0.1558288442@unil.ch> Dear Colleagues, Thank you for bringing the attached advert for PhD students and postdocs in my lab to the attention of candidates who may be interested. Many thanks Sophie Martin We are seeking outstanding and enthusiastic candidates to join the group of Sophie Martin at the Center for Integrative Genomics of the University of Lausanne, Switzerland. Applicants should have a Bachelor?s degree or equivalent (PhD position) or PhD degree (postdoc position) in a relevant discipline (biology, genetics, etc.) Our group studies molecular mechanisms of cell polarisation and cytosketal function, using the fission yeast, S. pombe, as a model system. Several potential projects are available, integrating live-cell imaging, genetic and biochemical experimental approaches. For more information, see http://www.unil.ch/cig/page44769.html, or contact Sophie.Martin at unil.ch The Center for Integrative Genomics is a new, dynamic institute with international and interactive research groups and world-class facilities in imaging, genomics and proteomics. The working language is English. The Center is located in Lausanne (Switzerland), a beautiful city by Lake Geneva that offers excellent opportunities for cultural and outdoor activities. Please send a CV and 2 letters of recommendation to: Sophie.Martin at unil.ch ______________________________________ Sophie Martin, PhD Center for Integrative Genomics University of Lausanne Genopode Building CH-1015 Lausanne Switzerland email: Sophie.Martin at unil.ch http://www.unil.ch/cig/page44769.html From marti5_kupiec at yahoo.com Wed Aug 8 15:07:02 2007 From: marti5_kupiec at yahoo.com (Martin Kupiec) Date: Wed, 8 Aug 2007 07:07:02 -0700 (PDT) Subject: [Pombelist] Looking for wt pombe Message-ID: <41452.95036.qm@web34307.mail.mud.yahoo.com> Dear Fission People, We are looking for wild strains of pombe for a variability study. Surprisingly, most people have just Leupold's isolates. If you happen to have one, or you know who might, would you pls send them to me? Thanks a lot! Martin Martin Kupiec Dept. of Molecular Micro & Biotech, Tel Aviv University, Ramat Aviv 69978, Israel. Phone: 972-3-640-9031 FAX: 972-3-640-9407 E-mail: martin at post.tau.ac.il http://www.tau.ac.il/lifesci/departments/biotech/members/kupiec/kupiec.html ____________________________________________________________________________________ Boardwalk for $500? In 2007? Ha! Play Monopoly Here and Now (it's updated for today's economy) at Yahoo! Games. http://get.games.yahoo.com/proddesc?gamekey=monopolyherenow -------------- next part -------------- An HTML attachment was scrubbed... URL: From juergen.stolz at wzw.tum.de Mon Aug 20 15:07:54 2007 From: juergen.stolz at wzw.tum.de (Juergen Stolz) Date: Mon, 20 Aug 2007 16:07:54 +0200 Subject: [Pombelist] used micromanipulator Message-ID: <93A5C9CF-BB04-4C4C-9344-A8A3BE05B3D9@wzw.tum.de> Dear all, We are looking for a micromanipulator for yeast tetrad dissection. A used but functional instrument would just be fine. I have worked with Singer instruments before, but other offers are equally welcome. Thans a lot, Juergen stolz at wzw.tum.de _____________________________ Dr. J?rgen Stolz Lehrstuhl f?r Ern?hrungsphysiologie Molecular Nutrition Unit Technische Universit?t M?nchen Am Forum 5 85350 Freising-Weihenstephan -------------- next part -------------- An HTML attachment was scrubbed... URL: From val at sanger.ac.uk Wed Aug 22 15:16:08 2007 From: val at sanger.ac.uk (Valerie Wood) Date: Wed, 22 Aug 2007 15:16:08 +0100 Subject: [Pombelist] NEW Pfam release (Version 22) Message-ID: <46CC4528.7080101@sanger.ac.uk> This weeks update of GeneDB has uses the new Pfam release (Version 22). This provides Pfam families/domains for an additional 40 fission yeast proteins. Three of these were previously sequence orphan: SPAC144.15c Vps51/Vps67 Golgi complex component 1 (ortholog of YGL223C), still 1 subunit of this complex missing- COG7 SPAC3G6.10c Vps51/Vps67 family (ortholog of YKR020W VPS51) SPAC4G9.06c Histone chaperone domain CHZ (ortholog of YER030W CHZ1) From h.yamano at mcri.ac.uk Wed Sep 5 09:41:26 2007 From: h.yamano at mcri.ac.uk (Hiro Yamano) Date: Wed, 5 Sep 2007 09:41:26 +0100 Subject: [Pombelist] Post-doc position available Message-ID: Dear colleagues A post-doctoral position is available in my lab to work on the mechanisms of the APC/C-dependent ubiquitylation and proteolysis using fission yeast and frog egg extracts. I would be very grateful if you could post the attached advert on your notice board, and bring it to the attention of any motivated student/post-doc who may be interested in your lab or department. Many thanks, Hiro Yamano ______________________________________________________________________ This email has been scanned by the MessageLabs Email Security System. For more information please visit http://www.messagelabs.com/email ______________________________________________________________________ -------------- next part -------------- A non-text attachment was scrubbed... Name: Postdoc Ad 2007.doc Type: application/applefile Size: 377 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Postdoc Ad 2007.doc Type: application/octet-stream Size: 26112 bytes Desc: not available URL: -------------- next part -------------- ************************** Hiro Yamano, Ph.D. Head, Cell Cycle Control Laboratory Marie Curie Research Institute, The Chart, Oxted, Surrey RH8 0TL, UK Tel: +44 (0)1883 722306 Fax: +44 (0)1883 714375 Email: h.yamano at mcri.ac.uk http://www.mcri.ac.uk/research/cellcycle.asp From jianqiu.wu at yale.edu Thu Sep 6 19:18:38 2007 From: jianqiu.wu at yale.edu (Jian-Qiu Wu) Date: Thu, 06 Sep 2007 14:18:38 -0400 Subject: [Pombelist] New contact and postdoc position Message-ID: <20070906141838.vy26rkth7kkwg4cs@www.mail.yale.edu> Dear All, I just started a new laboratory at The Ohio State University. The below is my new address. Please see below or the attached file for postdoc positions in my lab. Thanks. Jian-Qiu Wu Assistant Professor Department of Molecular Genetics The Ohio State University Biological Sciences Building, Room 976 484 West 12th Avenue Columbus, OH 43210-1292 Phone: 614 247-6680 Email: wu.620 at osu.edu Postdoctoral Positions Funded postdoctoral positions are available immediately in Jian Qiu Wu's laboratory at Ohio State University to study the molecular mechanism of cell division in the fission yeast S. pombe using a combination of molecular, cellular, biochemical, genetic, and confocal microscopic approaches. More information can be found at http://www.osumolgen.org/faculty/index.php/profile/jianqiu_wu Highly motivated and energetic candidates with strong background in molecular biology, cell biology, or genetics are desired. Please email a cover letter, curriculum vitae, research experience and interests, reprints of publications, and names and contacts of three references to wu.620 at osu.edu. The Department of Molecular Genetics at OSU is a vigorous and highly interactive department that plays a central role in the molecular life sciences on campus. The department consists of faculty members studying important problems in molecular, cellular, and developmental biology using a variety of model organisms including plant and animal viruses, fungi, plants, worms, insects, mice and humans. Departmental faculty members participate in numerous campus-wide collaborations and focus groups such as the Cell Biology Group, the Developmental Genetics Group (http://groups.yahoo.com/group/dgmeet/), and the RNA group. The Ohio State University is the flagship institution of the state's higher education system. It is located in the state capital, Columbus, the 15th largest city in the US. Columbus and its many suburbs have been ranked as one of the country's best places to live and work. -------------- next part -------------- A non-text attachment was scrubbed... Name: Postdoctoral