BISC 219/2009: Mod 1 Lab 5

Lab 5: SCORE!

Mapping: Count all adult and L4 progeny from one plate, scoring as either wild type , Dpy , Unc or Dpy Unc. Also score the second plate unless you have counted >100 total animals. Remember to remove each animal after you have determined its phenotype.

How would you get the single mutant class if you started with linked genes d u/+ +?

You will determine map distances using the formula: RF (recombinant frequency) =the number of single mutants (both dpy and unc single mutants) divided by the total number of worms counted * 100 (to obtain RF in % recombinants and thus in map units).

Congratulations! You now have an idea about the location and, maybe, the name of your MB? dpy mutation. To learn more you can enter the gene name (if you found an allelic association through your complementation analysis and now know the gene name)into the C. elegans database: | Wormbase at http://www.wormbase.org Wormbase.

Click on the link to Wormbase above and enter your dumpy gene name into the box at the top of the page and click Search. It will either bring you directly to that page or it will bring you to a page with mutiple hits - click on the link that provides a definition for what the gene does.

On this new page should be all the known information about this particular gene. Its name, who named it, what the gene encodes - if that is known, and much more. At the bottom will be a list of references - or a link to a list of references. Check this out. Does it appear that you are working with a new gene or one that has been well characterized?

If you aren't sure of your dumpy gene name because found complementarity with all of the 4 dumpy reference strains or other confusing complementation results, you can find out more about your dumpy gene on Wormbase from the location of your linked unc gene. You can start looking up the unc reference gene. Since you know that your dumpy gene is on the same chromosome and is a certain number of map units away from this known unc reference gene; therefore, you might can use location information about the genes around your linked unc gene to see if there is a well characterized dumpy gene in the position you have mapped it (+/- the number of map units) on that chromosome. Enter the unc reference gene name in Wormbase and click on Mapping Data. Scroll down the page until you find the mapping data for that gene and see if there is a known dumpy gene at the location you have mapped your mutation relative to this unc gene. If there is, you now know the name of your dumpy gene and you can enter that gene name in Wormbase to learn more about it. If you find no known dumpy associated gene at this map location, it is possible that you have found a new dumpy gene or a new function for an otherwise characterized gene. Your next step would be to see what is known about that location on the chromosome and see if what's known fits in at all with your observations. If it does, great and, if not, you have some thinking to do. DO NOT write a paper about "sources of error" in your experimental design!!!!

Spend some time with Wormbase and marvel at all the hard work and years of research that went into discovering all this information about this tiny little nematode that causes us no harm (non-parasitic). Why do you think so many smart people have devoted so much of their time and energy to working out the genetics of "appearance or movement challenged" little worms? We will talk more about model organisms and the power of functional and comparative genomics in our next series.

This is the end of Series 1. You will write a partial scientific paper about the work you did to characterize an unknown dumpy mutation created from random mutagenesis. See Assignment 2- mapping partial paper in the the Assignment section of the Wiki. See the Weekly Planner and Lab Calendar section of the wiki to see when this paper is due. We will be beginning our RNA interference (RNAi) Series today.

C. elegans General Information
Tools and Techniques
Lab 1: Welcome to C. elegans and Mutant Hunt
Lab 2: Linkage Test and Backcross
Lab 3: Linkage Test, Backcross and Mapping
Lab 4: Mapping Part 2