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geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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stringent response GO:15968 #488

Closed gocentral closed 9 years ago

gocentral commented 21 years ago

Obsolete request for stringent response GO:15968

any of the given set of environment like pH, nutrition, hormone, temp, etc can be a stringent condition for a strain in an experiment.

All the response factors are stringent in some way or the other if the amount applied or the act carried out is on the either side (+/-) of optimal/normal.

I suggest making it obsolete.

Pankaj

Reported by: jaiswalp

Original Ticket: "geneontology/ontology-requests/488":https://sourceforge.net/p/geneontology/ontology-requests/488

gocentral commented 21 years ago

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The term 'stringent response' in GO describes the specific global change in cellular metabolism (the downregulation of nucleic acid and protein synthesis, and the simultaneous upregulation of protein degradation and amino acid synthesis) that occurs in bacteria in response to starvation. This is a specific type of response - even though it can be induced by a wide range conditions - so I think we should keep it. I will improve the defintion though.

Original comment by: jl242

gocentral commented 21 years ago

Original comment by: jl242

gocentral commented 21 years ago

Logged In: YES user_id=561361

References : general http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list\_uids=12399897&dopt=Abstract

More refs: http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list\_uids=12399897&dopt=Abstract Experiments suggest that phylogenetically different bacteria sustained the functional activities in these ecosystems in response to increasingly stringent nutrient limitation

Ref: Non bacterial http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list\_uids=12393680&dopt=Abstract With more stringent response criteria and using 4 months as time to evaluate response, this analysis confirms superiority of the cyclosporine regimen regarding the response rate in all patients treated (70% vs. 41%, with or without cyclosporine; P=0.015) as well as in patients with severe aplas-tic anemia (65% vs 31%; P=0.011).

I think that it is the response shown by an organism (phenotype) which has been placed in a specific environment e.g. nutritional/drug/temp/humidity etc. where the environment crosses the thresold of highest/lowest limits acceptable for a normal grwoth/lifecycle. In that way the response is recoded in terms of stringent levels of the amount of applied environmental factor. Environment (both biotic/abiotic) could be anything in/outside the organism's body. If I am not wrong in GO we intend capture the response to such factor and not its amount (e.g. stringent amounts). It could be framed as "response to stringency", but stringency to what ?

"What" can be replaced by all the drugs/light/temp/water/humidity/anything you can think of. Improtantly the amounts will vary at an individual to a population-species level.

Original comment by: jaiswalp