From jschumac from mdanderson.org Tue Dec 2 17:18:03 2008 From: jschumac from mdanderson.org (jschumac@mdanderson.org) Date: Tue Dec 2 17:39:04 2008 Subject: [Zbrafish] Assistant Professor-UT MD Anderson Cancer Center Message-ID: <33a7ec5b-b633-47cd-bc73-d60a86c7ba2e@k8g2000yqn.googlegroups.com> Available immediately: One Tenure-Track Faculty Position at Assistant Professor Level The Department of Genetics at The University of Texas M. D. Anderson Cancer Center seeks an outstanding and highly interactive basic research scientist. The successful candidate's research uses genetic approaches in model organisms (e.g., C. elegans, Drosophila, yeast, zebra fish, mouse). The department seeks to complement its existing programs in developmental biology, DNA repair, RNA splicing, cell division and human and mouse cancer genetics. Applicants must hold a Ph.D. and/or M.D. degree, and will be expected to develop an internationally recognized, extramurally funded research program. We offer a very attractive recruitment package, active graduate and postdoctoral training programs and the unmatched scientific environment of the Texas Medical Center, the world’s largest biomedical center. To apply, please send, in a single pdf file: Cover Letter Curriculum vitae Short Research Summary (three page maximum) Contact information for three references Deadline for application is December 31, 2008. Send to: GeneticModelSearch@mdanderson.org Jill M. Schumacher, Ph.D. Associate Professor Department of Genetics The University of Texas M. D. Anderson Cancer Center 1515 Holcombe Blvd., Unit 1010 Houston, TX 77030 From noopur.mandrekar from gmail.com Wed Dec 3 02:51:12 2008 From: noopur.mandrekar from gmail.com (Noopur) Date: Wed Dec 3 12:02:40 2008 Subject: [Zbrafish] high fat diet Message-ID: Dear All, For one of my experiments, I would like to give my fish a high fat diet . Can anyone suggest me a recipe (for high fat diet) for the same? Thanking you in advance, With Best Wishes, Noopur Mandrekar Piramal Life Sciences Limited Mumbai, India. From jocelyn.mcauley from gmail.com Wed Dec 3 17:46:21 2008 From: jocelyn.mcauley from gmail.com (Jocelyn) Date: Wed Dec 3 18:41:32 2008 Subject: [Zbrafish] seasonal mortality? Message-ID: <4f90c044-4746-438b-9df9-ed600a20cc8c@a37g2000pre.googlegroups.com> I'm curious how many people here subscribe to the belief of seasonal mortality with regards to nursery set ups and baby fish (one month old or less). If so, which is your worst season for survivability? From Christian.Lawrence from childrens.harvard.edu Thu Dec 4 06:50:29 2008 From: Christian.Lawrence from childrens.harvard.edu (Lawrence, Christian) Date: Thu Dec 4 12:16:26 2008 Subject: [Zbrafish] seasonal mortality? Message-ID: <54F197250C79354BA5A2D4584D8D9FDA3FAD1770AC@CHEXCCRV1.CHBOSTON.ORG> I am deeply skeptical of this. I have worked with these fish for over nine years in different physical locations and have never observed such patterns. Still it would be interesting to look at any long term data sets that people out there may have to look at trends. In instances where such trends are apparent, my guess would be that human factors are at the root of it, not seasonality. Chris Lawrence ----- Original Message ----- From: zbrafish-bounces@oat.bio.indiana.edu To: bionet-organisms-zebrafish@moderators.isc.org Sent: Wed Dec 03 17:46:21 2008 Subject: [Zbrafish] seasonal mortality? I'm curious how many people here subscribe to the belief of seasonal mortality with regards to nursery set ups and baby fish (one month old or less). If so, which is your worst season for survivability? _______________________________________________ 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 jeedward from yahoo.com Thu Dec 4 11:17:14 2008 From: jeedward from yahoo.com (John Edward) Date: Thu Dec 4 12:16:56 2008 Subject: [Zbrafish] BCBGC-09 call for papers Message-ID: <3926.683.qm@web45904.mail.sp1.yahoo.com> BCBGC-09 call for papers ? The 2009 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-09) (website: http://www.PromoteResearch.org ) will be held during July 13-16 2009 in Orlando, FL, USA. We invite draft paper submissions. 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/20081204/b2db3874/attachment.html From jocelyn.mcauley from gmail.com Thu Dec 4 14:17:33 2008 From: jocelyn.mcauley from gmail.com (Jocelyn) Date: Thu Dec 4 14:18:45 2008 Subject: [Zbrafish] Re: seasonal mortality? References: Message-ID: <5b8452f9-f447-4978-b1eb-18a0ed61c4e2@z6g2000pre.googlegroups.com> My experience: + I've worked with zebrafish for 14 years in two locations. + I do believe in seasonal mortality: early fall The University of Oregon maintains a good database of nursery stats. I'd love to see what they have to say regarding this. From Christian.Lawrence from childrens.harvard.edu Thu Dec 4 14:28:06 2008 From: Christian.Lawrence from childrens.harvard.edu (Lawrence, Christian) Date: Thu Dec 4 14:34:35 2008 Subject: [Zbrafish] Re: seasonal mortality? In-Reply-To: <5b8452f9-f447-4978-b1eb-18a0ed61c4e2@z6g2000pre.googlegroups.com> Message-ID: Perhaps if Bill T. is out there reading this he might chime in... In the meantime, what exactly do you see? What are your thoughts as to why this might be happening? What do you mean by "seasonal mortality"? I've been thinking about this a bit, and perhaps this type of thing could be happening if the environment wasn't very well-controlled, i.e. your building's parameters are not well-buffered from seasonal change. Even if this were the case, it makes more sense in terms of downticks in spawning behavior, etc. but larval survival is harder for me to understand. This doesn't mean that it isn't happening. I'm just skeptical. CL On 12/4/08 2:17 PM, "Jocelyn" wrote: My experience: + I've worked with zebrafish for 14 years in two locations. + I do believe in seasonal mortality: early fall The University of Oregon maintains a good database of nursery stats. I'd love to see what they have to say regarding this. _______________________________________________ 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 david from zebrafish.org Thu Dec 4 14:43:17 2008 From: david from zebrafish.org (David Lains) Date: Thu Dec 4 16:58:25 2008 Subject: [Zbrafish] Re: seasonal mortality? In-Reply-To: <5b8452f9-f447-4978-b1eb-18a0ed61c4e2@z6g2000pre.googlegroups.com> References: <5b8452f9-f447-4978-b1eb-18a0ed61c4e2@z6g2000pre.googlegroups.com> Message-ID: <002101c95648$90aed220$b20c7660$@org> Hi Jocelyn I think there are a few factors that could be effecting this including seasonal variations in HVAC systems or source water conditions... Best Fishes David Lains <}}}>< Aquaculturist, Research Assistant Zebrafish International Resource Center 5274 University of Oregon Eugene, Or 97403 Email: david@zebrafish.org pH: (541) 346-6028 ext. 18 fax: (541) 346-6151 -----Original Message----- From: zbrafish-bounces@oat.bio.indiana.edu [mailto:zbrafish-bounces@oat.bio.indiana.edu] On Behalf Of Jocelyn Sent: Thursday, December 04, 2008 11:18 AM To: bionet-organisms-zebrafish@moderators.isc.org Subject: [Zbrafish] Re: seasonal mortality? My experience: + I've worked with zebrafish for 14 years in two locations. + I do believe in seasonal mortality: early fall The University of Oregon maintains a good database of nursery stats. I'd love to see what they have to say regarding this. _______________________________________________ Zbrafish mailing list Zbrafish@net.bio.net http://www.bio.net/biomail/listinfo/zbrafish From dgw5079 from u.washington.edu Thu Dec 4 15:36:33 2008 From: dgw5079 from u.washington.edu (David G. White) Date: Thu Dec 4 16:59:00 2008 Subject: [Zbrafish] Re: seasonal mortality? In-Reply-To: Message-ID: Hello, we have never noticed a problem in the fall except in one lab that does not have a RO/DI water source. In this small lab we have to filter city tap water ourselves. During the fall our filters and dosing systems are running at maximum capacity. The city may switch reservoirs, or reservoir quality may change with the rainy season, or