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

The idea of increasing/promoting scientific innovation was more appealing than the other options because it ruffled the least amount of feathers, meaning that it required less change from the everyday actions of the average human beings. The other options required humans to change their actions to “save the planet” and scientific advances would be a more gradual change for people, which would make the process easier.

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

My group discussed incentivizing the creation of eco-friendly cars as well as changing the stigma regarding eco-friendly choices.

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 liked it–in high school in order to get our honors credit for English class, we had to participate in a big socratic seminar. In class, we regularly had Socratic seminars as well. They helped brainstorm and develop ideas, which would be great for solving problems like what to do in the face of climate change. I don’t think I would moderate them ever, but I would not be opposed to participating in a Public Deliberation from time to time.

1 May 2019 ✷ Independent Research Presentation Practice

Procedure

• The class was broken up into 3 chunks consisting of 2-3 research groups
• The chunks went to different classrooms and practiced their presentations
• The group that wasn’t presenting critiqued the presenting group and then the roles reversed
• Presentations were adjusted according to the feedback
  • Fonts were increased
  • images were made larger
  • all of the AM-specific genes were re-BLASTed to see how many hit with high GC bacteria or only AM phages
  • charts/tables were updated with this new information

Results

image of the rubric

Conclusion

We need to be more specific in parts of the presentation that we understand really well but others won’t; better and more concise explanation will make the presentation flow smoother.

Future plans

Finalize and present!

24 April 2019 ✷ Independent Research

Procedure

• Every AM-specific gene was run through NCBI’s BLASTp in order to search for low-GC bacteria it shares genes with
  • this is evidence of horizontal gene transfer
• The abstract was edited and finalized
• the presentation was created and work was started for it

Results

Genes 6, 22, 40, 43, 45, 47, 48, 49, 51, 60, 85, and 96 had hits with low-GC bacteria.

the abstract:

Conclusion

Many of the AM-specific genes hit with viruses or bacteria with low %GC. This could be indicative of lateral gene transfer, which could explain why the AM phages have a much lower GC content than the other Arthrobacter phages and Arthrobacter host.

Future plans

Work on presentation

2. 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.

Part of the issue surrounding FDA approval was the stigma associated with phage therapy–because the use of bacteriophages for medicinal purposes was relatively uncommon to doctors in the United States, the standards for approving any phage cocktail were relatively unclear. There was no clear set of guidelines for what boxes needed to be checked for the treatment to be cleared by the FDA, so the leadership was able to come up with unrealistic questions to vet the doctors involved in Intralytix. Perhaps another decade or so of analysis of bacteriophages and their life cycles, habits, and safety in humans will allow researchers to get FDA approval for phage therapy. Knowing the answers to any possible question that the FDA could fire at them could streamline the approval process. Doctors and researchers understand antibiotics to a great extent, but they don’t know a great deal about phages and people tend to be afraid of things they do not understand.

Additionally, Kuchment writes, “‘We used to look for phages in sewers on the street,’ he said, by removing manhole lids or drain covers. But passersby would stop to ask what they were looking for, and when Roy replied “viruses,” they looked alarmed” (109). The public would need to be unbothered by this because there is no use fighting for the approval of a drug that people refuse to use because it is so ‘strange.’ This mindset is likely widespread and can veil the FDA in their vetting of phage therapy as well as potential phage therapy patients. Again, further research can allow people to understand the many benefits and overall value of phage therapy and allow it to be welcomed into the United States.

17 April 2019 ✷ More Independent Research

Procedure

• Gene 97 was blasted again to see what bacteria CDD matched it with
• Gene 97 hit with stapholococcus virus psi12
• articles found by the group noted that GC content was lower in Staphylococcus
• an abstract was written
• gene 62 was looked at, but it hit with a high GC bacteria
• an abstract was completed

Results

the abstract

Conclusion

Having a gene that is shared with phages of other clusters and is similar to a virus with a lower CG supports the idea that horizontal gene transfer could be responsible for the low GC content associated with AM phages.