Position in the Wu lab.pdf Type: application/x-unknown-application-pdf Size: 52433 bytes Desc: not available URL: From mohan at tll.org.sg Mon Sep 10 09:25:33 2007 From: mohan at tll.org.sg (Mohan Balasubramanian) Date: Mon, 10 Sep 2007 15:25:33 +0700 Subject: [Pombelist] Asia-Pacific Regional Fission Yeast Meeting July 25-27 2008 SINGAPORE Message-ID: Dear Colleagues We plan to host a Asia-Pacific regional fission yeast meeting in July 2008 in Singapore. The dates of the meeting are July 25-27. We hope this meeting will be of interest to fission yeast researchers in the Asia-Pacific region (and elsewhere as well). We will have two special lectures to start this meeting, given by 1. Richard Losick (HARVARD) and 2. Randy Schekman (UC BERKELEY) In addition, Paul Nurse, Masayuki Yamamoto and Mitsuhiro Yanagida will attend and give talks. We plan to keep the costs low. I would appreciate knowing the extent of enthusiasm; this will allow us a better estimate of the prices. Please write to any of us listed below Best Regards Mohan Balasubramanian (mohan at tll.org.sg) Snezhana Oliferenko (snejana at tll.org.sg) and Jianhua Liu (liujh at gis.a-star.edu.sg) -- Mohan K. Balasubramanian Temasek Life Sciences Laboratory 1 Research Link The National University of Singapore Singapore 117604 Tel: 65-6872-7478: Fax: 65-6872-7007 e-mail: mohan at tll.org.sg http://www.tll.org.sg/mohan.asp -------------- next part -------------- An HTML attachment was scrubbed... URL: From forsburg at usc.edu Tue Oct 9 18:44:40 2007 From: forsburg at usc.edu (SLForsburg) Date: Tue, 09 Oct 2007 10:44:40 -0700 Subject: [Pombelist] Regional Pombe meeting Message-ID: North American Pombe Meeting 2008 University of Southern California, Los Angeles, 6-8 June Organizers: Nick Rhind and Susan Forsburg Webiste: http://www-rcf.usc.edu/~forsburg/pombemeeting.html Information: USCpombe at gmail.com {} {} {} {} {} {} {} {} {} {} {} {} {} {} S L Forsburg PhD, Professor University of Southern California Molecular & Computational Biology Ray R Irani Hall 1050 Childs Way, RRI 201B Los Angeles, CA 90089-2910 vox: 213-740-7342 fax: 213-740-8631 forsburg at usc.edu www.pombe.net -------------- next part -------------- An HTML attachment was scrubbed... URL: From vogel at mpi-cbg.de Wed Oct 10 14:08:35 2007 From: vogel at mpi-cbg.de (Sven Vogel) Date: Wed, 10 Oct 2007 15:08:35 +0200 (MEST) Subject: [Pombelist] Microtubule stabilizing drug? Message-ID: <54215.10.1.238.4.1192021715.squirrel@webmail.mpi-cbg.de> Dear all, do you know a microtubule stabilizing drug that works in S.pombe? I heard that taxol does not, yet I did not try it myself so far. If you have experience with taxol or if you know any drug that does a similar job as taxol, please let me know. I will be happy about any comments :-) Thank you Sven -- Sven Kenjiro Vogel PhD Student, Tolic-Norrelykke group Max Planck Institute of Molecular Cell Biology and Genetics Dresden Pfotenhauerstr. 108 D-01307 Dresden phone: +49-351-210-2541 fax: +49-351-210-2020 From Marc_Buehler at hms.harvard.edu Wed Oct 24 16:32:47 2007 From: Marc_Buehler at hms.harvard.edu (Buehler, Marc) Date: Wed, 24 Oct 2007 11:32:47 -0400 Subject: [Pombelist] postdoctoral position Message-ID: <34D3E13342E7144D8E1A05032097A27A0880B05F@MAILSERVER02.MED.HARVARD.EDU> Dear Colleagues, Thank you for bringing the attached advert for an open postdoc position in my lab to the attention of candidates who may be interested. Many thanks Marc B?hler Postdoctoral Position Yeast Live-Cell Imaging Applications are invited for a postdoctoral position in the group of Dr. Marc B?hler to study chromatin-dependent gene silencing mechanisms. This research aims at the elucidation of "co-transcriptional gene silencing" (CTGS) on a single-cell level (B?hler et al. 2007, Cell 129:707-721), focusing on the mechanisms linking RNA turnover to chromatin-dependent gene silencing. The project will employ genetic, biochemical, molecular biological, advanced live-cell imaging and proteomic approaches. Candidates should have extensive experience in live-cell imaging techniques. Although not required, previous experience of working with yeast is preferred. The ability to work independently is essential and applicants are expected to have a high level of organisational and communication skills and to become involved in the supervision of graduate students. The FMI, part of the Novartis Research Foundation, is an international biomedical research centre with 300 members pursuing fundamental research in Neurobiology, Cell Growth and Signalling, and Epigenetics (www.fmi.ch). A competitive salary and access to state-of-the-art research facilities will be provided. The FMI is situated in Basel, a city offering an outstanding scientific and cultural environment in the centre of Europe. Applications, including a detailed CV, the names and contact details of three referees and a summary of current and future research interests should be addressed to Dawn Hammond, Friedrich Miescher Institute, Maulbeerstrasse 66, 4058 Basel, Switzerland (dawn.hammond at fmi.ch). Marc B?hler Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 4058 Basel Switzerland -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Advert_FMI_Buehler.pdf Type: application/octet-stream Size: 14732 bytes Desc: Advert_FMI_Buehler.pdf URL: From ccc at cict.fr Thu Oct 25 07:46:13 2007 From: ccc at cict.fr (Colloque Cycle Cellulaire et Cancer (CC&C)) Date: Thu, 25 Oct 2007 08:46:13 +0200 Subject: [Pombelist] CCC2008 Message-ID: <51869DA6-26DE-4AD3-9EB9-DE3702426CCB@cict.fr> EARLY BIRDS REGISTRATION ENDS NOVEMBER 15th !.... CELL CYCLE & CANCER March 25-28, 2008 TOULOUSE (FRANCE) The objective of this international conference is to highlight the latest advances in research into the mechanisms that control the cell cycle, their alterations in cancer, and their potential utility as targets for anticancer therapies. Organisers : B. Ducommun ( Toulouse) and C. Prigent (Rennes) with the French Society of Cell Biology Scientific sessions : DNA replication, Cytoskeleton and chromosomes segregation, Mitosis, Niche-dependent cell cycle and Cancer, Genome stability, Targeting cell-cycle in cancer therapy Keynote speakers : T. Hunt (Nobel prize 2001, London), M. Barbacid (Madrid), M. Kastan (Memphis), D. Lane (Dundee) Speakers : J. Bischoff (Madrid), J. Blow (Dundee), S. Doxsey (Worcester), W. Earnshaw (Edinburgh), I. Hagan (Manchester), J. Lazo (Pittsburgh), J. Lukas (Copenhagen), J. Maller (Denver), M. Malumbres ( Madrid), M. Mechali (Montpellier), R. Medema (Utrecht), L. Meijer (Roscoff), E. Nigg (Mertinsried), M. Roberge (Vancouver), J. Roberts (Seattle), C. Sardet (Montpellier), A. Senderowicz (betshesda), M-H. Verlhac (Paris) Short communications will be selected from the abstracts. Poster sessions Additional informations available at http://ccc-2008.univ-rennes1.fr REDUCED RATE FOR EARLY BIRDS ENDS NOVEMBER 15th !.... ___________________________________ CELL CYCLE and CANCER Cycle Cellulaire et Cancer March 25th-28th, 2008 TOULOUSE - FRANCE by the French Society of Cell Biology Contact the organizer: ccc at cict.fr http://ccc-2008.univ-rennes1.fr ___________________________________ Merci de penser ? l'environnement avant d'imprimer cet e-mail -------------- next part -------------- An HTML attachment was scrubbed... URL: From nick.rhind at umassmed.edu Fri Oct 26 19:20:23 2007 From: nick.rhind at umassmed.edu (Nick Rhind) Date: Fri, 26 Oct 2007 14:20:23 -0400 Subject: [Pombelist] The Schizosaccharomyces octosporus genome Message-ID: The first draft of the Schizosaccharomyces octosporus genome sequence is now available. The genome was sequenced at The Broad Institute as part of the Fungal Genome Initiative, a project funded by NHGRI. The current sequence consists of 25-fold coverage by 454 sequencing. The assembled genome contains 355 contigs with an N50 of 72 kb. Early next year, we intend