1
vote
1answer
18 views

How to identify the genes that distal enhancers pair?

I am writing a project proposal and I have to talk about this problem: how to identify the genes that distal enhancers pair? I am really new to this topic and I don't know what it is all about. I ...
2
votes
1answer
55 views

Using RNA-seq to compare gene expression across patients instead of between Control and Experimental conditions

I am working with RNA-seq data from the Cancer Genome Atlas TCGA and I have been reading about how people have compared gene expression levels measured by RNA-seq. Many of the papers I have read talk ...
2
votes
1answer
34 views

Why does the pET- expression vector contain a LacI gene additionally to the one in the genome?

The pET plasmid is used for protein expression with T7 promotor in expression strains, such as E.coli BL21(DE3) It contains a lacI gene which codes for the lac repressor protein, a protein of ...
3
votes
2answers
110 views

How can CI repressor both activate and repress $P_{RM}$ promoter found in $\lambda$ phage?

I'm reading a paper where the authors constructed a toggle switch that uses bidirectional $P_R/P_{RM}$ promoter found in the $\lambda$ phage. There are 3 binding sites - $O_R1$, $O_R2$, $O_R3$ - ...
6
votes
1answer
279 views

How much does the distance between a transcription factor binding site and a promoter influence transcription?

Assume we have a synthetic construct with a minimal (inducible) promoter that requires activation for significant transcription to occur. Realistically, how important is the distance between an ...
4
votes
1answer
60 views

What is the relation between plasmid concentration and mRNA levels?

Suppose a simple synthetic construct, consisting of a constitutive promoter and a single gene: One of the simplest ways to model GFP transcription is to use an ODE: $\frac{d [GFP_{mRNA}]}{dt} = a - ...
0
votes
2answers
118 views

How to determine the actual flux in the human metabolic model of a cell line?

The problem to be solved is to determine what the flux values are for the different reactions in the human metabolic model. As far as I understand, a good way to do that would be to use gene ...
1
vote
1answer
109 views

Shine-Dalgarno sequence and expressing proteins

Shine-Dalgarno sequence present in the prokaryotic mRNA plays a role in initiation of translation. In eukaryotes a Shine-Dalgarno like sequence is present but does not play an important role in ...
2
votes
1answer
545 views

Lyonization and X-linked disorders?

Lyonization or X-chromosome inactivation is the conversion of all but one, X-chromosomes in Females into non-coding heterochromatin (i.e. deactivated) leading to the formation of one or more Barr ...
2
votes
1answer
448 views

Optogenetics - How do microbial opsins work?

I'm just introduced to the optogenetics method and am having some trouble grasping the genetics (of the optogenteics) part of things. So we have Retinal and Opsin that form Rhodopsin molecule that ...
2
votes
1answer
387 views

Manipulation of gene expression using VP16 fusion and engrailed fusion to a transcription factor?

Today, a presenter briefly mentioned that gene expression in sea urchins during development might be manipulated using VP16 and engrailed fusions. On a slide, it said that expression might be ...
7
votes
1answer
45 views

circulating microRNAs are functional?

In plasma and other body fluids, miRNAs can be found. They not only originate from dying cells but also from active secretion and are usually 'packed' into vesicles/lipo-proteic structures (i.e. ...
6
votes
1answer
102 views

Bicoid regulation of hunchback

I'm learning about development via the example of Drosophila embryogenesis. I understand that bicoid regulates hunchback, among other genes. My question whether the regulation is direct or indirect? ...
9
votes
1answer
200 views

How are there alternative initiation codons?

According to wikipedia and the original complete sequence of the K-12 genome, there are multiple non-AUG start codons such as GUG and UUG. How is this possible? I'm particularly curious about the ...