Much of the fish we eat is not stolen from the sea by fisherman who heroically fight the waves in search for areas where fish outnumber pieces of pastic, but rather are farmed. This farming can be done in ponds, in big barrels, in parts of fjords that are surrounded by nets, etc.
Fish that is farmed this way needs food, and many of our ′left-overs′ are good fish food. Farm fish has been crossed to make them genetically optimal for dealing efficiently with left-overs from the human food industry that otherwise would become waste.
In crossing fish often de novo mutations are observed (i.e. residues are observed in the offspring that are not observed in either of the parents).
Rather than growing a few thousand fish and then finding out what went wrong, fish farmers want to sequence just one fish egg and determine from the DNA sequence whether to continue with this batch or not.
To make life easy for the researchers, this work is first tried on zebrafish and will later be repeated on the real farm fish (tilapia, etc).
One sub-project of this enormous endeavour is the analysis of mutations in the a fish nuclear hormone receptor. The fish farmers often observe that mutations in the retinoic receptors more easily lead to phenotypic changes than mutations in many other proteins (including most other nuclear hormone receptors).
The sequence of interest is available from SwissProt as RARGA_DANRE:
MFDCMEALGM GPRQLYDVTN RGACMLRKAS PFYAGLDPFA WTGTASVRSV ETQSTSSEEM VPSSPSPPPP PRVYKPCFVC QDKSSGYHYG VSSCEGCKGF FRRSIQKNMV YTCHRDKNCQ INKVTRNRCQ YCRLQKCFEV GMSKEAVRND RNKKKKDVKD EVIPPESYEL SGELEELVNK VSKAHQETFP SLCQLGKYTT NSSSDHRIQL DLGLWDKFSE LSTKCIIKIV EFAKRLPGFT TLTIADQITL LKSACLDILM LRICTRYTPE QDTMTFSDGL TLNRTQMHNA GFGPLTDLVF AFAGQLLPLE MDDTETGLLS AICLICGDRM DLEEPERVDR LQEPLLEALK IYARRRRPNK PHMFPRMLMK ITDLRGISTK GAERAITLKM EIPGPMPPLI REMLENPEAF EDQSESTEKK PEPEPPAPPP PALLTMKKEQ EDEDDSWATE NGSEPSPEEE DDDDEDGEEE RGTDSDGEAW GGQEPNADVS RKSHGGRAQ* |
Many mutations have been observed, and the examples that we want you to study are listed below. The first box holds mutations that behave almost the same as the genetic knock-out variant (that is not a happy fish, by the way), albeit that one of these is milder. (The middle residue of the pentamer is the one that got mutated).
cqDks 82 -> L ssCeg 94 -> G ffRrs 124 -> Q |
The second box holds a series of mutations that seem more related to the regulation of RARGA_DANRE:
agFgp 292 -> Y cgDrm 328 -> N mlMki 369 -> G tlLks 251 -> S |
You will work in groups of three. And remeber, all three group members get the same grade...
We start each of the four last days at 9:15 at the CMBI with a discussion. What you do with your time after that, is up to you.
Write a short article (in the style requested by FEBS letters) about these mutations. Use font Calibri and no smaller than 12 pitch. The article should, including figures, tables, references, etc., not be longer than 10 pages. Mail the article before the deadline to vriendgert@gmail.com. Mail it as PDF and as MS word file (.doc or .docx, not .odf). Add to this mail the model(s) you used for drawing the conclusions about the mutants.
In the article I expect to find an abstract, and at least one page introduction, about the molecule we work on. The methods section should be roughly one page. The results section should be split in two parts, at least one page about making the model and validating it, and a big part about the results. Try to have a one page discussion that does not repeat things that were written earlier already. Acknowledgements and references close the article. I would like to see as appendix a cut-n-paste of the sections of the validation report that you thing are relevant for the (quality of) the project. Send me your coordinates later today, then you get the complete validation report from me later tonite.