to add end-paired reads from genomic clones which should increase contig length and allow the contigs to be assembled into larger scaffolds. The octosporus assembly is available at http://www.broad.mit.edu/annotation/genome/schizosaccharomyces_japonicus.3 The site includes information about the S. octosporus project and assembly, along with the S. pombe and S. japonicus genomes, tools for downloading the genome sequences, BLASTing against the genome assemblies, and searching and browsing for features of the genomes. The S. octosporus genome will be automatically annotated at The Broad Institute and manually annotated in collaboration with the fission yeast community. Annotations will be released as they become available. Please share this release notice with anyone you think may be interested. Sincerely, Chad Nusbaum Nick Rhind From Simon.Labbe at USherbrooke.ca Mon Oct 29 14:10:42 2007 From: Simon.Labbe at USherbrooke.ca (Labbe Simon) Date: Mon, 29 Oct 2007 10:10:42 -0400 Subject: [Pombelist] Tenure Track position - University of Sherbrooke Canada Message-ID: STRUCTURAL BIOCHEMISTRY and BIOINFORMATICS ASSISTANT PROFESSOR The Department of Biochemistry invites applications for tenure-track positions at the Assistant Professor level starting in 2008 and 2009. The Department is composed of young scientists who are well-known for their innovation. For more details, visit http://www.usherbrooke.ca/biochimie/ . The successful candidates are expected to develop an externally funded research program in Structural biochemistry (e.g. crystallography) and Computational biology, and eventually contribute to teaching at the graduate and undergraduate levels. Curriculum vitae and description of future research goals along with the names and contact information of three references can be submitted by mail to: Comit? de recrutement D?partement de biochimie Facult? de m?decine et des sciences de la sant? Universit? de Sherbrooke 3001, 12e avenue Nord Sherbrooke (Qu?bec) J1H 5N4 Canada For further information : Simon Labb?, Ph.D. (Simon.Labbe at usherbrooke.ca) In accordance with Canadian Immigration requirements, priority will be given to Canadian citizens and permanent residents of Canada. The Universit? de Sherbrooke is committed to the principle of equity in employment and offers equal employment opportunities to qualified applicants. Simon Labb?, Ph.D. Professeur agr?g? / Associate Professor D?partement de Biochimie (Biochemistry) Facult? de m?decine Universit? de Sherbrooke 3001, 12e Avenue Nord Sherbrooke (Qu?bec) Canada J1H 5N4 Tel.: (819) 564-5281 (Secretariat) Tel.: (819) 820-6868 ext.: 15460 (Bureau / Office) Tel.: (819) 820-6868 ext.: 15461 or 15841 (Labs) Fax: (819) 564-5340 e-mail: Simon.Labbe at USherbrooke.ca Web site: http://www.med.usherbrooke.ca/labo_labbe -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Ad for structural biochemistry and bioinformatics person.doc Type: application/msword Size: 33280 bytes Desc: Ad for structural biochemistry and bioinformatics person.doc URL: From gsmith at fhcrc.org Mon Oct 29 17:18:59 2007 From: gsmith at fhcrc.org (Gerald Smith) Date: Mon, 29 Oct 2007 10:18:59 -0700 (PDT) Subject: [Pombelist] postdoctoral position at the Hutchinson Center (Seattle) Message-ID: Postdoctoral Research Position Fred Hutchinson Cancer Research Center, Seattle A postdoctoral research position to study genetic recombination and DNA break repair is available in the lab of Gerald R. Smith in the Division of Basic Sciences at the Fred Hutchinson Cancer Research Center in Seattle. Our research uses both S. pombe and E. coli to investigate the mechanism and control of recombination. Both genetic and biochemical approaches are used. In S. pombe our research is on meiotic recombination. Emphasis is placed on the control of recombination by hotspots, meiotic DNA double-strand break (DSB) hotspots, such as M26, in S. pombe and Chi in E. coli. Additional research is on chromosome segregation in meiosis, with emphasis on the roles of chromosome pairing and recombination. For further information, see our websites: http://myprofile.cos.com/smithabc102 http://www.fhcrc.org/science/labs/gsmith/ Experience in genetics or biochemistry is required. Experience with microbes is valuable but not essential. Stipends follow the NIH guidelines for postdoctoral fellows. Starting date is flexible. The Division of Basic Sciences has approximately 30 labs pursuing research with organisms as diverse as bacteria, yeast, plants, worms, flies, fish, mice, and humans, in areas as diverse as protein structure, enzymology, evolution, development, behavior, and suspended animation. Close collaborations with the University of Washington, close by, are frequent. Seattle is outstanding for its culture and proximity to mountains and oceans for outdoor activities. Gerald R. Smith Division of Basic Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Avenue North, A1-162 P.O. Box 19024 Seattle, WA 98109-1024 United States of America Tel. 206-667-4438 FAX 206-667-6497 e-mail gsmith at fhcrc.org ______________________________________ Gerald R. Smith Fred Hutchinson Cancer Research Center 1100 Fairview Avenue North, A1-162 P.O. Box 19024 Seattle, WA 98109-1024 Tel. 206-667-4438 FAX 206-667-6497 From Janni.petersen at manchester.ac.uk Wed Oct 31 14:35:30 2007 From: Janni.petersen at manchester.ac.uk (Janni Petersen) Date: Wed, 31 Oct 2007 14:35:30 +0000 Subject: [Pombelist] Post-doc position Message-ID: Hi Would you please bring the attached to the attention of anyone that you think maybe interested. Many thanks Janni DOCTORAL RESEARCH ASSOCIATE ? YEAST CELL BIOLOGY (Environmental control over cell division and polarised growth) (Ref LS/121/07) You will join a research team investigating environmental control over cell division and polarised growth, using the fission yeast S.pombe as a model system. For more background information see Petersen, J. and Hagan, I. M. Nature. 435:507-512. 2005. Petersen and Nurse. 2007 Nature Cell Biology (advance online publications). You will focus on characterising the means by which kinase signalling regulates cytoskeletal transitions, using a wide range of contemporary molecular cell biology, biochemical and bio-imaging techniques. This position is available from 1 December 2007. The closing date for applications is 8 November 2007 ***************************************************** Janni Petersen University of Manchester Faculty of Life Sciences Michael Smith Building C.4255 Laboratory C.4223 Oxford Road Manchester M13 9PT United Kingdom Phone: 0161-275-5512 Lab: 0161-275-5107 FAX: 0161-275-5082 e-mail: Janni.Petersen at manchester.ac.uk ***************************************************** -------------- next part -------------- A non-text attachment was scrubbed... Name: DOCTORAL_RESEARCH_ASSOCIATE.doc Type: application/msword Size: 56320 bytes Desc: not available URL: From M.Luetzelberger at tu-bs.de Fri Nov 2 13:56:22 2007 From: M.Luetzelberger at tu-bs.de (Martin Luetzelberger) Date: Fri, 02 Nov 2007 14:56:22 +0100 Subject: [Pombelist] Q: V5-tag in fission yeast Message-ID: <472B2C86.60101@tu-bs.de> Dear all, I'd like to ask if any of you have experience with the V5 epitope tag (KPIPNPLLGLDST) in fission yeast. We used this tag for N-terminal tagging of two essential genes. Both constructs are driven by the thiamine-repressible nmt1-8 promoter. We observe that strains within which the respective genes were exchanged with their V5-tagged version grow normally as compared to the wildtype. Thus, we have no indication that the V5 tag interferes with protein function. However, when we switch off the nmt1-8 promoter by addition of thiamine, cells arrest early. Whereas the V5-tagged strains stop growth already 10 hours after addition of thiamine, strains with an HA- or myc-tag and the same genetic background arrest only after 12-14 hours. Thus, the V5-tagged proteins appear to be short-lived and might have faster turn-over rates. Since we observed this behavior with two different proteins, we don't think that it is a gene-specific effect. Has anyone of you ever used the V5-tag in S.pombe and made similar observations? Best regards, Martin Luetzelberger Institute of Genetics Technical University of Braunschweig Spielmannstr. 