The climate change public deliberation forum today in class was very enlightening and engaging. It was an opportunity to learn from classmates about their thoughts on these issues, as well as share my own. Climate change can be a very controversial topic, and it was refreshing to have an opportunity to discuss without the conversation becoming a debate.

The three options for climate choices offered in the forum were all very interesting. Each option on their own seems to provide only part of a solution and each have many trade-offs that make them hard to sell to other individuals in the community. However, a combination of all three options seems to be a more feasible option. Combining innovative strategies with the preparation and protection of our communities will better prepare us for the future and the different possible outcomes. New innovations could provide methods of reducing carbon emissions that have fewer drawbacks and are more accessible to the average individual. While there are still trade-offs with the three options, combining the approaches will allow individuals to take different routes in their personal approaches to the issues of climate change.

The issue of societal participation and cooperation seems to be a considerable issue when thinking of climate change and ways to stop it or prepare for it. Many individuals are very set in their ways and are resistant to change. Because of this, it could prove to be difficult to have all individuals adapt to the new innovations and preparation measures. One method of gaining higher levels of cooperation would be incentivizing the changes that need to be made. When people feel a reason for making a change, they are more likely to do it. Just hearing about the potential effects of climate change does not motivate every person. Providing easy steps or small changes individuals can implement, especially if there is an incentive behind the change, will bring greater support to the issue of climate change.

Another potential societal drawback is cost. Many individuals do not feel that it is worth it to change to a cleaner form of energy if it will cost them more, even if it is only a small amount. Accelerating new innovation could lead to lower costs, which in itself would be an incentive to individuals. Also, having companies develop ways to show people the impact they could have would also take away from the drawback of cost. If people can see how their efforts contribute to the solution, they are more likely to become involved.

Climate change is a pressing issue that we need to begin preparing for in a serious manner. Whether this involves preparations or new innovations, we can begin implementing changes today. From this forum, I learned that there are many individuals in the community and in my class that care about climate change. Hearing this makes me more confident we can have an impact in the future.

Purpose: The purpose of this lab was to practice the final presentation and correct any mistakes.

Tools/Procedures:

Tools:

• Powerpoint
• NCBI BLAST

Procedures:

1. The final presentation was presented to other groups for practice.
2. Feedback was given on the presentation.
3. Corrections were made to the presentation.

Results:
This lab allowed for presentation practice. Changes were made to the presentation based on feedback. A new graph was made to highlight the research findings.

Conclusion:
In conclusion, this lab allowed for feedback to be given on the presentation, and for corrections to be made.

Future Work: 
Future work will include finalizing the presentation and presenting it.

Purpose: The purpose of this lab is to complete the final project presentation.

Tools/Procedures:

Tools:

• Google Slides
• Excel
• DNA Master

Procedures:

1. An outline for the final presentation was created.
2. Tables and graphs were made for the data section of the presentation.
3. Work was done on each section of the presentation, editing the slides and adding visuals to each slide.
4. Transitions were added to the slides.
5. The presentation was looked over one last time and then completed.

Results:
The results of this lab included finalizing the final presentation and creating figures and visuals to make the presentation more visually appealing.

Picture of a slide from the presentation.

Conclusions: 
In conclusion, the presentation was finished and is ready to present on Wednesday.

Future Work:
Future work will include practicing the presentation for the final presentation on May 3rd. Also, after the practice presentation on Wednesday, final edits will need to be made to the presentation.

Purpose: The purpose of this lab is to continue working on the presentation for the final project, and update the abstract.

Tools/Procedures:

Tools:

• NCBI BLAST
• Google Docs

Procedures:

1. More work was done to find other hosts and species that matched with AM specific genes from NapoleonB.
2. The abstract was edited and corrected. Suggested changes were made, and the abstract was updated to reflect the current evidence found by the project.
3. Work was begun on the presentation slides for the final presentation.

Results:
The results of this lab include finishing the research and data collection for the presentation, as well as finishing the abstract for the project. The results of the BLAST search found that 12/51 of the AM-specific genes of NapoleonB matched with genes from low %GC hosts and other species, such as roundworms and viruses.

Conclusions:
From this lab, it was concluded that a potential reason for the lower %GC of AM phages from their host is horizontal gene transfer, and this was reflected in the abstract.

Future Work: 
Future work will include creating the final project presentation. The presentation will also need to be rehearsed with the other group members.

Purpose: The purpose of this lab is to continue to work on the independent research project, as well as write an abstract for the final project.

