Rationale

Today we will create 4 possible research questions for an Independent Research Project.

Procedure

• The tools and ideas provided on Canvas were looked through to see if any generated interest
• After consideration, %GC and repeats were found to be most interesting to the group and four research questions were created around the topic.

Results

The questions created are presented below.

1. Is there a correlation within NapoleonB between the %GC of genes and the %GC of gaps with no coding potential?
2. In NapoleonB’s genome, are there many repeated sequences within the gaps between genes, as opposed to within the genes?
3. Is there a correlation within NapoleonB between the %GC of genes with known functions and genes with no known function?
4. Can the number of repeated sequences in phage genomes from different clusters indicate evolutionary relationships?

Conclusions/Next Steps

Next, we will narrow down the proposed questions to one final question for independent research. We will then begin research for the finalized topic.

Rationale

Final touches were worked on in the poster today and independent research projects were introduced to the class.

Procedure

• Remaining edits to the poster were discussed and made
• Groups were assigned to work under a “Coach”
• Tools and topics were explored for use in individual research projects

Results

The group of Lily, Lucy and I found the difference of %GC between no known function genes and genes with a function to be a potential research topic.

Conclusion/Next Steps

Next, we will dive more into the topic of %GC and the tools used to research it. It will be determined if %GC is a good research topic for the group.

Rationale

Today we will discuss what needs to be worked on in our poster and fix any issues before printing for Scholars Day.

Procedure

• Discuss what changes need to be made to the poster as a class.
• Different parts of the poster that needed to be revised were assigned to different groups in class.
• Each section was edited to an acceptable standard.

Results

The updated poster is shown below.

Conclusion/Next Steps

Next, the remaining section of the poster will be added and the poster will be looked over for final revisions. After approval by the others, the poster will be presented for Scholars Day.

1. Having a state health system in Russia during the 1940s-1950s led Russia to experience less freedom in the healthcare system. Due to the heavily controlled access to medicine that the people of the USSR faced, antibiotics were hard to come by during the time period. There was a considerably less amount of antibiotics available in the USSR in comparison to the United States. While the West did aid in the introduction of antibiotics to the USSR during World War II, their contributions were halted after the end of the war. This greatly slowed the strides that the USSR was making towards manufacturing proper antibiotics for consumption by the population. The state health system led to a lack of resources being allocated to the study of antibiotics during the time, which reduced the number of antibiotics available to the common population. Instead, herbs and more natural remedies were offered, and the absence of antibiotics paved the way for bacteriophage therapy to be more commonly used in the USSR.
2. Out of the three main organizations discussed in the novel, the Eliava Institute, the Phage Therapy Center, and the Hirszfeld Institute, there are somewhat different outcomes of each organization that have allowed for the differentiation between them. The Eliava Institute and the Hirszfeld Institute were both organizations that were impacted by the Russian government. The quote provided by Hirszfeld was given as a result of the struggles and tragedy that the family had to endure as a result of World War II and their struggles in Poland. The two organizations are similar in their struggles but greatly differ from the Phage Therapy Center. The Phage Therapy Center did not endure obstacles to the same degree as the Eliava Institute or the Hirszfeld Institute and it focused more on the treatment of patients. The Eliava Institute focused more on the research behind bacteriophages and their use.
3. Merril’s experiment utilized lambda phage and infected the blood of mice with it. After seven hours of infection, the surviving bacteriophage was isolated and reinjected into the bloodstream. This process was repeated eight times to allow for phages that lasted longer to be present in the bloodstream. Two phages called Argo1 and Argo2 were deemed to be the two phages present at the end of the rounds of serial passaging. Mice with E. coli were treated with Argo1 and Argo2, as well as W60, or lambda phage, in the experiment. The results were compared against a control group that received no phage therapy. The control group had a lower survival rate than those treated with phage therapy. The figures in the article showed that those treated with Argo1 and Argo2 showed significantly fewer symptoms of disease in comparison to the W60 group or the control group.
4. Despite the promising results that phage therapy has brought, antibiotics still seem to be the prevalent use of treatment today. More experimentation must be done on phage therapy before it can be widely accepted for use by others and the FDA. It appears as if phage therapy has been tested on a smaller scale, but few experiments have occurred on a large scale, which is needed in order to make strides towards more frequent use. In order to ensure safety for the public, more clinical trials must be performed as well as experimenting on what mixtures of phages are best for use for the differing diseases. There are undoubtedly unique circumstances that occur where one specific phage is needed, however developing a mixture of phages to combat the more common diseases would be beneficial for the general public. The company GangaGen recognizes the need for increased use in phage therapy and is working to treat infectious diseases that have a high level of antibiotic resistance. GangaGen is looking into combating multiple species of bacteria that are harmful to humans, and with enough published and accepted experimentation, the company, as well as others, may change the public outlook on phage therapy in the future.