7 38 106 Braunschweig Germany Phone: +49 531 391 5784 or 5796 Fax: +49 531 391 5765 Email: M.Luetzelberger at tu-bs.de From hoffmacs at bc.edu Fri Nov 2 14:09:23 2007 From: hoffmacs at bc.edu (Charles Hoffman) Date: Fri, 02 Nov 2007 10:09:23 -0400 Subject: [Pombelist] Q: V5-tag in fission yeast In-Reply-To: <472B2C86.60101@tu-bs.de> References: <472B2C86.60101@tu-bs.de> Message-ID: We have not noticed any deleterious effects of V5-tagging, however I am not sure that we have any equivalent experiment to what you are describing, which may be a more sensitive assessment of function and stability. Charlie Hoffman Boston College "I'd rather be fission." | On Fri, 02 Nov 2007 14:56:22 +0100 | Martin Luetzelberger wrote: | Dear all, | | I'd like to ask if any of you have experience with the V5 epitope tag (KPIPNPLLGLDST) in fission yeast. | We used this tag for N-terminal tagging of two essential genes. Both constructs are driven by the | thiamine-repressible nmt1-8 promoter. | We observe that strains within which the respective genes were exchanged with their V5-tagged version | grow normally as compared to the wildtype. Thus, we have no indication that the V5 tag interferes with | protein function. | However, when we switch off the nmt1-8 promoter by addition of thiamine, cells arrest | early. Whereas the V5-tagged strains stop growth already 10 hours after addition of thiamine, strains | with an HA- or myc-tag and the same genetic background arrest only after 12-14 hours. Thus, the V5-tagged | proteins appear to be short-lived and might have faster turn-over rates. Since we observed this behavior with | two different proteins, we don't think that it is a gene-specific effect. | | Has anyone of you ever used the V5-tag in S.pombe and made similar observations? | | Best regards, | | Martin Luetzelberger | | Institute of Genetics | Technical University of Braunschweig | Spielmannstr. 7 | 38 106 Braunschweig | Germany | Phone: +49 531 391 5784 or 5796 | Fax: +49 531 391 5765 | Email: M.Luetzelberger at tu-bs.de | | _______________________________________________ | Pombelist mailing list | Pombelist at sanger.ac.uk | http://lists.sanger.ac.uk/mailman/listinfo/pombelist From forsburg at usc.edu Fri Nov 2 14:28:31 2007 From: forsburg at usc.edu (SLForsburg) Date: Fri, 02 Nov 2007 07:28:31 -0700 Subject: [Pombelist] Q: V5-tag in fission yeast In-Reply-To: <472B2C86.60101@tu-bs.de> References: <472B2C86.60101@tu-bs.de> Message-ID: <7AE83148-F54E-4E8F-B65C-2E9D3EC1C901@usc.edu> We have used the tag quite a bit, at the C-terminus., without problem. We have not used it at the N-terminus. Could it be that your construct has a sequence that invokes the N-end rule and thus increases protein turnover? On Nov 2, 2007, at 6:56 AM, Martin Luetzelberger wrote: > Dear all, > > I'd like to ask if any of you have experience with the V5 epitope > tag (KPIPNPLLGLDST) in fission yeast. > We used this tag for N-terminal tagging of two essential genes. > Both constructs are driven by the > thiamine-repressible nmt1-8 promoter. > We observe that strains within which the respective genes were > exchanged with their V5-tagged version > grow normally as compared to the wildtype. Thus, we have no > indication that the V5 tag interferes with > protein function. > However, when we switch off the nmt1-8 promoter by addition of > thiamine, cells arrest > early. Whereas the V5-tagged strains stop growth already 10 hours > after addition of thiamine, strains > with an HA- or myc-tag and the same genetic background arrest only > after 12-14 hours. Thus, the V5-tagged > proteins appear to be short-lived and might have faster turn-over > rates. Since we observed this behavior with > two different proteins, we don't think that it is a gene-specific > effect. > > Has anyone of you ever used the V5-tag in S.pombe and made similar > observations? > > Best regards, > > Martin Luetzelberger > > Institute of Genetics > Technical University of Braunschweig > Spielmannstr. 7 > 38 106 Braunschweig > Germany > Phone: +49 531 391 5784 or 5796 > Fax: +49 531 391 5765 > Email: M.Luetzelberger at tu-bs.de > > _______________________________________________ > Pombelist mailing list > Pombelist at sanger.ac.uk > http://lists.sanger.ac.uk/mailman/listinfo/pombelist {} {} {} {} {} {} {} {} {} {} {} {} {} {} S L Forsburg PhD, Professor University of Southern California Molecular & Computational Biology Ray R Irani Hall 1050 Childs Way, RRI 201B Los Angeles, CA 90089-2910 vox: 213-740-7342 fax: 213-740-8631 forsburg at usc.edu www.pombe.net -------------- next part -------------- An HTML attachment was scrubbed... URL: From bisht at webmail.imtech.res.in Fri Nov 2 17:25:31 2007 From: bisht at webmail.imtech.res.in (Kamlesh Bisht) Date: Fri, 2 Nov 2007 22:55:31 +0530 (IST) Subject: [Pombelist] Q: V5-tag in fission yeast In-Reply-To: <7AE83148-F54E-4E8F-B65C-2E9D3EC1C901@usc.edu> References: <472B2C86.60101@tu-bs.de> <7AE83148-F54E-4E8F-B65C-2E9D3EC1C901@usc.edu> Message-ID: hello martin i am convinced with SLForsburg that v5 tag invokes N-end degradation.just because of curiosity i have submitted V5 sequence to "ProtParam tool" available at http://www.expasy.ch/tools/protparam.html. it predicts half life of any protein depending on the nature of the amino acid at the amino terminus. considering K (lys)of V5 tag is coming at N-terminal of v5 tag sequence itself is showing half time of only three minutes in yeast.means its presence at n-terminal most likely destabilise the protein of interest. Estimated half-life:of (KPIPNPLLGLDST) The N-terminal of the sequence considered is K (Lys). The estimated half-life is: 1.3 hours (mammalian reticulocytes, in vitro). 3 min (yeast, in vivo). ****************************************** Kamlesh Kumar Bisht Research Scholar Yeast Molecular Biology Group IMTECH (CSIR) CHANDIGARH INDIA 160036 contact numbers: Personal +91-09872811845 Office : +91-0172-2690004 Extn 443 ********************************************* On Fri, 2 Nov 2007, SLForsburg wrote: > We have used the tag quite a bit, at the C-terminus., without problem. We > have not used it at the N-terminus. > > Could it be that your construct has a sequence that invokes the N-end rule > and thus increases protein turnover? > > > > > On Nov 2, 2007, at 6:56 AM, Martin Luetzelberger wrote: > >> Dear all, >> >> I'd like to ask if any of you have experience with the V5 epitope tag >> (KPIPNPLLGLDST) in fission yeast. >> We used this tag for N-terminal tagging of two essential genes. Both >> constructs are driven by the >> thiamine-repressible nmt1-8 promoter. >> We observe that strains within which the respective genes were exchanged >> with their V5-tagged version >> grow normally as compared to the wildtype. Thus, we have no indication that >> the V5 tag interferes with >> protein function. >> However, when we switch off the nmt1-8 promoter by addition of thiamine, >> cells arrest >> early. Whereas the V5-tagged strains stop growth already 10 hours after >> addition of thiamine, strains >> with an HA- or myc-tag and the same genetic background arrest only after >> 12-14 hours. Thus, the V5-tagged >> proteins appear to be short-lived and might have faster turn-over rates. >> Since we observed this behavior with >> two different proteins, we don't think that it is a gene-specific effect. >> >> Has anyone of you ever used the V5-tag in S.pombe and made similar >> observations? >> >> Best regards, >> >> Martin Luetzelberger >> >> Institute of Genetics >> Technical University of Braunschweig >> Spielmannstr. 