perhaps our dosing the change is a problem but we do see a slight down turn in survival in younger sensitive fish. We do not see any differences in our other labs with a source water coming from large commercial RO/DI systems. So perhaps its in the water, but if your in full control of your environment I do not believe in seasonality in the fish. David G White Research Coordinator H225 Zebrafish Lab University of Washington Department of Biological Structure HSB G514 Box 357420 1959 NE Pacific Street Seattle, WA 98195-7420 Tel. 206-685-7512 FAX 206-543-1524 On Thu, 4 Dec 2008, Lawrence, Christian wrote: > Perhaps if Bill T. is out there reading this he might chime in... > > In the meantime, what exactly do you see? > > What are your thoughts as to why this might be happening? > > What do you mean by "seasonal mortality"? > > I've been thinking about this a bit, and perhaps this type of thing could be happening if the environment wasn't very well-controlled, i.e. your building's parameters are not well-buffered from seasonal change. > Even if this were the case, it makes more sense in terms of downticks in spawning behavior, etc. but larval survival is harder for me to understand. This doesn't mean that it isn't happening. I'm just skeptical. > > CL > > > On 12/4/08 2:17 PM, "Jocelyn" wrote: > > My experience: > + I've worked with zebrafish for 14 years in two locations. > + I do believe in seasonal mortality: early fall > > The University of Oregon maintains a good database of nursery stats. > I'd love to see what they have to say regarding this. > > _______________________________________________ > 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. > > > > > > > _______________________________________________ > Zbrafish mailing list > Zbrafish@net.bio.net > http://www.bio.net/biomail/listinfo/zbrafish > From mwinandy from ulg.ac.be Fri Dec 5 03:23:35 2008 From: mwinandy from ulg.ac.be (Marie Winandy) Date: Fri Dec 5 11:41:10 2008 Subject: [Zbrafish] Re:seasonal mortality? In-Reply-To: <200812041703.mB4H3CV23913@net.bio.net> References: <200812041703.mB4H3CV23913@net.bio.net> Message-ID: <200812050923350109.001FBFAF@smtp.ulg.ac.be> Hi all, I didn't notice seasonal mortality in the larvae, but a strain effect : some strain survive very well, while other don't. I suspect it's related to the transgene or mutation they have. On the other hand, at each end of summer, I notice a decrease in eggs production. Did someone expreience something similar? Best regards, M. Winandy Marie Winandy, PhD Universitι de Liθge GIGA B34 - Zebrafish Platform Avenue de l'Hτpital 1 B-4000 Liθge - Sart Tilman Belgique Tιl: +32.4.366.99.71 +32.4.366.33.38 +32.476.97.25.33 Fax: +32.4.366.41.98 email : mwinandy@ulg.ac.be or zebrafish.giga@ulg.ac.be http://www.giga.ulg.ac.be/extranet/services.htm From anandc from missouri.edu Fri Dec 5 15:01:04 2008 From: anandc from missouri.edu (Anand) Date: Fri Dec 5 15:05:38 2008 Subject: [Zbrafish] Tenure-track position at Oklahoma Message-ID: <86e353a7-6dcc-4491-9be6-176102e8925e@t11g2000yqg.googlegroups.com> Hi, I am forwarding this email about a faculty search at Oklahoma. Best wishes, Anand We are searching for a developmental biologist. We are a "neuroethology-friendly" department. Please forward to appropriate colleagues and/or post the job ad below. Thanks, Ari ************************************************** Ari Berkowitz, Ph.D. Associate Professor Director, Cellular & Behavioral Neurobiology Ph.D. Program Department of Zoology University of Oklahoma 730 Van Vleet Oval Norman, OK 73019 Phone: 405-325-3492 Fax: 405-325-6202 E-mail: ari@ou.edu Web: http://faculty-staff.ou.edu/B/Robert.A.Berkowitz-1/ http://www.ou.edu/cbn/ ************************************************** University of Oklahoma Department of Zoology Developmental Biologist The Department of Zoology, University of Oklahoma, invites applications for a tenure-track position at the Assistant Professor level, beginning August 2009. We seek an outstanding researcher and teacher with broad interests in developmental biology to join an integrative zoology department. Preference will be given to applicants whose research and teaching interests complement our existing strengths in development, neurobiology, cell signaling, behavior, ecology and evolutionary biology. We expect the applicant to establish an externally- funded research program and contribute to undergraduate and graduate teaching, including a core undergraduate course in developmental biology each year. In alternate semesters, the candidate will have the opportunity to develop a specialty course(s) in her/his area of interest. Our successful candidate will have a PhD and demonstrated ability to conduct significant independent research as judged by publications. Send curriculum vitae, reprints/preprints, and research and teaching statements, and arrange to have three letters of recommendation sent to Chair, Developmental Biology Search Committee, Department of Zoology, The University of Oklahoma, 730 Van Vleet Oval, Norman, OK, 73019, or as PDFs to zoology@ou.edu. Further information about the Department of Zoology is available at zoology.ou.edu. Screening of candidates will begin December 15, 2008 and will continue until the position is filled. The University of Oklahoma is an Equal Opportunity/Affirmative Action Employer. Women and minority candidates are encouraged to apply. From Poem.Turner from gmail.com Mon Dec 8 11:46:58 2008 From: Poem.Turner from gmail.com (lyrik162) Date: Mon Dec 8 12:34:18 2008 Subject: [Zbrafish] Post-doc Position at NCSU Message-ID: The laboratory of Dr. Jeffrey Yoder in the Department of Molecular Biomedical Sciences at North Carolina State University invites outstanding applications for an NIH funded Postdoctoral Research Associate. This position will be on an initial one-year contract, with a possibility of renewal. The broad objective of the project is to develop light-activated tools for the regulation of gene function in cell culture and zebrafish embryos. To be considered, applicants must have a Ph.D. in a biological or related discipline. Experience with modern molecular biology and cell culture techniques is required and expertise in RNA biology and/or gene regulation is preferred. The ideal candidate will be highly motivated, open-minded, and enthusiastic about working in the laboratory with scientists at all levels of training. Compensation is commensurate with experience. Applications should include a detailed cover letter, curriculum vitae, and the names and contact information for at least two references. Application materials must be submitted online at http://jobs.ncsu.edu, referencing position B-96-0819. Informal inquiries are encouraged and should be directed to Dr. Jeffrey Yoder, Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough Street, Raleigh, NC 27695, jeff_yoder@ncsu.edu. The position will remain open until a suitable candidate is found. North Carolina State University is an Equal Opportunity/Affirmative Action Employer. In addition, NC State University welcomes all persons without regard to sexual orientation. From wtpenber from mac.com Sat Dec 6 16:32:09 2008 From: wtpenber from mac.com (W. Todd Penberthy) Date: Mon Dec 8 12:34:45 2008 Subject: [Zbrafish] td-tomato vs mcherry as a red fluo reporter In-Reply-To: References: Message-ID: I have seen incredibly bright results with tandem dimer-tomato, but have not made a germ-line animal yet. Animals harboring apparently single tdT (+) neurons were easily detected even with a 2.5 objective. We did not find the signal to be too interfering to visualization of neighboring cells when expressed in just a few cells, however, when it was expressed in skin we could not see through tdT very well when using the TR filter. Best, W. Todd Penberthy On Oct 21, 2008, at 11:22 AM, Philippe Herbomel wrote: > Dear All, > > We are wondering about the best red fluorescent reporter to make > transgenic zebrafish with. > If one does not want to target the protein to a particular > compartment (membrane or nucleus), DsRed2, the most used > presently, is probably the best (very bright, with reasonable > maturation time). > If otherwise, the most used presently is mCherry, which is quite (4- > fold) less bright. > Now from the Tsien lab papers' data, td-Tomato appears both much > (over 5-fold) brighter than mCherry, and still compatible with > membrane or nuclear targeting; > and indeed at least two papers then provided evidence that td- > tomato was not only far superior to mcherry but even to GFP (in > terms of brightness) as a reporter in transgenic mice. > Now surprisingly, when a colleague of us injected either mcherry or > tdtomato mRNA into 1-cell zebrafish embryos, > she found td-Tomato to be less bright than mcherry. > So my question is: has anyone found this too, and/or tried to make > transgenic zebrafish with td-Tomato as reporter ? And what about > its actual brightness (and decay upon illumination) in zebrafish > embryos/larvae, as compared to the mcherry and dsred2 ? > > Thanks in advance for your testimonies on this. > I will post a summary of your responses ! > > Philippe Herbomel > > > ––––––––––––––––––––––––––––––––––––––––– > Philippe Herbomel > Unite Macrophages et Developpement de l'Immunite > Departement de Biologie du Developpement > Institut Pasteur > 25 rue du Dr Roux, 75724 Paris cedex 15, France > > tel. : 33 1 44 38 95 29 mobile: 33 6 73 35 74 20 > fax : 33 1 45 68 89 21 > http://www.pasteur.fr/recherche/RAR/RAR2006/Mdi-en.html > –––––––––––––––––––––––––––––––––––––– > Change the world one loan at a time - visit Kiva.org to find out how > > > > _______________________________________________ > Zbrafish mailing list > Zbrafish@net.bio.net > http://www.bio.net/biomail/listinfo/zbrafish -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.bio.net/bionet/mm/zbrafish/attachments/20081206/152a2221/attachment.html From wtpenber from mac.com Sat Dec 6 16:32:09 2008 From: wtpenber from mac.com (W. Todd Penberthy) Date: Mon Dec 8 12:35:26 2008 Subject: [Zbrafish] td-tomato vs mcherry as a red fluo reporter In-Reply-To: References: Message-ID: I have seen incredibly bright results with tandem dimer-tomato, but have not made a germ-line animal yet. Animals harboring apparently single tdT (+) neurons were easily detected even with a 2.5 objective. We did not find the signal to be too interfering to visualization of neighboring cells when expressed in just a few cells, however, when it was expressed in skin we could not see through tdT very well when using the TR filter. Best, W. Todd Penberthy On Oct 21, 2008, at 11:22 AM, Philippe Herbomel wrote: > Dear All, > > We are wondering about the best red fluorescent reporter to make > transgenic zebrafish with. > If one does not want to target the protein to a particular > compartment (membrane or nucleus), DsRed2, the most used > presently, is probably the best (very bright, with reasonable > maturation time). > If otherwise, the most used presently is mCherry, which is quite (4- > fold) less bright. > Now from the Tsien lab papers' data, td-Tomato appears both much > (over 5-fold) brighter than mCherry, and still compatible with > membrane or nuclear targeting; > and indeed at least two papers then provided evidence that td- > tomato was not only far superior to mcherry but even to GFP (in > terms of brightness) as a reporter in transgenic mice. > Now surprisingly, when a colleague of us injected either mcherry or > tdtomato mRNA into 1-cell zebrafish embryos, > she found td-Tomato to be less bright than mcherry. > So my question is: has anyone found this too, and/or tried to make > transgenic zebrafish with td-Tomato as reporter ? And what about > its actual brightness (and decay upon illumination) in zebrafish > embryos/larvae, as compared to the mcherry and dsred2 ? > > Thanks in advance for your testimonies on this. > I will post a summary of your responses ! > > Philippe Herbomel > > > ––––––––––––––––––––––––––––––––––––––––– > Philippe Herbomel > Unite Macrophages et Developpement de l'Immunite > Departement de Biologie du Developpement > Institut Pasteur > 25 rue du Dr Roux, 75724 Paris cedex 15, France > > tel. : 33 1 44 38 95 29 mobile: 33 6 73 35 74 20 > fax : 33 1 45 68 89 21 > http://www.pasteur.fr/recherche/RAR/RAR2006/Mdi-en.html > –––––––––––––––––––––––––––––––––––––– > Change the world one loan at a time - visit Kiva.org to find out how > > > > _______________________________________________ > Zbrafish mailing list > Zbrafish@net.bio.net > http://www.bio.net/biomail/listinfo/zbrafish -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.bio.net/bionet/mm/zbrafish/attachments/20081206/152a2221/attachment-0003.html From aquagopal from gmail.com Mon Dec 8 21:10:44 2008 From: aquagopal from gmail.com (A. Gopalakrishnan) Date: Tue Dec 9 11:45:33 2008 Subject: [Zbrafish] Proceedings of the XIth International Pigment Cell Conference, Sendai Message-ID: Dear sir, Please send me the following articel "Proceedings of the XIth International Pigment Cell *Conference*, Sendai" It will be usefull to my study on fish tumour. Rewgards Sincerely, A. Gopalakrishnan -- __________________________________ Ayyaru GOPALAKRISHNAN, M.Sc., M.Sc.,M.A.,Ph.D., Lecturer (Coastal Aquaculture & Livelihood) Centre of Advanced Study in Marine Biology Annamalai University, Parangipettai 608 502 Tamil Nadu, India Mobile:09443537538 Email: ag_krishnan@yahoo.com aquagopal@gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.bio.net/bionet/mm/zbrafish/attachments/20081209/0ddaeee9/attachment.html From estelle.hirsinger from pasteur.fr Tue Dec 9 10:29:39 2008 From: estelle.hirsinger from pasteur.fr (Estelle Hirsinger) Date: Tue Dec 9 11:45:52 2008 Subject: [Zbrafish] Antibodies against Integrin beta-1, alpha-5 and alpha-6 Message-ID: Dear All, Would someone know of antibodies against Integrin beta-1, alpha-5 and alpha-6 that work in zebrafish in immunofluorescence ? Thank you very much for your precious help ! Best, Estelle From jocelyn.mcauley from gmail.com Wed Dec 10 18:16:28 2008 From: jocelyn.mcauley from gmail.com (Jocelyn) Date: Wed Dec 10 18:18:55 2008 Subject: [Zbrafish] Re: seasonal mortality? References: Message-ID: Off list I received three emails indicating a shared experience of increased nursery mortality in fall. More about our parameters: + we have an RO/DI water source. + we have consistent personnel year round (ie full time staff, no student workers). + we feed powdered AP diet and raise brine shrimp for our nursery fish (no paramecia, rotifers, etc ). + another zebrafish facility in the same building reported anecdotally about similar problems at the same time. Will seasonal changes in city water persist through a RO/DI system? I'm coming to think so? thanks for your feedback. As always, its been interesting. From jocelyn.mcauley from gmail.com Wed Dec 10 18:42:46 2008 From: jocelyn.mcauley from gmail.com (Jocelyn) Date: Wed Dec 10 18:43:52 2008 Subject: [Zbrafish] IACUC help Message-ID: <84da77bf-e675-496f-af04-1c910d3c8892@u18g2000pro.googlegroups.com> Is it normal for an IACUC to request and maintain a copy of our fish database? They are very keen on wanting to know all of our stain names and numbers. Also, any hints on dealing with a mammal biased IACUC? - ex: how do I support that "harem breeding" (IACUC phrase: more than one fish of opposite sex) is not unusual/harmful to fish? thanks From dgw5079 from u.washington.edu Wed Dec 10 18:57:47 2008 From: dgw5079 from u.washington.edu (David G. White) Date: Wed Dec 10 19:48:59 2008 Subject: [Zbrafish] Re: seasonal mortality? In-Reply-To: Message-ID: Hello, if your on a purely RO water supply I would guess not. That system would just have a higher reject volume, water not passing through the membrane. You might notice this if your RO pressure or volume is lower than normal, unless you have ample capacity. With a purely DI system yes, it does not reject water and only removes ions in the water. Water will pass through the resin of a DI system regardless of quality (even if