User:Weinjule

"Have a good time!" - Wules Jeinstein

Discussion Questions

Week 1

• Can we trust these measured stem cell replications rate to be relatable to stem cell replication rates in the human tissue environment? Could a difference in measured and actual replication rates matter for interpretation of this metadata analysis?
• Specific tissues have very different cellular and chemical environments in the human body. It’s feasible that these factors may contribute to cancer rates. Are such factors adequately covered by the E factor discussed in the paper? If these factors may mediate stem-cell replication rate are they meaningfully separate from the R factor?
• Specifically why would the hypothesized introduction of the R variable for cancer risk require such strong measures as a direct response from WHO? How might a lay person who peripheral came into contact with this paper view it differently than those with a scientific background? Is such a strong response reasonable or disproportionate (or somewhere in-between)?
• What are ways to build on this basic relationship between divisions and cancer risk into a more encompassing theory for real cancer behavior? What additional variables are needed?

Week 2

• Due to the potential for link rot utterly disrupting the connectivity between information sources in among publications, how might we further organize older work for future accessibility? In addition to the well known DOI number, what other methods are effective?
• Currently Journals have been trending more and more towards electronic media than physical media. Due to the intrinsic non-permanence of electronic media, what may happen when smaller, predominantly electronic journals go online in the future? How will this data be accessible?
• What different challenges are there in maintaining proper data identification for a bioinformatics analysis with a very large data set compared to a traditional basic science project?
• Who (or what organization) can be charged in enforcing proper data labeling and use? Presumably individual researchers will not be perfect at data stewardship despite that being the ideal outcome.

Maureen 13:09, 10 October 2017 (PDT)great Qs. Looking forward to discussion

Week 3

• TZAP appears to be correlated to telomere shortening, and the presence of TZAP is confirmed in cell lines with shorter telomeres. Is it likely that TZAP itself contains catalytic properties for directing shortening the telomere loops? Or would it aid in the recruitment or activation of other enzymes?
• On Figure 2C, mutations are made in TRF2 to identify if the TZAP binding region recognizes the same telomeric repeat and can be used to restore function in TRF2 missing its binding domain. Why does chromosomal fusion occur when TRF2 fails to bind? Is there a different phenotype between TRF2 and TRF-Zinc chimera? - Potential answer, the open 3'prime strand in telomere loop formation bind could bind to nonspecific regions of other chromosomes in the absence of TRF2 DNA binding proteins. Phenotypes to me do look different in terms of chromosomal packing, however there is sufficient function to result in fairly normal looking chromosomes
• If we assume that TZAP is directly implicated in shortening telomere length, what process would result in the longer telomeres sometimes found in older (higher replication number) cells? Would TZAP be expressed to a similar amount along a cell’s life time? Is there a “sweet spot”, as seen in the 5 KB and 20Kb celllines, where TZAP will not contribute to shortening?

Week 4

Presenter this week, no questions

Week 5

• CRISPR is not nearly as clean as it is frequently made out to be. Aside from using a "high quality" CRISPR repeat target region (referenced as above 85% quality score) what can the authors do to control for the effects of off target breaks? How might they ensure off-target breaks are not contributing to any observed phenotypes in the mouse disease models?
• Will alteration of TAD structure through large scale insertions or deletions result in differential methylation, acetylation and phosphorylation profiles within an otherwise conserved sequence? This would result in differences in expression and repression that is distinct from the disruption of spacial relationships. How could the influence of one or the other be confirmed?
• Is it possible for Tad structural rearrangement to ever be beneficial? Appears to be frequently lethal or otherwise deleterious as per this paper, but would a simpler eukaryotic organism have more room for rearrangements? The fact that Tads are highly conserved between humans, mice, and even chicks apparently makes the possibility of change unlikely but alterations could lead to new gene interactions with powerful effects.

