From mwinandy from ulg.ac.be Fri Jun 5 09:37:03 2009 From: mwinandy from ulg.ac.be (Marie Winandy) Date: Fri Jun 5 11:51:07 2009 Subject: [Zbrafish] delay in development or high mortality Message-ID: <4A292D8F.5050504@ulg.ac.be> An HTML attachment was scrubbed... URL: http://www.bio.net/bionet/mm/zbrafish/attachments/20090605/6c47901a/attachment.html -------------- next part -------------- A non-text attachment was scrubbed... Name: mwinandy.vcf Type: text/x-vcard Size: 398 bytes Desc: not available Url : http://www.bio.net/bionet/mm/zbrafish/attachments/20090605/6c47901a/mwinandy.bin From wmebane from mbl.edu Fri Jun 5 15:59:27 2009 From: wmebane from mbl.edu (William Mebane) Date: Fri Jun 5 16:12:54 2009 Subject: [Zbrafish] delay in development or high mortality In-Reply-To: <4A292D8F.5050504@ulg.ac.be> Message-ID: <1704506154.1716061244235567160.JavaMail.root@mail> Marie, I think what you may be experiencing is "suspension" in development possibly due to exposure to low oxygen levels in the rearing dishes (easy to occur esp. if the dishes are covered and the room is warm). Keep the surface area to depth ratio high in your dishes. Developing embryos will actually rotate w/in the egg towards areas of higher O2 when an egg is partially imbedded in gel! Personally I have not seem this but folks here who are working with micro DO probes have. This "suspended animation" quirk happens w/many fish species, perhaps as a method of "holding on" until environmental conditions improve. I'm preaching to the choir w/this next statement, but making new cells is an extremely aerobic process. No oxygen...things slow down...then die. Good paper on this by Christopher Ton and colleagues "Physiological Genomics" 13:97-106, 2003 good luck! ----- Original Message ----- From: Marie Winandy To: zbrafish@magpie.bio.indiana.edu Sent: Fri, 5 Jun 2009 10:37:03 -0400 (EDT) Subject: [Zbrafish] delay in development or high mortality Hi all, since a few weeks, some PhD students in our lab have got problems with their wild type, non injected embyos: - some have a delay in development (14 somites instead of 24); - in some dishes, there are 3 or more different developmental stages at 24hpf (while the eggs were collected at the same time, with a 15 minutes interval between each clutch); - some clutches show >50 % mortality at 24hpf. We also have some pairs laying only dead eggs. This occurs in 25-30% of the clutches. At this time, the transgenics eggs don't seem to be affected. It seems that this occurs more frequently with eggs collected in the afternoon. The parent fish are 9-12 months old. Recently, there has been some NH4+/NH3 and NO2 in the system, but now it's decreased. We pay attention to let only 50 eggs in the 8cm petri dishes, change water at least once a day, discard unfertilised eggs at 4hpf. Have you any idea of the possible cause(s) of this? Do you think that the N ions could have influenced individuals at different levels, making some of them produce good eggs and other no? Thank you in advance for any shared idea and help. best regards, Marie -- William N. Mebane Superintendent Aquaculture Engineering Divison Marine Resources Center, Marine Biological Laboratory 7 MBL Street Woods Hole, MA 02543 phone (508) 289-7683 fax (508) 289-7900 MBL website - www.mbl.edu Haiti website http://www.mbl.edu/mrc/outreach/sustainable_aquaculture/index.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.bio.net/bionet/mm/zbrafish/attachments/20090605/c6cadaed/attachment.html From guschungman from gmail.com Tue Jun 9 11:10:12 2009 From: guschungman from gmail.com (Gus Chan) Date: Tue Jun 9 11:12:34 2009 Subject: [Zbrafish] vivo-morpholino Message-ID: I found that gene tools is now providing vivo-morpholino for knockdown in adult animals. I would like to whether it is possible to knockdown a specific gene in a specific organ, like heart or liver. Also, would it be possible to directly inject the vivo-morpholino into the liver or heart for gene knockdown? Gus -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.bio.net/bionet/mm/zbrafish/attachments/20090610/0a68d8a3/attachment.html From weibinz from med.umich.edu Wed Jun 10 14:18:10 2009 From: weibinz from med.umich.edu (Weibin Zhou) Date: Thu Jun 11 10:41:33 2009 Subject: [Zbrafish] caspase antibody Message-ID: <4A2FCEB3.8167.0008.0@med.umich.edu> Hi, could someone recommend an antibody for activated caspase-3 that works on zebrafish? We would like to examine apoptotic cells with whole-mount IF. Thank you very much. ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues From driever from biologie.uni-freiburg.de Thu Jun 11 13:38:49 2009 From: driever from biologie.uni-freiburg.de (Wolfgang Driever) Date: Thu Jun 11 13:42:29 2009 Subject: [Zbrafish] Animal Physiology / Neurophysiology Professorship at University of Freiburg Message-ID: <41D31816-B781-4603-BAFE-C34F263217E2@biologie.uni-freiburg.de> I would like to bring the following position to your attention: The Faculty of Biology at the Albert-Ludwigs-University Freiburg invites applications for the position of Professor (W3) in Animal Physiology / Neurophysiology (Professorship in Zoology, formerly held by Prof. Klaus Vogt) The applicant’s research should be in the area of systemic neurosciences and should focus on questions of neural coding and brain functions in relation to behaviour. The application of modern neurobiological experimental techniques, including genetic labeling methods, is desirable. The tasks associated with the position include teaching biology students in the field of animal physiology. German Habilitation or proof of equivalent scientific qualification is required. Close interactions and cooperations with the neuroscience research centers and institutions of the university are expected. For further information please visit the homepage of the faculty of biology at http://www.biologie.uni-freiburg.de and of the Freiburg Neuroscience Centers at http://www.sfb780.uni- freiburg.de and http://www.bcf.unifreiburg.de Please submit your application – preferentially in electronic form (with CV, structured list of publications, short description of previous and future research and teaching activities, copies of three most important publications) not later than June 15, 2009 to: Dean of the Faculty of Biology Albert-Ludwigs-University Freiburg Schaenzlestrasse 1 D-79104 Freiburg, Germany The University of Freiburg aims to increase the percentage of women in research and teaching, and therefore encourages female candidates meeting the above qualifications to apply. Handicapped candidates with equivalent qualifications will be given preference. see also: http://www.nature.com/naturejobs/science/jobs/96729-Professor ******************************************************* Prof. Dr. Wolfgang Driever Developmental Biology Unit Department of Biology I University of Freiburg Hauptstrasse 1 D-79104 Freiburg GERMANY Tel: internat.: (49)-761 203 2587 admin. office. -2588 Fax: internat.: (49)-761 203 2597 email: driever@biologie.uni-freiburg.de http://www.biologie.uni-freiburg.de/data/bio1/driever/index.html ********************************************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.bio.net/bionet/mm/zbrafish/attachments/20090611/1b4844a5/attachment.html From kristen from neuro.utah.edu Thu Jun 11 14:03:50 2009 From: kristen from neuro.utah.edu (Kristen M Kwan) Date: Thu Jun 11 14:06:10 2009 Subject: Fwd: [Zbrafish] caspase antibody References: Message-ID: <0F361704-ECDE-422F-AD38-313DB479F1D7@neuro.utah.edu> Hi there, Here is the information for an activated caspase-3 antibody that I have used successfully for whole-mount IF on zebrafish: BD Pharmingen Rabbit Anti Active Caspase-3, catalog number 559565. Good luck! Kristen Kwan > Begin forwarded message: > >> From: Weibin Zhou >> Date: June 10, 2009 1:18:10 PM MDT >> To: "zbrafish@magpie.bio.indiana.edu" >> >> Subject: [Zbrafish] caspase antibody >> >> Hi, >> could someone recommend an