7 >> 38 106 Braunschweig >> Germany >> Phone: +49 531 391 5784 or 5796 >> Fax: +49 531 391 5765 >> Email: M.Luetzelberger at tu-bs.de >> >> _______________________________________________ >> Pombelist mailing list >> Pombelist at sanger.ac.uk >> http://lists.sanger.ac.uk/mailman/listinfo/pombelist > > > {} {} {} {} {} {} {} {} {} {} {} {} {} {} > S L Forsburg PhD, Professor > University of Southern California > Molecular & Computational Biology > Ray R Irani Hall > 1050 Childs Way, RRI 201B > Los Angeles, CA 90089-2910 > > vox: 213-740-7342 > fax: 213-740-8631 > forsburg at usc.edu > www.pombe.net > > > From ibimbsm at bio.uni-stuttgart.de Tue Nov 13 09:32:59 2007 From: ibimbsm at bio.uni-stuttgart.de (Stefan Mangold) Date: Tue, 13 Nov 2007 10:32:59 +0100 Subject: [Pombelist] scFv-fusionprotein in S.pombe Message-ID: Dear Sir or Madam, in the Department of Molecular Biology at the University of Stuttgart, I have recently started my diploma thesis with the aim to express and secrete an scFv-fusion protein in Schizosaccharomyces pombe. The project is supervised by PD Dr Christina Wege in the group of Prof. Holger Jeske. The idea for this project has arosen since we have already used S. pombe for expression of a number of plant proteins, and in a collaborating institute, the Institute of Cell Biology and Immunology, scFv-fusion proteins have been expressed either in bacteria or in animal cells. Now, we want to try to combine our systems - but do not have any experience in antibody expression in yeast-based systems at all yet. Therefore, the first step of my work is to find out about an appropriate signal sequence, which should ensure the translocation of the scFv into the lumen of the ER and its entry into the secretory pathway. We hope to get functional antibodies for different applications by this method. During my literature research, I have now found a number of interesting publications. Since, however, I was not able to find any recent report on successful antibody production in S. pombe, I like to ask you if you might have any know-how or operating experience in expression and secretion of heterologous proteins in S. pombe, or perhaps even with scFv-antibodies or scFV-fusion proteins, respectively. Or maybe you can recommend somebody else who might have this experience? Helpful tips or information would assist us greatly and maybe avoid choosing a strategy which is not likely to be successful. At the moment, my main concern is the choice of a promising signal peptide sequence, as mentioned already. If you were interested, I would appreciate giving you a report about my experience later! Sincerely yours and best regards from Stuttgart, Stefan Mangold ----------------------------------------------------------- Stefan Mangold Department of Molecular Biology and Plant Virology Institute of Biology University of Stuttgart Pfaffenwaldring 57 D-70550 Stuttgart E-mail: stefan.mangold at bio.uni-stuttgart.de From nick.rhind at umassmed.edu Thu Nov 15 16:29:14 2007 From: nick.rhind at umassmed.edu (Nick Rhind) Date: Thu, 15 Nov 2007 11:29:14 -0500 Subject: [Pombelist] Searching for octosporus genes Message-ID: Those of you looking for your favorite gene in the octosporus genome at http://www.broad.mit.edu/annotation/genome/schizosaccharomyces_japonicus.3 should be aware that the octosporus genome has not yet annotated, so there are no predicted proteins or transcripts available. Therefore, you should not use BLASTP or BLASTX, and when you use BLASTN or TBLASTN, you need to search against the genomic sequence, not the transcripts. The octosporus automated annotation will be performed after the final draft assembly is released, hopefully early next year. Nick From jejasmin at ucsd.edu Tue Nov 20 08:24:54 2007 From: jejasmin at ucsd.edu (Jean-Nicolas Jasmin) Date: Tue, 20 Nov 2007 00:24:54 -0800 Subject: [Pombelist] growth on non-fermentable substrates Message-ID: <200711192022.lAJKMbIL009561@biomail.ucsd.edu> Dear all, I am working with Sz pombe strains FY261 and FY254 and I find it difficult to grow them on a non-fermentable substrate. On 5% YE and 2% glycerol and ethanol it takes about 2 weeks to get large colonies and the colonies show very high variation in size. I have tried solid media with yeast extract (1 to 5%) and glycerol (1 to 3%) and/or ethanol (1 to 3%), plus amino acids, and I obtain about the same result. Is this normal for these genotypes? Which strain should I use to obtain better growth on non-fermentable substrates? Is there another non-fermentable susbstrate that pombe use better? Note that I have previously posted this question at yeast at net.bio.net. I have received only one answer, advising me to use 0.1% glucose in the media. I am looking for other solutions as I need to grow pombe on non-fermentable substrates to select for resistance to erythromycin and chloramphenicol (mtDNA encoded resistances). Many thanks, Jean-Nicolas EBE, Biological Sciences, UCSD From nick.rhind at umassmed.edu Mon Nov 19 21:57:03 2007 From: nick.rhind at umassmed.edu (Nick Rhind) Date: Mon, 19 Nov 2007 16:57:03 -0500 Subject: [Pombelist] growth on non-fermentable substrates In-Reply-To: <200711192022.lAJKMbIL009561@biomail.ucsd.edu> Message-ID: Hi Jean-Nicolas, A lot of information on carbon source utilization by pombe is available at NCYC and CBS I don't know the genotypes of FY261 and FY254, but I doubt that you will find any differences in carbon source utilization between different strains; the lab strains of pombe are very homogeneous. Is your purpose to grow pombe on a non-fermentable carbon source to prevent mitochondrial loss during drug selection? If so, you may not have to worry. pombe is petit negative, and so should not be able to survive without mitochondrial function, even on a fermentable carbon source. Nick -- Nick Rhind Assistant Professor Biochemistry and Molecular Pharmacology University of Massachusetts Medical School 364 Plantation Street, LRB904 Worcester MA 01605 USA 1 (508) 856-8316:vox 1 (508) 856-8358:fax www.umassmed.edu/bmp/faculty/rhind.cfm From bonnefoy at cgm.cnrs-gif.fr Tue Nov 20 13:19:49 2007 From: bonnefoy at cgm.cnrs-gif.fr (Nathalie Bonnefoy) Date: Tue, 20 Nov 2007 14:19:49 +0100 Subject: [Pombelist] growth on non-fermentable substrates In-Reply-To: <200711192022.lAJKMbIL009561@biomail.ucsd.edu> References: <200711192022.lAJKMbIL009561@biomail.ucsd.edu> Message-ID: Hi Jean-Nicolas, For sure pombe cells do not grow well on glycerol. However, they will grow much better if they are ura4+: ura4 mutants are already rather compromised for growth on glycerol. If your strains are ura4- and if this marker is not necessary for your experiment, segregate it out. We use a mixture of ethanol glycerol that helps a bit: 1% yeast extract, 0.5% casaminoacids, 3% glycerol, 3% ethanol, 40 microg/ml adenine. However S. pombe respiratory chain mutants don't grow on galactose, which can be considered as a non-fermentable carbon source like for human cells even if it's fermentable for S. cerevisiae. Thus we also use galactose as non-fermentable carbon source, our medium is 1% yeast extract, 1% bactopeptone, 0.1% glucose, 2% galactose, 20 microg/ml adenine (the peptone here comes from an old cerevisiae recipe, it could be eliminated). But you can also try galactose without the 0.1% glucose (they will be slower to start growing), or you can reduce the glucose to 0.05%. I hope this helps, if you have any other questions please feel free to write again, I can forward you a review on pombe and mitochondrial studies, best wishes, Nathalie ________________________________________________________________________________ Nathalie Bonnefoy Centre de G?n?tique Mol?culaire CNRS B?timent 26 Avenue de la Terrasse 91198 Gif-sur-Yvette cedex Tel: (33) 1 69 82 31 75 Fax: (33) 1 69 82 31 60 e-mail: bonnefoy at cgm.cnrs-gif.fr >Dear all, > >I am working with Sz pombe