Project weirdness and grant: Do we have the skillz to pay the billz?

Today I tried running two consequently batches of ComM- mutants for a transformation assay but every single flask failed to grow ಠ_ಠ

8 cultures, 4 strains, 2 fresh preperations of sBHI all stalled out. Anouther lab member had two out of four HI cultures stall as well. What could it be? Sometimes bact is fussy in poorly understood ways and decides to not grow, yogurt and sourdough colonies can do this as well occasionally, and HI can be especially capricious but this is ridiculous something has to be going on. I originally thought the culprit could be a newly made batch of sBHI, but I remembered I did an overnight with it yesterday and the colonies turned out perfect this morning. What could of happened? More clues will surely come tomorrow. Also at some point I should lay out what exactly I’m doing for the blog

The lab is busying itself with grant work, the submission is due Sunday and there’s still a lot to do. I spent the other part of my day in the office going through a recent revision.  The proposal can be divided into five main goals(not necessarily in the order they are present in the grant):

1) Identifying genes responsible for DNA uptake in HI. The lab found that 25 genes are upregulated when competence is induced, so they’re probably involved in competence somehow but no one really knows what they do, so we’re testing what happens when you knock them out.

2) Finding out what determines uptake specificity. In HI there’s this little sequence, AAGTGCGGT, that makes up the core of a motif that appears in the genome 1471 times. DNA pieces containing this sequence get taken up by competent HI at a much greater rate than pieces without it. But why? How? What proteins actually grab onto this sequence?

3) There’s  a related species with a related but slightly different motif, and they both prefer their own brand. What makes them different? Cross-complementation tests will help determine this

4) Is there anything special about those sequences that allows them to enter the cell? DNA is long and stiff, and the secretin pores it has to go through are small, and we know plasmids can squeeze through so DNA must be getting kinked somewhere in order to fit through these small opening. Do the sequences not only give the proteins something familiar to grab onto, but also allow the DNA to bend more easily at that spot? The sequence runs slower in a gel than a sequence made up of a random assortment of those same bases, so maybe the sequence is structurally special?

5) What forces do the uptake proteins exert?  This will be the laser trap work done at SFU

More information about the grant can be found on Rosies blog

On Fridays there’s a evolution discussion group at noon and I really want to go to this weeks. The paper is titled “The evolution of sex-specific grandparental harm. ” by Rice et al 2010. I haven’t read it yet but looks awesome. Finally some theoretical work behind the issue of grandchild harming phenotypes. Realies. Most of my studies in Ohio dealt with selfish gene evolution so maybe I’ll even have something to contribute.  Best line of the abstract = “We use the logic of Hamilton’s rule to develop a new ‘no-cost-to-self nepotism rule’ that greatly simplifies the determination of the invasion criteria for mutations that cause grandparents to harm grandchildren.” Oh my.

5 Comments (+add yours?)

  1. Clem
    Feb 25, 2011 @ 07:30:23

    Where in Ohio?


  2. dnogas
    Feb 25, 2011 @ 14:47:37

    Nope, Andrea Case’s lab. I don’t think I ever met Prof. Woolverton. Why do you ask?


  3. Clem
    Feb 28, 2011 @ 04:43:28

    I’m in central Ohio. Daughter went to UD and sons to OSU. I don’t know Chris personally, but have seen some of his pubs and thought there might be a connection.


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