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Topic: Zebrafish

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	Zebrafish
		The zebrafish (Danio rerio) is a tropical fresh water fish originating from southeast Asia.
		Zebrafish are not only a favorite of many home aquaria, but figure prominently as a vertebrate model for developmental, genetic, and biomedical research.
		Through comparative approaches, the zebrafish and human genomes are shown to share extensive conserved syntenic fragments and many zebrafish genes and their human homologs share structural and functional similarities.
	www.ou.edu /wanglab/Zebrafish.html (299 words)

	Zebrafish - Wikipedia, the free encyclopedia
		The zebrafish is especially useful to biologists because the body of the developing embryo is transparent.
		Zebrafish, published by Mary Ann Liebert, Inc., is the only peer-reviewed journal to focus on the zebrafish and other aquarium fish model species including medaka, Fugu and Xiphophorus.
		Due to its favorable qualities, the zebrafish has become one of the primary model species used for human disease-related research that is supported by the National Institutes of Health.
	en.wikipedia.org /wiki/Zebrafish (276 words)

	Zebra Danio - Wikipedia, the free encyclopedia
		The Zebra Danio or Zebrafish (Brachydanio rerio or Danio rerio) is a tropical fish, commonly kept in aquaria and used for scientific research, belonging to the minnow family (Cyprinidae).
		The fish is named for its five uniformly, pigmented, horizontal blue stripes on the side of the body; all extending to the anal fin onto the end of caudal fin rays of its tail.
		The arrival of zebrafish as a major model for studying developmental biology co-incided with a large scale mutagenesis screen.
	en.wikipedia.org /wiki/Zebra_Danio (805 words)

	Zebrafish FAQs
		Zebrafish, Danio rerio, are freshwater fish that were originally found in slow streams and rice paddies and in the Ganges River in East India and Burma.
		Because zebrafish are more closely related to humans, they are more likely to be similar to them in many biological traits than a more distantly related organism.
		Zebrafish originate from fast moving rivers and streams in northeastern India and the water quality in that area is very good.
	www.neuro.uoregon.edu /k12/FAQs.html (6989 words)

	Zebrafish and the Guide (Site not responding. Last check: )
		Zebrafish kept together for breeding should have some means to escape from more aggressive fish, in the form of either more space or plantlike materials to be used as hiding spaces.
		To prevent zebrafish from eating their eggs, the tank bottom should be fitted so as to make the eggs (~1.0–1.5 mm diameter) inaccessible to the fish, yet easy to collect—for example, a layer of marbles, an array of closely spaced rods, mesh, or a box containing marbles or covered with mesh.
		Zebrafish genetic composition is determined from the records of the parents that generated the fish, phenotypic classifications of the fish and their siblings, and genetic and molecular tests to determine if fish carry particular recessive traits.
	iacuc.cwru.edu /resources/zebrafish.html (5553 words)

	Model organisms: Fish
		However, zebrafish development is more rapid than in the frog, the organisation of the embryo is simpler and (like worms and fruit flies) the embryo is transparent.
		Like the mouse, the zebrafish is amenable to genetic analysis and has a similar generation interval (2-3 months).
		The zebrafish (Danio reiro) is amenable to genetic analysis and has a generation interval of 2 to 3 months.
	genome.wellcome.ac.uk /doc_wtd020806.html (559 words)

	NCRR Reporter Spring 2004—Critical Resources: A Resource for the Zebrafish Connoisseur
		Zebrafish currently are used in a wide range of studies, including research on blood diseases, fetal alcohol syndrome, the genetics of polycystic kidney disease, and developmental errors that lead to cleft palate.
		Chosen partly for its hardiness, small size, and brief life span, the zebrafish possesses an additional trait that endears it to researchers: zebrafish eggs are transparent, allowing direct visualization of the embryo.
		To maintain zebrafish lines, researchers must manage many fish tanks, a logistical headache because the standard 10-gallon glass aquarium is heavy, breakable, difficult to clean and move, and must be plumbed by hand.
	www.ncrr.nih.gov /newspub/may04rpt/stories4.asp (1178 words)