the resin is spent). DI is more common then RO water in my experience. Sounds like you are on a centralized system. I would contact whomever services the system. It might require more frequent maintenance during the fall, carbon filters, resin or membranes. David G White Research Coordinator H225 Zebrafish Lab University of Washington Department of Biological Structure HSB G514 Box 357420 1959 NE Pacific Street Seattle, WA 98195-7420 Tel. 206-685-7512 FAX 206-543-1524 On Wed, 10 Dec 2008, Jocelyn wrote: > Off list I received three emails indicating a shared experience of > increased nursery mortality in fall. > > More about our parameters: > + we have an RO/DI water source. > + we have consistent personnel year round (ie full time staff, no > student workers). > + we feed powdered AP diet and raise brine shrimp for our nursery fish > (no paramecia, rotifers, etc ). > + another zebrafish facility in the same building reported anecdotally > about similar problems at the same time. > > Will seasonal changes in city water persist through a RO/DI system? > I'm coming to think so? > > thanks for your feedback. > As always, its been interesting. > > _______________________________________________ > Zbrafish mailing list > Zbrafish@net.bio.net > http://www.bio.net/biomail/listinfo/zbrafish > From dgw5079 from u.washington.edu Wed Dec 10 19:21:53 2008 From: dgw5079 from u.washington.edu (David G. White) Date: Wed Dec 10 19:49:20 2008 Subject: [Zbrafish] IACUC help In-Reply-To: <84da77bf-e675-496f-af04-1c910d3c8892@u18g2000pro.googlegroups.com> Message-ID: Is this a ABSL1 lab? I would think your IACUC would be happy to just know your tracking your fish i.e. population and mortality. Anything above a ABSL1 lab perhaps. Your institute needs a aquatic veterinarian to combat the mammals. As for your example I would say that zebra fish are aggressive spawners particularly males. In order to divide a "alpha" males attention it is often necessary to spawn them with other fish, females and other males (if need be). This also supports the social structure of the fish. An aggressive male fish can kill a female on a pair-wise cross, thank goodness for dividers. Have them come in to your lab just after lights on and have them watch some fish spawning or tape it for them. Harem breeding is very common in the zebra fish world and safe. David G White Research Coordinator H225 Zebrafish Lab University of Washington Department of Biological Structure HSB G514 Box 357420 1959 NE Pacific Street Seattle, WA 98195-7420 Tel. 206-685-7512 FAX 206-543-1524 On Wed, 10 Dec 2008, Jocelyn wrote: > Is it normal for an IACUC to request and maintain a copy of our fish > database? > They are very keen on wanting to know all of our stain names and > numbers. > > Also, any hints on dealing with a mammal biased IACUC? > - ex: how do I support that "harem breeding" (IACUC phrase: more than > one fish of opposite sex) is not unusual/harmful to fish? > > thanks > > _______________________________________________ > Zbrafish mailing list > Zbrafish@net.bio.net > http://www.bio.net/biomail/listinfo/zbrafish > From Christian.Broesamle from med.uni-muenchen.de Thu Dec 11 03:26:31 2008 From: Christian.Broesamle from med.uni-muenchen.de (Christian Broesamle) Date: Thu Dec 11 12:23:21 2008 Subject: [Zbrafish] IACUC help In-Reply-To: References: Message-ID: This may be a somewhat dangerous argument to make. The IACUC may turn it around and even require you to do group breedings. I'd rather go with proven safety and the fact that in nature ZF are schooling fish and occur in rel. high densities and probably 'harem breed' there too. Christian >As for your example I would say that zebra fish >are aggressive spawners particularly males. In >order to divide a "alpha" males attention it is >often necessary to spawn them with other fish, >females and other males (if need be). This also >supports the social structure of the fish. An >aggressive male fish can kill a female on a >pair-wise cross, thank goodness for dividers. >Have them come in to your lab just after lights >on and have them watch some fish spawning or >tape it for them. > >Harem breeding is very common in the zebra fish world and safe. > > >David G White >Research Coordinator >H225 Zebrafish Lab >University of Washington >Department of Biological Structure >HSB G514 Box 357420 >1959 NE Pacific Street >Seattle, WA 98195-7420 >Tel. 206-685-7512 >FAX 206-543-1524 > >On Wed, 10 Dec 2008, Jocelyn wrote: > >>Is it normal for an IACUC to request and maintain a copy of our fish >>database? >>They are very keen on wanting to know all of our stain names and >>numbers. >> >>Also, any hints on dealing with a mammal biased IACUC? >>- ex: how do I support that "harem breeding" (IACUC phrase: more than >>one fish of opposite sex) is not unusual/harmful to fish? >> >>thanks >> >>_______________________________________________ >>Zbrafish mailing list >>Zbrafish@net.bio.net >>http://www.bio.net/biomail/listinfo/zbrafish >> > > > > >_______________________________________________ >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 Christian.Lawrence from childrens.harvard.edu Wed Dec 10 21:35:53 2008 From: Christian.Lawrence from childrens.harvard.edu (Lawrence, Christian) Date: Thu Dec 11 12:24:33 2008 Subject: [Zbrafish] Re: seasonal mortality? In-Reply-To: Message-ID: I see the logic in seasonal changes in water supply, but I guess the reason why I tend to not be much of a believer in this affecting survival in controlled facilities is that these changes, if and when they occur, should be for the most part be detected by routine water quality testing. However, I suppose at least one problematic parameter that would go undetected in most facilities (ours included) is chloramines/chlorines. One could certainly imagine a scenario in which there is an increase in the use of such chemical treatments during the fall in certain regions, and if you're not testing for it (because you don't expect it to be there), AND your RO water service provider (if you have one) isn't checking for it, or isn't maintaining the RO system properly, then it could get through and be causing a problem. In such circumstances, one could simply test for it to see if this might be the case and ensure that RO units be serviced regularly. But changes in other parameters, like pH, alkalinity, salinity, etc. should be readily observable and therefore correctable. The other issue is that aside from toxins or heavy metals, zebrafish - even larval and juvenile stages - are very tolerant of variable conditions. Or they should be, at least. If they aren't, poor tolerance for challenges is likely indicative of an underlying problem more serious in nature. CL On 12/10/08 6:16 PM, "Jocelyn" wrote: Off list I received three emails indicating a shared experience of increased nursery mortality in fall. More about our parameters: + we have an RO/DI water source. + we have consistent personnel year round (ie full time staff, no student workers). + we feed powdered AP diet and raise brine shrimp for our nursery fish (no paramecia, rotifers, etc ). + another zebrafish facility in the same building reported anecdotally about similar problems at the same time. Will seasonal changes in city water persist through a RO/DI system? I'm coming to think so? thanks for your feedback. As always, its been interesting. _______________________________________________ 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.Lawrence from childrens.harvard.edu Wed Dec 10 22:40:11 2008 From: Christian.Lawrence from childrens.harvard.edu (Lawrence, Christian) Date: Thu Dec 11 12:24:52 2008 Subject: [Zbrafish] IACUC help In-Reply-To: <84da77bf-e675-496f-af04-1c910d3c8892@u18g2000pro.googlegroups.com> Message-ID: I think this is the sort of thing you will see more and more of as the model matures. In the past, most IACUCs wouldn't want to touch zebrafish with a ten foot pole, and so as long as the floors and tanks were clean and logbooks filled out during semiannual inspections, everything was