2. In the planned experiment parts, I'm curious what do ACAT inhibition and Statins do and how do they related to the cholesterol binding with STING?
Thank you!

 Based on your results, do you think aspirin is worth considering as a preventive treatment for NAFLD?

In order for effective therapies to be developed I assume in vivo human testing would have to be done at some point. How could these therapies be safely tested in human beings? 

 

1. It was mentioned in the beginning that dental prosthetics are not ideal solutions to tooth decay, especially due to their expensive nature. I'm not sure if you would know this at all, but realistically do you see cell therapy treatments such as this being a cheaper alternative, or would they just be preferable from a comfort/lower infection risk perspective?

2. Are there any other mechanisms that regulate the HIPPO pathway that could impact cell proliferation/differentiation? If so, what impact would this have on YAP expression?

2. What other possible reasonings are there for your observed results and what controls did you use to rule out other possibilities for why there were more observed genomic similarities among prolate phages than prolate-phage and non-prolate phages. 

 

How could the results of your research be applied towards making effective cancer treatments in the future? 

What potential confounds did you have to control for when performing your experiment? 

2. Would it be correct for me to say that wound healing being upregulated is an instance of an oncogene mutation or expression change? Meaning that the gene expression change promoted cell survival and could possibly explain why HPV is implicated in cancer research?

1. Is there a limit to the amount of protection against ischemic injury that mitochondrial fission can induce (or does more exercise always yield greater protection)? 

2. Is there reason to suspect drug-initiated mitochondrial fission significantly differs from exercise-induced mitochondrial fission?

2. I know you mention on the poster the differences between the old and new guidelines and I was wondering is this a typical thing that happens in microbiology? Are different groups of organisms and in this case innate immune system responders frequently being reclassified on the basis of their evolutionary relationships?


Great work again! Thanks
-Andre

2. How do the properties of Aspirin (anti-inflammatory) and (lowing cholesterol levels in blood) connect to their effects on the mice's changes in fat mass, weight gain, and TG levels?
Great work, thank you!!

Secondly, while these specific drugs and pathway targets may not be applicable to other types of tumor cells, could this style of treatment (as in altering intracellular pH) potentially be used to treat other types of cancer? If there were another type of tumor cell that also had an obligate pH range for survival, do you think similar approaches could be used to treat those cancers?

Also, I think your experimental design was great in that you measured the effects of the drug before and after disease onset.  Another question I have is what did you do to characterize disease onset? Was there also a certain amount of fat buildup to be considered “steatosis”? Overall, I really enjoyed learning about your research. The applications of PharmOmics sounds very promising. I would love to see what else it can do for other diseases that might not have any specific drugs developed for it or even maximize the potential of known drugs.

Also I wonder how significant these proton pump proteins are especially in a living organism since there may be other factors that can influence the intracellular pH. If you inhibit these proteins to prevent acidification, do you think there could be a possibility that the cell can respond by going through other anaerobic pathways to cause acidification? I am really curious on how effective these inhibitors, such as acetazolamide, truly are in general in controlling the cell pH over a period of time.

I hope that further research can be done on this because this sounds like it has a lot of potential. I wonder if a similar method can be applied to other types of cancers that also accumulate tumors in hypoxic conditions as well.

2. Why do the CAIX inhibitor and NHE-1 inhibitor not significantly affect cells grown at normoxia conditions? How might these cells respond and adapt to not have a buildup of H+ ions? Do you think these results could change over a longer time period? 

Thanks!

On a separate note, you mentioned an alternative was that a cholesterol pool could be originating from the Golgi (instead of the ER as hypothesized). If the evidence in favor of the pools originating from the golgi were to be found, what would this mean for the proposed mechanism?  Would it just mean that the cholesterol from the Golgi must diffuse/travel to the ER to inhibit and prevent the translocation of STING? 

P.S. Good job from a fellow CTSI-RAP Student! (I'm a PhySci major so my questions may be somewhat uneducated haha)

Loved your poster/abstract video! I won't be able to attend your presentation time tomorrow but just wanted to post a few quick questions:

1.) Was there a reason in these initial experiments that the K562 BFP+ cells were not treated with equimolar amounts (as mentioned on the poster) in order to try and allow fair comparisons of editing between the Cas 9 fusions?  Was there a particular reason or benefit to the non-equimolar amounts used in these initial experiments?

