Brooke and Maggie will be presenting the following papers:
Zhang Y, Shang L, Zhang J, Liu Y, Jin C, Zhao Y, Lei X, Wang W, Xiao X, Zhang X, Liu Y, Liu L, Zhuang MW, Mi Q, Tian C, Wang J, He F, Wang PH, Wang J. An antibody-based proximity labeling map reveals mechanisms of SARS-CoV-2 inhibition of antiviral immunity. Cell Chem Biol. 2022 Jan 20;29(1):5-18.e6. doi: 10.1016/j.chembiol.2021.10.008. Epub 2021 Oct 20. PMID: 34672954; PMCID: PMC8527578. Reviews: •Varnaitė R, MacNeill SA. Meet the neighbors: Mapping local protein interactomes by proximity-dependent labeling with BioID. Proteomics. 2016 Oct;16(19):2503-2518. doi: 10.1002/pmic.201600123. Epub 2016 Jul 27. PMID: 27329485; PMCID: PMC5053326. • The Proteome: Discovering the Structure and Function of Proteins: Jill Adams (2008). https://www.nature.com/scitable/topicpage/theproteome-discovering-the-structure-and-function-613/
16 Comments
Huixian Qiu
3/10/2024 08:36:15 pm
what is the role of biotinylation in this experiment?
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Joely Swanson
3/18/2024 02:27:11 pm
How can this study be used in the future? Just for identifying drugs to lessen COVID symptoms?
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Rohan Babaria
3/18/2024 09:25:36 pm
They mentioned the overlap for the datasets were low on the study for sars-cov2, I was wondering what could be the cause of that?
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Dianna
3/19/2024 01:20:06 pm
In Zhang et al.’s article, they revealed the viral infection mechanisms of SARS-CoV-2, does that found similar in other species?
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3/19/2024 02:06:29 pm
For BioID, what is the method commonly used to lower the interference, like the behavior change caused by biotinylation.
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Sara Fritz
3/19/2024 02:35:32 pm
In Zhang et al.’s article, they tested drug treatment with SARS-CoV-2 infection and got results on the expression of proximal proteins, this is shown in Figure 7B, what exactly is the connection between the upregulation/downregulation of these proteins and the SARS-CoV-2 infection/severity?I also thought it was really interested that estradiol is one of the drugs that alleviates COVID-19 symptoms, I wish the researchers had expanded on this more.
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Julia Carey
3/20/2024 08:39:48 pm
What is the maximum proximity for the BioID protein identification?
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Perla Larios
3/20/2024 09:22:11 pm
In the Zhang supplemental info they tells us that they see a very high p-value and gene ratio in within the organic anion transport but its not mention on the paper, why is this the case?
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Rebecca Wright
3/20/2024 09:34:54 pm
Another BioID question: Can you go into more detail about Figure 2 in the Zhang et al. paper? I understand that they're explaining how they verified the efficacy of the model, but why are they using a Myc antibody in a biotinylation experiment?
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Samuel Kivi
3/20/2024 11:06:32 pm
In the article from Zhang et al., are any of the examined drugs (such as in Fig. 7) currently used to as a treatment for COVID?
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Miles Giehtbrock
3/21/2024 12:11:10 am
So to my understanding it has been proven that BirA tags do don effect the tagged proteins cellular localization. Could it affect biotin- related protein's function if i researcher decided to use this tag to investigate the function of a biotin interacting enzyme?
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Zoe Zwick
3/21/2024 01:11:25 am
One thing mentioned in the main paper was that when compared to 3 other papers, "Of the 1,388 high-confidence proximal proteins in this study, 1,092 proteins with biotinylated sites were not covered". Why might this be?
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Kate Stack
3/21/2024 08:58:11 am
In the Zhang et al.’s article they found that COVID-19 may be affecting host gene expression regulation through epigenetic signaling. How common is this phenomenon with other types of viruses? Is this part of what made COVID-19 so severe?
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Michelle Conte
3/21/2024 11:16:36 am
For the proteins E, NSP1, ORF3b, and ORF6, which had no interaction, is there a hypothesis for why this is the case? Since they are viral proteins, what could they have in common to be an isolated group from this interaction network?
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Praneeth
3/21/2024 11:51:06 am
how do the advancements in proximity-dependent labeling techniques like BioID, as reviewed by Varnaitė and MacNeill, contribute to our understanding of viral-host interactions compared to earlier methods?
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Madeline Blum
3/21/2024 11:53:20 am
In Zhang et. al, four drug compounds were assayed for virus inhibition, one being a control. The three experimental were recommended for clinical trials. Do you know why Azacitidine would be recommended for clinical trial, despite the significant cell toxicity demonstrated in their data, as well as mentioned in their analysis?
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