OK. The use of zebrafish has grown to such an extent that now, at the end of the day, there is no conceptual difference between mice and rats and zebrafish in terms of the way they are being utilized. So they will be increasingly held to the same standards. Inspections will be naturally much tougher, but also more useful, as painful as they may be. An example of this trend is in the tracking of numbers and accounting of different strains. This is standard stuff for mammalian model animals, and at some institutions (ours included), it is now for zebrafish as well. Think about it. In some facilities, you might have hundreds of Tg and mutant strains, including no small number that show associated clinical defects, etc. This is clearly the kind of information that an institutional animal care program needs to be monitoring. The trick with dealing with a "mammal based" IACUC is to work with and ultimately educate them. Their actions should be grounded in science, just as they are with mice, rats, etc. I believe that institutions with zebrafish programs (an ever increasing number) have the responsibility to ensure that their IACUCs are trained in the basics of fish biology, aquaculture, basic zebrafish research techniques, etc., and/or are consulting with an expert in these matters to help inform their oversight of zebrafish programs. In many instances, this is not yet the case, but the "user" side can and should push back on this issue so that regulation makes the most sense for the care of the animals and the integrity of the research. Christian Lawrence Aquatic Resources Program Children's Hospital Boston 320 Longwood Avenue Boston, MA 02115 617.919.2738 617.730.0836 (fax) christian.lawrence@childrens.harvard.edu On 12/10/08 6:42 PM, "Jocelyn" wrote: Is it normal for an IACUC to request and maintain a copy of our fish database? They are very keen on wanting to know all of our stain names and numbers. Also, any hints on dealing with a mammal biased IACUC? - ex: how do I support that "harem breeding" (IACUC phrase: more than one fish of opposite sex) is not unusual/harmful to fish? thanks _______________________________________________ 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 rburdine from Princeton.EDU Thu Dec 11 09:48:58 2008 From: rburdine from Princeton.EDU (Burdine, Rebecca D) Date: Thu Dec 11 12:25:26 2008 Subject: [Zbrafish] Re: seasonal mortality? References: Message-ID: <04AF14C4EF3CF34682460FB1FDBA98C02B4794@MBCLUSTER.pu.win.princeton.edu> Our system is purely RO and we aren't seeing this seasonal issue. I would suggest checking on two things. First, when does the RO system get serviced? Is there a connection between servicing and your seasonal issue? Second are you monitoring room temp? Our facility is in an older building and it takes forever for the temperature to even itself out, even in temp maintained rooms. Is it possible that you are having a severe temp spike (up or down) in the fall? Becky --------------------------------------------------- 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) 258-1343 Email: rburdine@princeton.edu Admin Assistant: Cathy Falk (609) 258-1604 ________________________________ From: zbrafish-bounces@oat.bio.indiana.edu on behalf of David G. White Sent: Wed 12/10/2008 6:57 PM To: Jocelyn Cc: bionet-organisms-zebrafish@moderators.isc.org Subject: Re: [Zbrafish] Re: seasonal mortality? Hello, if your on a purely RO water supply I would guess not. That system would just have a higher reject volume, water not passing through the membrane. You might notice this if your RO pressure or volume is lower than normal, unless you have ample capacity. With a purely DI system yes, it does not reject water and only removes ions in the water. Water will pass through the resin of a DI system regardless of quality (even if the resin is spent). DI is more common then RO water in my experience. Sounds like you are on a centralized system. I would contact whomever services the system. It might require more frequent maintenance during the fall, carbon filters, resin or membranes. David G White Research Coordinator H225 Zebrafish Lab University of Washington Department of Biological Structure HSB G514 Box 357420 1959 NE Pacific Street Seattle, WA 98195-7420 Tel. 206-685-7512 FAX 206-543-1524 On Wed, 10 Dec 2008, Jocelyn wrote: > Off list I received three emails indicating a shared experience of > increased nursery mortality in fall. > > More about our parameters: > + we have an RO/DI water source. > + we have consistent personnel year round (ie full time staff, no > student workers). > + we feed powdered AP diet and raise brine shrimp for our nursery fish > (no paramecia, rotifers, etc ). > + another zebrafish facility in the same building reported anecdotally > about similar problems at the same time. > > Will seasonal changes in city water persist through a RO/DI system? > I'm coming to think so? > > thanks for your feedback. > As always, its been interesting. > > _______________________________________________ > Zbrafish mailing list > Zbrafish@net.bio.net > http://www.bio.net/biomail/listinfo/zbrafish > _______________________________________________ Zbrafish mailing list Zbrafish@net.bio.net http://www.bio.net/biomail/listinfo/zbrafish -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.bio.net/bionet/mm/zbrafish/attachments/20081211/fee07498/attachment.html From dgw5079 from u.washington.edu Thu Dec 11 14:21:57 2008 From: dgw5079 from u.washington.edu (David G. White) Date: Thu Dec 11 14:27:31 2008 Subject: [Zbrafish] Re: seasonal mortality? In-Reply-To: Message-ID: Chloramine maybe a factor here. The stability of this molecule can be troublesome. Here is a thought, during the fall the first few rains might "wash" the watershed clean increasing turbidity as it makes its way to the local water treatment plant. The plant that may already use chloramine to treat the water may increase the dosage during these times. Chloramine may do damage to fish over time and/or may have a more direct impact on your nursery fish survival. I would also imagine that chloramine would be harmful to your biofilter. Activated carbon isn't 100% effective at removing chloramine. A bigger problem might be if you or someone else is treating the water for chlorine and you have chloramine. You would be producing a harmless chloride ion and toxic ammonia. But this would show up on routine testing. Whomever maintenance's your source water may not know the parameters needed for fish. There is a lot of background noise in trying to figure this out. The reason why most buildings even have a source of clean water RO/DI is for the HVAC system surely these systems operate differently as we pass from summer to fall. Since another fish lab in your building has a similiar problem one thing you probably both have in common is source water. David G White Research Coordinator H225 Zebrafish Lab University of Washington Department of Biological Structure HSB G514 Box 357420 1959 NE Pacific Street Seattle, WA 98195-7420 Tel. 206-685-7512 FAX 206-543-1524 On Wed, 10 Dec 2008, Lawrence, Christian wrote: > I see the logic in seasonal changes in water supply, but I guess the reason why I tend to not be much of a believer in this affecting survival in controlled facilities is that these changes, if and when they occur, should be for the most part be detected by routine water quality testing. > > However, I suppose at least one problematic parameter that would go undetected in most facilities (ours included) is chloramines/chlorines. One could certainly imagine a scenario in which there is an increase in the use of such chemical treatments during the fall in certain regions, and if you're not testing for it (because you don't expect it to be there), AND your RO water service provider (if you have one) isn't checking for it, or isn't maintaining the RO system properly, then it could get through and be causing a problem. In such circumstances, one could simply test for it to see if this might be the case and ensure that