janapix

Hello,


Let's say I'm using intracellular staining of IFN-gamma to identify CD8+ T-cells which have been stimulated by a peptide...
I'm just curious about how this works, that is, using synthetic peptides to stimulate the T-cells, because I thought T-cells
could only recognise peptide in the context of MHC.

Please explain how incubating these cells with free-floating peptides (if that is how its done at all...) results in the activation of
effector T-cells. Peptides on MHC-I, tethered at both ends are meant to loop upwards, providing a recognizable shape in the
CONTEXT of MHC... what am I missing here? I would be very grateful if someone could explain this, or even point me to an
appropriate article.


(p.s.: I do understand how the cytokines produced are trapped inside the cell, and how staining proceeds.)


Thanks.

Looking up this mouse strain, I found this website (http://jaxmice.jax.o...ain/000664.html) describing the strain as one providing a
"permissive background for maximal expression of most mutations"

What does this mean?
Do any of you know the molecular/genetic basis of creating a mouse that allows this?
Do you know any good papers/references which might answer my question?

I'm just a curious undergraduate...

Hello,  I'm studying proteomics at uni and am trying to create an all-encompassing workflow, bearing in mind that the techniques chosen along the way will depend on the specific scenario. This is what I've come up with so far... is there anything that should be added  in here?
I don't want to include obscure technology.

Also, I understand that the categories I've used here are flexible, allowing their components (in boxes)  cross-over into each other, if I've made major mistakes, do let me know, but I am aware that the field doesn't allow for creation of an exceedingly strict workflow.
Alternatively, If you already have a workflow similar to what I'm looking for, I'd love to see it.



image link: http://i317.photobuc...icworkflow1.png

What makes metablomics more complicated than proteomics?
Why are there so very few people/labs that are good at it? Do the complexities arise from the nature of the cell itself
or researchers just waiting for high-thoroughput technology to come along and make life easier?

Just curious because I'm studying proteomics right now, and my lecturer has included a rather short section on metablomics
... but I'm given to understand that metabolites actually provide the best 'snapshot' of what is going on inside a cell.


edit:  ALSO... when extracting samples fro tissues, how do you make sure you're not getting any components of the 'proteome' in there?
Is it something along the lines of using molecular sieves to retain the smallest compounds?

Question: I split one sample (cells) into two, extract mRNA from one, proteins from another and analyse. Why are there differences between mRNA levels and protein abundance?

This isn't homework. Just studying for an exam and I'd like to know ALL the variables. The question (from a past paper) asks for biological and technical reasons. I only have 3 biological (Bi) and one technical (T) reason(s).

• [mRNA] not connected to protein turnover (Bi)
  
• gene expression doesn't always lead to protein products (Bi)
  
• long-life proteins may be present while their mRNAs could be degraded and absent due to the related gene being switched off at the time of sampling. (Bi)
  
• integral membrane proteins are difficult to extract and would show deceptively low abundance (T)