From weibinz from med.umich.edu Wed Apr 1 13:50:03 2009 From: weibinz from med.umich.edu (Weibin Zhou) Date: Wed Apr 1 13:58:59 2009 Subject: [Zbrafish] Latest Zebrafish Microarray? Message-ID: <49D37F1A.8167.0008.0@med.umich.edu> Dear Colleagues: Although Affimatrix is marketing a microarray set for zebrafish expression analysis, it seems to me that its design is kind of outdated as their webpage shows the chip was designed according to the genome release of 2003. so I am looking for an up-to-date version of microarray for zebrafish. If you happen to know any information about this, I'd appreciate if you could reply. Thanks a lot. Weibin ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues From georg.otto from tuebingen.mpg.de Wed Apr 1 14:35:43 2009 From: georg.otto from tuebingen.mpg.de (Georg Otto) Date: Wed Apr 1 14:36:46 2009 Subject: [Zbrafish] Latest Zebrafish Microarray? In-Reply-To: <49D37F1A.8167.0008.0@med.umich.edu> References: <49D37F1A.8167.0008.0@med.umich.edu> Message-ID: Dear Weibin, afaik the most updated zebrafish microarray is the one from Agilent, which I think has been designed 2007. Check their website here: http://www.chem.agilent.com/en-us/products/instruments/dnamicroarrays/ zebrafisholigomicroarraykit/pages/default.aspx Hope that helps, Georg On 1 Apr 2009, at 20:50, Weibin Zhou wrote: > Dear Colleagues: > > Although Affimatrix is marketing a microarray set for zebrafish > expression analysis, it seems to me that its design is kind of > outdated as their webpage shows the chip was designed according to > the genome release of 2003. so I am looking for an up-to-date > version of microarray for zebrafish. If you happen to know any > information about this, I'd appreciate if you could reply. > > Thanks a lot. > > Weibin > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and > should not be used for urgent or sensitive issues > > _______________________________________________ > Zbrafish mailing list > Zbrafish@net.bio.net > http://www.bio.net/biomail/listinfo/zbrafish From jfreema from purdue.edu Wed Apr 1 15:29:56 2009 From: jfreema from purdue.edu (Freeman, Jennifer L) Date: Wed Apr 1 15:32:22 2009 Subject: [Zbrafish] Latest Zebrafish Microarray? In-Reply-To: <49D37F1A.8167.0008.0@med.umich.edu> References: <49D37F1A.8167.0008.0@med.umich.edu> Message-ID: <00DAC672DD52D748A0D603373F2EA0D40680FEE1@EXCH06.purdue.lcl> There is also a Zv7 (2007) expression array available from NimbleGen (http://www.nimblegen.com/products/exp/eukaryotic.html). Jennifer ******************************************* Jennifer L. Freeman, Ph.D. Assistant Professor of Toxicology Purdue University School of Health Sciences 550 Stadium Mall Dr. CIVL-1277 West Lafayette, IN 47907 E-mail: jfreema@purdue.edu Phone: (765) 494-1408 Fax: (765) 496-1377 ******************************************* -----Original Message----- From: zbrafish-bounces@oat.bio.indiana.edu [mailto:zbrafish-bounces@oat.bio.indiana.edu] On Behalf Of Weibin Zhou Sent: Wednesday, April 01, 2009 2:50 PM To: zbrafish@oat.bio.indiana.edu Subject: [Zbrafish] Latest Zebrafish Microarray? Dear Colleagues: Although Affimatrix is marketing a microarray set for zebrafish expression analysis, it seems to me that its design is kind of outdated as their webpage shows the chip was designed according to the genome release of 2003. so I am looking for an up-to-date version of microarray for zebrafish. If you happen to know any information about this, I'd appreciate if you could reply. Thanks a lot. Weibin ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues _______________________________________________ Zbrafish mailing list Zbrafish@net.bio.net http://www.bio.net/biomail/listinfo/zbrafish From julien.roux from unil.ch Thu Apr 2 02:21:41 2009 From: julien.roux from unil.ch (Julien Roux) Date: Thu Apr 2 11:18:18 2009 Subject: [Zbrafish] Re: Latest Zebrafish Microarray? References: Message-ID: <0cc3dfc2-4ae7-452f-9ed1-3f2dfcee1b96@y7g2000yqa.googlegroups.com> Dear Weibin, Even if the design is outdated, you can find an up-to-date mapping of the probesets to the latest genome assembly in EnsEMBL (http:// www.ensembl.org/Danio_rerio/Info/Index) You can retrieve this mapping with Biomart for example (http:// www.ensembl.org/biomart/martview/) Hope this helps Julien From miguelfiliperamos from gmail.com Fri Apr 3 16:54:07 2009 From: miguelfiliperamos from gmail.com (esbinho) Date: Fri Apr 3 17:04:02 2009 Subject: [Zbrafish] Bacterial fish pathogens models Message-ID: Hi all I am doing my PhD with bacterial fish pathogens, and I am thinking in using Zebrafish as a model! As anyone in the group has done this, that is willing to take me for a few weeks and teach me?!?! I have my own funding, and need to learn how to develop infection models in zebra fish! Thanks in advance for all your help Miguel From anne_streit from web.de Wed Apr 8 08:50:51 2009 From: anne_streit from web.de (Anne Streit) Date: Wed Apr 8 11:34:31 2009 Subject: [Zbrafish] FW: where to get zebrafish Message-ID: <1338558473@web.de> > -----Urspr?ngliche Nachricht----- > Von: "Anne Streit" > Gesendet: 08.04.09 15:09:55 > An: zbrafish@magpie.bio.indiana.edu > Betreff: where to get zebrafish > > Dear all! > > Do you know where you can get adult zebrafish from, apart from T?bingen? I would > like to get T?-WT... I established some techniques in my lab but need to build up a new > aquaria system with new fish, but I don?t know where to get them from.. > > best regards Anne __________________________________________________________________________ Verschicken Sie SMS direkt vom Postfach aus - in alle deutschen und viele ausl?ndische Netze zum gleichen Preis! https://produkte.web.de/webde_sms/sms From Christian.Lawrence from childrens.harvard.edu Wed Apr 8 11:40:55 2009 From: Christian.Lawrence from childrens.harvard.edu (Lawrence, Christian) Date: Wed Apr 8 12:04:41 2009 Subject: [Zbrafish] FW: where to get zebrafish In-Reply-To: <1338558473@web.de> Message-ID: ZIRC www.zebrafish.org University College London http://www.ucl.ac.uk/zebrafish-group/fishfacility.php On 4/8/09 9:50 AM, "Anne Streit" wrote: > -----Urspr?ngliche Nachricht----- > Von: "Anne Streit" > Gesendet: 08.04.09 15:09:55 > An: zbrafish@magpie.bio.indiana.edu > Betreff: where to get zebrafish > > Dear all! > > Do you know where you can get adult zebrafish from, apart from T?bingen? I would > like to get T?-WT... I established some techniques in my lab but need to build up a new > aquaria system with new fish, but I don?t know where to get them from.. > > best regards Anne __________________________________________________________________________ Verschicken Sie SMS direkt vom Postfach aus - in alle deutschen und viele ausl?ndische Netze zum gleichen Preis! https://produkte.web.de/webde_sms/sms _______________________________________________ Zbrafish mailing list Zbrafish@net.bio.net http://www.bio.net/biomail/listinfo/zbrafish The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. From v-ambriz from windstream.net Wed Apr 8 14:57:46 2009 From: v-ambriz from windstream.net (v-ambriz@windstream.net) Date: Wed Apr 8 14:58:28 2009 Subject: [Zbrafish] Paramecium Message-ID: <20090408145746.64TLB.679212.root@ispmxfep13-z01> Does any one has a good protocol for breeding and feeding paramecium for fry? I being using the one that it comes with the culture, however, I don't get enough reproduction. Plus I will like to know if some one has a better food, than the wheat grains that my culture comes with. From Christian.Lawrence from childrens.harvard.edu Wed Apr 8 15:04:10 2009 From: Christian.Lawrence from childrens.harvard.edu (Lawrence, Christian) Date: Wed Apr 8 15:05:27 2009 Subject: [Zbrafish] Paramecium In-Reply-To: <20090408145746.64TLB.679212.root@ispmxfep13-z01> Message-ID: ZIRC does. Their protocol is up on their website. www.zebrafish.org On 4/8/09 3:57 PM, "v-ambriz@windstream.net" wrote: Does any one has a good protocol for breeding and feeding paramecium for fry? I being using the one that it comes with the culture, however, I don't get enough reproduction. Plus I will like to know if some one has a better food, than the wheat grains that my culture comes with. _______________________________________________ Zbrafish mailing list Zbrafish@net.bio.net http://www.bio.net/biomail/listinfo/zbrafish The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. From Christian.Broesamle from med.uni-muenchen.de Thu Apr 9 09:05:40 2009 From: Christian.Broesamle from med.uni-muenchen.de (Christian Broesamle) Date: Thu Apr 9 11:37:46 2009 Subject: [Zbrafish] anaesthetic for physiology Message-ID: Hi all, Does anyone know of an anaesthetic that can be used in an electrophysiology paradigm in fish? We are interested in measuring nerve conductance velocity. Tricaine/Mesab/MS-222 blocks action potentials and therefore is useless for us. Has anyone used curare to block movements? What about analgesics? Thanks, Christian -- *********************************** Christian Br?samle Department of Biochemistry Ludwig-Maximilians-Universit?t M?nchen Schillerstrasse 44 80336 M?nchen Germany tel: +49 89 2180 75-451 fax: +49 89 2180 75-415 *********************************** From jasmine.blight from adelaide.edu.au Wed Apr 15 00:37:54 2009 From: jasmine.blight from adelaide.edu.au (jasmine.blight@adelaide.edu.au) Date: Wed Apr 15 11:24:56 2009 Subject: [Zbrafish] HA, FLAG and GFP tags in zebrafish Message-ID: Has anyone ever encountered any problems with detecting HA, FLAG or GFP tags in zebrafish expressing constructs containing these tags? I have used HRP conjugated anti-HA and FLAG antibodies as well as a non-conjugated anti-HA mouse antibody and have consistently got the same non-specific banding. From Christian.Broesamle from med.uni-muenchen.de Thu Apr 16 04:25:27 2009 From: Christian.Broesamle from med.uni-muenchen.de (Christian Broesamle) Date: Thu Apr 16 11:06:04 2009 Subject: [Zbrafish] HA, FLAG and GFP tags in zebrafish In-Reply-To: References: Message-ID: Did you deyolk your embryos? If you detect the same non-specific bands with different secondary ABs, it could be that you have some very highly abundant, sticky proteins in your prep. Did you try immunostainings? You may see whether the same structures are stained. Regarding tags: we detected background labelling on very few, but clearly stained neurons using an anti-myc-tag AB in non-transgenic larvae/embryos. Clearly, one has to be careful and do the approriate controls! Christian >Has anyone ever encountered any problems with detecting HA, FLAG or >GFP tags in zebrafish expressing constructs containing these tags? > >I have used HRP conjugated anti-HA and FLAG antibodies as well as a >non-conjugated anti-HA mouse antibody and have consistently got the >same non-specific banding. > >_______________________________________________ >Zbrafish mailing list >Zbrafish@net.bio.net >http://www.bio.net/biomail/listinfo/zbrafish -- *********************************** Christian Br?samle Department of Biochemistry Ludwig-Maximilians-Universit?t M?nchen Schillerstrasse 44 80336 M?nchen Germany tel: +49 89 2180 75-451 fax: +49 89 2180 75-415 *********************************** From ihussain from lincoln.ac.uk Fri Apr 17 06:00:31 2009 From: ihussain from lincoln.ac.uk (Issam Hussain) Date: Fri Apr 17 11:20:29 2009 Subject: [Zbrafish] cryosectionning methods Message-ID: <05EB201423015E4CBC59DF30AE7687EB0F0B60@AEXCMS03.network.uni> Hi everyone I am searching for standard cryosectionning protocol, I am actually doing chondrogenic differeniation using stem cells. Is any one got a cryosectionning protocol? Thank you Issam From jeedward from yahoo.com Sun Apr 19 10:50:51 2009 From: jeedward from yahoo.com (John Edward) Date: Mon Apr 20 11:15:07 2009 Subject: [Zbrafish] Extended draft paper submission: BCBGC-09 call for papers Message-ID: <527802.29049.qm@web45906.mail.sp1.yahoo.com> Extended draft paper submission: BCBGC-09 call for papers ? This Extended Call for Papers for the 2009 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-09) (website: http://www.PromoteResearch.org ) is for those who didn't get a chance to submit the papers for the earlier call for papers. The papers received and accepted in response to this extended call for papers will be included in the final version of the respective conference proceedings. These proceedings will be either ready by the time of the conference (i.e., they will be available during the conference) or soon after the conference (before the end of August 2009), based how fast the proceedings can be prepared. Note: If you have already submitted a paper (whether accepted or rejected or currently under review) for MULTICONF-09, please DO NOT submit that paper again to this extended call for papers. IMPORTANT DATES: Draft paper submission date: May 11, 2009 Acceptance/rejection decision: May 21, 2009 Camera ready paper and copyright and pre-registration due: May 28, 2009 Conference dates: July 13-16, 2009 ? ? BCBGC-09 will be held during July 13-16 2009 in Orlando, FL, USA. The conference will take place at the same time and venue where several other international conferences are taking place. The other conferences include: ????????? International Conference on Artificial Intelligence and Pattern Recognition (AIPR-09) ????????? International Conference on Automation, Robotics and Control Systems (ARCS-09) ????????? International Conference on Enterprise Information Systems and Web Technologies (EISWT-09) ????????? International Conference on High Performance Computing, Networking and Communication Systems (HPCNCS-09) ????????? International Conference on Information Security and Privacy (ISP-09) ????????? International Conference on Recent Advances in Information Technology and Applications (RAITA-09) ????????? International Conference on Software Engineering Theory and Practice (SETP-09) ????????? International Conference on Theory and Applications of Computational Science (TACS-09) ????????? International Conference on Theoretical and Mathematical Foundations of Computer Science (TMFCS-09) ? The website http://www.PromoteResearch.org contains more details. ? Sincerely John Edward Publicity committee -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.bio.net/bionet/mm/zbrafish/attachments/20090419/683ff080/attachment.html From MultiliteUSA from cs.com Tue Apr 21 18:27:09 2009 From: MultiliteUSA from cs.com (MultiliteUSA@cs.com) Date: Wed Apr 22 12:00:31 2009 Subject: [Zbrafish] Thought I'd pass along bulb pricing Message-ID: Mike, Keep us in mind for your Osram HBO 103W/2 requirements, we can offer them for $105.00 each. Regards, Dale Butler Multi-Lite USA, Inc. 408 426-1443 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.bio.net/bionet/mm/zbrafish/attachments/20090421/9f50efad/attachment.html From samiramiss.s from gmail.com Fri Apr 24 23:47:21 2009 From: samiramiss.s from gmail.com (samiramiss.s@gmail.com) Date: Tue Apr 28 11:14:27 2009 Subject: [Zbrafish] zebrafish breeding Message-ID: hello Can anybody help me for zebrafish breeding? From rburdine from Princeton.EDU Tue Apr 28 11:20:55 2009 From: rburdine from Princeton.EDU (Burdine, Rebecca D) Date: Tue Apr 28 11:25:22 2009 Subject: [Zbrafish] zebrafish breeding In-Reply-To: References: Message-ID: <790DAC09623D0A47ACDB126E3C52D8B614D96A@MBCLUSTER.pu.win.princeton.edu> Probably. What is your question'/problem? --------------------------------------------------- Rebecca D. Burdine, Ph.D. Assistant Professor Dept. of Molecular Biology Princeton University Washington Road Mof 433 Princeton, NJ 08544? ? Phone:?