antibody for activated caspase-3 that >> works on zebrafish? We would like to examine apoptotic cells with >> whole-mount IF. Thank you very much. >> >> >> >> ********************************************************** >> 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 > Kristen M. Kwan, PhD Department of Neurobiology and Anatomy University of Utah 409 Wintrobe 20 N 1900 E Salt Lake City, UT 84112 (801) 585-1702 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.bio.net/bionet/mm/zbrafish/attachments/20090611/48a20070/attachment.html From chi-bin.chien from neuro.utah.edu Fri Jun 12 11:43:50 2009 From: chi-bin.chien from neuro.utah.edu (Chi-Bin Chien) Date: Fri Jun 12 11:47:10 2009 Subject: [Zbrafish] Imaging Zebrafish In-Reply-To: <8f8dff4a-7965-485e-ad72-ea576199f16e@l32g2000vba.googlegroups.com> References: <8f8dff4a-7965-485e-ad72-ea576199f16e@l32g2000vba.googlegroups.com> Message-ID: <1A550405-8A42-4AD2-8F85-B5E67D9ADBF2@neuro.utah.edu> Hi Sarah, If you are talking about live 5 dpf fish, you will need to mount in some way; otherwise, they will float up because of their inflated swim bladders. Anesthetizing with tricaine and mounting in low-melt agarose is simple and effective. best wishes, Chi-Bin Chien < Dept. Neurobiology and Anatomy | office: 1-801-585-1701 > < Univ. Utah Medical Center | lab: 1-801-585-1702 > < 20 North 1900 East, 401 MREB | fax: 1-801-581-4233 > < Salt Lake City, UT 84132 | chi-bin.chien@neuro.utah.edu > < http://chien.neuro.utah.edu > On May 22, 2009, at 6:27 AM, FritzXC23 wrote: > Hi All! > > My name is Sarah Fritz and I am undergraduate student from Gettysburg > College. I am currently working on a research project that involves > imaging fluorescent zebrafish hair cells. I am wondering if anyone has > suggestions about the best way to get 5 dpf fish to lay on their sides > without having to mount them. Thanks! > > Sarah Fritz > > _______________________________________________ > 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/20090612/68b3d34c/attachment-0001.html From borsani.unibs from gmail.com Sun Jun 14 08:19:21 2009 From: borsani.unibs from gmail.com (Giuseppe Borsani) Date: Mon Jun 15 11:53:24 2009 Subject: [Zbrafish] MO rescue guidelines Message-ID: I'm relatively new to zebrafish and, coming from genetics, working on this animal model is often for me more an art than a science. We are trying to rescue a MO-induced phenotype through the injection of capped mRNA. I have a number of questions with apparently no obvious answers (i.e.: shall I make a construct with or without the 5' UTR? What about the 3' UTR? Is it convenient to inject a fusion transcript that includes a reporter gene such as GFP? Since GFP often alters the functional properties of the gene of interest, what about bicistronic mRNAs? Shall we inject as a control a mRNA containing a gene inactivating mutation? I'm wondering if there is a paper-review-web site with some guidelines for the strategy to be used. Thank you for your help Giuseppe Borsani University of Brescia From paramecia.vap from gmail.com Mon Jun 15 19:10:49 2009 From: paramecia.vap from gmail.com (Vladimir Apekin) Date: Wed Jun 17 11:12:03 2009 Subject: [Zbrafish] parameciavap.com Message-ID: <767e8c0b-a74b-4d35-b1b6-994fb63ad9aa@x29g2000prf.googlegroups.com> To whom it may concern. Dear Colleagues, If you are interested in improving the way you grow zebrafish in your lab, we at - parameciavap.com- (formerly known as Fish and Frogs Co.) are excited to be of service to you. Packaged under oxygen, the culture is stable for an additional week. Our product has been successfully tested and is relied on by many research Laboratories in Boston and across the US. For instance, Zon Lab has been buying our Paramecia every week for 7 years, the Sive Lab for 8 years, O’Malley Lab for 5 years and so on. (Ben Pratt :“..Reliable, Consistent, Convenient, and Economical”). If you know a lab that might be interested in our product, please forward this