Week 6

• Promoter elements and enhancer elements with high levels of histone acetylation tended to refold faster. While promotes this makes sense to ensure gene expression, why would enhancer elements be held to a similar standard? Would repressor-rich histone modification regions be expected to also fold faster?
• Is it possible that there are mammalian regions of high-density repressor elements in a similar way to super-enhancer regions? Why may or may not these be necessary. If they do exist would we expect them to exhibit similar characteristics to the superenhancer’s non-cohesion mediated interaction activity?
• The final model demonstrates that removing extrusion actually results in greater compartmentalization of chromosomal regions. In lecture we discussed how the fractal globule-model is the correct model of chromosomal organization rather than the equilibrium globule, and how a potential mechanisms that contributes to this organization was CTCF and cohesion mediated loop formation. Are these two concepts at odds? Does extrusion of chromosome into loop simultaneously encourage organized, but not highly compartmentalized, chromosomal structures?

Week 7

• HSP70 and HSP90 are two general chaperone proteins, involved in many refolding pathways. However, there are a great number of chaperones involved in normal cell function with greater specificity. Might it be possible to determine the cause of variable expression among individual genetic defects by analyzing specific chaperones involved in the process?

Answer: This is an interesting possibility. Chaperones have very different functions. In this study protein folding is the targeted mechanism, but depending on the nature of the chaperone involvement is more or less likely. HSP90 and 70 appear especially relevant do to their broad involvement, others may have more nuance to their involvement.

• Fanconi Anemia is a very useful disease for this study due to the massive number of genes involved in its phenotype, as well the the large body of work on it across the years. However this research could be carried out on other genetic disorders to reinforce the divergent HSP70 and HSP90 severity phenotypes across systems. What other candidate disorders would allow this experimental process to be repeated?

Answer:

• What are the implications of this research in possible carcinogenesis? I can imagine that HSP90 bound proteins could be involvement in cellular regulation, and stress mediated HSP90 reduction then may allow uncontrolled growth if other mutations exist.

Week 9

• How much stock can we put in results that include extremely low N (2 to 4, see figure 3)? Clearly low N is bad, but for single cell data RNAi is this more excusable? What would be an acceptable way to navigate this situation? Is the use of error bars intellectually honest?
• Does this divergent process of cell cycle mediation likely involve those cell single pathways, such as Ras, Myc,EF2, to contribute to daughter cell fate? What are other possible existing cellular protein types that could be responsible for this observed behavior?
• P53 is implicated in a variety of factors relating to control of cell lifespan involving DNA damage. Due to it's breadth of function in cell cycle and cell death, is it an ideal marker for DNA damage occurance? Should short term DNA damage response in the cell cycle through ATM/ATR also be analyzed?

Week 10

• Why didn't the authors carry out M6A methylation level testing data in concert with the shock-mediated transcription alteration experiments in heat shock and FTO knockout situations?Would have been helpful to include that experiment side by side to tie together M6A's activity more directly to HSP70 behavior.
• RNA capping is used in more than enabling the construction of the transcription complex, it is a key signal in nuclear export and maintains RNA stability. What mechanisms may contribute these uncapped mRNAs to survive towards transcription once outside the nucleus?
• Conceivably there are a great number of additional signals that can result in non-cap dependent transcription. Might this be mediated by the same group of elF proteins, or associated complex? What RNA structural changes could allow this?

Week 11

• One of the strong possibilities with using RT-qPCR for identifying Dengue and Zika viruses is that it is possible to easily create different levels of specificity to a given strain or set of strains fro qPCR probe design using flexible bases. However the CAS-9 guide RNA tends to possibly more specific than qPCR primers. How might this SHERLOCK system be adapted to variable specificity across viral species?
• The prospects of applying SHERLOCK in the field are very attractive. While sherlock reactions are clearly more feasible than qPCR in the field, how do they compare to a simple ELISA? Is the increased specificity offered by the guide RNA necessary for field analysis?
• Good question for Pat but ELISA requires more lab stuff and cold chain. Maureen 11:00, 14 December 2017 (PST)