RO units be serviced regularly. > > But changes in other parameters, like pH, alkalinity, salinity, etc. should be readily observable and therefore correctable. > > The other issue is that aside from toxins or heavy metals, zebrafish - even larval and juvenile stages - are very tolerant of variable conditions. Or they should be, at least. If they aren't, poor tolerance for challenges is likely indicative of an underlying problem more serious in nature. > > CL > > On 12/10/08 6:16 PM, "Jocelyn" wrote: > > Off list I received three emails indicating a shared experience of > increased nursery mortality in fall. > > More about our parameters: > + we have an RO/DI water source. > + we have consistent personnel year round (ie full time staff, no > student workers). > + we feed powdered AP diet and raise brine shrimp for our nursery fish > (no paramecia, rotifers, etc ). > + another zebrafish facility in the same building reported anecdotally > about similar problems at the same time. > > Will seasonal changes in city water persist through a RO/DI system? > I'm coming to think so? > > thanks for your feedback. > As always, its been interesting. > > _______________________________________________ > 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. > > > > > > > _______________________________________________ > Zbrafish mailing list > Zbrafish@net.bio.net > http://www.bio.net/biomail/listinfo/zbrafish > From galus.michal from gmail.com Mon Dec 15 14:55:38 2008 From: galus.michal from gmail.com (Michal Galus) Date: Mon Dec 15 15:08:20 2008 Subject: [Zbrafish] IHC/HE Assistance Message-ID: <1121b1b0812151155s2bb86f2sd51d310c1c8d52b4@mail.gmail.com> Hello, I have recently finished an exposure where we have prepared adult zebrafish for IHC/HE whole mount slides. We will be subjecting the samples to serial longitudinal sections and we are attempting to find a protocol to decalcify the fish for sectioning. I am inquiring if anyone is aware of any protocols or would be able to point me in the right direction of where I would be able to find some. Thank you for your time, Sincerely Mike From jocelyn.mcauley from gmail.com Mon Dec 15 15:54:44 2008 From: jocelyn.mcauley from gmail.com (Jocelyn) Date: Mon Dec 15 16:21:17 2008 Subject: [Zbrafish] PETA's fish campaign Message-ID: Finally, PETA is taking fish protection seriously... er or not: http://www.peta.org/sea_kittens/ Yes, PETA is trying to rebrand fish as Sea Kittens. I think I need to go change my zebrafish logos now. From lasse from scienceshow.dk Tue Dec 16 04:27:26 2008 From: lasse from scienceshow.dk (Lasse) Date: Tue Dec 16 11:53:55 2008 Subject: [Zbrafish] Re: IHC/HE Assistance References: Message-ID: <2e990bda-e184-4874-993c-96cfcbae21ff@f3g2000yqf.googlegroups.com> On Dec 15, 8:55?pm, "Michal Galus" wrote: > Hello, > I have recently finished an exposure where we have prepared adult > zebrafish for IHC/HE whole mount slides. We will be subjecting the > samples to serial longitudinal sections and we are attempting to find > a protocol to decalcify the fish for sectioning. I am inquiring if > anyone is aware of any protocols or would be able to point me in the > right direction of where I would be able to find some. > > Thank you for your time, > > Sincerely > Mike HI Mike I have a bit experience with IHC on adult tissues. I usually fix whole adult fish with their bellies opened, or smaller sections in 4% PFA at 4 degrees overnigh, then decalcify for one week at RT in EDTA prior to dissection/finer sectioning. I have also decalcified in acid (formic acid: citric acid; 1:1) for 24 hours, but this will degrade RNA if you need to do combined ISH/IHC. I know that some protocols refix after decalcification, some do dot decalcify at all and others decalcify for longer time (>1 month in EDTA). My protocol is not good if endogenous flourescent proteins needs to be identified - especially dsRed is no longer appearent after 1 week at RT, but the tissues are much easier to finely cut into sections compared to other decalcification procedures. Hope this helps :). Feel free to contact me off-list if you like, and I can send you more detailed protocols :). lasse.jensen@ki.se. Sincerely: -Lasse From emond.4 from osu.edu Tue Dec 16 18:01:51 2008 From: emond.4 from osu.edu (Michelle Emond) Date: Tue Dec 16 18:32:52 2008 Subject: [Zbrafish] DNA preps for injections Message-ID: <4948335F.2000800@osu.edu> Hi, We've been trying to find a reliable kit for cleaning up DNA for injections. Qiagen miniprep DNA does not seem to be clean enough to inject straight off the column, as the embryo survival rate is very low. So, we've been running the DNA over one of their PCR purification columns to further "clean" the DNA, and that seems to result in higher survival rates. However, we'd like to streamline our methods to cut costs. We'd love to hear what other labs do for DNA preps (plasmids and BACs), both for larger preps of known constructs (midi or maxi), and for miniprep quantities for screening potential constructs. Thanks very much, Michelle Emond, Ph.D. email: emond.4@osu.edu Center for Molecular Neurobiology Ohio State University From esanders1229 from gmail.com Tue Dec 16 22:06:49 2008 From: esanders1229 from gmail.com (esanders1229@gmail.com) Date: Wed Dec 17 11:07:28 2008 Subject: [Zbrafish] Re: high fat diet References: Message-ID: <41c2df50-e447-40a2-8e2e-7a9f40a534ed@v39g2000pro.googlegroups.com> Noopur, No commercially available formulated diet springs to mind. However, using drosophila maggots would be a cheap source of food with a very high lipid content. From jalister from vcu.edu Wed Dec 17 08:24:38 2008 From: jalister from vcu.edu (James Lister) Date: Wed Dec 17 11:07:49 2008 Subject: [Zbrafish] DNA preps for injections In-Reply-To: <4948335F.2000800@osu.edu> Message-ID: Hi Michelle, Actually, we use Qiagen spinprep DNA (or more recently the equivalent kit from Fermentas) for pretty much everything with no problem. True, we might get better results with cleaner preps of DNA but it hasn't been an area we've felt a need to optimize. We routinely are injecting in the range of 10-50 pg per embryo, and certainly see toxicity at the upper range of that, but for the most part get sufficient survival/normal development to work for us (experiments perhaps similar to what you are talking about -- screening potential promoters/enhancers with GFP, etc.?) I assume you've already tried titrating down the amounts you are injecting to be sure it's a DNA quality (vs quantity, or other parameter) problem? As for BACs, there may be something better on the market for this now, but when I last did this a few years ago I basically used the Qiagen midi kit with a 100 ml culture to get a miniprep-sized yield (10-20 micrograms). The only adjustment to the protocol that was made was to pre-heat the elution buffer to 65C. For quick screening one can do a 2-5 ml culture and use the Qiagen reagents for the early steps, but instead of the column step do a phenol/chloroform extraction followed by an isopropanol precipitation (there used to be a protocol for this on a web site somewhere but I can't seem to find it now). As you might expect this is going to be dirtier than a column purification but the yield is much better. And my experience with BACs is that you don't need to inject very much even though they're much larger, because they will express much more strongly than a plasmid that has a relatively short promoter. Hope this helps (I'm curious to hear what others do as well), Jim > -----Original Message----- > From: zbrafish-bounces@oat.bio.indiana.edu > [mailto:zbrafish-bounces@oat.bio.indiana.edu] On Behalf Of > Michelle Emond > Sent: Tuesday, December 16, 2008 6:02 PM > To: zbrafish@magpie.bio.indiana.edu > Subject: [Zbrafish] DNA preps for injections > > Hi, > > We've been trying to find a reliable kit for cleaning up DNA for > injections. Qiagen miniprep DNA does not seem to be clean enough to > inject straight off the column, as the embryo survival rate is very > low. So, we've been running the DNA over one of their PCR > purification > columns to further "clean" the DNA, and that seems to result > in higher > survival rates. However, we'd like to streamline our methods > to cut costs. > > We'd love to hear what other labs do for DNA preps (plasmids > and BACs), > both for larger preps of known constructs (midi or maxi), and for > miniprep quantities for screening potential constructs. > > Thanks very much, > Michelle Emond, Ph.D. > email: emond.4@osu.edu > Center for Molecular Neurobiology > Ohio State University > > _______________________________________________ > Zbrafish mailing list > Zbrafish@net.bio.net > http://www.bio.net/biomail/listinfo/zbrafish > From tgenade from gmail.com Wed Dec 17 05:11:30 2008 From: tgenade from gmail.com (Tyrone) Date: Wed Dec 17 11:08:19 2008 Subject: [Zbrafish] antibodies against zebrafish leukocyte any one? Message-ID: Hello, I'm looking for a antibody that recognizes zebrafish microglial epitopes. I'm aware of the 4C4 atnibody employed by Becker & Becker (J. Comp. Neurobiol. 