message along to them. Thanks! Vladimir Apekin From lasse from scienceshow.dk Wed Jun 17 12:21:22 2009 From: lasse from scienceshow.dk (Lasse) Date: Wed Jun 17 12:22:27 2009 Subject: [Zbrafish] Fish/trout serum for zebrafish cell culture Message-ID: Dear All A collegue and I are trying to establish fish cell lines, and in preparation for that I have found several papers strongly promoting the addition of Fish/trout/salmonoid serum and/or embryo extracts to the culture medium. I was wandering if anyone have experience with using fish serum for cell culture and if so, have a tip to where I can purchase fish serum relatively cheaply (preferably a european company). Alternative if you have a good protochol for how to obtain cell culture-grade fish serum from whole blood? I would also appreciate any other comments or expertise/know how you might like to share regarding fish cell culture, although I can be more specific at this time as I have just started myself. All my best, and thanks alot in advance!! Lasse From wclements from ucsd.edu Wed Jun 17 15:10:10 2009 From: wclements from ucsd.edu (Wilson Clements) Date: Wed Jun 17 15:16:34 2009 Subject: [Zbrafish] Re: Defeating the swimbladder Message-ID: <2CD233FF-6365-41D6-89B1-B71EDC6037B4@ucsd.edu> Dear Fish Gurus, For some of our fluorescent transgenic lines, it would be useful to be able to easily screen individuals at, for example, 5 dpf. Unfortunately, this process is inhibited by variable swimbladder inflation. I can tricaine my fish, and many of them remain on the bottom of a petri dish where I can easily observe and sort them. However a certain number of individuals have inflated swimbladders causing them to float out of microscopic focus and move around in the media. I was wondering if anyone had ever come up with a trick to cause temporary swimbladder deflation in a plate. Best, Wilson Clements -------------------------------------------------------------------------------------------- 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 From j.burris from cellbio.duke.edu Thu Jun 18 12:33:32 2009 From: j.burris from cellbio.duke.edu (Jim Burris) Date: Thu Jun 18 12:36:58 2009 Subject: [Zbrafish] Re: Defeating the swimbladder In-Reply-To: <200906181704.n5IH4dp28027@net.bio.net> References: <200906181704.n5IH4dp28027@net.bio.net> Message-ID: <887ED24B-8ADB-42F7-BC91-C01CBB59B052@cellbio.duke.edu> Wilson, When possible we sort nearly all of our fluorescent transgenic fish at 3 dpf to avoid this problem. Best Fishes, Jim Burris Zebrafish Facility Manager Department of Cell Biology Duke University Medical Center Durham, NC 27710 (919)684-6092 (843)344-1887 (cell) j.burris@cellbio.duke.edu On Jun 18, 2009, at 1:04 PM, zbrafish-request@oat.bio.indiana.edu wrote: > Send Zbrafish mailing list submissions to > zbrafish@net.bio.net > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.bio.net/biomail/listinfo/zbrafish > or, via email, send a message with subject or body 'help' to > zbrafish-request@net.bio.net > > You can reach the person managing the list at > zbrafish-owner@net.bio.net > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Zbrafish digest..." > > > Today's Topics: > > 1. Fish/trout serum for zebrafish cell culture (Lasse) > 2. Re: Defeating the swimbladder (Wilson Clements) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 17 Jun 2009 10:21:22 -0700 (PDT) > From: Lasse > Subject: [Zbrafish] Fish/trout serum for zebrafish cell culture > To: bionet-organisms-zebrafish@moderators.isc.org > Message-ID: > > Content-Type: text/plain; charset=ISO-8859-1 > > Dear All > > A collegue and I are trying to establish fish cell lines, and in > preparation for that I have found several papers strongly promoting > the addition of Fish/trout/salmonoid serum and/or embryo extracts to > the culture medium. I was wandering if anyone have experience with > using fish serum for cell culture and if so, have a tip to where I can > purchase fish serum relatively cheaply (preferably