1. Did any of the Options appeal to you more than the others?
   • I found the option about “making communities self-sufficient by building independent power grids and creating strong local agricultural production” pretty useful. Even though to implement this, it might take a while it will useful in the long run, as each community will be able to have control over their power. Also if changes need to be made to make it efficient, it would be easier if the changes affected a smaller group of people since they maybe could be easier to influence rather than a larger group.
2. Did you hear or think of any new way of addressing the issues associated with the warming of the climate?
   • The group talked about using incentives towards the people to make them buy the energy efficient option. One such incentive was making the energy efficient products cheaper, which I thought was an interesting way to facilitate or influence people to buy the option better for the environment.
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 thought that the Public Deliberation was insightful since I was able to hear many opinions, and different takes of possible solutions from people who experienced different weather conditions. I think that it could be useful to hear perspectives that one has not hear before.I think that it would interesting or fun to facilitate something like this in the future, since anyone can learn a lot about a topic in a short amount of time.

Rationale:

Powerpoint was presented and feedback and changes were  given for the final presentation on May 3rd 2019.

Tools:

• Excel

Procedure :

1. Groups were split into different coaches
2. Listened to another presentation, and feedback was provided for them.
3. Presented the powerpoint, and feedback was given.
4. Changes were made regarding the feedback given.

Results:

New Graphs were added :

Conclusions:

Graphs were added in the presentation to make it less wordy

Future Work:

Presentations will be practiced and required changes will be made.

Rationale:

A power point presentation was created for the CURES in Bio Symposium

Tools:

• Excel
• Power Point

Procedure :

• Power point was created and shared with the other members of the group.
• Different parts of the presentation were created.
• Information and figures such as phylogenetic trees were included.
• New information observed from data collected were added into the presentation as well

Results:

There appear to be no results pertaining to the question researched about, but trends considering phages within each cluster was found.

Conclusion:

Even though nothing was found for the question, a trend was found in the start codons usually the very first few genes and last few genes for most of the clusters. The trends appeared to be consistent through all the cluster except cluster AU, which seemed to not follow any specific trend.

Future Work:

The PowerPoint will be presented and feedback will be given for the final presentation.

Rationale:

Abstract was worked on and perfected for the independent group project. 

Tools: 

• Excel  
• Google Doc 

Procedure: 

1. Previous abstract was used, and corrections were viewed.  
2. Individually corrections were made.  
3. Group decided upon the best abstract and created the final abstract  
4. Results were noted on a google doc about observations obtained from the data collected

Results: 

Some of the results that were found in the study: 

Abstract:

Conclusion: 

The results did not provide enough certainty to sub-cluster the phages based off start codons, but other interesting common features were found within each phage of the cluster.  

Future Work:  

Power point will be made and presentations will be practiced for our independent group project.  

As a scientist, describe the main experiment you would like to see performed before phage therapy is approved for human use. What are the risks involved with using phage therapy? 

The Forgotten Cure discusses about many experiments that have been conducted by GangaGen and Intralytix to test the effectiveness of phages. One of such experiment pertains about salmonella which was tested using chicks by Perdue, a large poultry producer, and Intralytix. To ensure that the food was free of bacteria, antibiotics were registered to the chickens, but the FDA banned the production of many antibiotics such as fluoroquinolones and Baytril. To test if bacteriophages would serve as a better alternative to antibiotics, Perdue decided to test salmonella in chickens, since it produced a greater effect on humans compared to chickens. The procedure was conducted by spraying and injecting phages onto and into the chick eggs on the 17th day, when the immune system is developed and working. At the same time medicine was injected into the chick’s egg. Vaccinations were also provided to the chicks after they were born and sprayed with phages one more time. As a scientist, I would like to see the results of this experiment, but also, I would like to see phage therapy used in treating Staphylococcus aureus. As mentioned in The Forgotten Cure, “staph aureus is highly virulent, and can infect patients who are completely healthy,” (89). Staph aureus is known to cause infections, and boils, but if it enters the bloodstream can even cause an infection to the heart- valve. Maybe a concoction of phages or phages and vaccines, as used in the experiment about salmonella, could help treat staph aureus.  