strains FY261 and >FY254 and I find it difficult to grow them on a >non-fermentable substrate. On 5% YE and 2% >glycerol and ethanol it takes about 2 weeks to >get large colonies and the colonies show very >high variation in size. I have tried solid media >with yeast extract (1 to 5%) and glycerol (1 to >3%) and/or ethanol (1 to 3%), plus amino acids, >and I obtain about the same result. > >Is this normal for these genotypes? > >Which strain should I use to obtain better >growth on non-fermentable substrates? > >Is there another non-fermentable susbstrate that pombe use better? > >Note that I have previously posted this question >at yeast at net.bio.net. I have received only one >answer, advising me to use 0.1% glucose in the >media. I am looking for other solutions as I >need to grow pombe on non-fermentable substrates >to select for resistance to erythromycin and >chloramphenicol (mtDNA encoded resistances). > >Many thanks, > >Jean-Nicolas >EBE, Biological Sciences, UCSD > >_______________________________________________ >Pombelist mailing list >Pombelist at sanger.ac.uk >http://lists.sanger.ac.uk/mailman/listinfo/pombelist -- ________________________________________________________________________________ From hoffmacs at bc.edu Tue Nov 20 14:42:35 2007 From: hoffmacs at bc.edu (Charles Hoffman) Date: Tue, 20 Nov 2007 09:42:35 -0500 Subject: Fwd: [pombelist] Culturing S.pombe without glucose References: Message-ID: <2E9C0345-3BE5-4AA2-B237-486645E93061@bc.edu> This seems to be a popular topic that comes up ever few years. I will simply paste a previous exchange on carbon sources. I strongly agree with Nathalie that to get reasonable growth on glycerol, you need Ura+ cells. Cheers, Charlie Hoffman Begin forwarded message: > From: "Kurt Runge, Ph.D." > Date: June 11, 2004 1:07:56 PM EDT > To: hoffmacs at bc.edu, cynthia.turcotte.1 at UMontreal.CA > Subject: Re: [pombelist] Culturing S.pombe without glucose > > I have been also growing pombe in glycerol, but we have followed > the old Gutz et al. Handbook of Genetics (c. 1974) recipes. > > Basically, growth on a non-fermentable carbon source requires the > inclusion of replacements for citric acid cycle intermediates. In > the Gutz handbook for some recipes, this replacement was 0.37% mono > sodium glutamate (which is changed to alpha keto-glutarate by B6- > mediated transamination). This approach is the yeast version to > the old, difficult-to-understand adage in your biochemistry > textbooks "fats burn in the flame of carbohydrates", but done > without glycosis. > > Being an S. cerevisiae person by training, I have grown up an h- > ade6 ura4 leu1 his7 strain in 0.67% Yeast nitrogenbase with 150 mg/ > l supplements for auxotrophies plus 3% glycerol + 0.37% mono sodium > glutamate (from a 7.4% MSG filter-sterilized stock). After 2 > weeks, cells reach about 4e7 cells/ml by hemocytometer counts, > where as 3% glucose gives 6 e7 in similar medium without MSG. > > When I have done EMM2, I only get about 1 e8 cells per ml. > However, cell survival in EMM2 is better than the above medium > (called SDC). > > > Kurt Runge > > > > > Kurt Runge, Ph.D., Associate Staff > Cleveland Clinic Foundation > Lerner Research Institute > Dept. of Molecular Biology > 9500 Euclid Avenue, NC20 > Cleveland, OH 44195 > (216) 445-9771 FAX: (216) 444-0512 > http://www.lerner.ccf.org/molecbio/runge/ > >>>> "Charles S. Hoffman" - 6/8/04 10:54 AM >>> > You can use sucrose, maltose, or raffinose for somewhat reasonable > growth. > You can also grow on gluconate, but that is basically as poor as > glycerol. > > Cheers, > > Charlie Hoffman > Boston College > "I'd rather be fission." > > --On Tuesday, June 8, 2004 10:43 AM -0400 Cynthia Turcotte > wrote: > >> Dear PombeList >> >> I would like to have some advice on the culture of S. pombe with >> other >> carbon sources than glucose or glycerol. >> >> We tried already the following conditions: >> >> Both EMM and YE media >> with 0.35% lactic acid, or 2% lactic acid + EtOH, or potassium >> acetate or >> sodium >> acetate >> with or without 0.05% glucose, in each case. >> >> The only cultures that grew contained 0.05% glucose and they could >> not be >> diluted in a media lacking glucose. Moreover, these cultures did not >> grow to saturation; they attained the same O.D. as cultures >> containing >> only 0.05% glucose. >> >> >> Any suggestion will be greatly appreciated >> >> Thank you >> >> Cynthia Turcotte >> Dr. Luis A. Rokeach's laboratory >> Universit? de Montr?al >> >> >> >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From blewettn at mail.nih.gov Tue Nov 20 14:51:52 2007 From: blewettn at mail.nih.gov (Nathan Blewett) Date: Tue, 20 Nov 2007 09:51:52 -0500 Subject: [Pombelist] growth on non-fermentable substrates Message-ID: Jean-Nicolas, Our lab routinely uses Yeast Extract -dextrose + 3% glycerol as a growth assay for S. pombe. We have a strain, yYH1 which is ura4-, leu+, carrying a suppressor tRNA, and nonsense adenine allele, this strain grows well on this media, @ 32 and 37 degrees C. We also have several deletion strains which exhibit growth defects on non-fermentable carbon, both at elevated temperature, and the standard 32 deg.C. Generally, our wt strain will come up on these plates on day 3-4. Here is a link to the Forsburg lab page, a great resource for all things Pombe: http://www-rcf.usc.edu/~forsburg/media.html We use the YES recipe (0.5%YE), and subsitute glycerol for glucose. Not sure what your strains are, they may have a phenotype in this regard? I can also tell you that I have not been able to see growth on minimal media (EMM) with only non-fermentable carbon, only rich YEGly. Regards, Nate Blewett From forsburg at usc.edu Tue Nov 20 15:16:55 2007 From: forsburg at usc.edu (SLForsburg) Date: Tue, 20 Nov 2007 07:16:55 -0800 Subject: [pombelist] Culturing S.pombe without glucose In-Reply-To: <2E9C0345-3BE5-4AA2-B237-486645E93061@bc.edu> References: <2E9C0345-3BE5-4AA2-B237-486645E93061@bc.edu> Message-ID: I will post a summary of this discussion on the media page at pombe.net . Please keep the comments coming., and Jean-Nicolas, please if you could summarize any useful omments you got that were not sent to the list, that would be helpful. GEneral note: it's really helpful for the community if the conversations include the whole list. regarding pombe.net: if you notice errors or you have additions or protocols to add to the site, please email me! North American regional meeting in Los Angeles June 6-8 2008 http://www-rcf.usc.edu/~forsburg/pombemeeting.html {} {} {} {} {} {} {} {} {} {} {} {} {} {} S L Forsburg PhD, Professor University of Southern California Molecular & Computational Biology Ray R Irani Hall 1050 Childs Way, RRI 201B Los Angeles, CA 90089-2910 vox: 213-740-7342 fax: 213-740-8631 forsburg at usc.edu www.pombe.net -------------- next part -------------- An HTML attachment was scrubbed... URL: From forsburg at usc.edu Wed Nov 21 17:15:08 2007 From: forsburg at usc.edu (S L Forsburg) Date: Wed, 21 Nov 2007 09:15:08 -0800 Subject: [Pombelist] pombe.org and web notes Message-ID: Hi everyone, I use the domain name pombe.net for our main pombe pages, though I also own the domain pombe.org. Since everyone uses pombe.net to visit our site, I see no reason to hold onto pombe.org My ownership will expire at the end of this month, so if anyone wants to pick up pombe.org for more pombe on the web, it will be available on Nov 30. Happy Thanksgiving! susan PS: I have summarized the recent discussion of growth on non- fermentable carbon sources at http://www-rcf.usc.edu/~forsburg/media.html#glycerol If you have other information, protocols, or suggestions for the pombe pages, please let me know. I would like to keep this as up to date and useful for the community as possible. I also rely on you to tell me about broken links, etc. we hae over 50 pages on our web site and I rely on