User:Kromine

Kyle Romine's Discussion Page

Week 1 Discussion Questions

1. In the second article, do you think the assumption that: “…the increase in mutations resulting from poor diet is identical to the increase resulting from smoking cigarettes” is accurate or fair?

2. Do you think this mathematical model has a means of accounting for replicative diseases that impart resistance to certain cancers? Alternatively, mutations that make you more prone to cancers?

3. I don’t think this model accounts very well for the variability in division rates in cancers and sub-types, what are your thoughts on this?

Week 2 Discussion Questions

1. One concern I have with switching to DOI’s is the risk of losing information if databases become compromised. What are your thoughts on this? Should we move to alternate identifiers?

2. With the development of large repositories across multiple centers, how can we develop a uniform method of creating sample identifiers? Who should make these decisions and how can we keep in mind Protected Health Information with these identifiers?

3. What obstacles do you think will be the hardest to overcome for the creation of global identifiers?

Maureen 13:27, 10 October 2017 (PDT)Great questions for your faculty mentor today!

Personal thoughts: I think this paper is a bit dry to read but brings up some very important topics. I have found in my own studies that, especially working with clinical samples, there is a huge issue in keeping identifiers both unique and consistent. This can be very frustrating and hard to deal with. I have also had issues in previous labs about losing data due to having slightly different identifiers in a larger data bank (i.e date first, organism second, vice versa, etc.)

Week 3 Discussion Questions

1. What are the implications of the discovery of TZAP as a telomere trimming protein? How should we proceed forward with research? Whats the next big question?

2. What do you hypothesize are the identities of the “additional factors” that must regulate TZAP?

3. Do you think this telomere upper limit associated with TZAP will be uniform across species? Families? etc.

Week 4 Discussion Questions

1. Why would it be evolutionary beneficial to keep transposons if they are 'parasitic', as the authors describe?

2. Since Rhino is not conserved outside of Drosophila, what do you predict will be found in humans?

3. How will this research change how we perform transposon-based gene knockout experiments?

4. How should we continue forward with heterochromatin research?

Week 5 Discussion Questions

1. What do you hypothesize are some of the “other unknown factors” that contribute to the receptiveness of the promoter to respond to an enhancer? Do you think that its structural or more small-molecule effects (I.e protein cascades, etc.). My guess is that there are some post-translational modifications due to differential signaling.

2. I feel like the paper is kind of stuck in a loop analogous to the question of whether the chicken came first or the egg. Do you think TADs evolved as a result of the requirements of enhancer:promoter interactions? Or did enhancer:promoter interactions evolve as a result of the already present topology conserved in the genome? I realize this question isn’t really answerable, but I think it would be an interesting discussion. I am inclined to believe that it is the latter as it makes sense to have evolved to have these TADs regardless of enhancer:promoter interactions such as these (such as regulatory elements, etc.).

3. The authors seemed to be convey pretty clearly that they believe that TAD disruption plays a critical role in disease etiology so, knowing their experimental methods, would you say it is realistically feasible (financially and timely) to create diagnostic tools to evaluate patients for these abnormalities? The authors even specify in the last paragraph of the discussion how these analyses will provide valuable diagnostic info from patient cells, but what can/should we do with this information?

4. Slightly off topic question, is it possible TADs are conserved regions for recombination or am I just off the deep end?

Week 6 Discussion Questions

1. Do you think it would ever be evolutionarily beneficial to NOT preserve the contact domains in chromatin?

2. Are there known organisms or lineages that have a lower level of contact domain preservation?

3. What would be the effect of a higher affinity cohesin protein with respect to loop termination? What would the consequences be if the cohesion molecule did not fall off properly?

Note: It really just surprises me that the loops can be so easily removed. If this is so important biologically it is shocking that you can knockout a single protein in the complex (Rad21) and completely shut down the chromatin topology. If you look at other extremely important biological processes there are lots of redunancies and rescue mechanisms but this paper shows that the mechanism is pretty much entirely dependent on CTCF and Cohesin and that there are no biological "backups"

Week 7 Discussion Questions

1. I know from working in leukemia research that palbociclib (and the other -ciclibs) are considered to be somewhat “dirty” when it comes to hitting the CDK4/6 complex. Should they have used siRNA or CRISPR to knockout/down CDK4/6 instead of using a drug based method? I am thinking that a knockout would possibly be too deleterious to the cell and that is why they went with inhibitors…

2. They mention situations where there needs to be a fixed number of cells generated, such as in wound healing (which I am assuming is NOT referring to all their p53 work), but don’t do any experiments or cite any regarding whether or not this model stands in those situations. Have you found any evidence to support this?

3. Can this model be used as an early detection diagnostic tool? Lots of blood cancers specifically have mutated CDK4/6 signaling so I wonder if we should be looking at the ratio of CCND1 and p53 mRNA in pre-cancerous cells.

Side Notes:

Can you explain to me how you make something siRNA resistant?

How does mRNA get transferred to the daughter cells here? Is it passive? Would it have been possible to block mRNA transfer?

Week 8 Discussion Questions

1. What are some hypothetical evolutionary benefits to creating (or allowing) a system to translate uncapped RNA’s? Do you think this is a result of faulty ribosomal RNA translation that just never got fixed?

2. There are probably hundreds of thousands of RNAs in a cell but the authors state that there only “a few hundred” that utilize the 5’-UTR methyl-Adenines. Are these specific RNAs that are conserved? I would imagine that, if the hypothesis were true, then they would be genes absolutely critical to protecting against cellular stresses and for cellular maintenance.

3. Why do you think that interferon had no effect on m6-A levels but heat-shock and UV did?

Notes:

I liked the papers hypothesis and the data presented is compelling but I felt like there were a lot of experiments missing. The ‘claim’ is mostly that there is an increase in cap-independent translation using the m6-A residues in the 5’-UTR, which is due to stress. But, they did little to no challenging of the eIF3 protein, which is supposedly absolutely required for m6-A recognition. What happens if we use cells with normal eIF4 activity (HeLa have reduced activity)? Is eIF3 more heat stable than eIF4? Are there certain genes that will predominantly be cap-independent?