Did any of the Options appeal to you more than the others?

I think my favorite options were #2 and #3, the second option was great because it does perhaps the most to actually protect our communities, and the third option invests in our future. While it is hard to change the past, it is easy to decide what our future is.

Did you hear or think of any new way of addressing the issues associated with the warming of the climate?

I still choose to remain skeptical on the topic itself, merely because of a lot of politically charged misinformation. However, I am glad to have discussed with my classmates to reach common ground on a couple of issues. Our group mainly agreed that the problem is inaction and hypocrisy.

What are your thoughts on the use of Public Deliberation in the classroom or the community? Is this something you would like to facilitate?

I loved the deliberation, I wished we had done this more often during the school year. I think it would be very beneficial to utilize this during next years SEA-PHAGES class.

Title: Compiling a Presentation

Date: 24 April 2019

Rationale: With the present results, a presentation will be compiled that will be presented at the CURE in Bio symposium.

Procedure: A powerpoint presentation was compiled that summarized the introduction, methods, and results of the research done in the lab this semester. The presentation still needs to be refined with additional figures and background information, as well as practiced thoroughly to ensure smoothness.

Results/Observations: As a final result, our group decided that the sequence is most likely a regulator or promoter sequence, this is reflected in the elimination of many other functions in our presentation.

Conclusions/Next Steps: The presentation needs work and practice, and will be worked on in the next few days. Otherwise, this will conclude lab work for this semester.

One of the biggest problems in phage therapy has been in the approval process. Describe the trouble surrounding FDA approval and recommend some suggestions to improve the process of phage therapy approval.

To begin, it appears that any process that appears in front of the FDA must be simplified before doing so. For example, Intralytix’s phage cocktail wasn’t projected to make it through simply because it had multiple ingredients. Instead, they focused on a small market topical treatment, which would open up a corridor for more development within the field that would be expanded. In general, it is very difficult to make it through FDA approval due to the thoroughness it requires to be approved. Not only do research and results have to be thorough, but funding and personnel have to be thorough as well. If a company doesn’t have the necessary expertise or funds to complete an experiment to the extent at which the FDA requires, the company stands very little chance of passing through. However, pertaining specifically to phage therapy, the field is underserved. As we have learned, the attention given to phage research has dropped off again, and although it is beginning to pick back up it still hasn’t blossomed to its full potential. As a result, not as many people have done research on phages, nor has a significant amount of funding been directed towards discovering a way to effectively incorporate phage therapy into modern medicine. Perhaps making the public and the FDA more aware of the process and efficiency of phage therapy, would our country then more readily accept this changing form of medical treatment.

Title: Individual Research Continued

Date: 17 April 2019

Rationale: The purpose of this lab was to find a tool that can predict a function for our sequence, as well as look more into literature and write a rough draft of an abstract.

Procedure: The group members perused NCBI PubMed for articles that pertained to or revealed information for our sequence or those like it. The promoter prediction method on DNA Master appeared helpful and will be utilized further as the group ran out of time for this day. The group also worked to write an abstract that will be used for the presentation.

Results/Observations: The promoter finder revealed that there may be a promoter in the region of our sequence, but no hard results were found as we were not able to pinpoint the sequence on DNA Master yet, we had just figured out how to use the tool right as time ran out. The group was able, however, to fully devise an abstract that explains our progress so far.

Conclusions/Next Steps: In the next lab session, we will likely be focusing primarily on the promoter finder on DNA Master as well as refining our abstract to reflect any potential findings from it. We will also likely be trying to find any more supporting literature for our project in order to defend our results.

Title: Individual Research

Date: 15 April 2019

Rationale: The purpose of this lab was to continue searching for evidence of a potential function for the sequence of interest that the project is focused upon.

Procedure: The group continued to search for literature on NBCI PubMed that could support a function or a possible meaning for the conserved sequence. Tools such as transposon finder and others were utilized and an outline for a presentation was made. The group also consulted with research coaches in order to get a better idea of the scope and future direction of the project.

Results/Observations: While we still have negative results for a function of the sequence, the possibility of the sequence being a promoter or a regulatory sequence shows promise. The options for confirming these functions are fairly limited, however.