a european > company). Alternative if you have a good protochol for how to obtain > cell culture-grade fish serum from whole blood? > > I would also appreciate any other comments or expertise/know how you > might like to share regarding fish cell culture, although I can be > more specific at this time as I have just started myself. > > All my best, and thanks alot in advance!! Lasse > > > > ------------------------------ > > Message: 2 > Date: Wed, 17 Jun 2009 13:10:10 -0700 > From: Wilson Clements > Subject: [Zbrafish] Re: Defeating the swimbladder > To: zbrafish@magpie.bio.indiana.edu > Message-ID: <2CD233FF-6365-41D6-89B1-B71EDC6037B4@ucsd.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > Dear Fish Gurus, > > For some of our fluorescent transgenic lines, it would be useful to be > able to easily screen individuals at, for example, 5 dpf. > Unfortunately, this process is inhibited by variable swimbladder > inflation. I can tricaine my fish, and many of them remain on the > bottom of a petri dish where I can easily observe and sort them. > However a certain number of individuals have inflated swimbladders > causing them to float out of microscopic focus and move around in the > media. > > I was wondering if anyone had ever come up with a trick to cause > temporary swimbladder deflation in a plate. > > Best, > Wilson Clements > ---------------------------------------------------------------------- > ---------------------- > 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 > > > > > ------------------------------ > > _______________________________________________ > Zbrafish mailing list > Zbrafish@net.bio.net > http://www.bio.net/biomail/listinfo/zbrafish > > End of Zbrafish Digest, Vol 49, Issue 8 > *************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.bio.net/bionet/mm/zbrafish/attachments/20090618/d963e442/attachment.html From jocelyn.mcauley from gmail.com Thu Jun 18 18:03:54 2009 From: jocelyn.mcauley from gmail.com (Jocelyn) Date: Thu Jun 18 18:16:01 2009 Subject: [Zbrafish] Re: Defeating the swimbladder References: Message-ID: One of our grad students uses a typical 20x100 petri dish poured with agarose to create a slanted bottom (ie varying depth). She transfers the tricained fish to the shallow end of the petri dish to better stabilize them for visualizing. They are kept at this shallow depth briefly. From cwyatt42 from googlemail.com Fri Jun 19 05:17:45 2009 From: cwyatt42 from googlemail.com (Cameron Wyatt) Date: Fri Jun 19 11:21:47 2009 Subject: [Zbrafish] Lipophilic tracers and MeOH preserved embryos Message-ID: I have recently received a batch of 3 days post fertilisation zebrafish embryos in which I had intended to trace the optic projection with DiI or DiO. Unfortunately the embryos were preserved in MeOH. Can anyone direct me to a protocol for rehydration which would make the embryos suitable for tracing or has the MeOH rendered them unusable? Any suggestions will be greatly appreciated. ~ Cameron From chi-bin.chien from neuro.utah.edu Mon Jun 22 03:33:13 2009 From: chi-bin.chien from neuro.utah.edu (Chi-Bin Chien) Date: Mon Jun 22 11:14:33 2009 Subject: [Zbrafish] Lipophilic tracers and MeOH preserved embryos In-Reply-To: References: Message-ID: <0FC37E0B-FB61-4BC8-BD6A-645DB3982C59@neuro.utah.edu> Rehydration will not help--the problem is that lipophilic dye tracing in fixed embryos depends on the fact that aldehyde fixation (like PFA) crosslinks proteins but leaves plasma membranes (like axonal membranes) intact. If you extract lipids, they are gone and not retrievable. Chi-Bin On Jun 19, 2009, at 11:17 AM, Cameron Wyatt wrote: > I have recently received a batch of 3 days post fertilisation > zebrafish embryos in which I had intended to trace the optic > projection with DiI or DiO. Unfortunately the embryos were preserved > in MeOH. > Can anyone direct me to a protocol for rehydration which would make > the embryos suitable for tracing or has the MeOH rendered them > unusable? > Any