Tools/Procedures:

Tools:

• DNA Master
• PhagesDB
• NCBI BLAST

Procedures:

1. Research was done to determine if there was any evidence of horizontal gene transfer in NapoleonB. It was found that gene 62 showed high similarity with Streptomyces bacteria and that gene 97 showed similarity with a Streptococcus virus.
2. More research was done to show that %GC and genome length of phage are inversely related.
3. An abstract was written for the final project, including information collected from this lab and previous labs.

Results:
The research done in this lab helped to provide evidence for horizontal gene transfer and its role in the %GC of NapoleonB. NapoleonB’s gene 97 matched with a Streptococcus virus. Streptococcus is a low GC bacteria in the phylum Firmicutes. The correlation with gene 97 provides evidence that horizontal gene transfer could be a reason the phage has a %GC much lower than its host, arthrobacter. It was also found that %GC and genome length are inversely related. As NapoleonB and most AM phages have longer genomes, around 150,000 base pairs, this is another possible explanation for the lower GC content.

Conclusion:
In conclusion, this lab helped to provide possible evidence for why AM phages have a lower %GC than their arthrobacter host.

Future Work:
Future work will include continuing research on GC content of phage and host. It will also include beginning to create a final presentation for the project and drawing conclusions from the data and sources collected.

Purpose: The purpose of this lab was to begin outlining the presentation for the research project and the final presentation in May.

Tools/Procedures:

Tools:

• Google Drive
• PubMed/NCBI
• PhagesDB

Procedures:

1. The data from the last lab was analyzed and discussed to determine the next step in the project.
2. It was decided that a literature search would need to be done to learn more about the %GC in host and phage genome, and the relationship between their GC content.
3. Articles were found discussing the phage and hos GC content.
4. A project outline was created for the presentation.
5. An abstract was started, and a background information section was also begun. The results are not finished, but the current findings were compiled. The conclusion was also begun.

Results:
An outline for the project was created, with elements such as the abstract, background information, and conclusion. The articles found showed that in most bacteriophage there is a correlation between their %GC and that of their host. It was also found that the longer the phage genome was, the lower the %GC. It was also found that the average %GC of Arthrobacter sp. ATCC 21022 is 63.41%.

Conclusions:
In conclusion, it was determined that more literature needed to be read to try and determine the reason that the AM phage %GC is so much lower than that of its host. An outline was created for the final presentation.

Future Work:
Future work will include learning more about the GC correlation of phage and their host species through literature searches. Also, more work will need to be done for the final presentation.

Purpose: The purpose of this lab is to continue work on the final project, collecting and analyzing data.

Tools/Procedures:

Tools:

• DNA Master
• PhagesDB
• PhageNotes

Procedures:

1. The genes of NapoleonB were analyzed to determine which genes were specific to the AM cluster, and which were not.
2. Statistical analyses were performed on the data found in the last lab.
3. It was found that the AM-specific genes had a statistically significant lower %GC than the non-AM genes.
4. No significant difference was found for the %GC3 of the AM and non-AM cluster genes.
5. It was also determined that the arthrobacter AM cluster phages have a significantly lower %GC than all non-AM arthrobacter phages.

Results: 
The analyses of the data collected show that AM cluster phages have %GC that are lower than the average arthrobacter phage %GC. While all of the genes in NapoleonB have a lower average %GC, the AM-specific genes have an even lower average than the non-AM specific genes.

Conclusions:
In conclusion, it was found that AM cluster genes have lower %GC than most other arthrobacter phage clusters.

Future Work:
Future work will include gathering more data about AM cluster genes, and trying to determine why they have a lower %GC than other genes. This could include looking at genes not found in AM phage, as well as looking at what makes AM phages different from the other arthrobacter clusters.

Prompt: 

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.

The FDA approval process is long and daunting for any new drug or therapy treatment. Only about 18% of medicines make it to Phase I of clinical trials, according to the Forgotten Cure. Because of the rigorous tests the drugs must pass, it is hard for them to advance past this phase. Another problem is the cost and time of development and FDA approval. On average, it costs $800 million for development and approval of new treatments. This makes the large pharmaceutical companies not want to invest in this research themselves, leaving it for others to do.

The researchers who want to conduct an FDA trial must first submit an application for their trial to be approved. In the case represented in the Forgotten Cure, the researchers submitted an application and then had to undergo a series of questions relating to the trial, to show they were serious and to help prove that their trial would be beneficial, and would not cause further problems. In phage therapy, some of the concerns for FDA trials were lytic phages and the scientist’s ability to identify different phages. The FDA was concerned that temperate phages, that undergo the lysogenic cycle, could exchange genes with other organisms and cause problems during and after testing.