2.)  I know you said that the current experiments aren't necessarily a fair comparison due to Cas9 fusions not being expressed equally within the K562 cells, but even if treated with equimolar amounts, is it possible that there would be unequal uptake of the plasmids? 

P.S. I'm not too knowledgeable or experienced with genetic editing and the experimental methods you described so I apologize if my questions are kind of dumb/odd.

2. What are the difficulties around using pharmacological therapy for NAFLD? Why do you believe there has been no FDA-approved drugs yet? 

2. I understand that ILC, NK, CDC, and macrophage can be found in the adipose tissue, but what do they tell us about the samples? Do they each have specific roles or has only their general effect been researched? 

I was also curious, what the current advantages of using whole genome nucleotide similarity are? 

Thanks for the great presentation!!

2. How did you account/control for variations in HMCs across different individuals in order to generalize your conclusions. 

P.S. I do not know much about HMCs so if my questions don't make sense or are not applicable, I apologize. 

Also, could you use a combination of these DNA repair factor sequences to both recruit HDR proteins and inhibit NHEJ?

Thanks for the amazing summary of your project!

2. What other factors are there that can offset the the effect that human adipose tissue inflammation has on the innate human immune system?

2. What other factors must be taken into consideration besides ability to regulate pH in a MM cell's ability to survive?

This is a clarifying question: What were the positive and negative controls that you used when analyzing differential gene expression via RNA seq between the HPV18 positive and negative cells? 

Were there any results that surprised you or that you especially did not expect?

You mentioned that proteins E5, E6, and E7 are associated with viral carcinogens and that E5 regulates a gene involved in the HPV mechanism. Do you have future plans to continue studying the E5 protein and its role in cancer development?

Thanks for your hard work, Andres!! This was so interesting.

1. At this point in time what do you believe are potential treatments that could be used to combat HCMV? In the abstract you mentioned that there no preventive measures, but how could that change once the glycoprotein is uncovered?

2. When a preventive treatment is created who should be the first one to receive the treatment? (For example, what demographic and age ranges)

Notably, in Figure 3, LilSpotty had 35.8% shared GC with Awesomesauce, and in Figure 6 Group W had 35.6%. With these measurements being so close to the 35.0% cutoff from the guidelines, were there any extra controls/tests run to ensure this specific measurement? I know you mentioned it in your conclusions that this may not be significant. Are you planning to follow up with any tests if not done so already?

Seeing as this project centered around recategorizing singleton phages into their appropriate clusters, do you feel like there is a lot of work to be done in terms of planning for the future? Do you see categorizing singleton phages having a drastic clinical or bioinformatic effect?

2. According to this research there is a significant link between obesity and type 2 diabetes how does diet change this trend between the two?

2)Is there an indication that those who take aspirin regularly are less likely to develop NAFLD? Just wondering because aspirin is a fairly widely used drug already..

3)I wonder what allows fluvastatin to prevent the onset of NAFLD? Is it clear what exactly it targets in order to prevent the disease onset besides preventing weight gain and fat mass increase?

Thanks!

2. Also, were you using only one type of nucleic acid for your bacteriophages (such as ssDNA bacteriophages) or was this just a large mix of bacteriophages?

3. I wish I could attend your presentation and hear more about the splitstree and how that is done, can you please explain it in the padlet a little for those of us who have not taken an MIMG lab?
 
Thank you for all the work you put into this presentation and I look forward to your answers!

You discussed how the two clusters shared the same tail proteins. Did you begin to hypothesize why this might be?

How did you build the big table in the center of the poster?

2. In the literature, it suggested there was an inverse relationship between GC content and genome length, while you all found that there was no correlation. What do you think may have caused that difference? Could it be from the pool of phages you investigated?

2. For someone who has not taken an MIMG lab (me) what is the significance of the molar ratios of what was put into the sample for this experiment?

3. How will using equimolar amounts on K562BFP cells help make the analysis better?

Thank you for your research and this presentation! I hope to see more research from you in the future, and I look forward to your answers!

2. Can you describe the mechanism that explains how the resulting GEPs are mostly biased towards astrocytes?

3. I'm curious as to what the next steps might be as to how to get this into a clinical study after your findings were presented?

