Gergana Vandova

3,698 reputation

1634

bio	website	linkedin.com/profile/…
	location	Palo Alto, CA
	age	27
visits	member for	1 year, 5 months
	seen	May 11 at 0:28
stats	profile views	199

Visiting scholar at Stanford Genome Technology Center. Interested in synthetic biology.

	3,698 reputation	bio	website	linkedin.com/profile/…	visits	member for	1 year, 5 months
1634 badges		location	Palo Alto, CA		seen	May 11 at 0:28

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Dec 19	comment	How many people's DNA were involved in the compilation of the reference human genome? Wow, I read so many papers regarding this matter, but never wikipedia. Thanks. But do you think it is really unknown exactly from which source the DNA came?
Dec 19	comment	How many people's DNA were involved in the compilation of the reference human genome? Can you please give me a link to the source of this text?
Dec 19	asked	How many people's DNA were involved in the compilation of the reference human genome?
Dec 19	answered	How are the boundaries of a gene determined?
Dec 19	awarded	Critic
Dec 19	awarded	Nice Question
Dec 16	comment	What determines a successful protein expression in E. coli? The two subunits are on the same plasmid. The plasmid sequence starts with T7 promoter, RBS1, subunit beta, RBS2, subunit alpha. The RBS sequences are a little bit different, so I was thinking of making them the same, but this shouldn't have a great effect on the protein expression. (they are very close to the consensus sequence).
Dec 16	awarded	Commentator
Dec 16	comment	What determines a successful protein expression in E. coli? But this still doesn't explain why the other subunit expresses better, as well as other proteins from the same native organism are well expressed in E. coli. That's why I think it is more of a question about the control elements of transcription and translation, rather than rare codon usage.
Dec 16	comment	What determines a successful protein expression in E. coli? Thanks, Mad Scientist! Yes, I have thought about codon optimization and this is definitely on my to do list. Sorry I forgot to mention it. DNA 2.0 has a software which will convert your sequence into optimized one. I have also heard about Rosetta BL21, but I have never used it. We might also want to stick to our own strain, because it is the heterologous producer of of or drug of interest. I am a little concerned about codon optimization, precisely because of misfolding but I thing we should do it.
Dec 16	asked	What is causing my problem with very low yields when isolating a 42kb yeast plasmid?
Dec 16	asked	What determines a successful protein expression in E. coli?
Dec 16	comment	Which sequence characteristics influence the transcription efficiency of T7 polymerase? Well, the protein expression also depends on the strength of the ribosome binding site.
Dec 16	answered	bi-directional transcription experiment
Dec 15	comment	What is the criticality of the ribosome binding site relative to the start codon in prokaryotic translation? What I am also concerned about, are secondary structures formed between the RBS and the upsream or dowstream sequence. Any thoughts on that? Thanks again :-)
Dec 15	comment	What is the criticality of the ribosome binding site relative to the start codon in prokaryotic translation? Thanks for your thorough answer. I guess I haven't realized that the RBS end is determined by this U base. Does this mean that it can be 100 bases away from ATG? I am actually asking this question, because I have a synthetic construct with RBS annotated on it and some of them are really far away from the start codon. Which could mean either wrong annotation of the following gene sequence, or that the distance doesn't matter that much. But on the other hand I thought that the ribosome should bind both the RBS and the start codon at the same time which I don't see possible with long sequences.
Dec 15	accepted	What is the criticality of the ribosome binding site relative to the start codon in prokaryotic translation?
Dec 15	comment	bi-directional transcription experiment What organism is it? And how big the genes A and B are?
Dec 14	comment	Has anyone tried Gibson Assembly Optimizations? Thanks. Yes, I have heard of the Gibthon software, haven't tried it yet. We have been using the IDT predictor of secondary structure of the primers. Might be worth comparing it to the Gibthon tool. It would have been nicer if some optimizations of the reaction conditions make the use of such predictors obsolete. Not to mention that their precision is questionable.
Dec 14	awarded	Scholar