433:131--147, 2001) but the then suppliers, Drs. Dowding and Scholes no longer have stocks of it. The original monoclonal line is maintained at the European Collection of Cell Cultures at Porton Down UK as 7.4.C4 but is priced well out of the reach us poor humble researchers in South Africa. I am not working in zebrafish, but Nothobranchius, so I'm looking for an antibody sample to test with. Anyone out there who thinks they could help? Thanks Tyrone UCT Human Biology Department From jeanpierre.baudoin from crg.es Wed Dec 17 11:52:25 2008 From: jeanpierre.baudoin from crg.es (Jeanpierre 686. Baudoin) Date: Wed Dec 17 12:34:00 2008 Subject: [Zbrafish] anti-cFos. Message-ID: Hi all, Does anyone know if any antibody anti-cFos works for Zebra? I found two potential ones, from abcam and Santa-Cruz, which may work, but i have no experience with these antibody, so if someone has it would help me. thank you a lot! Cheers, JP. Jean-Pierre BAUDOIN, PhD Centre for Genomic Regulation (CRG) C/ Dr. Aiguader, 88 08003 Barcelona, Spain Tel. +34 93 316 01 30 Fax +34 93 316 00 99 jeanpierre.baudoin@crg.es | http://pasteur.crg.es !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! New call for La Caixa Fellowships CRG International PhD Program Deadline: January 18, 2009 More on: http://pasteur.crg.es !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.bio.net/bionet/mm/zbrafish/attachments/20081217/a81798f0/attachment.html From Caitlin.Stewart_swift from tufts.edu Wed Dec 17 15:17:19 2008 From: Caitlin.Stewart_swift from tufts.edu (Caitlin Stewart-Swift) Date: Wed Dec 17 15:20:07 2008 Subject: [Zbrafish] Re: high fat diet In-Reply-To: <41c2df50-e447-40a2-8e2e-7a9f40a534ed@v39g2000pro.googlegroups.com> References: <41c2df50-e447-40a2-8e2e-7a9f40a534ed@v39g2000pro.googlegroups.com> Message-ID: <49495E4F.8090707@tufts.edu> Dear All, I would not recommend letting Drosophila maggots getting anywhere near a zebrafish facility. Unfortunately I cannot recommend an alternative high fat feed, I can offer experience with a fly infested fish lab, which is highly unpleasant and almost impossible to correct. Hence why I would discourage flies. Cheers and Best Wishes, Caitlin Stewart-Swift Zebrafish Facility Manager Tufts University Boston, MA esanders1229@gmail.com wrote: > Noopur, > > No commercially available formulated diet springs to mind. However, > using drosophila maggots would be a cheap source of food with a very > high lipid content. > > _______________________________________________ > Zbrafish mailing list > Zbrafish@net.bio.net > http://www.bio.net/biomail/listinfo/zbrafish -- Caitlin Stewart-Swift Senior Research Technician/Zebrafish Facility Supervisor Department of Craniofacial and Molecular Genetics Tel(617)636-4011 Caitlin.Stewart_swift@tufts.edu From wilson.clements from gmail.com Wed Dec 17 18:55:04 2008 From: wilson.clements from gmail.com (Wilson Clements) Date: Wed Dec 17 19:03:01 2008 Subject: [Zbrafish] Re: DNA preps for injections Message-ID: Dear Michelle, For injection of DNA, I use regular old minipreps (Qiagen, Eppendorf, whatever) or midipreps. Then I phenol extract (add equal volume of 24:25:1 phenol:chloroform:isoamyl alcohol, vortex, spin 3', pull off aqueous (top) phase) them twice and ethanol precipitate (add 10% vol. of 3M sodium acetate, pH 5.2, mix, add 2.5 vols. 100% ethanol, mix, -20C 15' to overnight, spin full speed 15' at 4C, pull off supe, and resuspend pellet in appropriate vol. H2O). I have no problems with injected DNA cleaned up in this manner and the clean-up is cheap and amenable to reasonably high throughput. For BACs, we set up 5ml o/n cultures. We spin down the cultures, resuspend them in Qiagen midiprep buffer P1, lyse them with P2 (5', r.t.), neutralize with P3, spin down the garbage, transfer the supe (~750ul) to a new tube, add equal vol. isopropanol, spin 30' at 4C, wash with 70% EtOH, and resuspend in 50ul H2O. This prep is pretty dirty, but can be further cleaned up with phenol extraction and EtOH precipitation. Hope this helps. Best, Wilson ------------------------------------------------------------------------ -------------------- Wilson Clements, Ph.D. wclements@ucsd.edu Dept. of Biology Section of Cell and Developmental Biology University of California at San Diego 9500 Gilman Dr. Natural Sciences Building 6105 La Jolla, CA 92093-0380 TEL (858) 534-6955 LAB (858) 822-4658 FAX (858) 822-5740 Message: 1 Date: Tue, 16 Dec 2008 18:01:51 -0500 From: Michelle Emond Subject: [Zbrafish] DNA preps for injections To: zbrafish@magpie.bio.indiana.edu Message-ID: <4948335F.2000800@osu.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi, We've been trying to find a reliable kit for cleaning up DNA for injections. Qiagen miniprep DNA does not seem to be clean enough to inject straight off the column, as the embryo survival rate is very low. So, we've been running the DNA over one of their PCR purification columns to further "clean" the DNA, and that seems to result in higher survival rates. However, we'd like to streamline our methods to cut costs. We'd love to hear what other labs do for DNA preps (plasmids and BACs), both for larger preps of known constructs (midi or maxi), and for miniprep quantities for screening potential constructs. Thanks very much, Michelle Emond, Ph.D. email: emond.4@osu.edu Center for Molecular Neurobiology Ohio State University From jason.cockington from gmail.com Wed Dec 17 18:52:42 2008 From: jason.cockington from gmail.com (Leviathan) Date: Wed Dec 17 19:05:56 2008 Subject: [Zbrafish] Re: PETA's fish campaign References: Message-ID: <367bad2c-538c-4492-b5b6-223751733a59@w39g2000prb.googlegroups.com> Maybe i should think about changing mine also... Adelaide Zebra Sea Kitten Facility what do you think!?! :Op From zfinadmin from gmail.com Thu Dec 18 17:17:35 2008 From: zfinadmin from gmail.com (zfinadmin@gmail.com) Date: Thu Dec 18 17:18:56 2008 Subject: [Zbrafish] Fish facility care information Message-ID: <4a30e550-c56d-4c2d-b966-39eddd62f636@t39g2000prh.googlegroups.com> Dear Zebrafish Investigators, I am writing to ask for information from U.S. investigators regarding the care of their zebrafish facilities. Since my arrival at Berkeley, I have cared for my facility myself, with oversight and approval from the Office of Laboratory Animal Care. We have been very happy with this arrangement; however, the arrangement is currently under review, and I would like to obtain information from other investigators as to whether or not they care for their own fish, and whether they are pleased with the level of care. If you could take a few moments to answer a couple questions, or forward the email to a member of your lab who could, I would greatly appreciate your help. I will be happy to share the collected information with the community. A response as soon as possible would be much appreciated. Please respond to my email, amacher@berkeley.edu Lab Name(s) & University: Approx. size of fish facility: Recirculating or flow-through: Who cares