Even though phage therapy seems to be a possible alternative, there are many risks that come with it. Phage therapy could potentially be harmful if the bacteria releases toxins into the body which could lead to septic shock. Phages can switch from being lytic to lysogenic and cause a potential risk to the body. If the phage turns to be lysogenic, it can alter the bacteria’s genes and can possibly create a pathogenic bacterium. Also, there could be some doubts from the public and there could be various reactions knowing that they are being injected with phages. When viruses were added onto food, people tend to be scared about the thought of viruses in the food they eat , since people would usually avoid viruses and bacteria. The FDA could also provide risks for phage therapy especially humans, since the process to attain anything is very long, and requires a lot of clinical work. Many tests must be done on animals then humans and then shown to the FDA for approval. Even if approval is achieved, sufficient funding is required to be able to proceed and implement phage therapy, experienced by Intralytix after the British Company stopped funding them.  

Rationale: 

Start Codons for each of the phages in the AU Cluster were collected, and saved on an Excel sheet.  

Tools: 

• PhagesDB 
• Excel 
• DNA Master 

Procedure:  

1. AQ Cluster phage FastA files were downloaded from PhagesDB, and opened in DNA Master.  
2. Start codons were noted, and percent of each of the start codons were noted.  
3. Abstract for the independent project was written and submitted.  

Results:  

Start Codons for CapnMurica:  

Conclusion:  

Similarities have been found within most of the phages in the cluster. Creating a phylogenetic tree may be useful to view these results, and to sub-cluster phages.  

Future Work:  

Since most of the data has been collected, a tree including all of the phages in the cluster will be made to possibly  sub-cluster these phages. 

Rationale: 

Start Codons for AQ Cluster were finished, and average amounts of each start codon and GC content for each phage were calculated and noted.  

Tools: 

• PhagesDB 
• DNA Master 
• Excel  

Procedure:  

1. FastA file of each of the phages in AQ Cluster were downloaded.  
2. The FastA file was opened in DNA Master.  
3. Start codons for each of the phages were noted onto Excel.  
4. Averages of each start codon for the phages were calculated.  
5. GC content for each of the phage was obtained from PhagesDB.  

Results:  

Example of data collection of start codon for phage Anasi:  

Conclusion:  

It was observed and reported in an article that the start codon ATG, GTG, and TTG were respectively 45%, 45%, and 7%. However when looking at the data that was collected, the percent of ATG was much higher, usually about 80%, in each phage, and the GTG and TTG start codons, which was about 5-10% each. 

Future Work:  

Start codons for AU cluster will be collected, and a phylogenetic tree will be constructed to see if there any way the phages could be sub-clustered.  

Rationale: 

Start codons for the phages 0f the AQ cluster were collected.  

Tools:  

• PhagesDB 
• DNA Master 
• Excel 

Procedure:  

1. FastA file was downloaded from PhagesDB 
2. File was opened in DNA Master.  
3. Start Sequences of phages were noted on Excel.  
4. Genomes of AR Cluster phages were copied onto a word document to help in creating a phylogenetic tree.  

Results:  

More start codons for AQ Cluster phages were collected: 

Conclusion:  

There were similarities of start codon preferences found in the start and end of the phage AQ and all that were recorded had 82 genes. There could be some kind of trend that is present between all phages in a cluster, and maybe in between clusters. 

Future Work:  

More start codon sequences will be collected and be used to create a phylogenetic tree.  

Rationale:

Start codons for AR cluster phages were collected, and research articles were searched to be used for project.  

Tools:  

• DNA Master 
• PhagesDB 
• Excel 
• Baylor OneSearch  

Procedure:  

1. Collection of start Codons for AM Cluster phages were completed.  
2. Research Articles were explored through Baylor OneSearch, and bibliographies for the five articles were created.  
3. AR cluster phage start codons were collected.  

Results:  

More data was collected for start codons, and more articles were found.  

Conclusion:  

Some unique characteristics found among all of AM Cluster phages were noted such as the start sequences of the last four genes of every phage were the same.

Future Work:  

More start codons for phages of other clusters will be collected in hopes of finding similarities between phages and clusters to further cluster the phages.  

Rationale:  

Plan for the rest of the semester was discussed about and data was collected on start codons.  

Tools: 

• PhagesDB 
• DNA Master  
• Excel 

Procedure: 

1. A plan for the remainder of the semester was talked about, and decisions on goals to reach each day were discussed.  
2. Research articles on topics were found, and title ideas were discussed about.  
3. Ideas were formulated on how to strategically obtain all the data.  
4. A FastA file was downloaded from PhagesDB, and start codon was noted on an Excel sheet for AM cluster phages.  

Results: 

Start Codons for Phages were collected, and below is an example of start codons collected for Phage Arcadia

Conclusion: 

Some similar observations were noted of the start codon of AM Cluster Phages that have been collected.  

Future Work: 

Start Codons of other phages including different cluster and different hosts will be collected and used to possibly create a phylogenetic tree.