Dear all colleagues,
I am new in the cell biology field. Could someone recommend me the technique or method to investigate the mechanism between pathogen and protein expression (of the host)?
Thanks in advance
Well, you could try western blotting. Say that there is a particular protein that this organism expresses that is interesting to you, if an antibody has been developed for it then you buy the antibody that's been developed against that protein and perform a western blot. You compare the expression of that protein with and without the presence of the pathogen and if there is no visible difference by western blot then the pathogen doesn't affect its protein expression. If there is a difference then the pathogen is affecting this protein expression.
If you don't know which protein to consider then consider a housekeeping protein which is a protein that is absolutely essential for "maintaining house" or keeping the organism alive. Consider a protein like one in glycolysis pathway. That's pretty essential for living organisms. If you want to look at total protein levels, you can run your cell lysate on an SDS PAGE gel and stain it with Coomassie to look at all the proteins on the gel. If protein expression is really low overall then you can silver stain the gel instead. If one band corresponding to a protein is interesting to you then you can cut it from the gel out with a razor and submit it to a collaborator for mass spectrometry analysis. Otherwise total protein can be measured with a spectrophotometer and the Bradford assay.
If say you incubate your pathogen with a plant and observe that plants grown with the pathogen have shriveled up leaves but plants grown without the pathogen do not, then the pathogen is affecting the leaves specifically. So a housekeeping gene expressed in the shoot or roots probably isn't useful to study. You need something that affects leaf growth and water retention in that case.
Ade Oktiviyari what exactly do you want? Do you want correlation (which sounds like you want a method to observe infection progress) or mechanism (how does the infection happen)?
Maybe try to be more specific and then we can discuss your options.
I'm thinking of two approaches: NGS of mRNA expression (to assess changes on transcription level) and differential proteomics (e.g., 2D-DIGE) to find changes on protein level
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