27 March 2019 ✷ Independent Research Project Topics

Procedure

• The questions created in the previous class were discussed with Dr Adair
• Ultimately, it was decided to combine the first two questions to make a question that is a bit broader and that can be expanded
• tools to analyze repeats and % GC were researched and some bumps in using DNA Master were worked out

Results

Conclusion

The question we created is more substantial and will allow for in-depth research of NapoleonB.

Future plans

Research into NapoleonB’s genome will begin.

25 March 2019 ✷ Independent Research Project Topics

Procedure

• The class discussed the qualities of a “good” research question and then groups worked to craft research questions
• The idea of % CG composition was looked upon favorably and thus most of the 4 questions revolved around that idea
• 4 questions were created and discussed
• the questions were submitted

Results

The group came up with the following questions:

Conclusion

The questions generated will need some refinement, but they should lead to some meaningful research.

Future plans

The questions will be looked over by Dr Adair to ensure the question is “good.” Then, research will begin.

20 March 2019 ✷ Final Poster Making + Research Projects

Procedure

• The group poster was edited because a new gene was added (96b)
  • The discussion was edited to reflect this
• Groups were assigned and potential topics were discussed
  • comparing the %CG between functional genes and nkf genes is a potential idea discussed within the group

Results

updated discussion

current poster (m&m is being edited to have better phrasing of each step)

Conclusion

The results section is incomplete, but should be fine by Friday. The materials and methods needs some refining so it will be inserted before Friday as well.

Future plans

This poster will be updated and edited until it reflects what is to be presented at Scholar’s Day. Research for independent projects will begin.

18 March 2019 ✷ Final Poster Making

Procedure

• The 4 posters were combined into one and students were broken into groups for delegated tasks.
  • The discussion section was turned into a similar image as the materials and methods section
  • symbols were added to the headers of each section
  • The materials and methods section was expanded and edited several times to include more information on the in silico portion of the lab

Results

materials and methods new edit

discussion

image of our poster

Conclusion

Some groups still need to add in their portions, but other groups had a lot more work to do than others in order to complete this. The final poster will be created in the following class periods.

Future plans

This poster will be updated and edited until it reflects what is to be presented at Scholar’s Day.

Forgotten Cure

1. How did having a state health system influence the treatment of infectious disease in 1940s-50s Russia?

The state health care system created by the USSR during wartime created many issues in the treatment of infectious disease. The conditions created by World War II spurred many outbreaks of bacterial infections. Then, non-traditional medicine became more popularized and this sparked an increased interest in phage therapy because it was viewed as natural or non-traditional. The government was communist at this time and thus people were distrusting of the government as a general rule. The government had interfered with antibiotic development and inserted itself into personal healthcare, so trust of the government wasn’t common. Antibiotic use in Russia was difficult to obtain at first, but then it turned to being available on shelves without prescriptions and this contributed to the growing number of antibiotic resistant bacterial strains and thus increased use of phage therapy.

2. The Hirszfeld Institute is also intertwined with Russian history. A tragic quote is given on page 66 by Hirszfeld about the death of his daughter.  Even so, the outcome of these 2 centers has been very different.  Discuss why you think this is so.

Contrast the Phage Therapy Center in Wroclaw with the Eliava Institute in Tbilisis.

Both the Hirszfeld Institute and the Eliava Institute came about because of oppressive regimes in eastern Europe and both had to overcome differing ideologies in regards to phage therapy. The Hirszfeld Institute found more success in its longevity because the Eliava Institute had only a short period of popularity and scientific discovery. Unfortunately, in order for institutes such as these to exist and experiment, they need funding and support. The geographical locations of the two made this immensely difficult when compared to similar places in countries like the United States; the Eliava Institute is located in Georgia, which is small and fell under Soviet rule in the days the institute was established. Thus, the Phage Therapy Center, located in Poland, has found more success than the Eliava institute because being rooted in Poland gives it more connection to the western world and thus more opportunity to receive funding from more developed countries and the donors that reside in them.

3. Research in the USA often differs from other countries because of regulations by the FDA and private investments. Describe the experimental design that Merril used to determine how to select for phages that were not removed by the liver and spleen.

Review the Merril, Carlton, and Adhya PNAS paper, focusing on interpreting their figures.

Mice were injected with phage and a bacteria and the blood was tested after several hours and the phages that survived were isolated and propagated in order to increase the number of them. This was repeated 8 times until the remaining phages were able to survive for 18 hours within the mouse. The figures in the paper reflect the strength of the symptoms associated with the bacterial infection relative to the dose and type of phage used to treat the mouse. Mice treated with only antibiotic had reduced symptom presence, but mice treated with phage had the least symptoms.

4. The most convincing argument for using phage is tied to the increasing problem of antibiotic resistance. Even so, many still consider phage therapy an alternative therapy.  Chapter 8 describes several start-up companies:

Phage Therapy, Phage Biotics, GangaGen, Exponential Biotherapies.  Research these companies and discuss the potential for phage therapy in modern Western medicine. What experiments need to be done?

