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PhD student in chemical engineering


Jul
28
comment Phagemid display
Wow! Thanks for answering such an old question. I'm not entirely sure if this solves the avidity issues though.
Apr
3
comment E coli cotransformation efficiency
I've always understood for this process to be incredibly low. When you consider how much DNA is added and how many competent cells there are, if you have even 1% transformation efficiency, you'll always get lawns. Since we don't, that gives a rough estimate of the process.
Mar
4
comment Does the MS2 RNA binding protein have any translational repression effects?
Probably because I asked this question back in 2012 and was more of a curiosity question rather than an actual experimental question. More specifically, I'm concerned more about generating a tuneable analog type of repression system where you can generate a range of repress rather than perform a complete knockdown using CRISPR.
Mar
3
comment What is the fastest way to build an alanine scanning library?
@GerganaVandova, not really but it might be of interest to the broader community.
Mar
3
comment Does the MS2 RNA binding protein have any translational repression effects?
The idea would actually be to repress translation via the mecahnism that you suggest. Hence, the rationale of putting the MS2 hairpin upstream of the ORF.
Mar
3
comment What implications has the missing 2'-OH on the capability of DNA to form 3D structures?
This answer is incorrect for a variety of reasons. For one, it makes the assessment that RNA is more flexible. It isn't; DNA is. The role described in the Aleadam paper thus is minimal. The comments about degradation has little to do with the ability to adopt 3D structures. It is more of a reflection of the presence of specific defensive mechanisms via DNases and RNases.
Jan
21
comment How straightforward is in vitro compartmentalization?
Thanks! Since it has been awhile since I've asked this question, I now get the impression that certain reactions like transcription and smPCR work well. When concentrations and size become more important or translation is important things go south.
Dec
13
comment Is there a PSI-BLAST for nucleotide sequences?
why not blastn?
Dec
11
comment Finding RNA Loops
As an improvement to what @WYSIWYG mentioned, PARS is fairly low resolution since it is still enzyme based. The newer in vivo SHAPE or DMS-seq methods are much better and more informative.
Sep
6
comment Does RNA polymerase move around DNA or does DNA rotate benath the polymerase?
I think he is asking a different question. At some point the RNA should be wound around the DNA if the RNAP is spinning around the DNA.
Sep
6
comment Is there any database with RNA classification?
Probably scor.berkeley.edu
Sep
6
comment Why Only DNA can Contain Hereditary Material?
@shigeta, certainly there are RNA viruses that are excellent examples of RNA functioning as hereditary materials.
Jul
15
comment How to obtain bacteria samples?
@Jonsca, shall we start the reopenning process?
Jul
12
comment How to obtain bacteria samples?
@Jonsca, I'm actually ok with this type of question. The alternative way to ask how to achieve such things but not exactly from whom, which is a reuseuable question. (ie how to appropriate go about contacting certain people)
Jun
10
comment Providing small molecules to cells on a filter plate
@WYSIWYG, Batch should be fine. The question is what would be the setup to do so. Would it be as simple as reversing a 96 well lid over and placing the filter plate on top? What about the wetting?
Jun
7
comment Removing bacterial contaminants from resin
I am an engineer by training. The default option is always to fix it yourself. Usually with duct tape.
Jun
6
comment Removing bacterial contaminants from resin
@Shigeta, alas it wasn't my column. I guess it's time to buy some new resin.
Jun
1
comment Removing bacterial contaminants from resin
I'm going to try the high salt. That's a good suggestion. The reverse flow probably won't work since I've repacked the column a few times by now
May
28
comment cell uptake prediction
cLogP? I would imagine that's a fast dirty way to get an estimate. en.wikipedia.org/wiki/Partition_coefficient
Apr
17
comment Are there any examples of sudden leaps in evolution?
I believe that the technical term is a "Hard Sweep".