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

The options that appealed to me the most were the ones focusing on awareness and innovation, such as the options we spoke about pertaining to increasing the efficiency of the “dirtier” fuel sources we currently have so that society has more time to come around to clean fuel sources naturally while also giving those energies time to be improved as well. I also think it’s important to spread the severity of this issue and talk about the little things that they can do to be part of the solution and not get harmed by some effects of climate change.

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

We read a lot of ways that co2 emissions could be limited but a lot of them involved taxing or limiting freedoms of people and overall we decided that these were not going to be first choices.

3. 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 think that deliberation instead of argument is a lot more effective at getting to the problem and how to solve it without emotions getting people riled up. It makes it so that everybody is on the same side instead of competing and I think that our time was very productive.

Final Abstract

Date: 4-24-19

• Rationale
  • The rational for this lab is to rewrite the abstract for the project based on constructive criticism.
• Procedure
  1. Each group member individually edited a version of the previous abstract.
  2. The group compared individual versions and chose the aspects and sections that were the best from each to form a final abstract.
• Results
  • 

    Final abstract

    

  • A short summary of results found
• Future Plans
  • The next step is to continue to create a powerpoint presentation to present data.

Question:

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.

One of the hardest parts about FDA approval or approval from any government agency for that matter is that they are all very picky when it comes to funding. This is understandably because there is only so much money to go around; however, they don’t make it easy to prove oneself to these agencies in order to receive funding. Since agencies like the FDA want to see results before deciding to throw money at a concept, groups like Intralytix and GangaGen were forced to cater to unreasonable requests without funding to begin with or give up on phage therapy for humans. Also understandably, this pushes groups like these two to the latter option, since in the world we live in there isn’t a very easy way up without monetary support. Given that the FDA doesn’t understand precisely the nature of phage (something that none of us fully understand yet, but something that some see more of than others) and asks for unreasonable results, combined with the fact that they won’t provide funding without these results, and lastly the fact that government agencies are basically comprised of red tape, the FDA has proven to be a fairly immovable roadblock.

Honestly, the only thing that I can think of that will help raise the understanding of phage usage and push for FDA approval is to continue what these companies are doing already and making products and testing on things other than humans. The more tests that are performed and the more basic knowledge that is accumulated, the more likely results will appear that give agencies like the FDA faith in this concept. All things take time. For example, funding wasn’t focused on renewable energy sources for a long time since faith and understanding was in coal. Obviously, the world has started to change its stance on that issue, and something like this will follow when the world is more ready to embrace it. The more data these groups can accumulate and the farther they can spread this information, the sooner it will be funded and the positive feedback loop occurring from this will provide Intralytix, GangaGen, and any other company like them the support they need to make real breakthroughs on phage therapy in humans.

Abstract and Final Data Collection

Date: 4-19-19

• Rationale
  • The rational for this lab is to finish gathering data to use for our independent research project as well as write an abstract for the project.
• Procedure
  1. DNAMaster was used to determine the start codon used for each gene by each phage in the AU cluster.
  2. Findings were recorded on a Google Sheets page and tendencies were calculated.
  3. The group worked together on a abstract for the project, functioning as a summary and introduction to our research.
• Results
  • Start codons are nucleotide sequences that are found at the beginning of protein-coding genes of DNA. In bacteriophage, these start with the base pairs ATG, GTG, or TTG. Generally, ATG and GTG codons are used at the same frequency, and TTG is used in 7% of cases. This study aims to discover trends between this start-codon tendency and evolutionary relationships between phages within the clusters AM, AQ, AR, and AU. As phage genomics is a recently repopularized field, not much is known about them or how they work. If trends like these are discovered, we can more easily characterize and group phages into subclusters, which in turn would allow future analysts to perform more focused research. Data was gathered using the database PhagesDB and was recorded and expressed using Microsoft Excel, DNAMaster, and SplitsTree4. Start codon preferences were calculated on a spreadsheet and compared to the unrooted phylogenetic trees created with SplitsTree. Our results were inconclusive in regard to a trend between start-codon preferences and evolutionary relatedness being useful as subclustering criteria. However, an interesting trend was discovered in the clusters studied. In each cluster, there is a cluster-specific, highly conserved pattern of start-codon usage at specific locations within the genome that span four to five genes. Although our results were inconclusive, if a study were to recreate ours with data analysis focused on phage within a chosen geographical area, it’s possible that a trend could emerge between start-codon tendency and relationships of phages discovered in this close proximity.
  • The following is an example of the start codons used by CapnMurica, an AU phage.
  • 

• Future Plans
  • The next step is to continue to compare the data we’ve collected and search for trends or surprising discoveries.