the readers to keep it current. >>>>>>>>>>>>>>>>>>>>>>>>>>> Susan L Forsburg PhD Professor, Molecular & Computational Biology Chair, Molecular Biology Graduate Committee University of Southern California RRI 201 1050 Childs Way Los Angeles CA 90089-2910 -------------- next part -------------- An HTML attachment was scrubbed... URL: From marti5_kupiec at yahoo.com Mon Dec 3 15:48:42 2007 From: marti5_kupiec at yahoo.com (Martin Kupiec) Date: Mon, 3 Dec 2007 07:48:42 -0800 (PST) Subject: [Pombelist] FACS Message-ID: <533334.14499.qm@web34314.mail.mud.yahoo.com> Hi everybody! We are new to the field of FACS in pombe, and I have the following observation: After adding hydroxyurea my favorite mutant stays in G2, but slowly/surely the peak spreads to the right (to what appears as higher and higher DNA content). Somehow this "smells" like some sort of artifact, and not endoreduplication (I don't see a 2C peak turn into a 4C, rather a migration of the distribution, that also gets wider as time passes). Has anybody seen this before? It seems as if for some reason the cells accumulate higher propidium iodide content, although they are not particularly longer... Any ideas/suggestions? Thanks! Martin Kupiec Dept. of Molecular Micro & Biotech, Tel Aviv University, Ramat Aviv 69978, Israel. Phone: 972-3-640-9031 FAX: 972-3-640-9407 E-mail: martin at post.tau.ac.il http://www.tau.ac.il/lifesci/departments/biotech/members/kupiec/kupiec.html ____________________________________________________________________________________ Be a better pen pal. Text or chat with friends inside Yahoo! Mail. See how. http://overview.mail.yahoo.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From ssazer at bcm.edu Mon Dec 3 16:44:29 2007 From: ssazer at bcm.edu (Shelley Sazer) Date: Mon, 3 Dec 2007 10:44:29 -0600 Subject: [Pombelist] FACS In-Reply-To: <533334.14499.qm@web34314.mail.mud.yahoo.com> References: <533334.14499.qm@web34314.mail.mud.yahoo.com> Message-ID: <9640309A-C9EC-45CC-8899-AC3C091148FD@bcm.edu> Martin, I published a paper on this very topic: Sazer S, Sherwood SW. Mitochondrial growth and DNA synthesis occur in the absence of nuclear DNA replication in fission yeast. J Cell Sci. 1990 Nov;97 ( Pt 3):509-16 Let me know if you have other questions. Shelley Dr. Shelley Sazer Associate Professor Department of Biochemistry Room BCM 375A Mail Stop BCM 125 Baylor College of Medicine 1 Baylor Plaza Houston, Texas 77030 U.S.A. e-mail: ssazer at bcm.edu phone: (713) 798-4531 FAX: (713) 796-9438 -------------- next part -------------- An HTML attachment was scrubbed... URL: From huberman at buffalo.edu Mon Dec 3 17:05:50 2007 From: huberman at buffalo.edu (Joel Huberman) Date: Mon, 03 Dec 2007 12:05:50 -0500 Subject: [Pombelist] FACS In-Reply-To: <533334.14499.qm@web34314.mail.mud.yahoo.com> References: <533334.14499.qm@web34314.mail.mud.yahoo.com> Message-ID: Dear Martin, What mutant are you looking at, and what concentration of HU are you using? Answers to these questions are needed in order to provide a complete response to your inquiry. Wild-type fission yeast cells accumulate with an approximately haploid (1C) DNA content when incubated in high concentrations of HU (approximately 10 mM and higher). In fact, these cells have a slightly greater than 1C DNA content, because they're really in early S phase. Early origins fire in HU, and replication forks move a few kb away from those early origins before slowing down due to dNTP depletion. Even after the forks have slowed, they continue to move slowly (in wild-type cells), and their rate of movement appears to be inversely correlated with the HU concentration. Note that when fission yeast cells enter S phase in the presence of HU, the cells are initially binucleate. Although each nucleus has a DNA content of approximately 1C, the cell has a DNA content of approximately 2C. A short time (30-50 minutes) after entry into S phase, these cells go through cytokinesis and become mononucleate, with approximately 1C DNA in each cell. It is this accumulation of mononucleate cells with approximately 1C DNA content that is most noticeable when log phase fission yeast cells are incubated with HU for long times (greater than an hour). Are you sure that the peak you're describing as 2C is truly 2C and not 1C? Whether 2C or 1C, the slow rightward progression could be a consequence of either or both of the following two factors: (i) slow ongoing nuclear and mitochondrial DNA synthesis, because HU does not completely block DNA synthesis (unlikely if your HU concentration is 20 mM or greater); or (ii) changes in cell shape and size, which in turn affect the intensity of the fluorescence signal perceived by your flow cytometer. Generally, even when the DNA content of a cell remains constant, the fluorescence signal will become larger as cell size increases. In both cases, the width of the distribution will increase with time, due to heterogeneity among cells in rate of DNA synthesis and/or rate of cell size increase. I hope this information helps you. If you would be willing to send me your flow cytometry profiles by e-mail, I could attempt to provide a more educated guess. With best wishes, Joel Huberman On Dec 3, 2007, at 10:48 AM, Martin Kupiec wrote: > Hi everybody! > We are new to the field of FACS in pombe, and I have the following > observation: After adding hydroxyurea my favorite mutant stays in > G2, but slowly/surely the peak spreads to the right (to what appears > as higher and higher DNA content). Somehow this "smells" like some > sort of artifact, and not endoreduplication (I don't see a 2C peak > turn into a 4C, rather a migration of the distribution, that also > gets wider as time passes). Has anybody seen this before? It seems > as if for some reason the cells accumulate higher propidium iodide > content, although they are not particularly longer... > Any ideas/suggestions? > Thanks! > > Martin Kupiec > Dept. of Molecular Micro & Biotech, > Tel Aviv University, > Ramat Aviv 69978, Israel. > Phone: 972-3-640-9031 > FAX: 972-3-640-9407 > E-mail: martin at post.tau.ac.il > http://www.tau.ac.il/lifesci/departments/biotech/members/kupiec/kupiec.html > > > Be a better friend, newshound, and know-it-all with Yahoo! Mobile. > Try it now._______________________________________________ > Pombelist mailing list > Pombelist at sanger.ac.uk > http://lists.sanger.ac.uk/mailman/listinfo/pombelist -------------- next part -------------- An HTML attachment was scrubbed... URL: From nick.rhind at umassmed.edu Mon Dec 3 21:40:52 2007 From: nick.rhind at umassmed.edu (Nick Rhind) Date: Mon, 03 Dec 2007 16:40:52 -0500 Subject: [Pombelist] FACS In-Reply-To: <533334.14499.qm@web34314.mail.mud.yahoo.com> Message-ID: Hi Martin, The rightward drift you see over time as your cells elongate in the HU arrest is most likely, as you suspect, due to the accumulation of cytoplasmic background not DNA replication and is, as Shelly points out, an old problem in pombe flow cytometry. We avoid the problem by analyzing isolated nuclei instead of whole cells. This approach is not much more difficult than the standard whole-cell prep and gives much cleaner data. Our protocol is adapted from Carlson et al. (1997) Yeast 13:1329 and can be found in Forsburg and Rhind (2006) Basic methods for fission yeast. Yeast 23(3):173 The surprising result is that your favorite mutant arrests in G2; that is not a phenotype I have ever seen before. One would expect cells to arrest in early S as ~1C. As Joel points out, cells just arresting in S will be binucleate and thus have 2C DNA content. I guess it is possible that your mutant is failing to complete cytokinesis. The isolated nuclei protocol would sort that out, as would microscopic examination of your arrested cells. Another, perhaps more likely, explanation is that you are getting enough rightward drift that at the first time point your arrested cells have already drifted over from 1C, where they should be, to 2C. Good luck, Nick From tongke at bc.edu Tue Dec 4 22:26:43 2007 From: tongke at bc.edu (Kevin Tong) Date: Tue, 04 Dec 2007 17:26:43 -0500 Subject: [Pombelist] Spot assays Message-ID: Hi everyone! I am having a little bit of a technical issue when trying to perform some spots assays using strains of S.pombe on different types of solid media (i.e. YEA, EMMG, 5FOA, etc.). I find that I am unable to make consistent circular spots on my plates. Spots on some plates will spot perfectly. Some spots on other plates will hardly spread out at all and remain very small and compact. Others will "bleed" into each other or make amoeba-like shapes. I have tried drying the plates in a variety of ways (quickly, slowly, wetter, drier), but nothing seems to work very well. Does anybody know why this is happening and what I can do to generate more consistent spots? I've noticed that different types of plates will spot differently as well. Does it have something to do with the type of media being used? Thanks in advance, Kevin .???