1. A new procedure for determining the genetic basis of a physiological process in a non-model species, illustrated by cold induced angiogenesis in the carp PhD dinner seminars John Herbert
2. Why angiogenesis due to cold temperature? It is more difficult for muscles to utilise O 2 at lower temperatures
3. What Evidence? Cold induced angiogenesis has been shown in mammals and vertebrates 25 o C 5 o C
4. In the non-model species carp (no genome and little transcriptome ~20K EST sequences), ortholog relationships and microarray re-analyses were used to predict identity of cold induced angiogenic genes
5. Functionally linked together by orthologs Basic strategy overview What is an ortholog and how to create this link with 20K anonymous carp DNA sequences Model species Angiogenic genes Non-model species Cold induced genes
7. How to find orthologs? Kuzniar A, van Ham RC, Pongor S, Leunissen JA: The quest for orthologs: finding the corresponding gene across genomes . Trends Genet 2008, 24 (11):539-551.
9. BLASTO illustrates limitations with public available software Zhou Y, Landweber LF: BLASTO: a tool for searching orthologous groups . Nucleic Acids Res 2007, 35 (Web Server issue):W678-682 Database from 2007 Singular, just one sequence Limited filtering options
16. How to improve on this? Zebrafish Another model species Genome is almost complete Currently 6 million ESTs 28 thousand Refseq proteins Carp……….only…. 20K ESTs Diverged 50 MYA Use zebrafish as stepping stone (SRBH)
18. Teleost genome duplication: can be seen with genes important in endothelial biology Human chromosome 11 Zebrafish chromosome 18 (on other strand) Zebrafish chromosome 16
24. Gracey et al. 2004: Coping with cold: An integrative, multitissue analysis of the transcriptome of a poikilothermic vertebrate. 17,825 sequences on chip This data set proved appropriate for meta-analysis to predict cold-induced angiogenic genes in skeletal and heart muscle tissues. Cold induced genes
25. Carp gene expression cooling regimen B) 57 genes up-regulated on initial cooling 567 total non-redundant genes up-regulated A) 547 persistently up-regulated genes