	HHMI News: Mutant Zebrafish Provide Clues About Human Anemia
		Zebrafish with the sauternes mutation develop a disease identical to CSA, a condition that reduces the number of red blood cells and lowers levels of hemoglobin in both fish and humans.
		Even though adult zebrafish are only one inch long, researchers can tell whether the fish's blood cells are making hemoglobin by examining the live fish under a microscope.
		While a lack of infrastructure had stalled zebrafish genetics studies, a recent $5 million grant from the National Institutes of Health to fund the Zebrafish Genome Initiative should encourage more work in the field.
	www.hhmi.org /news/zon.html (789 words)

	"Physiological genomics": mutant screens in zebrafish -- Warren and Fishman 275 (1): 1 -- AJP - Heart and Circulatory ... (Site not responding. Last check: )
		The real advantage of zebrafish for genetic research is the ease with which one can carry out large-scale screens.
		Mutations in zebrafish genes affecting the formation of the boundary between midbrain and hindbrain.
		Cloche, an early acting zebrafish gene, is required by both the endothelial and hematopoietic lineages.
	ajpheart.physiology.org /cgi/content/full/275/1/H1 (3665 words)

	The Syntenic Relationship of the Zebrafish and Human Genomes -- Barbazuk et al. 10 (9): 1351 -- Genome Research
		The zebrafish is an important vertebrate model for the mutational analysis of genes effecting developmental processes.
		An example of the extent of syntenic correspondence of zebrafish and human genomes is shown in Figure 1.
		that the zebrafish msxb gene (LG1) is orthologous to MSX1 (Hsa4)
	www.genome.org /cgi/content/full/10/9/1351 (4171 words)

	MOLECULAR DISSECTION OF CRANIOFACIAL DEVELOPMENT USING ZEBRAFISH -- Yelick and Schilling 13 (4): 308 -- Critical ... (Site not responding. Last check: )
		Expression of contact, a new zebrafish DVR member, marks mesenchymal cell lineages in the developing pectoral fins and head and is regulated by retinoic acid.
		Diversity of expression of engrailed-like antigens in zebrafish.
		Combinatorial expression of zebrafish Brn-1- and Brn-2-related POU genes in the embryonic brain, pronephric primordium, and pharyngeal arches.
	crobm.iadrjournals.org /cgi/content/full/13/4/308 (8123 words)

	Zebrafish
		The zebrafish (Danio rerio) is an ideal model organism for studying development and gene function in vertebrates, due to its small physical size, large clutches, transparent embryos, and ease of genetic and experimental manipulation.
		Sequencing of the complete zebrafish genome is ongoing at the Sanger Institute using a combined clone and whole genome shotgun strategy.
		To identify duplicate genes and identify the sequence differences that distinguish duplicates, we are generating finished sequence for zebrafish BACs known to contain duplicate genes.
	www-shgc.stanford.edu /resources/zebrafish.html (218 words)

	BBC NEWS \| Health \| Key gene 'controls skin colour'
		Zebrafish are ideal for research because they share many similar genes with humans.
		The researchers found a variant of the zebrafish, called golden, had fewer, smaller and less heavily pigmented melanosomes than normal fish.
		This mutation appears, like the zebrafish, to result in fewer, smaller and lighter melanosomes.
	news.bbc.co.uk /2/hi/health/4531966.stm (525 words)

	Instructions for Authors - Zebrafish
		Zebrafish is a quarterly peer-reviewed journal focusing on research using zebrafish and other aquarium species including medaka, Fugu and Xiphophorus as models for studies of vertebrate development, toxicology and human disease.
		The Journal will serve as a forum for papers discussing research on comparative genomics and evolution, the genetic analysis of embryogenesis and disease and the cellular and molecular mechanisms of cell growth, differentiation and gene expression in these model species.
		Zebrafish is published by Mary Ann Liebert, Inc., 140 Huguenot Street, 3rd Floor, New Rochelle, NY 10801-5215.
	www.liebertpub.com /manuscript.aspx?pub_id=122 (868 words)

