How many of the cells are competent?

›
We're collaborating with some physicists on a cool laser-tweezers experiment. The tests are done on single cells, so it's important...
3 comments:

Our vindication is on hold...

›
The result I was raving about a couple of weeks ago turns out to not be as solid as I had thought. This was the comparison of hypercompetent...

Ramifying motif searches

›
I began using the Gibbs motif search program just to get a better estimate of 'the' USS consensus. But as I get into it (necessary t...

Make the bacteria do the work

›
The best geneticists are smart but lazy; they use genetics to avoid laborious and tedious analyses, and in the process produce very elegant ...
4 comments:

Folding variations

›
The server I've been using for USS motif searches has been down, so I've been playing around with variations in how sxy mRNA might ...

Deconstructing the structure?

›
A lab meeting presentation yesterday got me worrying about how having an explicit technical drawing of a structure makes it difficult to thi...
1 comment:

The first good searches for USS motifs

›
With more help from the motif-software expert, I now have the program running well. I can use fragmentation masks to control where the progr...
3 comments:

No-fault motif searching

›
Yesterday the very helpful guy who wrote the motif-search program I'm using sent me an improved version that eliminated the segmentation...

Vindication!

›
About 15 years ago I hypothesized that Haemophilus influenzae takes up DNA mainly for its content of nucleotides, and predicted that the ge...
3 comments:

Waiting for illumination...

›
The five double mutant strains I constructed appear to be correct. They should have the purR knockout combined with each of our five sxy ...
1 comment:

Part two of the puzzle

›
Iakov's comment to yesterday's post is right; the card images I posted yesterday fit a binary code. The card #9 we created worked f...
4 comments:

Not a genetic code

›
If you're visiting from Tangled Bank #62 you've probably already noticed that this isn't your usual science blog. I rarely post...
1 comment:

Mutants R US

›
My transformations worked, and I have thousands of what should be sxy purR double mutants. In fact I have thousands of double mutants for ...
2 comments:

Little steps

›
The purR knockout cells grew on the kanamycin agar, and I purified DNA from them. Today I'll grow up the hypercompetent mutants, give ...
2 comments:

Maybe PurR does repress a competence gene after all

›
In a post last month I wondered whether the purine repressor PurR might repress competence genes, and concluded that this was probably a de...
2 comments:

Sneaking around the segmentation fault....

›
Now we have our Perl script to chop the genome sequence into short-enough fragments, and we have the motif-search program running on the fas...

How hard can it be?

›
Sunday evening I sent the post-doc who's been learning Perl an email asking if we could write a little 'script' that would take ...
4 comments:

G-USSs and R-USSs (C-USSs and U-USSs?)

›
One of the projects we're working on will produce a paper titled "Defining the Haemophilus influenzae uptake signal sequence"...
2 comments:

Still looking for equilibrium

›
Today I thought more about an algorithm (a rule, a test, a way to calculate) I'd outlined that would decide when our Perl simulations of...
2 comments:

Is the origin of biological chirality a no-brainer?

›
One argument invoked by creationists for a magical origin of life is that the observed homochirality (definition below) of biological molecu...
4 comments: