Sam and Madeline will be presenting the following papers:
Choi S, Engelke R, Goswami N, Schmidt F. Proteomic profiling of metformin effects in 3T3-L1 adipocytes by SILAC-based quantification. Proteomics. 2022 Jun;22(11-12):e2100196. doi: 10.1002/pmic.202100196. Epub 2022 Mar 22. PMID: 35275438. Reviews: • Ong SE1, Mann M.A practical recipe for stable isotope labeling by amino acids in cell culture (SILAC). Nat Protoc. 2006;1(6):2650-60. • Geiger T, Wisniewski JR, Cox J, Zanivan S, Kruger M, Ishihama Y, Mann M. Use of stable isotope labeling by amino acids in cell culture as a spike-in standard in quantitative proteomics. Nat Protoc. 2011 Feb;6(2):147-57. doi: 10.1038/nprot.2010.192. PMID: 21293456.
15 Comments
HUIXIAN QIU
3/24/2024 11:03:38 am
What's the purpose of using both light and heavy medium and what's the difference between them? Why is the separation of using light & heavy medium necessary for this method and how does this step compare to oher proteomics methodls?
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Maggie Chrostowski
3/29/2024 12:57:09 pm
SILAC is labeled in a cell culture with heavy forms of amino acids. What are the amino acids they typically use?
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perla larios
4/2/2024 10:02:00 am
Why would body regulation be downregulated during celiac disease? what pathway is affected to cause this change?
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Miles Giehtbrock
4/2/2024 01:26:21 pm
In "Proteomic profiling of metformin effects in 3T3-L1 adipocytes by SILAC-based quantification" how did they know what peptides belonged to which protein after trypsin digestion?
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Joely
4/2/2024 02:16:56 pm
How could the findings from the primary paper be utilized for therapeutic strategies?
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Brooke Fuerstenau
4/2/2024 07:40:47 pm
They say that "although many clinical studies are suggestive of the effects of metformin, the biological alterations caused by metformin are unclear," so why would this drug be so commonly used if the effects are still unclear?
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Sara Fritz
4/3/2024 12:42:40 pm
In SILAC, ~97% of proteins that grow in the labeled isotope media will have the heavy isotopes. For the ~3% that appear to come from the normal cell culture (but actually are not), are these proteins composition completely due to chance or are there specific proteins that might be more likely to be unlabeled due to their rate of translation or abundance? What sort of error could occur as a result of this?
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Zoe Zwick
4/3/2024 06:54:30 pm
For the primary paper, they only used cells with insulin resistance. Do you think it would have been beneficial to also look at normal, healthy adipocytes as well?
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Michelle Conte
4/3/2024 11:03:34 pm
Will spike-in SILAC strategy provide different results than classical SILAC?
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Dianna
4/4/2024 08:18:48 am
Can SILAC be used to treat or detect other diseased cells/symptoms besides metabolic diseases?
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Rohan
4/4/2024 08:28:30 am
In the paper "a practical recipe for stable isotope labeling by amino acids in cell culture" they mention that their can be some inter conversion between proline and arginine in some lines- how can researchers get around this obstacle?
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Rebecca Wright
4/4/2024 08:57:25 am
In the SILAC paper, the authors found that metformin treatment significantly altered levels of many different kinds of proteins. Since metformin is used to treat type 2 diabetes, many of the regulated pathways, such as appetite, body weight, and metabolism, made sense to me. However, the authors also found that some proteins may regulate ER stress and protein folding. How would this be beneficial in treating type 2 diabetes?
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Praneeth
4/4/2024 12:06:19 pm
how do you assess the choice of 'heavy' amino acids used in their SILAC setup in terms of metabolic stability and quantification accuracy?
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Kate Stack
4/4/2024 12:17:11 pm
What are the reasons someone would use SILAC as opposed to traditional mass spectrometry or other quantitative proteomic methods?
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