Because phage therapy is to be used on humans, it is much more regulated by the FDA than other animals, and therefore harder to gain approval. The FDA was worried about transduction and that it would cause harm to humans who used the therapy if toxins were to be released. The companies described in the Forgotten Cure had more success in using phage therapy for animals such as chickens. Starting with cows and chickens, however, is one way to help gain public approval.

There are many ways that scientists can help improve the process of phage therapy approval. The work done by Ramachandran in the Forgotten Cure is an example of ways scientists can try to make phage therapy safer for humans. Ramachandran was able to inactivate endolysin, which allows phage to escape from the bacterial cell by weakening the cell wall. In his tests, all of the mice treated with this engineered vaccine survived, while 80% of those untreated did not (Forgotten Cure). Designing methods and techniques like Ramachandran will help the FDA to be more comfortable with giving bacteriophage to humans and will help speed and improve the approval process for scientists and doctors interested in the subject.

Scientific researchers are not the only ones needed for clinical trials. Physicians will need to be involved and collaborate with the researchers to have a successful phage research trial. If physicians do not think that phage therapy will work, or that it is not safe, it will be hard to conduct clinical trials. Helping to educate physicians on phage therapy will improve the approval process.

Another way to help improve phage therapy approval is to increase the understanding of phages general population and convince them of their safety and effectiveness. While gaining FDA approval can be hard, another step is getting patients to accept phage therapy as an acceptable treatment. This can be done by teaching individuals about bacteriophage, and then about phage therapy, making it seem like a common treatment, as it was for the Georgians, who even had vials of phage in first aid kits in the war. Another way to increase the public’s feelings of safety with bacteriophages is to continue to discover more about them, researching phage not only for their potential therapeutic uses but also to learn more about them so that scientists and others can better understand what they are researching and using.

Purpose: The purpose of this lab is to collect sources for the independent project, and to continue researching the project question.

Tools/Procedures:

Tools

• DNA Master
• PhagesDB
• Google Sheets

Procedures:

1. Sources were found for the project and citations were made for each of them.
2. %GC for all arthrobacter phage were compared and the average was found.
3. %GC and GC3 were found for all of NapoleonB’s genes., an AM cluster phage.
4. %GC and GC3 were found for all of Sonali’s genes, an FG cluster phage.
5. Averages and standard deviations were found for the above information.
6. %GC was compared for all AM specific genes to the %GC of non-AM specific genes.
7. Research was saved.

Results:
In this lab, data was collected for the %GC of genes in an AM cluster phage, the arthrobacter cluster with the lowest %GC, and for an FG cluster phage, the arthrobacter cluster with the highest %GC. The data will be analyzed in a future lab.
It was found that Arthrobacter phage have an average %GC of 59.7%, while AM phage have an average 0f 45.2%.
For NapoleonB, it was found that the phage had an average %GC for its genes of 44.9%, and GC3 of 43.97%
For Sonali, it was found that the phage had an average %GC for its genes of 67.7%, and GC of 89.6%

Conclusions: 
In conclusion, this lab was used to begin data collection on %GC and GC3 of different clusters and different Arthrobacter phage. Overall, it was found that the %GC in Arthrobacter clusters has a high standard deviation, meaning it has a wide range. However, the standard deviation for AM compared to other Arthrobacter clusters, had an even higher standard deviation. It was also found that the GC3 of Sonali’s genes differed sigificantly from the %GC of the genes, and from the average %GC.

Future Work:
Future work will include collecting more data for AM and non AM cluster phages, concerning their %GC. Also, in the future, the data collected will be analyzed, to see if there is a significant difference, and why.

Purpose: The purpose of this lab is to finalize the research question for the independent project, as well as begin finding sources and tools that can be used for project data collection.

Tools/Procedures:

Tools:

• PhagesDB
• Canvas
• PubMed and other resources

Procedures:

1. Research was done on the question for the project.
2. A new route was chosen for the project, focusing on the difference in %GC of AM cluster phages than non-AM.
3. Articles were found for the project from the research
4. A question was written
5. Bioinformatics tools were found for the project

Results: A new route was chosen for the project. Instead of focusing on coding and non-coding regions, the project will investigate the low %GC of AM phages compared to other arthrobacter phages.

Conclusion:
In conclusion, a plan for the final project was determined, as well as a question.

Future Work: 
Future work will include continuing to research more about the topic for the project, as well as beginning to collect data for analyzing and making conclusions.