suggestions will be greatly appreciated. > ~ Cameron > > _______________________________________________ > Zbrafish mailing list > Zbrafish@net.bio.net > http://www.bio.net/biomail/listinfo/zbrafish From zoltan from zebrafish.org Fri Jun 26 18:31:25 2009 From: zoltan from zebrafish.org (Zoltan) Date: Mon Jun 29 11:24:20 2009 Subject: [Zbrafish] Rome 09 Husbandry Workshop Announcement Message-ID: Dear friends and colleagues! We are very pleased to announce the "ZIRC, UCL, ZHA Husbandry Workshop" that will focus on nursery procedures and raising larvae, during the "6th European Zebrafish, Genetics, and Development Meeting" in Rome: Wednesday, July 15th, 2009 2 to 4 pm, In the "Sala Arte" of the Conference Center Subjects for discussion will include - 1. Aspects of larval rearing including nursery work and protocols, general tips & tricks. There will be 3 presentations on this topic followed by discussion. 2. EU and US legislation including imports/exports. There will be 2 brief presentations on this topic followed by brief discussion. For more Information, please see the Rome meeting website: http://www.zebrafish2009.org/scientific.htm Or the ZIRC web site: http://zebrafish.org/zirc/home/RomeZIRCWebAnnouncment.php We are very much looking forward to seeing you at the workshop! Best regards, Carole Wilson, Zoltan Varga From philosophyfreak from yahoo.com Mon Jun 29 10:57:34 2009 From: philosophyfreak from yahoo.com (ZebrafishMD) Date: Mon Jun 29 14:16:18 2009 Subject: [Zbrafish] Diseased Zebrafish Message-ID: Recently, we have noticed that our fish have been dying in a similar fashion. They get lathargic, rest on the bottom of the tank, bloat, and die. Sometimes it looks as if their scales are raising off of their bodies. Simultaneously, another problem seemed to be occurring, in which fish exhibited bent or curved spinal columns, making it difficult for them to swim. From the research I've done, our facility hasn't been the only one with this problem. I believe that our fish are infected by microsporidiosis, a disease in which a parasite releases spores that the fish eat, and which subsequently infect the host's hindbrain and spinal column. This disease seems to have symptoms our fish have: emaciation and a curved spinal cord. But this does not explain the bloating or lethargy. These symptoms seem to suggest that many of the fish have infected swim bladders, which research suggests usually occurs when the fish are immunosuppressed and bacteria makes their way from the gut to the swim bladder, which are connected in zebrafish. Is it possible that the spores are causing the immunosupression and, subsequently, our fish are getting infected swim bladders? Has anyone else had this problem? If so, how was it dealt with? What is the best way to eradicate the problem? Thanks in advance to any one who may have a solution or advive. From zohar.bm from gmail.com Tue Jun 30 13:52:51 2009 From: zohar.bm from gmail.com (zohar ben moshe) Date: Tue Jun 30 13:56:55 2009 Subject: [Zbrafish] cockroach gel bait in zebrafish facility Message-ID: <2032da8e-676c-419c-b787-862eb988fbf1@z9g2000yqi.googlegroups.com> Dear ZF community members, We have had an explosion of cockroach population (the big disgusting type) in our ZF facility and called a insect exterminator. For caution he used a gel bait, not spray. But, unsupervised, he placed gel spots inside the shelves and some of the spots are in contact with the water!! The active compound in the gel is Imidacloprid (2.15%). This compound is of very low acute toxicity to fish. However, we do not know about the prolonged exposure and whether the biofilter will take care of this or not. We will greatly appreciate any insight on the use of this compound, Imidacloprid, in a fish facility. Should we get hysteric or can we relax? Sincerely, Zohar, Yoav Gothilf's Laboratory Department of Neurobiology Tel Aviv University http://www.tau.ac.il/lifesci/departments/neuro/members/gothilf/gothilf.html