How where the two proteins, HHE-1 and CIAX identified and could there be other targets that you identified that could help in treating MM?

What concentrations of proton pump inhibitors were used, and have you tested different concentrations to find the most effective?

2. How was it determined that ischemia should be induced for an 1hr in the experiment?

Can mutations in the proteins and/or receptors involved in the immune system or in the adipose tissue allow rescue of function in those proteins, gaining back normal and healthy functioning of the human body, either to alleviate the symptoms of diabetes or to prevent the occurrence of it?

2.  What were the other drugs that were predicted for NAFLD and why weren't they used?

2. What are some methods that can be used to ensure that the unknown structure is the pre-fusion GB structure of interest?
Thanks again for sharing about your research, and I look forward to hearing more from your team!

2) What other diseases, if any, do you see this research potentially being beneficial to combat other than coronary artery disease?

2. In terms of a potential treatment, what aspects of the structure would you hypothesize could be targeted by a drug? Is there a hypothesized mechanism by which a potential drug can interact with the pre-fusion gb?  

As we can see in this study the MM cells use the CAIX and NHE-1 to regulate their internal ph. my question is, now that they have this mechanism, why do the cells that were incubated in normal in PH 6.7 have a higher rate of apoptosis than those that were incubated in PH 7.2?

I have a few questions regarding your results:

1. Fluvastatin resulted controlling weigh gain after treatment. However, it controls the weight better than in the control. What may have cause the stable weight compared to the control group? (referring to Fig. 4)

2. In conclusion, Fluvastatin and Aspirin treat NAFLD with Aspirin having a slightly greater effect. Fluvastatin is different because it also has an effect in regulating weight gain. Which treatment based on your research will be best suitable to treat NAFLD?  

what changes in gene expressions can lead to this behavior, and how do you think this change in behavior can benefit the Strongyloidiasis?

Are there potential inherent differences in the tissues of the umbilical cord and heart which may affect the experiment's results?

2) How did you set up the experiment to have it set where the mice would be in hypoxic conditions for an hour. Was this based on human results that showed significant ischemia?

Additionally, do you believe that this method of identifying HGT events could be combined with previous sequence based techniques such as gene synteny (order) to more accurately identify instances of HGT or is this method alone sufficient?

Again, excellent work on the project! Especially you Raneesh ;)

2. Since these drugs worked to prevent the NAFLD stage of steatosis, do you by any chance know that reason why it may not be effective on the later stages of NALFD?

I have a few questions regarding your figures: 

1. In the confocal microscopy figure, what is happening in the stimulated + added cholesterol images? What is the purpose of showing the different fluorescent colors? I ask this because i do not see a difference between the green and blue fluorescents. 

2. In the Statins qPCR* expected results, what does the result tell us if there is an increase in Fluvastatin and Atorvastatin? 

2) Also, how would your results have changed if the patient samples did have a good amount of muscle mass?

2) Why did the group decide to choose otherwise healthy patients for this research when type-2 diabetes can arise in patients with different forms of diseases?

2. You mentioned that the overexpression of YAP seemingly caused the dedifferentiation of the ameloblasts back into a progenitor state, which warranted you to conduct further experiments to determine the causality of YAP expression and ameloblast dedifferentiation. If YAP overexpression does in fact cause the dedifferentiation of these cells, will this impact the already existing structures that are present, and will there be a method to prevent this from happening in vivo? For the potential applications of this research, the dedifferentiation of the cells could suggest potential impacts in other tissues that could be beneficial, so will you continue to focus on dental tissues, or will you attempt to achieve this dedifferentiation in other tissues?

2. In the future directions you mention short-term vs. long-term HPV infection, would there be a way to model the different longevities of infection in vitro? What are some distinctive phenotypic differences between the two? 

Do you believe there is a way to have your tool PharmOmics determine whether the drug predicted to target the disease will be preventative or simply treat the disease? Was there any initial indication between Aspirin and Fluvastatin before the experiment that would have let you predict their different efficacies?

Thank you for your research and again excellent work!

Q1: So I understand that both the control and miR-24 overexpressed cells were isolated from the cancerous epithelial cell lines. Is there a reason why you guys sampled from the cancerous lining? In addition, were the miR-24 overexpressed cells naturally found from the cancerous epithelial cell lines or were normal cells induced/ engineered in someway to overexpress the miR-24?