Future plans

Find more data and work on presentation

15 April 2019 ✷ More Independent Research

Procedure

• Justification for why AM phages had such a low GC content when arthrobacter has a typically high GC content was researched on databases.
• An abstract was drafted
• it was decided that the remainder of the research would come from literature and databases including NCBI and PubMed were used to locate more information on GC and arthrobacter.

Results

A research outline was created

Conclusion

TGC is related to bond strength because of the three bonds between C and G. This allows DNA to be more resistant to high temperature. Horizontal gene transfer is responsible for a lot of the variation in GC content of bacteria and the phages that infect them.

Future plans

Find more data!

10 April 2019 ✷ Independent Research (again)

Procedure

• The genes were sorted by whether or not they were specific to AM and then averages and statistical analysis was performed by Lucy.
• In the search for a phage that was most similar to NapoleonB but from another cluster, group members noticed that the Pham numbers had changed and that more phages had been added, thus the data from the previous lab regarding the stats on the AM vs non-AM genes needed to be redone.
• Phams were checked against PhagesDB and the results were updated.

Results

Pictured is the data recorded today.

Conclusion

The P score for the average %GC of AM-specific genes vs non-AM-specific genes is low enough to indicate a significant difference between the two.

Future plans

Find more data!

8 April 2019 ✷ Independent Research

Procedure

• The new annotations (including inserted genes) was added into the DNA Master file for NapoleonB and the percent GC and GC3 of each gene was calculated by DNA master and recorded by group members.
• The genes were sorted by whether or not they were specific to AM and then averages and statistical analysis was performed by Lucy.
• This procedure was repeated for a phage from a different cluster.
• The average %GC for the entire genome (rather than by each gene) for all the clusters was provided by PhagesDB and statistical analysis was performed with this information as well.

Results

Pictured is the data recorded today.

Conclusion

AM phages have the lowest % GC of all the clusters. The genes that are AM specific seem to have a lower percent GC than those genes that exist in other clusters.

Future plans

Find more data!

3 April 2019 ✷ Scholars Week

Procedure

• Groups presented the poster prior to lab and it was judged
• the class debriefed the pros/cons of the poster and what could be improved upon
• research groups met and discussed what needed to be done to create a meaningful research project
• in an attempt to come up with a better question, the group noticed that AM phages have a significantly lower %GC than other clusters, so a question surrounding this fact was created and a plan to look at %GC and %GC3 was drafted

Results

QTM that was submitted (research plan created today):

AM phages have a significantly lower percent GC than other Arthrobacter phages. It also has

many AM-specific genes.

Look at the percent GC and percent GC3 of AM-specific genes and genes that occur in both AM

and non-AM phages within NapoleonB’s genome

QUESTION: What is the relationship between the percent GC and GC3 in AM-specific genes

and genes present in AM and non-AM phages?

TITLE: Identification of trends within %GC and GC3 within AM cluster specific genes present in

NapoleonB and non-AM cluster specific arthrobacter genes also present in NapoleonB.

SOURCES:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3923770/

https://www.omicsonline.org/open-access/the-gc-content-of-bacterial-genomes-2329-9002-2-

e108.php?aid=26236

https://www.pnas.org/content/111/39/E4096

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4576692/

BIOINFORMATICS DATABASES/TOOLS:

%GC Calculator:

https://www.biologicscorp.com/tools/GCContent/#.XKUcUZhKhPY

Phamerator

PhagesDB

DNA Master

PhageNotes

Ram’s database thing

Conclusion

Research for this question will be meaningful because many students had questions brought to them during the presentation of the poster regarding the high number of non-functional genes and this question and plan can help answer some of those questions.

Future plans

Research!

1 April 2019 ✷ Scholars Week

Procedure

• Each pair practiced presenting the poster and the class interrupted them and critiqued them to mimic the actual poster presentation
• each group took a turn

Results

Some groups need to coordinate and practice some more before presenting

final version of the poster

Conclusion

The poster presentation should be short (5-10 min) and presenters should be knowledgable on the topics covered by the poster. Practicing over and over again will help with this

Future plans

Research into NapoleonB’s genome will begin after presentations are complete.