AQ Data Collection and Project Outline

Date: 4-17-19

• Rationale
  • The rational for this lab is to continue gathering data to use for our independent research project as well as plan an outline for the project.
• Procedure
  1. DNAMaster was used to determine the start codon used for each gene by each phage in the AQ cluster.
  2. Findings were recorded on a Google Sheets page and tendencies were calculated.
  3. The group convened and discussed the parts of the project that needed to be worked on and an outline was formed.
• Results
  • The outline was made as follows:
  • Title:
    Subclustering of bacteriophage determined by start codon preference
    Guiding Question:
    Every phage has a different tendency to choose one of the following base pair sequences as start codons: ATG, GTG, or TTG. Given the percentage of each codon’s use in phages from clusters that infect Arthrobacter, can this preference be used to further cluster phages within existing clusters?
    Abstract:
    Start codons are nucleotide sequences that are found at the beginning of protein-coding genes of DNA. In bacteriophage specifically, they start with ATG, GTG or TTG start codons. In our experiment, we looked at the preferred start codons of bacteriophage that infect Arthrobacter in different clusters to examine the percentage of each start codon preferred in and between clusters. We found that within clusters, there were repeated patterns of preferred start codons that were unique to the cluster. In the AM cluster, the last four genes preferred the start codons GTG, GTG, ATG, and ATG in all 14 phages we looked at. With these discoveries, we can more easily characterize and group phages into their clusters based on their start codons as well as use these known patterns to reassure the clusterization of the phage.
    List of tools used:
    PhagesDB
    DNA Master
    Excel
    Splitstree
    Introduction (Background Information):
    In all DNA, genes start with specific three nucleotide sequences that promote transcription by a ribosome. These sequences are known as start codons and organisms can have specific preferences in start codons. Protein-coding genes of bacteriophages all start with either an ATG, GTG, or TTG start codon. On the Guiding Principles of Bacteriophage Genome Annotation, it mentions that, “… TTG is rarely used (about 7% of all genes). ATG and GTG are used at almost equivalent frequencies.”
    Types of Data Collected:
    Phage genomic sequences for clusters AM, AR, AQ
    Phylogenetic interrelatedness between phages within and between clusters
    Start codons for each gene of each phage within each cluster sampled
    Start codon usage percentage for the above phages
    Results (to date):
    Similarities of phages in each cluster were found. For example for all AM cluster phages the start codons for the last four genes were GTG ,GTG, ATG, and ATG. Phage Molivia, which belongs to AQ Cluster appears to be more closely related to AR and AM phages rather than to other AQ cluster phages. The average ATG, GTG, and TTG percentage within clusters don’t exactly align with the guiding principles mentioned by PhagesDB. The percentage of ATG and GTG were not similar; ATG was the most predominantly preferred start codon.
    Conclusions:
    No conclusions have been made to date
  • The following is an example of the start-codon preferences recorded for the AQ phage Anansi
  • 

• Future Plans
  • The next step is to continue gathering data for the AU cluster and compare the start codon data to phylogenetic data for each cluster.

Data Gathering – AQ and AR Clusters

Date: 4-10-19

• Rationale
  • The rational for this lab is to continue gathering data to use for our independent research project.
• Procedure
  1. PhagesDB was used to find the entire nucleotide sequence for phages in the AQ and AR clusters.
  2. SplitsTree was used to produce phylogenetic trees for the AQ and AR cluster phages.
  3. Start codon preferences for each phage were calculated and recorded on the google sheets page used in previous labs.
• Results
• 
  • Above is a screenshot of a phylogenetic tree including every AR cluster phage. This was made using whole genome alignment between the phages.
• 
  • Above is a screenshot of a phylogenetic tree including every AQ cluster phage. This was made using whole genome alignment between the phages.
• 

  The preferred start codons of phage KBurrousTX

  

  The preferred start codons of phage Linus

• Future Plans
  • The next step is to continue gathering this data before attempting to further subcluster phages based on start codon preference.

Data Gathering

Date: 4-8-19

• Rationale
  • The rational for this lab is to continue gathering data to use for our independent research project.
• Procedure
  1. PhagesDB was used to find the entire nucleotide sequence for phages in the AM cluster.
  2. SplitsTree was used to produce a phylogenetic tree for the AM cluster phages.
  3. Start codon preferences for each phage were calculated and recorded on the google sheets page used in previous labs.
• Results
• 
  • Above is a screenshot of a phylogenetic tree including every AM cluster phage. This was made using whole genome alignment between the phages.
• 

  NapoleonB’s preferred percentages of each start codon

  

  Mudcat’s preferred start codon of each gene

• Future Plans
  • The next step is to continue gathering this data before attempting to further subcluster phages based on start codon preference.

URSA Scholars Week

Date: 4-1-19

• Rationale
  • The rational for this lab is to practice poster presentations and test understanding of our research poster.
• Procedure
  1. Presentation groups took turns practicing poster presentations.
  2. The class critiqued each group and gave tips for presenting.
• Results
• 
  • The poster above was learned and ready to be presented over.

• Future Plans
  • The next step is to focus on independent research projects.

Final Research Question

Date: 3-27-19

• Rationale
  • The rational for this lab is to decide on a final idea for a research project over the genome of Arthrobacter ATCC 2102.
• Procedure
  1. Groups met together to decide on which question was the best out of the four that were braingstormed during the previous lab.
  2. Group leaders were asked for direction and whether or not the final question was specific and testable.
• Results
  • A final question was decided on.

• Future Plans
  • The next step is to refine this question and work towards gathering data in order to answer it.