Conclusions/Next Steps: We will search for a promoter finder or another program that can lead us towards evidence for a function. In terms of the presentation, one conclusion that can be made is that in order to discover if the sequence functioned as a regulator. Our next steps will be to further search in literature as well as find a program that can predict the possibility of a promoter.

Title: Protein Prediction

Date: 10 April 2019

Rationale: With the discovery of the pham abnormality, further inspection will be done on the proteins to see if any more information can be found on the proteins and their relation to the sequence.

Procedure: The proteins were BLASTed and loaded into HHpred in order to inspect the possible matches or structure of the proteins. Further inspection was done on surrounding sequences and proteins in order to possibly discover more about the sequence of interest.

Results/Observations: There were no significant BLAST hits for the proteins, but more research will be done to discover the nature of the proteins.

Conclusions/Next Steps: More tools like RaptorX or other protein structuring tools will be utilized to possibly draw comparisons between proteins that could show a reasoning for the sequence of interest.

Title: Transposon Searching

Date: 8 April 2019

Rationale: We will continue to search for a purpose or additional information that can define the 45-bp sequence (with 6-bp palindromic flanks)

Procedure: Upon BLASTing the sequence again on PhagesDB, it was found that 11 out of 14 phages contain the sequence, with 2 phages, NapoleonB and Kardesai, containing 2 copies of the sequence. The phamerator maps were inspected and more research was done to find literature that could support the finding being a promoter or transposon, or otherwise.

Results/Observations: All phages, except for the 2 mentioned above, that contained the sequence had a gene sequence consensus of a gene in pham #37812 followed by pham #1350. However, the 2 phages that contained a copy of the sequence had a gene in pham #37812 followed by a gene in pham #620. It is worth noting that only NapoleonB and Kardesai have copies of this gene phamily.

Conclusions/Next Steps: All of the sequences will be inspected to look at the flanking regions as well as searches conducted on the internet to find programs that may be able to predict transposons or promoters.

Title: Independent Research

Date: 27 March 2019

Rationale: The four previous research topics will be reconsidered and one topic will be selected as the final project

Tools: 

• DNA Master
• Gepard
• NCBI BLASTn

Procedure: After discussing as a group, the decided upon topic was repeat sequences in NapoleonB’s genome. Therefore, Gepard and DNA Master were used to locate sequences of interest that repeated throughout NapoleonB’s genome. Once a potential repeated sequence was identified, it was entered into DNA Master’s “Scan” feature to check if it repeated a significant number of times. Potential repeat sequences were also BLAST’ed by NCBI’s BLAST database to see if they appeared in other phage genomes.

Results/Observations: One 51-base pair sequence was shown to repeat twice in NapoleonB’s genome, as well as show BLAST results for many other AM cluster phages. No other found repeat sequences showed significance.

Conclusions/Next Steps: Gepard will be used continuously throughout the experiment in order to locate sequences of interest. The specific location of the repeat will also give clues as to why the repeat exists. The main point of the project is to investigate whether or not a repeat sequence can be used as a “tag” in order to reverse an “NKF” call made on the annotation of NapleonB.

Title: Research Topics

Date: 25 March 2019

Rationale:  A research topic will be discussed and eventually conferred upon

Procedure: With group members, the available information and tools were considered in order to formulate a research topic. Four different topics were decided upon that would be narrowed down at a later time.

Results/Observations: The four topics for research were: 1. Repeats in NapoleonB’s genome. 2. attP sites in NapoleonB’s genome. 3. Stoperator genes in NapoleonB’s genome. 4. GC% content and its phylogenetic connection to the AM cluster.

Conclusions/Next Steps: Since 4 topics have been determined, they will be investigated once more in order to decide upon one topic that will be pursued for future research

Title: Individual Projects and Poster Reflection

Date: 20 March 2019

Rationale: The purpose of this lab was to reflect on the poster making process and begin formulating a question for a research project

Procedure:

• Written reflection was done on the process of making the poster individually and as a group
• Literature and tools were explored to begin formulating a question for the research project

Results/Observations:

• Initial discussions yielded a common interest in attP sites and Start Site Commonality
• More research and collaboration will be done to narrow this down

Next Steps/Conclusions:

• More sources need to be consulted to fully formulate a question for the research project
• The provided tools will be explored in order to discover more information on the eventual research project