Rationale: I currently only have half the data I need to make the graph so I’m going to be searching for the database call and making the graph today.

Tools: Excel, DNAMaster, phagesDB, Phamerator, Javascript, Meteor, MySQL, CLion, Purdue Robotics Operating System(PROS)

Procedure:

1. Sifted through phamerator code to locate call to Meteor script. Followed meteor script call to 236th line of code in Phamerator. Copied the 236th line of code into PROS to do further analysis.

2. Broke single line of code into a more readable format using PROS which resulted in 467 pages of code.

3. Read through the code to find database call which led me to the Hatfull database which is written in MySQL.

4. Used the Hatfull database to collect data on which AM phages are in each pham that the genes for NapoleonB were called to.

5. Graphed results in Excel.

Results:

Conclusions and Future Work: The Hatfull database is extremely useful and could be used for a lot more bioinformatic endeavors. The coming weeks we will be conducting our individual research in a group under the guidance of Aadil.

Rationale: In order to collect the  data needed to create a graph to display the comparison between the amount of AM phages that are a member of a pham against non-AM phages that are members I need data from the phamerator and phagesDB databases.

Tools: Excel, DNAMaster, phagesDB, Phamerator, Javascript, Meteor, MySQL, CLion, Purdue Robotics Operating System(PROS)

Procedure:

1. Loaded the phagesDB database into Excel to test to see if I could access the pham data from there. That ended up not working.

2. Went to phamerator and started analyzing  code of the website using Meteor, Javascript, and PROS. Meteor is built on Javascript and is what phamerator is built with.

3. Exported the pham map of NapoleonB as a .svg file then used Atom to change it in to a text file that could be parsed using a C script.

4. Gave the parameters to parse by to Rachel to write a code in CLion to locate the gene number, pham, and total members in the pham.

Results:

N/A

Conclusions and Future Work: There is still much more digging that I need to do to get all the data required. Over the coming days I will analyze more code to find where the database call is in the phamerator code.

1. The USSR had a state controlled system of health care. During the cold war, since a lot of money was going into the arms race, there wasn’t anymore ability for the government to supply antibiotics. Therefore, phage therapy became a more popular solution to the issue of bacterial infections. Also, antibiotics were mostly being shipped from the western market, so antibiotics were dissuaded against using propaganda.

2. Stalin was a big proponent of Lysenkoism, which stifled scientific research greatly for Hirszfield. Furthermore, due to the Jewish lineage of Hirszfield and his associates  and the persecution of Jews at the time in Poland the Hirszfield institute was severely stifled in their ability to release any of their research in comparison to the Eliava institute. However, after Stalin died, the Polish government supported the Hirszfield institute. The Eliava institute on the other hand received more support during the war in order to develop therapies for soldiers in war. Later when the Phage Therapy Center opened up they differed in their support as the PTC has access to the research funding pooling effort of the European Union. This contributes to a large portion of research funding of almost all labs in the EU.

3. Merril treated mice with different versions of Lambda phage: the parent strain, Argo1, and Argo2. After the phage had been in the blood stream for some time she took blood samples and isolated the phages from the samples. She grew and propagated the phages then repeated the process for a total of 8 times. The result was  phages that were able to be injected in mice and survive filtration and kill bacteria. They tested the effectiveness on rats infected with E. Coli and Argo1 and Argo2 resulted in a drastic reduction in symptoms.

4. I personally feel like the biggest limiting factor to phage therapy in western medicine is the immense R&D cost preventing initial profit to keep a start-up going. That’s why the current system in place for some of these companies looks extremely promising for getting to the point where we can start producing phage therapy. First R&D needs to go into a more readily understood product such as in the case of EBI production of certain peptides for therapeutic use. The sale of said product can then be used to fund the research into phage therapy. What needs to be researched in my opinion is efficient means of production for phage therapy, as the first issue for any and all new products is development cost. To encourage more research to go into more effective therapy, research into more effective production must occur.

Rationale: We are practicing presenting the posters to pick the best design, as well as, to get a feel for presenting.

Tools: N/A

Procedure:

1. Presented posters and gave feedback on design choices.
2. Voted on the best one and made a plan for imporvements.

Results:

N/A

Conclusion and Future Work: We decided Lily Goodman’s group poster was the best overall design and plan to improve on it. I will begin to work on using the phagesDB api to make a chart correlating phams of the genes in NapoleonB to phage cluster.

Rationale: Continuing to prepare for the presentation, we are combining poster ideas in order to make a better poster.

Tools: Excel, Powerpoint

Procedure:

1. Joined with another group and worked on fitting both poster ideas together.
2. Finished making the sunburst graph to look visually appealing.

