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visits member for 2 years, 7 months
seen Aug 15 '13 at 16:22

Aug
27
comment Do twins “run in the family”?
I am still catching up on this topic but there are (atleast) 3 documented towns with greater than average rate of twinning: Cândido Godói, Kodinhi and Igbo-Ora. A published study on the Brazilian town might also be of help. It might be informative to look at familial twinning in these examples as beginning clues.
Aug
21
comment What makes a wet dog so stinky?
The "after rain" smell is technically called "petrichor". In summary, compounds from plants emitted during dry periods get absorbed into rocks. Rain releases these compounds and the smell derives from these compounds. The wikipedia page is a good place to read more about petrichor.
Aug
20
comment Why is GTP gamma S non hydrolyzable?
I'm almost certain its got something to do with the amino acid in the P-loop that contacts the gamma phosphate, however without a reference I am not going to post it as an answer yet. I can ask my PI but then its more fun to find it out myself ;)
Aug
20
comment Is the EC50 of an activating protein for an enzyme a good indicator for the binding affinity Kd?
bobthejoe, just thought I'd say this: You've laid out really well why interpreting Km is not always trivial. Exactly why I chose to focus on EC50 (with the trivial(?) assumption that substrate far exceeds enzyme concentration). I'm going to accept your answer, given the richness of detail that you've laid out!
Aug
16
comment Is the EC50 of an activating protein for an enzyme a good indicator for the binding affinity Kd?
bobthejoe: I like the detail in your answer, especially the hGH example is very surprising. However, my question pertains to comparing affinities and EC50 measurements, both being derived from in vitro assays with purified proteins. I would think the avidity argument might hold, especially when the same system were compared in a vesicular environment versus detergent solution.
Aug
6
comment Absorption ratios 260/280 and 260/230 for RNA
For the sake of completeness and relevant detail: The aromatic amino acids (Phe, Trp and Tyr) are the primary contributors to the ability of proteins to absorb at 280nm. Cysteine double bonds can also absorb but its both rare and the extinction coefficient is smaller in comparison to the aromatic residues.
Aug
4
comment What is itching?
I have seen two answers posted and then "disappear" after a couple of days.. Can someone tell me whats happening or was I dreaming? :-)
Jul
30
comment How would I explain different properties of the same protein in different species?
The NCBI protein database or UniProtKB would be the first places I would search. Other databases exist, but these are my personal favourites
Jul
30
comment How would I explain different properties of the same protein in different species?
Have you checked sequence similarity/identity, especially of the nucleotide contacting regions (otherwise known as the P-loops I think)?
Jul
24
comment How to compute properties of peptides ?
The introductory chapter of Proteins by Thomas Creighton (books.google.com/books/about/Proteins.html?id=hu8T_kI1LrkC) would be a great place to start. It was my Bible for introductory biochemistry in college!
Jul
1
comment How do I deal with sticky and viscous samples from cell lysates?
Definitely your suggestions will make things much better. I think Mad Scientist was looking for a quick and dirty way to do it when doing small scale checks for protein expression from a new construct.
May
10
comment Do gene expression levels necessarily correspond to levels of protein activation?
@Daniel: +1 for ending it at "..high throughput (which is all the rage these days)"!
May
10
comment Protein construct design
I used the x-ray structure to determine known loop regions that connect structured domain regions (pt #1)
May
10
comment How does a cell know its size?
Of particular interest to this question might be the latest issue of Curr Biol that has a special section devoted to this topic: Curr Biol, Vol 22 Issue 9 (cell.com/current-biology/issue?pii=S0960-9822%2812%29X0009-5)
May
3
comment Generating custom human DNA sequences based on traits such as eye colour?
"maybe" is the keyword ;-)
Apr
30
comment Does anyone have any TOPO directional cloning tips?
From what I read, @Ben seems to be saying that he is not looking to troubleshoot the original (traditional) method which failed and is only looking for tips on using the TOPO kit as a first-timer..
Apr
14
comment Compressing structural information in PDB files
It sounds to me that apart from the fact that it is PDB files that are under discussion here, this is not really a biology question per se but more of a programming question and you are likely to get better responses from that forum.
Mar
22
comment How does a cell know its size?
Rebecca Heald and her group at Berkeley do very interesting work looking at how organelle sizes are controlled by comparing two Xenopus species, very much related to the question here. Check out Nuclear size is regulated by importin alpha and NTF2 in Xenopus
Feb
27
comment Which cryogenic vials and caps are ideal for storing glycerol stocks?
I routinely store my stocks in plain vanilla 1.5ml eppendorfs and see no issues with it. I would be curious also to know what/why these special vials are "special"