Rohan and Joely will be presenting the following papers:
Pastuzyn ED, et al., The Neuronal Gene Arc Encodes a Repurposed Retrotransposon Gag Protein that Mediates Intercellular RNA Transfer. Cell. 2018 Jan 11;172(1-2):275-288.e18. doi: 10.1016/j.cell.2017.12.024. David Lee, Oliver Redfern & Christine Orengo, Predicting protein function from sequence and structure Nature Reviews Molecular Cell Biology 8, 995-1005 (December 2007) | doi:10.1038/nrm2281 Overview of back to back papers in Cell: http://www.cell.com/cell/fulltext/S0092-8674(17)31509-X Popular Press Article (A recommended read): https://www.theatlantic.com/science/archive/2018/01/brain-cells-can-share-informationusing-a-gene-that-came-from-viruses/550403/
16 Comments
HUIXIAN QIU
2/11/2024 09:47:17 pm
In the article Predicting protein function from sequence and structure, the author mentioned comparing the sequence of the protein is used to predict the function of protein. What is the accuracy of the prediction compared to the experimental data? How does this method relate to the genomic sequencing that we covered before?
Reply
Rebecca Wright
2/13/2024 11:29:43 pm
One thing I found rather difficult to conceptualize is the relevance of the findings of the Neuronal Gene Arc paper. The findings are very interesting, particularly the data about revealing a new signaling pathway, but I'm having trouble understanding where it fits in to the larger picture. Is it useful for disease research? Virology? Something else? Could you elaborate on this please?
Reply
Perla Larios
2/14/2024 02:02:22 pm
"The Neuronal Gene Arc Encodes a Repurposed Retrotransposon Gag Protein that Mediates Intercellular RNA Transfer" article explained that they used HEK cells, why did they choose this specific cell line. Also this is a embryonic kidney line not a cancer line why was this the route?
Reply
Sara Fritz
2/14/2024 05:42:30 pm
In "The Neuronal Gene Arc Encodes a Repurposed Retrotransposon Gag Protein that Mediates Intercellular RNA Transfer" the researchers have evidence that RNA is needed for the capsid development of the Arc protein and that RNA is transported by the Arc capsid. The RNA that is encapsulated is said to be collected in a stochastic process or that the most abundant RNAs are captured. What do the researchers talk about for what this means for intercellular signaling? Is this fast or slow? What types of information are communicated this way.
Reply
Samuel Kivi
2/14/2024 07:18:47 pm
Do any other genes encode similar virus-like capsids to Gag proteins in animals? If not, why is Arc the only known gene to encode something like this? Does it have anything to do with the fact that the function is only present in/between neurons?
Reply
Zoe Zwick
2/14/2024 09:37:46 pm
In "The Neuronal Gene Arc Encodes a Repurposed Retrotransposon Gag Protein that Mediates Intercellular RNA Transfer," they mention that there could be Arc-dependent intercellular signaling in systems other than the nervous system. Is the function in these other cells similar or does the mRNA that they carry affect the cells that they are signaling to differently?
Reply
Michelle Conte
2/14/2024 11:55:54 pm
In the Western Blots that show the absence of the Arc protein, is that because the protein was degraded as a result of the transfections and experiments or because it was blocked from being released?
Reply
Dianna Xie
2/15/2024 12:48:12 am
In ”The Neuronal Gene Arc Encodes a Repurposed Retrotransposon Gag Protein that Mediates Intercellular RNA Transfer”, does dArc1 have the same RNA-binding mechanism/function as dArc2, since they are structured differently?
Reply
Maggie Chrostowski
2/15/2024 08:49:49 am
In “The Neuronal Gene Arc Encodes a Repurposed Retrotransposon Gag Protein that Mediates Intercellular RNA Transfer,” I wondered if Arc is related to the structure of microglia? I only think this because microglia are responsible for pruning neurons.
Reply
Miles Giehtbrock
2/15/2024 09:44:00 am
In "Predicting protein function from sequence and structure" they mentions reasons why they may not be able to use homology related protein sequences to help predict function. They also mentioned PROTFUN, an algorithm that took post-translational modifications into account when predicting protein function. This led to my question, do simple BLAST based algorithms take into account intron sequence and other large insertion sequence data?
Reply
Maddy Blum
2/15/2024 10:03:44 am
In Pastuzyn et al., the Arc homolog in Drosophilia, dArc1, was mentioned to have been originated independently. The tests revealed both arc and darc1 assembled into homologs. Why do you suppose they only tested tetrapod arc capsulation after this similarity was confirmed?
Reply
Brooke Fuerstenau
2/15/2024 11:13:17 am
In “The Neuronal Gene Arc…” they talk a lot about the evolutionary pathway of Gag genes and their repurposing for other important tasks, how did these genes evolve separately in different organisms to function in the same way?
Reply
Julia Carey
2/15/2024 11:20:03 am
How do you think these Arc proteins could be used in treatments for various neurodegenerative disorders, such as Alzheimer's?
Reply
2/15/2024 11:22:59 am
In the article "The Neuronal Gene Arc Encodes a Repurposed Retrotransposon Gag Protein that Mediates Intercellular RNA Transfer", they mentioned that the closest relatives of Arc in the coelacanth, zebrafish, and carp genomes were encoded by prototypical Ty3/gypsy retrotransposons. Does that conclusion also obtained from the similar BLAST method we did on the lab or there are any other method. Additionally, since Arc capsids are caspid domain with Gag, is endocytosis also one of the similar function share between Arc and Gag.
Reply
Praneeth
2/15/2024 11:28:15 am
How do the discoveries about the Arc gene's role in intercellular RNA transfer and its evolutionary origins influence our understanding of neuronal communication and plasticity?
Reply
Kate Stack
2/15/2024 11:54:48 am
In the primary paper how might the results differ if they did not use mice as their model organisms? Zebrafish also appeared to be a close relative in their phylogenetic tree and I wonder how their difference in phylogeny would affect things.
Reply
Leave a Reply. |
AuthorDr. Ahna Skop Archives
April 2024
Categories |