Results: N/A

Conclusions and Future Work: Next we will practice presenting our posters to the class in order to find which poster is the best to use for Scholar’s Day.

Rationale: Since we determined good visuals are important for a good poster we will work on making aesthetically pleasing visuals.

Tools: Excel, Photoshop

Procedure:

1. Took all the data from the past year of research and attempted to make a chart for each relevant piece of data.
2. Made a sunburst chart to represent gene function calls, pie chart for soil composition and tree measurements
3. Cropped photos from wet-lab results to make them more visually appealing.

Results: N/A

Conclusion and Future Work: The visuals definitely need more work to look as visually appealing as I was shooting for. Therefore, I will work some more to make sure that the information is provided in an aesthetic way.

Rationale: To prepare for the Scholar’s Day presentation we will begin rough drafting our poster by hand.

Tools: N/A

Procedure:

1. Researched good poster making strategies and viewed posters from years prior.
2. Drew a rough outline on paper of what we wish the poster to look like at the end.

Results: N/A

Conclusions and Future Work: We decided that symmetry and visuals are key parts of the poster we want to work on. We will begin working on the poster next time.

Rationale: Now that we have completed our first draft of our annotation we’re going to take one last look before we hand it over to the TAs to revise it. We’re also going to write an abstract to submit for scholars day at Baylor.

Tools: Microsoft Word, DNAMaster, PhageNotes

Procedure:

1. Scrolled through each gene that has been annotated after copying the PhageNotes documentation over to DNAMaster.
2. Found a couple of mistyped starts and fixed them.
3. Compiled each group members individual abstracts into one abstract using Word.

Results:

None.

Conclusion and Future Work: Now that we have finished our abstract we will put together a presentation of our findings of NapoleonB. Furthermore, we will begin individual projects soon.

Rationale: There were some calls that were a bit difficult so as a team we revised certain genes assigned to us.

Tools: DNAMaster, NCBI, Phamerator, GeneMark, PhagesDB

Procedure:

1. Looked at gene 50’s reading frame to determine if I should elongate it to the LORF.
2. Checked starterator, blasted both lengths of the gene, and checked the Coding Potential coverage to determine I shouldn’t bring it back.
3. Also the better RBS score supported my call.

Results:

Conclusions and Future Work: The call was correct, there is no need to move the gene to its LORF. Next we will do a group-wide analysis of the entire annotation to make sure we don’t see any glaring issues. We will also begin the process of making a presentation of our findings.

1. Dysentery was a major problem among troops during World War I. This need opened up the avenue for d’Herelle to make the discovery that some people were being miraculously cured of dysentery. Relating to locusts, d’Herelle was originally studying bacteria that killed locusts when he discovered that  there were some parts of his plate that had died for no explainable reason. What we now know as plaques. d’Herelle found the same clear spots on his plates when he examined the stools of some sick soldiers. These findings led to money being put into research for this microbial antagonist to  bacteria, as  dysentery was wounding military forces so greatly. This in turn led to the discovery of bacteriophages.

2. Like every great scientist d’Herelle was driven by his curiosity and could not let a question go unanswered. However, more than that he was extremely dedicated and passionate to science and treated it as more than a job. For example, when he took up an unpaid position. He was not dissuaded from continuing forward despite so many people doubting him. Eliava was similar in a sense, but he was described as more laid back, but both men were extremely dedicated to their craft. Eliava ended  up being executed due to the Soviet Regime.

3. Phage therapy wasn’t very well understood, so under normal circumstances it would’ve been extremely hard to get government  funding for research into  phage therapy. However, war pushes governments to move forward with risky moves in the hopes of getting the technological edge over their opponents. Since many people were dying of diseases such as dysentery, it was very important for governments to find a way to fix this problem before the enemy. This led to phage therapy research getting funded despite being such a new concept. Also, had the push for finding a cure for dysentery not occurred d’Herelle may have never made the connection between the spots on his plate in the locust killing bacteria and the dysentery patients.

4. A big reason phage therapy didn’t take off is because antibiotics seemed to be a better solution at the time. They were quick and very successful in treating bacterial infections. They also weren’t specific to certain bacteria. This wasn’t the problem alone, however, as there was the issue with scientists not fully understanding phage therapy yet and success rates of trials for phage therapy being pretty bad. Together this led to phage therapy being completely overtaken in functionality by antibiotics.

5. They were extremely curious on how bacteriophages replicated, which is how they joined the Phage Group. They discovered that it was DNA that was the genetic material for phages rather than proteins. Furthermore, they also discovered the replication mechanism for bacteriophages. Eventually they moved on to studying the reproduction of higher order life forms, which caused phage research to die out.