April 26

4/26/17 Day 21: Independent Research Project

Name: Caroline Addison

Date: 4/26/17

Rationale of Today’s Work: We met for over 6 hours on Tuesday to analyze our data and determine consensus sequences across the different programs used, and then we compiled our data into a powerpoint. Today after lecture, we asked Dr. Adair to check our presentation, so after a few tweaks are made, we will present this to the class.

Tools Used/Methods: Google Slides

Results:

Dr. Adair helped us to tweak our powerpoint presentation and guide us in our explanations of our results, including the negative control of the AU cluster because we forgot to include the fact that the reverse genes had been deleted after auto-annotation. Due to this, we were looking in gaps that were not between a reverse and forward gene, and, therefore, this provided inconclusive results.

This is the link to our final presentation.

Conclusion/Next Steps:

On Friday, we will be presenting this to the CURES-IN-BIO Symposium.

“Our presentation is powerful.” –Christina Gaw, 2017

April 25

The Forgotten Cure – Part 3

Prompt 2:  The Food and Drug Administration (FDA) is one of the United States federal executive departments in charge of protecting people’s public health and safety. One of the most frustrating problems associated with the FDA is the regulations that a company must pass before clearing a product. It takes an immense amount of time to pass the regulations set forth by the FDA. Intralytix stated that “it took [the FDA] almost a year, from the time they said they had no more technical questions, to issue the regulation, and that’s a long time for a company of our size to be hanging out there.” GangaGen, another phage company, found a way to isolate a single phage component with a protein that could poke a hole in the bacterial wall. They reasoned that the FDA would more readily approve phage therapy if only a single phage component could destroy a bacterial cell as easily as a whole phage. When using phages in cows, companies determined that the viruses didn’t stay in the cow’s bodies, and Intralytix proved that their phage cocktail showed efficacy by having a 99% reduction in most foods. Despite these facts, people are still wary to use phage because the thought of eating viruses quickly turns people away. Both Intralytix and GangaGen are worried that the process of FDA approval, which comes with the long time-commitments and numerous expenses, could significantly impact the success of their company. Also, Dr. Wolcott petitioned to the FDA that phages are safe to use in wounds, and the FDA allowed him to proceed with the trial to test for efficacy. However, in order to complete this, the FDA stated they must put each phage through a separate trial, and the costs would be “astronomical.” In response, Wolcott said, “The FDA should approve the process, not the individual phages.”

Since phage therapy must pass through the FDA before it can be used legally in food or humans in the United States, it caused the development and progression of phage therapy to slow. I agree with Dr. Wolcott in that the FDA needs to approve the process of phage therapy rather than testing each and every phage separately. In the end, the FDA was ultimately making it nearly impossible to approve phage therapy because of the large costs and the lengthy regulation processes. Because of these factors, people look to antibiotics instead because they’re a quick and easy solution. However, this is causing more and more mutated, antibiotic-resistant bacteria, meaning that antibiotics are becoming increasingly less effective. In order to combat this problem, people need to utilize alternative therapies, including phage therapy. There are statistics to prove its efficacy, but people are wary of consciously putting viruses into their systems. If the FDA would simply approve the entire process of phage therapy, it would save time and money for companies to begin using this method in food processing and human treatment. Although there are few concerns with the use of phage therapy, having it approved could drastically improve the well-being of many patients who are in need of alternative therapy and, as a result, save many people’s lives. Additionally, scientists and researchers could work to improve the negative label associated with phage therapy by raising awareness of its value in the medical field.

April 24

4/24/17 Day 20: Independent Research Project

Name: Caroline Addison

Date: 4/24/17

Rationale of Today’s Work: After meeting over the weekend, we used MEME results to compare to Softberry putative promoter sequences for the phages it analyzed. We each took separate clusters (I had AK) and we highlighted all the similar regions in the papers and brought them to class today.

Tools Used/Methods: Google Docs, SoftBerry BPROM, MEME

Results:

Dr. Adair helped us yet again to decide a direction in which to proceed. At this point, we have no conclusive data. e will try to use DNAMaster’s putative promoter sequences to compare to our results.

Conclusion/Next Steps:

We will try to use DNAMaster’s putative promoter sequences to compare to our results.

April 19

4/19/17 Day 19: Independent Research Project

Name: Caroline Addison

Date: 4/19/17

Rationale of Today’s Work: After meeting a few times over Easter weekend, we realized that Arthrobacter was not ideal to use for this research project since the genome was too long and there isn’t much research on Arthrobacter promoter sequences.

