Tuesday, June 30, 2009

Periplasm Prep Planning II

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I tried a modification of a periplasmic protein prep to try and purify uptake DNA, which didn't work. There are several possible reason...

Periplasm Prep

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UPDATED BELOW Experimental plan for the day: Medium-scale periplasm prep test-- to purify double-stranded DNA in the “protected state” (the...
1 comment:
Friday, June 26, 2009

Plan for the next few weeks

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One proposal down, one to go... The next one isn’t due until August 8th, so I’ve got just over a month to get it done. This time, however,...
1 comment:
Thursday, June 25, 2009

But which would win in a fight?

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The budding and fission yeasts provide for several interesting comparisons. Some of these somewhat illustrate my considerable confusion abo...
1 comment:
Tuesday, June 23, 2009

Proposaling continues

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I continue on the saga of writing this soon-to-be-due proposal. I keep struggling with things that I think I understand in my head, but can...
2 comments:
Thursday, June 18, 2009

A taste of DNA

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I gave Rosie a draft of my grant application, so decided to dither with human USS motifs again. First, for fun, I looked at where several of...
1 comment:
Tuesday, June 16, 2009

They're eating our DNA!!!

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I am in the midst of proposal-writing, which makes blogging tougher, but when I hit a writing-block at the end of the day, I decided to dall...
1 comment:
Tuesday, June 9, 2009

Supragenomicisticexpialidocious

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Howzabout that “ supragenome ”? Polymorphic gene content Genome sequencing efforts have captured substantial variation in the gene content a...
1 comment:
Friday, June 5, 2009

Joint molecules...

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There are several classes of transformation event that could be mediated by natural competence and recombination. The first thing that I ha...

Searching for Cash (How I'll spend my summer vacation)

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So it’s time to outline my plans for the next several weeks... Grant-writing and preliminary data gathering! Two grant applications to do: ...
Wednesday, June 3, 2009

There's a lesson here somewhere

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A recent email exchange with a local computer expert, explaining one reason I normally avoid directly seeking help until I really need it (t...
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Friday, May 29, 2009

Enumerating their differences

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I took a break from working on GBrowse today to try and do some genome-wide alignments of the sequenced Haemophilus influenzae isolates, an...
2 comments:
Thursday, May 28, 2009

GBrowse Update (boring, except the bit about the fish)

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I finally succeeded in my attempt to put a functioning GBrowse installation on my computer. My problem turned out to be extremely trivial ...
3 comments:
Wednesday, May 27, 2009

As easy as that? Nahh...

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For one of our planned experiments, I want to purify periplasmic uptake DNA away from chromosomal DNA in a clean efficient manner. There a...
2 comments:
Monday, May 25, 2009

Congression versus linkage

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Yet again, I did a transformation of Haemophilus influenzae cells with slightly variant H. influenzae genomic DNA. I fed MAP7 DNA-- conta...
1 comment:
Thursday, May 21, 2009

Sequencing, Ho!

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In response to Rosie’s last post , I wanted to outline my take on two of our planned experiments that involve deep sequencing: Transform a s...
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Always check your concentrations (Edited)

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Okay, enough about the evolution of sex for now. I got some data again, but sadly discovered that I'd used the wrong selection for my t...
2 comments:
Wednesday, May 20, 2009

Interfering Clones

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Since I’m new around here, I thought I’d try and start reflecting on the big picture surrounding the Redfield lab’s research, starting with ...