`?.. ><((((?>`?.??.><((((?> Kevin Tong Annunziato Lab Boston College, Higgins Hall Rm. 400 140 Commonwealth Ave. Chestnut Hill, MA 02467 Lab Phone: (617) 552-3110 Fax: (617) 552-2011 .???`?.. ><((((?>`?.??.><((((?> From Alison.Pidoux at ed.ac.uk Wed Dec 5 00:00:42 2007 From: Alison.Pidoux at ed.ac.uk (Alison L Pidoux) Date: Wed, 05 Dec 2007 00:00:42 +0000 Subject: [Pombelist] Spot assays In-Reply-To: References: Message-ID: <20071205000042.c546zgt1c0g8cgkw@www.staffmail.ed.ac.uk> Dear Kevin, Different solid media do produce different spot shapes / sizes. However, the dryness of the plates is the most important thing. Freshly-poured plates are a disaster. They should be dried (we use a laminar flow hood for 30-60 min) until there is no liquid around the plate and dryness lines have begun to appear on the agar. Alternatively, leave plates out on the bench for a couple of days after pouring. Using a 48-pin 'hedge-hog' will give nice small consistent spots (probably 2-3 ul transferred). If you are pipetting with a multichannel pipettor, don't use more than 5 ul per spot. Spots will soak into the agar within a couple on minutes on a perfectly dried plate. Hope this helps. Alison Quoting Kevin Tong : > Hi everyone! > I am having a little bit of a technical issue when trying to > perform some spots assays using strains of S.pombe on different > types of solid media (i.e. YEA, EMMG, 5FOA, etc.). I find that I am > unable to make consistent circular spots on my plates. Spots on > some plates will spot perfectly. Some spots on other plates will > hardly spread out at all and remain very small and compact. Others > will "bleed" into each other or make amoeba-like shapes. I have > tried drying the plates in a variety of ways (quickly, slowly, > wetter, drier), but nothing seems to work very well. Does anybody > know why this is happening and what I can do to generate more > consistent spots? I've noticed that different types of plates will > spot differently as well. Does it have something to do with the > type of media being used? > > Thanks in advance, > Kevin > > .???`?.. ><((((?>`?.??.><((((?> > Kevin Tong > Annunziato Lab > Boston College, Higgins Hall Rm. 400 > 140 Commonwealth Ave. > Chestnut Hill, MA 02467 > Lab Phone: (617) 552-3110 > Fax: (617) 552-2011 > .???`?.. ><((((?>`?.??.><((((?> > > > > > _______________________________________________ > Pombelist mailing list > Pombelist at sanger.ac.uk > http://lists.sanger.ac.uk/mailman/listinfo/pombelist > > Alison Pidoux Allshire Lab Wellcome Trust Centre for Cell Biology, Insitute of Cell Biology, The University of Edinburgh, 6.4 Swann Building Mayfield Road Edinburgh EH9 3JR -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From steven.sanders at case.edu Wed Dec 5 01:18:08 2007 From: steven.sanders at case.edu (Steven Sanders) Date: Tue, 4 Dec 2007 20:18:08 -0500 Subject: [Pombelist] Spot assays In-Reply-To: References: Message-ID: Dear Kevin, >From our experience the best way to spot pombe is to use a multichannel pipette with 5ul spots. For some unknown reason we have never been able to get consistent results with "pinners". As others have mentioned dry plates are essential. You can use a hood but we just leave the plates on the beach for at least two days after pouring. Good luck, Steven Sanders On 12/4/07, Kevin Tong wrote: > > Hi everyone! > I am having a little bit of a technical issue when trying to perform > some spots assays using strains of S.pombe on different types of solid > media (i.e. YEA, EMMG, 5FOA, etc.). I find that I am unable to make > consistent circular spots on my plates. Spots on some plates will spot > perfectly. Some spots on other plates will hardly spread out at all and > remain very small and compact. Others will "bleed" into each other or make > amoeba-like shapes. I have tried drying the plates in a variety of ways > (quickly, slowly, wetter, drier), but nothing seems to work very well. Does > anybody know why this is happening and what I can do to generate more > consistent spots? I've noticed that different types of plates will spot > differently as well. Does it have something to do with the type of media > being used? > > Thanks in advance, > Kevin > > .???`?.. ><((((?>`?.??.><((((?> > Kevin Tong > Annunziato Lab > Boston College, Higgins Hall Rm. 400 > 140 Commonwealth Ave. > Chestnut Hill, MA 02467 > Lab Phone: (617) 552-3110 > Fax: (617) 552-2011 > .???`?.. ><((((?>`?.??.><((((?> > > > > > _______________________________________________ > Pombelist mailing list > Pombelist at sanger.ac.uk > http://lists.sanger.ac.uk/mailman/listinfo/pombelist > -- Steven L. Sanders, Ph.D. Assistant Professor of Biochemistry Case Comprehensive Cancer Center Case Western Reserve University 10900 Euclid Ave. Cleveland, OH. 44106-7285 Visitors and Deliveries: Wolstein Research Bldg. 3-503 Phone: 216 235 1858 Fax: 216 368 8919 steven.sanders at case.edu http://www.case.edu/med/sanders/sanderslab/Home.html -------------- next part -------------- An HTML attachment was scrubbed... URL: From WXJ580 at bham.ac.uk Wed Dec 5 14:22:10 2007 From: WXJ580 at bham.ac.uk (Jikai Wen) Date: Wed, 5 Dec 2007 14:22:10 +0000 Subject: [Pombelist] FISH protocol Message-ID: <169903AA38587249812CF4B7388131DED1786D221E@mbx5> Hi Everybody, I am going to do FISH in S.pombe to check my RNA localization by four 50 nt specific probes, which have C6 amino-modification on dT and could be labelled by Cy3. I get the yeast FISH protocol from my collegue that works excellent in budding. I am wondering that what's the difference for the cell spheroplasting between fission yeast and budding yeast, simply in budding, they always use lyticase and perform it in ~10 to 15 minutes after fixation but in Nurse-lab protocol, they use zymolyase and novozyme with 90 min incubation. Does somebody have the FISH protocol in pombe? Thank you very much! Cheers, Jikai From WXJ580 at bham.ac.uk Mon Dec 10 13:28:38 2007 From: WXJ580 at bham.ac.uk (Jikai Wen) Date: Mon, 10 Dec 2007 13:28:38 +0000 Subject: [Pombelist] about FISH in S.pombe Message-ID: <169903AA38587249812CF4B7388131DED1786D2225@mbx5> Hi everybody, I am going to do FISH in S.pombe to check my RNA localization by four 50 nt specific probes, which have C6 amino-modification on dT and could be labelled by Cy3. I get the yeast FISH protocol from my collegue that works excellent in budding. I am wondering that what's the difference for the cell spheroplasting between fission yeast and budding yeast, simply in budding, they always use lyticase and zymolyase, and perform it in ~10 to 15 minutes after fixation but in Nurse-lab protocol, they use zymolyase and novozyme with 90 min incubation. Does somebody have the FISH protocol in pombe? Thank you very much! Cheers, Jikai Wen Birmingham University, Edgbaston, Birmingham, UK. B15 2TT