Tools Used/Methods: Google Docs, SoftBerry BPROM, MEME

Results:

Lathan helped us find an article that used the MEME software to locate promoter sequences. The researchers were able to find a consensus sequence for their research, so we decided to incorporate it into our project. We also kept using BPROM to try and find results.

Conclusion/Next Steps: Dr. Adair helped us today try to figure out what to do since we weren’t obtaining ideal results with our research. We decided to try again and look for a better method to obtain better results.

April 12

4/12/17 Day 18: Independent Research Project

Name: Caroline Addison

Date: 4/12/17

Rationale of Today’s Work: Chrissy, Christina, and I continued to research our project.

Tools Used/Methods: Microsoft Word, Google Docs, SoftBerry BPROM

Results:

We will incorporate BPROM from Softberry into our research because it ranks promoters by their LDF and provides the -35 and -10 sequences that are necessary for promoter-finding.

Softberry result for Nubia

Conclusion/Next Steps: We will research further into this topic.

April 10

4/10/17 Day 17: Independent Research Project

Name: Caroline Addison

Date: 4/10/17

Rationale of Today’s Work: Chrissy, Christina, and I are in the independent research project together, and we thought about what topics we could research after our experience at LeTourneau.

Tools Used/Methods: Microsoft Word, Google Docs

Results:

We decided to go off of the poster we just presented about gap exploration and try to find promoter sequences within the Arthrobacter genome to compare to our phages, since we previously compared them to E. coli. We found different programs to use, such as Softberry BPROM, that may help us with this process.

Conclusion/Next Steps: We will research further into this topic.

April 5

4/5/17 Day 16: LeTourneau Symposium

Name: Caroline Addison

Date: 4/5/17

Rationale of Today’s Work: Chrissy, Daniel, and I will present our research on Saturday at LeTourneau. We reviewed everything for the poster, and our final result is pictured below.

Tools Used/Methods: Posters

Results:

Conclusion/Next Steps: We will finish the posters and practice presenting them for the LeTourneau Phage Symposium.

April 3

4/3/17 Day 15: LeTourneau Symposium Abstract

Name: Caroline Addison

Date: 4/3/17

Rationale of Today’s Work: I am in a group with Chrissy and Daniel to present our research at LeTourneau. We got together and wrote an abstract (with Lathan’s help, thankfully!!) for our gap exploration for promoter regions poster.

Tools Used/Methods: Microsoft Word

Results:

Abstract: Annotations of Arthrobacteriophage genomes Caterpillar, Nubia, and Shrooms displayed large gaps with no evidence of functionality. These large gaps tend to be abnormal for bacteriophage due to its relatively small genome. Here, effort was put into determining potential promoter sequences or repeats within these large gaps.  Little is known regarding promoter sequences for both the Arthrobacter host and its corresponding phages. Because of this, the E. coli sigma 70 promoter sequence was used to best predict the presence of both a forward and reverse promoter within a selected region. Using promoter analysis based on over 400 known E. coli promoters, putative promoters were identified between reverse and forward genes of each genome. Large gaps were then screened for these putative promoters of Arthrophages Caterpillar, Nubia, and Shrooms. Lastly, a test for repeats or inverted repeats was performed using dot-plot analysis.

Conclusion/Next Steps: We will finish the posters and practice presenting them for the LeTourneau Phage Symposium.

March 29

3/29/17 Day 14: URSA Scholars Week Presentation

Name: Caroline Addison

Date: 3/29/17

Rationale of Today’s Work: Christina, Jake and Niharika and I presented Figure B at URSA during our time slot.

Tools Used/Methods: Poster Presentations

Results:

We presented in front of a few people who had very good questions for us. I enjoyed having the real experience of presenting our research.

Conclusion/Next Steps: Up next is the LeTourneau Phage Symposium, so we will begin writing our abstracts for these posters next.

March 27

3/27/17 Day 13: URSA Poster Practice Presentations

Name: Caroline Addison

Date: 3/22/17

Rationale of Today’s Work: Pictured below are the two posters that the class picked to present for URSA. Christina, Jake and Niharika and I presented Figure B.

Tools Used/Methods: Microsoft PowerPoint

Figure A

Figure B

Results:

We learned how to explain the Gepard dot plot and how it relates to phage diversity and we learned the overall structure of the poster so we would be able to present it well.

Conclusion/Next Steps: We will be presenting at URSA Scholars Week.