	The zebrafish gene map defines ancestral vertebrate chromosomes -- Woods et al. 15 (9): 1307 -- Genome Research
		to facilitate the assembly of the zebrafish genome sequence.
		represent >10% of the genes in the zebrafish genome.
		Map positions for zebrafish genes were derived from this work, and those of Tetraodon were obtained from http://www.ensembl.org/Tetraodon_nigroviridis/.
	www.genome.org /cgi/content/full/15/9/1307 (5493 words)

	Zebrafish SSR Search
		This form searches for a Zv6 scaffold, Zv5 scaffold or finished BAC clone by accession number, derives all di-, tri-, and tetra- nucleotide repeats in the sequence, masks the sequence around the repeats for larger zebrafish repetitive sequences, and then designs unique primer pairs to amplify the simple sequence repeats.
		Due to the possibility of mis-assembly in zebrafish genome assemblies, marker linkage should be independently confirmed.
		Zebrafish repeat libraries compiled by Rick Waterman and Zhirong Bao.
	danio.mgh.harvard.edu /markers/ssr.html (226 words)

	Zebrafish Genome Resources
		The zebrafish (Danio rerio) is a small freshwater fish native to south Asia and is a common aquarium fish worldwide.
		It is an important model organism for the study of vertebrate development and disease, organ function, behavior, and toxicology.
		Some of the features that make the zebrafish so experimentally amenable include its short generation time, large numbers of embryos produced per mating, and the development of transparent embryos outside the mother, allowing all stages of development to be observed.
	www.ncbi.nlm.nih.gov /genome/guide/zebrafish/index.html (275 words)

	Zebrafish developmental genetics and central nervous system development -- Blader and Strähle 9 (6): 945 -- Human ... (Site not responding. Last check: )
		neurulation in the zebrafish resembles the secondary neurulation
		A schematized cross-section through a 24 h embryo (left) indicating general architectural features, including the overlying non-neural ectoderm, the roofplate (RP), dorsal-, inter- and motorneurons, the floorplate (FP) and the underlying notochord, is transposed onto a lateral view of a zebrafish embryo in two planes of focus (right).
		(1996) Mutations in zebrafish genes affecting the formation of the boundary between midbrain and hindbrain.
	hmg.oxfordjournals.org /cgi/content/full/9/6/945 (5094 words)

	Stanford Zebrafish Genome Project (Site not responding. Last check: )
		Comparisons of zebrafish and mammalian gene maps have revealed extensive conservation of syntenic relationships among vertebrates (Postlethwait and Talbot 1997; Postlethwait et al.
		Mammalian counterparts for all zebrafish chromosomes have been identified, and additional gene mapping studies will determine the extent to which gene order is maintained within conserved segments.
		The Talbot and Postlethwait groups are collaborating to localize zebrafish genes on an integrated genetic linkage map.
	zebrafish.stanford.edu /genome/Frontpage.html (292 words)

	The developmental miRNA profiles of zebrafish as determined by small RNA cloning -- Chen et al. 19 (11): 1288 -- Genes ...
		The zebrafish is an important model organism to study vertebrate
		zebrafish and were enriched in the fibroblast cell lines (Fig.
		Lippman, Z. and Martienssen, R. The role of RNA interference in heterochromatic silencing.
	www.genesdev.org /cgi/content/full/19/11/1288 (4006 words)

	MGH Zebrafish WWW Server
		Comparison of the zebrafish microsatellite map (Shimoda et al.) and the RAPD map (Postlethwait et al.).
		A zebrafish genetic linkage map consisting of 705 simple sequence-length polymorphism markers (SSLPs), using 44 F2 progeny from the AB x IN reference cross.
		A zebrafish yeast artificial chromosome (YAC) library using genomic DNA isolated from the inbred AB zebrafish strain.
	zebrafish.mgh.harvard.edu (179 words)