Rational

Today we will evaluate all 4 posters created by the class and determine which one is best fit for later use.

Procedure

• Presented poster and different style elements
• Evaluated each poster
• Determined which poster was to be worked on in the future by the class.

Results

The 4 posters are shown below. The first poster was chosen to be worked on further.

Conclusion/Next Steps

It was concluded that the poster made by Lily, Aman, Lucy, Sabin, Michael, and I was to be worked on for future use by the class. Next, we will improve more on the poster and work on presentation skills for URSA Scholars Day.

Rationale

Today we will finish creating the final posters in our groups before presenting them to the class.

Procedure

• Combined groups with Sabin, Aman, and Michael
• Shared our (Lily, Lucy, and I) poster with group 2
• Combined elements of the poster to create one cohesive presentation

Results

The final poster result is shown below.

Conclusion/Next Steps

It was somewhat difficult to create the poster and combine the elements of the two styles. The overall words and content that were used were previously created during the last lab, however small issues such as spacing and font sizes were reoccurring. Next, we will assess all the posters created as a class and determine which one will be used to continue our work.

Rationale

Today we will begin making a research poster to present our findings on NapoleonB.

Procedure

• Powerpoint was opened and a shared presentation was created for each person in the group to begin working on the poster.
• Each group member worked on different aspects of the poster, in order for it to come together and to maximize time.
• The outline and spacing of the poster was individually worked on, as well as the introduction.

Results

The created poster is shown below.

The poster is not finished, but due to time constraints, this was the result produced.

Conclusion/Next Steps

Next, we will continue to work on our poster and learn more about the art of poster making. We will also dive more into each section and what each of us wants to present in each section of the poster.

Rational

Today we will begin sketching a rough outline of our poster and planning the content that is in each section of the poster for URSA Scholars Day.

Procedure

• Previously created posters were shown and analyzed by the class.
• Students broke up into assigned groups to begin group poster planning.
• A rough outline of the poster was created and the sections to include on the poster were determined.

Results

Shown below is the outline of the poster.

Conclusion/Next Steps

Next, we will learn more about the components and small details that are included in poster making. We will also begin making the poster for NapoleonB on Powerpoint.

Rationale

Today we will look more closely at the entire completed genome of NapoleonB and learn more about the basics of scientific poster making.

Procedure

• The entire annotated genome of NapoleonB was looked over by the class.
• Large gaps were analyzed to determine if certain genes should be elongated or if new genes should be inserted.
• Mistakes that were made with inserting data into PhageNotes were fixed.
• After the genome was checked by the class, a quick overview of various scientific posters was given.

Results

The varying red flags that were raised were looked over by the class and fixed by those who originally annotated the gene. No corrections were made on genes 85-88.

Conclusion/Next Steps

Next, we will revise the abstracts submitted on 2/18/19. Posters will begin to be made in groups after evaluating what is important for each group member, in terms of poster content and design.

Rationale

Today we aim to check the annotations of NapoleonB and come together in groups to make an abstract of the research conducted last semester and this semester.

Tools

• DNA Master
• PhagesDB
• NCBI
• Phamerator
• Genemark
• HHPred

Procedure

• An abstract draft was made by combining the stronger parts of other student’s abstracts in the group.
• The annotations for gene 96 was re-evaluated due to a large gap present between genes 95 and 96.
• Coding potential, and PhagesDB and NCBI blast hits were re-evaluated to determine whether or not the large gap should be closed.
• Phamerator was employed to compare the different regions to various AM cluster phages.

Results

The revised abstract was submitted. The large gap between genes 95 and 96 was deemed to possess a lack of need to be altered.

Conclusion/Next Steps

Next, we will finalize the abstract draft made. We will also look more closely at the full annotated genome of NapoleonB before submitting.