molecular mechanism of inflammation

[lillianroam]

I'm planning to apply a research opportunity on molecular mechanism of inflammation, espacially on respiratory tract infection. As it is said in references, I should infect the sample and get tissue, extract mRNA and amplify cDNA. I've no idea about what to do next. How could I know which gene specially function during innate immunity?
Need your help~

[mith]

1. compare to housekeeping genes
2. investigate likely candidate genes - knockout etc

[JackBean]

Well, if you use DNA chips, than it's easy, you will investigate almost all human genes and after proper analysis you should come up with genes involved (either positively or negatively) in inflamation.
If you use qPCR, than you have to look to papers first for some candidates, but that should not be a problam, as inflamation is IMHO quite interesting area for medics.
The other way is to look to Gene Ontology (http://www.geneontology.org/:) and look for inflamation and either search involved genes on their site or go to Human Genome web site and look for some assignment of genes. I don't remember, where is it exactly, but I know, you can search for specific GO ID in there.

[lillianroam]

1. compare to housekeeping genes
2. investigate likely candidate genes - knockout etc

Thank you.

[lillianroam]

Well, if you use DNA chips, than it's easy, you will investigate almost all human genes and after proper analysis you should come up with genes involved (either positively or negatively) in inflamation.
If you use qPCR, than you have to look to papers first for some candidates, but that should not be a problam, as inflamation is IMHO quite interesting area for medics.
The other way is to look to Gene Ontology (http://www.geneontology.org/:) and look for inflamation and either search involved genes on their site or go to Human Genome web site and look for some assignment of genes. I don't remember, where is it exactly, but I know, you can search for specific GO ID in there.

Basically, I think I need to amplify new genes in immunology. Thank you for your suggestions. They are very useful.

[JackBean]

What do you mean by 'amplify new genes'?

[lillianroam]

What do you mean by 'amplify new genes'?

I mean I need to find out new funtional genes in this process.
Happy new year.

[JackBean]

Well, then use the DNA chips

[zami'87.]

Maybe you could include cancer in that research as it has been discovered connection between inflammation and tumor promotion..there are plenty nice articles at NCBI...Good luck!

[jwalin]

i don't know how useful will the below information will be. i had done a project on medicine (indian traditional) a while ago. a bit of copy paste i am doing right now.

there is what i know about general inflammation. you could use a few ideas. but its all about general inflamation only

Eicosanoid biosynthesis begins when cell is activated by mechanical trauma, cytokines, growth factors or other stimuli. (The stimulus may even be an eicosanoid from a neighboring cell; the pathways are complex.) This triggers the release of a phospholipase at the cell membrane. The phospholipase travels to the nuclear membrane. There, the phospholipase catalyzes ester hydrolysis of phospholipid (by A2) or diacylglycerol (by phospholipase C). This frees a 20-carbon essential fatty acid. This hydrolysis appears to be the rate-determining step for eicosanoid formation free fatty acid is oxygenated along any of several pathways.
anti inflammatory substances usually stop this biosynthesis
other few lower histamine levels or inhibit cyclooxygenase (COX) and lipoxygenase (LOX),

i have lost a file that talked about how eocosonoid, histamine, COX and LOX help in inflammation

i am sorry if it was a waste of time
but i meant to help