(609) 258-7515 Fax: (609) 258-6730 Email: rburdine@princeton.edu Admin Assistant: Anna Schmedel (609) 258-5028 > -----Original Message----- > From: zbrafish-bounces@oat.bio.indiana.edu [mailto:zbrafish- > bounces@oat.bio.indiana.edu] On Behalf Of samiramiss.s@gmail.com > Sent: Saturday, April 25, 2009 12:47 AM > To: bionet-organisms-zebrafish@moderators.isc.org > Subject: [Zbrafish] zebrafish breeding > > hello > > Can anybody help me for zebrafish breeding? > > _______________________________________________ > Zbrafish mailing list > Zbrafish@net.bio.net > http://www.bio.net/biomail/listinfo/zbrafish From zfinadmin from gmail.com Tue Apr 28 11:51:43 2009 From: zfinadmin from gmail.com (zfinadmin@gmail.com) Date: Tue Apr 28 12:38:37 2009 Subject: [Zbrafish] An imaging course at UCL Message-ID: <40986d97-0504-4dbf-b541-5b5d98c419cd@f41g2000pra.googlegroups.com> 3.5 days 8 – 11 June 2009 Applications are requested from students and post-docs who wish to attend a 3.5 day imaging workshop at UCL focusing on confocal microscopy techniques. The workshop will run from the morning of the 8th June to lunchtime on the 11th June. Registration and accommodation costs will be covered by the ZF-MODELS Integrated Project (www.zf-models.org). Course outline: Day 1 – lectures Basics of microscopy: setting up Koehler illumination, Phase contrast, DIC. Point spread functions and optical resolution. Objectives – what do all the codes mean? What are the benefits and drawbacks of the different objectives? Which one should I choose for what job? Introduction to confocal microscopy: Confocal principle, optical paths, signal cross talk. Digital images, optical vs digital resolution, pixels, voxels and grey levels. Digital and physical regions of interest - scanning and analysis. Optical sectioning and 3D reconstruction and rendering methods. Live cell imaging confocal and multiphoton confocal microscopy: FRET, FRAP, FLIP, FLIM. 2 photon concept, advantages and drawbacks. SHG and THG imaging. Image analysis and 3D reconstruction: Image composition and properties. Signal co-localization analysis. Deconvolution analysis. Application of algorithms to improve image quality – dangers! 3D reconstruction, volume rendering and visualization. Comparison of software packages available. Fluorescent probes and cell labeling: Basics of fluorescence, luminescence and spectral properties and consideration. Chemical fluorophores, fluorescent proteins (standard and advanced), FLAsh ReAsh bi-arsinical probes. Labelling techniques, bathing, AM dyes, electroportation, transfection microinjection, gene gun. Day 2 & 3 & 4 – circus of practical classes to rotate round in groups of 4 (to make sure everyone gets hands on experience). 1. Basic microscope set up and alignment for Koehler illumination, Phase contrast, DIC. Alignment of Hg lamps. Confocal basics – image acquisition, correct dynamics range, eliminate cross talk, Z series, lambda scan, image projection and rotation. 2. Live cell imaging FRAP and FRET techniques. 3. Multiphoton and second harmonic imaging. 4. Image analysis and 3D reconstruction practical. 5. Zebrafish specific module - high-resolution fish brain imaging, including some detail on transgenics, mounting, imaging, reconstruction and presentation Deadline for applications: 10th May 2009 To apply, send a CV & cover letter explaining why you would like to attend and a letter of support from your lab to Steve Wilson (s.wilson@ucl.ac.uk) From zfinadmin from gmail.com Wed Apr 29 18:28:43 2009 From: zfinadmin from gmail.com (zfinadmin@gmail.com) Date: Wed Apr 29 18:32:59 2009 Subject: [Zbrafish] 6th European Zebrafish meeting Abstract Submission Deadline: April 30, 2009 Message-ID: Hello Everyone: Abstract submission and on-line registration for the 6th European Zebrafish meeting closes tomorrow, April 30. Abstract Submission Deadline: April 30, 2009. Abstracts submitted after the deadline will not be accepted. So please hurry and upload your abstracts for the meeting. http://www.zebrafish2009.org/home.html We look forward to seeing you in Rome. best fishes, The ZF2009 Organizing Committee e-mail: scientific.committee@zebrafish2009.org