for your facility: Are you pleased with the level of care: Comments: Thank you so much, Sharon From challa.anilkumar from gmail.com Sun Dec 21 00:20:31 2008 From: challa.anilkumar from gmail.com (Anil) Date: Mon Dec 22 12:14:13 2008 Subject: [Zbrafish] Shipping wt/tg zebrafish - Biosafety Message-ID: <04c8db0f-95e8-4917-8ddd-22ec6e3b6d50@u18g2000pro.googlegroups.com> I would like to know if any standard protocols have been established with SHIPMENT/TRANSPORTATION of wildtype and transgenic zebrafish. I would be thankful if I can get the protocols (or pointers to relevant information) in this regard. Thanks. Anil From david from zebrafish.org Mon Dec 22 13:27:40 2008 From: david from zebrafish.org (David Lains) Date: Mon Dec 22 13:30:51 2008 Subject: [Zbrafish] Shipping wt/tg zebrafish - Biosafety In-Reply-To: <04c8db0f-95e8-4917-8ddd-22ec6e3b6d50@u18g2000pro.googlegroups.com> References: <04c8db0f-95e8-4917-8ddd-22ec6e3b6d50@u18g2000pro.googlegroups.com> Message-ID: <037401c96462$fcf61c90$f6e255b0$@org> Hello Anil Here is the basic shipping protocol: http://zfin.org/zf_info/zfbook/chapt1/1.7.html Please feel free to contact me with specific details as I maybe able to help you further. Best Fishes David Lains <}}}>< Aquaculturist, Research Assistant Zebrafish International Resource Center 5274 University of Oregon Eugene, Or 97403 Email: david@zebrafish.org pH: (541) 346-6028 ext. 18 fax: (541) 346-6151 -----Original Message----- From: zbrafish-bounces@oat.bio.indiana.edu [mailto:zbrafish-bounces@oat.bio.indiana.edu] On Behalf Of Anil Sent: Saturday, December 20, 2008 9:21 PM To: bionet-organisms-zebrafish@moderators.isc.org Subject: [Zbrafish] Shipping wt/tg zebrafish - Biosafety I would like to know if any standard protocols have been established with SHIPMENT/TRANSPORTATION of wildtype and transgenic zebrafish. I would be thankful if I can get the protocols (or pointers to relevant information) in this regard. Thanks. Anil _______________________________________________ Zbrafish mailing list Zbrafish@net.bio.net http://www.bio.net/biomail/listinfo/zbrafish From chuntaoyuan from gmail.com Tue Dec 23 01:17:04 2008 From: chuntaoyuan from gmail.com (Chuntao Yuan) Date: Tue Dec 23 13:09:30 2008 Subject: [Zbrafish] Re: DNA preps for injections References: Message-ID: On 12ΤΒ18ΘΥ, ΙΟΞη7Κ±55·Φ, Wilson Clements wrote: > Dear Michelle, > > For injection of DNA, I use regular old minipreps (Qiagen, Eppendorf, > whatever) or midipreps. Then I phenol extract (add equal volume of > 24:25:1 phenol:chloroform:isoamyl alcohol, vortex, spin 3', pull off > aqueous (top) phase) them twice and ethanol precipitate (add 10% vol. > of 3M sodium acetate, pH 5.2, mix, add 2.5 vols. 100% ethanol, mix, > -20C 15' to overnight, spin full speed 15' at 4C, pull off supe, and > resuspend pellet in appropriate vol. H2O). I have no problems with > injected DNA cleaned up in this manner and the clean-up is cheap and > amenable to reasonably high throughput. > > For BACs, we set up 5ml o/n cultures. We spin down the cultures, > resuspend them in Qiagen midiprep buffer P1, lyse them with P2 (5', > r.t.), neutralize with P3, spin down the garbage, transfer the supe > (~750ul) to a new tube, add equal vol. isopropanol, spin 30' at 4C, > wash with 70% EtOH, and resuspend in 50ul H2O. This prep is pretty > dirty, but can be further cleaned up with phenol extraction and EtOH > precipitation. > > Hope this helps. > > Best, > Wilson > ------------------------------------------------------------------------ > -------------------- > Wilson Clements, Ph.D. > > wcleme...@ucsd.edu > > Dept. of Biology > Section of Cell and Developmental Biology > University of California at San Diego > 9500 Gilman Dr. > Natural Sciences Building 6105 > La Jolla, CA 92093-0380 > > TEL (858) 534-6955 > LAB (858) 822-4658 > FAX (858) 822-5740 > > Message: 1 > Date: Tue, 16 Dec 2008 18:01:51 -0500 > From: Michelle Emond > Subject: [Zbrafish] DNA preps for injections > To: zbraf...@magpie.bio.indiana.edu > Message-ID: <4948335F.2000800@osu.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi, > > We've been trying to find a reliable kit for cleaning up DNA for > injections. DNA does not seem to be clean enough to > inject straight off the column, as the embryo survival rate is very > low. So, we've been running the DNA over one of their PCR purification > columns to further "clean" the DNA, and that seems to result in higher > survival rates. However, we'd like to streamline our methods to cut > costs. > > We'd love to hear what other labs do for DNA preps (plasmids and BACs), > both for larger preps of known constructs (midi or maxi), and for > miniprep quantities for screening potential constructs. > > Thanks very much, > Michelle Emond, Ph.D. > email: emon...@osu.edu > Center for Molecular Neurobiology > Ohio State University Qiagen have different kit for different use. I think Qiagen miniprep is not so good as Qiagen spin. Qiagen spin is cell grade! From ulrike from mail.nih.gov Tue Dec 23 12:03:28 2008 From: ulrike from mail.nih.gov (Ulli) Date: Tue Dec 23 13:10:14 2008 Subject: [Zbrafish] Release of version 2.5 of caMOD - The Cancer Models Database Message-ID: <4ed71a59-2217-4cbe-9eb4-c45c28511ff3@f13g2000yqj.googlegroups.com> On behalf of the entire caMOD team, I am pleased to announce the availability of caMOD 2.5 at http://cancermodels.nci.nih.gov. caMOD 2.5 includes many improvements that facilitate searching for cancer models in caMOD as well as for submitting new models to the database. Search enhancements: - Significantly enhanced Search to better accommodate the increasing volume of data in caMOD - Broadened keyword search - Improved search for transgenes and targeted modifications - Addition of the PubMed publication identifier as a search criterion to the Advanced Search page - Enhanced customization of the Search Results list Submission enhancements: - Customization of the publication page for rat models - Improved PubMed data retrieval script - More flexible designation of URLs for associated microarray and image data A caGrid data service for caMOD 2.5 will be available in the coming weeks and will be announced via this listserv. For more information about caGrid, please see https://cabig.nci.nih.gov/workspaces/Architecture/caGrid/. Please refer to the release notes for additional information on caMOD 2.5, available from the application home page. For questions or suggestions, contact the NCICB application support team at http://ncicb.nci.nih.gov/NCICB/support. Thank you for your interest in caMOD! Ulli Wagner Internet Developer (Contractor) SAIC-Frederick, Inc. NCI Center for Bioinformatics Phone and Fax: (402) 502-9380 From jeedward from yahoo.com Sun Dec 28 15:46:59 2008 From: jeedward from yahoo.com (John Edward) Date: Mon Dec 29 12:26:00 2008 Subject: [Zbrafish] BCBGC-09 call for papers Message-ID: <48954.25147.qm@web45913.mail.sp1.yahoo.com> BCBGC-09 call for papers ? The 2009 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-09) (website: http://www.PromoteResearch.org ) will be held during July 13-16 2009 in Orlando, FL, USA. We invite draft paper submissions. 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/20081228/7b4fe576/attachment.html From joymurphyknapp from gmail.com Mon Dec 29 15:37:12 2008 From: joymurphyknapp from gmail.com (CryoDanio) Date: Mon Dec 29 17:31:10 2008 Subject: [Zbrafish] cryopreservation service Message-ID: Hello, I am interested in starting a business that would provide zebrafish cryopreservation services, including sperm freezing, storage and thawing for in vitro fertilization. I'm trying to get a feel for what level of demand exists in the zebrafish community. As a former technician myself, I know the amount of time and resources needed to perfect the skill of cryopreservation. It seems likely to me that some labs would rather pay to have this done professionally than incur the costs of learning it themselves. I would like to hear other peoples' thoughts on the idea. Thanks in advance for your feedback! Joy