	Biology - Wikipedia, the free encyclopedia
		Originating in embryology, modern developmental biology studies the genetic control of cell growth, differentiation, and "morphogenesis," which is the process that gives rise to tissues, organs, and anatomy.
		Model organisms for developmental biology include the round worm Caenorhabditis elegans, the fruit fly Drosophila melanogaster, the zebrafish Brachydanio rerio, the mouse Mus musculus, and the weed Arabidopsis thaliana.
		Physiology studies the mechanical, physical, and biochemical processes of living organisms by attempting to understand how all of the structures function as a whole.
	en.wikipedia.org /wiki/Biology (2858 words)

	OUP: UK General Catalogue
		Whole genome sequencing projects, such as the human genome project, have led to the isolation of tens of thousands of genes for which the in vivo function is unknown.
		It is therefore likely that an increasing number of researchers will turn to organisms such as the zebrafish to understand the in vivo requirement for the proteins these genes encode.
		Recent technical advances now allow the rapid testing of in vivo function of as yet uncharacterised genes in zebrafish in large numbers and at a speed that is impossible in other systems.
	www.oup.com /uk/catalogue/?ci=9780199638086 (507 words)

	Zebrafish cDNA Library Information (Site not responding. Last check: )
		Note: this is a Zebrafish Gene Collection library.
		Poly A+ RNA was isolatd from the ovaries of 2 female adult zebrafish (4-5 month old).
		Note: the tissue for this library was originally annotated as pharyngeal arch; however upon sequence analysis it is suspected that this is not the correct tissue source.
	image.llnl.gov /image/html/zfishlib_info.shtml (3783 words)

	Washington University - Zebrafish Genome Resources
		The efficient use of zebrafish to study developmental and physiological processes requires a variety of genomic and genetic tools.
		These GFP lines can then be used in biological analysis, or as visible genetic markers along chromosomes to aid in mapping experiments or generation of deletions.
		SL Johnson Zebrafish Lab, Department of Genetics, WashU
	zfish.wustl.edu (151 words)

	Trans-NIH Zebrafish Initiative
		The NIH established the Trans-NIH Zebrafish Coordinating Committee in the fall of 1997 in response to the scientific community’s recommendation to promote the use of zebrafish as a model organism for the study of vertebrate development and disease.
		When appropriate, items not in response to the Trans-NIH zebrafish initiatives, but which are deemed relevant, will be posted.
		Posting decisions are made by a subcommittee of the Trans-NIH Zebrafish Coordinating Committee.
	www.nih.gov /science/models/zebrafish (141 words)

	Center News
		However, a teleost species such as zebrafish or Fugu is typically used as the outgroup in current tetrapod comparative sequence analyses.
		The coelacanth was shown to have 49 protocadherin cluster genes organized in the same three ordered subclusters, alpha, beta, and gamma, as the 54 protocadherin cluster genes in human.
		Additionally, zebrafish protocadherins are far more prone to homogenizing gene conversion events than coelacanth protocadherins, suggesting that recombination- and duplication-driven plasticity may be a feature of teleost genomes.
	www-shgc.stanford.edu /news (4206 words)

	Zebrafish Comparative Genomics Blast Search
		This Blast server is maintained at the Massachusetts General Hospital Renal Unit by Iain Drummond and is hosted on a Sun Fire server, generously donated by Sun Microsystems.
		Batch retrieval of WGS traces is facilitated by using the form at the bottom of the blast results page.
		Batch retrieval of sequence data is made possible by a form at the bottom of the search output.
	danio.mgh.harvard.edu /blast/blast_grp.html (298 words)

	Affymetrix - Zebrafish Genome Array
		The Affymetrix GeneChip® Zebrafish Genome Array can be used to study gene expression of over 14,900 Danio rerio transcripts.
		This array was designed in collaboration with representative members of the Zebrafish community and the National Institutes of Health.
		Note: The DsRed probe set is provided with permission from BD Biosciences, and BD Biosciences grants users a limited license to utilize this probe set only on the Affymetrix array.
	www.affymetrix.com /products/arrays/specific/zebrafish.affx (166 words)

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