First of all, many of the phage therapy studies mentioned in the book were completed in European countries and did not follow typical protocol for studies to be completely accepted, such as using double-blind experiments. Experiments proving again the effectiveness of combining phage therapy with antibiotics but following guidelines for research that will make it more widely accepted in western medicine. Because the currently published studies were not conducted in such a manner, there is doubt from western doctors and thus doubt in the usage of phages to treat bacterial infections.

6 March 2019 ✷ Poster Making Cont.

Procedure

• The 4 posters were each presented by group members and the best parts were noted and other parts were critiqued/questioned
• The things I liked best about my group’s poster were questioned heavily by the class
• The 4 posters were voted on to determine which would be the best to work off of and ultimately, this poster won.
• The class had mixed feelings over the donut-pie chart, so it was edited to make it easier to comprehend.

Results

image of our poster

incompletely updated donut-pie chart; letters will be added to the pie portion in order to correspond to the gene function indicated in the key

Conclusion

The group was told it had a poster that was a great balance of pictures and words and that the graphics were creative.

Future plans

This poster will be updated until it reflects what is to be presented at Scholar’s Day.

4 March 2019 ✷ Poster Making Cont.

Procedure

• The small groups were paired up and the best parts of each poster were implemented.
• The other group shared a link to their poster with my group
• My materials and methods image and my donut-pie chart was included in the final poster
• The format of the other group’s poster was used
• everything was cleaned up on the poster using google slides
• the poster was downloaded and submitted

Results

image of our poster

Conclusion

The poster created in today’s lab was simple and easy to look at. It has a good balance of pictures and words and it will need slight changes, but overall, it is a strong candidate.

Future plans

This poster will be compared to the posters of those of other groups.

27 February 2019 ✷ Poster Making

Procedure

• The drawing from the previous period was referenced, but the dimensions and orientation ended up being changed to a large square.
• A shared powerpoint was created and group members edited each section.
• I was responsible for materials and methods and the pie chart in “data”
• I downloaded the entire Phamerator map and converted it to a .jpeg file in order to insert it
• The poster was saved and submitted

Results

image of our poster

Link to full resolution:

YAYAY poster-1gq3kgj

Conclusion

The poster created in today’s lab was simple and easy to look at. It has some spacing issues but more time to adjust it would benefit the group.

Future plans

The best parts of each poster will be combined into one amazing poster that will be printed and presented at Scholar’s Day.

25 February 2019 ✷ NapoleonB Poster Planning

Procedure

• Past posters were looked at and critiqued/analyzed
  • flaws were noted and kept in mind when planning for our own poster
• Students broke into groups to plan posters
• The ideal poster was drawn and what was going in each section was indicated; some research into software and what PowerPoint had to offer was looked into.

Results

Drawing of our poster

Conclusion

The poster should be simple but pleasant to look at with enough information on it for viewers to understand the project.

Future plans

The powerpoint version of our poster will be crafted in the following lab period.

18 February 2019 ✷ NapoleonB DNA Annotation Corrections + Abstracts

Procedure

• DNA master was opened and NapoleonB was auto-annotated
• PhageNotes was opened and each aspect of the DNA annotations for gene 23 was rechecked for the start codon. It was ultimately decided the start would not be moved because of the RBS scores and agreement with Starterator.
• Abstracts for research performed last semester and this semester were crafted prior to lab and members of the group combined the best parts of each abstract into one strong one
• Cooper’s abstract was used as the foundation for the group’s abstract, but the procedure from Kathryn’s was very strong and was included in the final draft. My introduction and final numerical values were included from my abstract, and Nathan’s procedure was also included.

Results

final annotation for gene 23:

The group’s abstract:

            ” Bacteriophages are a diverse, vast part of our biosphere that still have relatively little known about them. The 2018-2019 Baylor University SEA-PHAGES Cohort worked to isolate a collection of Arthrobacter phages and then annotated the genome of Arthrobacter phage NapoleonB. This study was conducted in order to discover and sequence a new bacteriophage. By collecting, purifying, and isolating the phage in a high-titer lysate, the fully sequenced genome of the phage was able to be annotated and analyzed. As a result of the annotations, completed on DNA Master, the annotations of NapoleonB showed 71 genes without a known function and 26 with a confirmed function. Among these 26, 7 genes suggested functions relating to tail proteins while 1 gene coded for holin, which makes NapoleonB the only phage in the AM cluster to have this gene. The genes that showed a function were supported by NCBI BLASTp, HHPred, and synteny from the Phamerator AM cluster phages and known phams. The unknown genes either showed ambiguous results or no significant results from an NCBI or PhagesDB BLAST, while the called genes showed evidence of basic bacteriophage functional proteins. The results of this sequencing and annotating suggest that while many different species, types, and clusters of bacteriophages have been discovered and analyzed thoroughly, there is much more to be discovered. However, the annotation of NapoleonB provides useful evidence that improves the general understanding of bacteriophages.”

Conclusion

Many of the genes annotated were no known function or tail proteins, so the study of the phage is largely centered around that.

Future plans

The annotation of NapoleonB’s genome will be completed, checked, and submitted to phagesdb. The information gathered from the annotation of the genome will lead to the creation of a research question and thus further research into phage biology involving NapoleonB.