Q2: I am aware that there is currently no cure for IBD. Do you think the findings from this research can be used to explore possible treatments for this disease?

Thank you!

2. Are there any current anti-cancer treatments that target this mechanism of excretion in order to combat the effects of the immunosuppression? If you are able to confirm the presence of the PD-L1 in the exosomes, what are the next steps for you? Will you attempt to find a mechanism to halt the export, or will you further analyze the cancer cells?

2. It is mentioned that further research could involve more Myoviridae phages. How do you anticipate these other phages to fit into the phylogeny and SplitsTree that you built for the Myoviridae family?

2)  Have you considered performing assays of isolated fusion proteins to possibly work around the problems of cells not properly expression the fusion proteins?

2) Will you consider testing the various subtypes of the single ventricle phenotype?

2. Not as related to the research itself, but do you believe that with the ever changing genomes of phages and increase use of digital media, a 2D diagram will eventually be replaced in accurately showing viral clusters? (is there a more viable way in your opinion).
Thank you and nice work!

2. Why did the clustering system guidelines change? Was it missing essential information?

2. Do you expect Seurat to be effective for all mycobacteriophages or are there any limitations to analyzing these phages?

3. Could any changes or adaptations be made to the Seurat tool in order to give you more comprehensive results for analyzing genomic diversity?

Thank you so much. And looking forward for your future study!

2) You stated that innate lymphoid cell, natural killer cells, and macrophages were present in adipose tissues as predisposition to the link between obesity and diabetes. I was wondering if these are also found in other types of tissues, such as skeletal muscle tissue?

Thank you!

2. What other HIF genes and cells besides the ones mentioned in t heir research study, if any, are associated with tumor progression and chemotherapy resistance? 

2) You mentioned that high similarities and intercluster conservation in Myoviridae Arthrobacter clusters may be explained by constant horizontal gene transfer. If this wasn't the case, is there another explanation for these similarities?

2. Potentially, is there a way to stop differentiation and/or proliferation once the inhibitor is removed? If the inhibitor is a large factor of how much YAP is produced, would adding Large Tumor Suppressor Kinase 1/2 to an environment subsequently slow down or even hinder cell growth, potentially making this a possible treatment for some forms of oral cancer?

Thank you very much for the presentation!

2. Outside of phage isolation, what other uses will finding these genetic differences be put towards?

2. Could some sort of soil treatment be used to disrupt the life cycle of the nematode? Possibly using a chemical (if it is discovered) that can inhibit the chemotaxis of the iL3 towards the soil bacteria?

3. As I understand, this mechanism of using bacteria for chemotaxis can be found in a wide range of organisms. How many of these research results can be generalized to other organisms with similar life cycles?

Thanks, and once again great job!

2. Was there a specific reason besides safety that live mices/rats could not be used for the experiment? It seems plausible to be able to measure activity levels of these animals by making them exercise and then extracted cells afterwards, but was there another obstacle to this?

2. Given that as everyone gets older, their cells start to slowly deteriorate. I was wondering if you knew how age affects each of these differences found in SV endothelial cells in comparison to the cells of a healthy individual?

3. Also, could you explain in a little more detail what is the importance of NOTCH1 proteins in having a healthy heart?

2. I thought that a good question to ask was whether or not did you do any comparison between Cluster I and Cluster F of mycobacteriophages? Since both go through lysogenic life cycles, we would expect them to have more similarities than those found with Cluster O, but for that same reason, the small differences that we find between them might actually  say something about why Cluster F was found to overlap more with Cluster O than Cluster I.

3. Since gene exchange happens all the time between microbes, I was wondering if you think whether your novel findings were due to an unaccounted exchange of genetic material?

2. I have read that aerobic-type exercise such as long-distance running and swimming is more beneficial to the cardiovascular system than anaerobic-type exercises such as short-distance sprinting. Based on this information, could different exercise types/styles have different impacts on the amount of mitochondrial fission in the heart tissue?

3. I am assuming that the Drp1 protein that causes mitochondrial fission does not act on just the heart (correct me if I am wrong). What effects could mitochondrial fission have on other bodily organs and the organism as a whole?

Thank you and great job!

what kind of limitations this method creates to test it on other phages ? 

From my understanding, there are two types of adipose tissue (white and brown). How do the immune response differ between the two?