Automated Analysis of Conserved Syntenies for the Zebrafish Genome

John Postlethwait,* Victor Ruotti, Michael J. Carvan, and Peter J. Tonellato *Institute of Neuroscience University of Oregon Eugene, Oregon 97403 Human & Molecular Genetics Center Medical College of Wisconsin Milwaukee, Wisconsin 53226 Great Lakes WATER Institute University of Wisconsin-Milwaukee Milwaukee, Wisconsin 5320 II. The Conservation of Zebrafish and Mammalian Genomes E. Conserved Chromosome Segments III. Using Genome Conservation in Zebrafish Research C. Conserved Chromosome...

Zebrafish Facilities for Small and Large Laboratories

Institute of Neuroscience University of Oregon Eugene, Oregon 97403 A. Size and Purpose Considerations B. Design Overview II. Zebrafish Biology B. Materials and Testing for Toxins A. Water Chemistry, Cycles, and Buffers E. Monitoring, Alarms, and Redundancies F. Adult Tanks and Their Functions J. Requirements of Standard Operations K. Utilities and Infrastructure L. Fish Record Keeping and Databasing VI. Mutagenesis Room VII. Treating Outflow B. Charcoal-Treated Outflow VIII. Disposing of the...

Mapping Maternal Effect Mutations

Mapping a mutation to a chromosomal position can be carried out either simultaneously with an F4 screen using natural crosses (see Section II.A) or at any time after the identification and recovery of the mutation. Specific details on mapping protocols have been previously described (Geisler, 2002 Talbot and Schier, 1999). Here we describe the modification of this approach for mapping maternal-effect mutations. Briefly, the approach consists of outcrossing a carrier for the mutation to a...

Lessons from Transgenic Zebrafish Expressing the Green Fluorescent Protein GFP in the Myeloid Lineage

Zebrafish Fluorescent Protein

Thomas Look,* and John P. Kanki* *Department of Pediatric Oncology Dana-Farber Cancer Institute Harvard Medical School Boston, Massachusetts 02115 Division of Hematology Oncology Beth Israel Deaconess Medical Center Harvard Medical School Boston, Massachusetts 02115 I. Introduction II. Myeloid Cells in Zebrafish III. Expression ofpu.1 in Myeloid Development IV. Analysis of the Zebrafish pu.1 Locus V. Germline Expression of Enhanced Green Fluorescent Protein (EGFP) Under Control...

Solutions Materials and Protocols

MESAB stock solution 0.2 ethyl-m-aminobenzoate methanesulfonate. Adjust to pH 7.0 with 1 M Tris pH 9.0. Keep at 4 C. MESAB working solution 7 ml stock solution per 100 ml fish water. Hank's solutions Stock solutions 1, 2, 4, and 5 and premix can be stored at 4 C. Stock solution 6 is prepared fresh and added to the premix to form the final Hank's solution. Solution 1 8.0 g NaCl, 0.4g KCl-in 100 ml double-distilled (dd) H2O. Solution 2 0.358 g Na2HPO4 anhydrous, 0.60 g KH2PO4, in 100 ml ddH2O....

Highly Efficient Zebrafish Transgenesis Mediated by the Meganuclease ISceI

Meganuclease

Clemens Grabher,* Jean-Stephane Joly, and Joachim Wittbrodt* European Molecular Biology Laboratory (EMBL) INRA, Institute de Neurobiologie A. Fessard CNRS B. Methods of Gene Delivery Overview C. Methods of Gene Delivery Microinjection II. Transgenesis by Meganucleases C. Meganuclease Transgenesis Protocol (Zebrafish) References Few technical achievements in biological sciences have opened up such possibilities as transgenesis technologies have. The ability to change selectively the genetic...

Bacterial Artificial Chromosome BAC Clones and the Current Clone Map of the Zebrafish Genome

Romke Koch,* Gerd-J rg Rauch, Sean Humphray, Robert Geisler, and Ronald Plasterk* Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 ISA, United Kingdom Max-Planck-Institut fur Entwicklungsbiologie D-72074 T bingen, Germany II. Physical Map of Fingerprinted Clones B. Restriction Digest Fingerprinting C. Contiguation of Fingerprinted Clones III. Screening Methods and Utilization of the Current Zebrafish Clone Map B. Screening Sequence Databases D. Fingerprinted...

Mcwrh V32

Automation of the analysis frees investigators to focus on the potential biological and functional interpretation. However, special problems arising from genome duplication require further refinement of the current algorithms before genomewide results become fully available. We thank NIH grants R01RR10715 and P01HD22486 for support. Abnet, C. C., Tanguay, R. L., Heideman, W., and Peterson, R. E. (1999). Transactivation activity of human, zebrafish, and rainbow trout...

Enu

Fig. 1 Target-selected mutagenesis in zebrafish. Approximately 100 adult male zebrafish are randomly mutagenized with N-Ethyl-N-nitrosourea (ENU) and outcrossed against wild-type females. A library of approximately 5000 F1 animals is constructed, in principle having independent mutations. Genomic DNA of these F1 animals is isolated and arrayed in 384-well PCR plates, suitable for robotic handling. The DNA is screened for mutations in target genes by resequencing or TILLING. Animals with...

V

Fig. 5 Phylogenetic network Bryant and Moulton, 2004 reconstructed from the sequences of the concatenated phylogenetic footprint cliques computed with the tracker program. From the noncoding DNA of respective HOX-A clusters we find strong support for the ''duplication first'' scenario, in which the duplication of the HOX clusters predates the divergence of the percomorph fishes pufferfish from the zebrafish lineage. Phylogenetic networks indicate the noise uncertainty by the width of the...