March 29

3-25-19 — Project Question Ideas

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Project Question Ideas

Date: 3-25-19

  • Rationale
    • The rational for this lab is to decide on four ideas for a research project over the genome of Arthrobacter ATCC 2102.
  • Procedure
    1. Groups met together to brainstorm ideas.
    2. Group leaders were asked for direction and whether or not a question was specific and testable.
  • Results
    • Four questions were formed.
      • The four questions that we came up with

  • Future Plans
    • The next step is to focus on one question and receive approval for a project based on one of the questions.
March 22

3-20-19 — Independent Research Project

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Independent Research Project

Date: 3-22-19

  • Rational
    • The rational for this lab is to brainstorm ideas for a research project over the genome of Arthrobacter ATCC 2102.
  • Procedure
    1. Groups of two or three were formed to work on individual projects.
    2. Ideas were discussed between group members.
    3. Arthrobacter phage data, including GC%, location found, cluster, and genome size was recorded from PhagesDB for phages that infect Arthrobacter ATCC 21022.
  • Results
    • A project idea of comparing relative phylogenetic relatedness between Arthrobacter phages was chosen.
  • Future Plans
    • The next step is to continue gathering data from PhagesDB in order to collect a large enough sample size to perform different genome enlightenment and data analysis.
March 22

3-18-19 — Poster Design

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Poster Design

Date: 3-18-19

  • Rational
    • The rational for this lab is to make work on final edits for the class poster.
  • Procedure
    1. The class worked in individual groups to fix parts of the poster.
    2. My group found high resolution images to be placed on the poster.
  • Results
    • The final poster design was worked on as a class.

 

An image of the final poster.

  • Future Plans
    • The next step is to begin working on individual research projects.
March 18

3-18-19 — The Forgotten Cure Part 2

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

One of the most important outcomes of the USSR having a state health care system was a focus on alternatives to antibiotics. Given the Russian culture of using natural remedies, the cost of antibiotics, and the association of antibiotics with major western countries, it was easy for the country and its doctors to switch to phage therapy, as it was natural, not costly, and was notably different from the antibiotic route the western countries were taking.

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 and Eliava Institutes were medical institutes whose founding shared a place in history with WWII. Although they both focused on phages and both involved being shadowed by regimes, the Hirszfeld Institute was successful while the Eliava Institute was not. This is partially due to their geographical locations. The Eliava Institute in Tbilisis was in a much smaller country with much less funding and control, and thus failed in the end. The Hirszfeld Institute was in Poland, a much larger country with more say in the western world. The location of this institution made it easier for it to receive funding for its specialized pursuits of bacteriophage research and immunology.

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.

Merril and his team took lood samples from animals, isolated the phage present, and injected them into mice. This process was repeated a number of times until their survival rate was much higher. These phages were named Argo1 and Argo2. Four mice were taken and injected with a lethal dose of bacteria. The mice that were injected with Argo1 and Argo2 were made slightly sick before recovering, the mouse that was treated with Lambda phage had a slightly more severe illness, and the mouse that went untreated died in two days. This supported his hypothesis of the relative strengths of passaged versus unpassaged phages.

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?

Although phage therapies are very promising, one major problem that most of these companies have in common is that they don’t follow the rules and regulations set out by the American government. Since they don’t follow the proper protocols, it’s impossible for them to make much progress in America. Because of this, western doctors are distrusting of the capabilities of phage therapy. A phage therapy institute has recently been opened in California, which shows promise since it would have to operate under American protocols and hopefully gain credibility. Large experiments with control groups following proper American protocol have to be performed in order to gain more support and credibility in the States.

March 8

3-6-19 — Group Poster Comparison

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Group Poster Comparison

Date: 3-6-19

  • Rational
    • The rational for this lab is to compare the four poster designs from each group to decide which features should be kept and which poster should be used as a base for the final poster.
  • Procedure
    1. All four final posters were presented to the class one by one.
    2. Likes and dislikes from each poster were recorded individually.
    3. A final poster was chosen to be the base for the final class poster.
    4. Additional features that the class thought should be added were recorded so that they can be integrated into the final poster design.
  • Results
    • A final poster draft was chosen to be edited and worked on as the final poster.

An image of the poster design chosen to be used for the final poster.

  • Future Plans
    • The next step is to finalize the chosen poster design, adding and removing liked and disliked features until a fully refined poster is created.
March 8

3-4-19 — Final Group Rough Draft Poster Design

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Final Group Rough Draft Poster Design

Date: 3-4-19

  • Rational
    • The rational for this lab is to continue working on the poster design from the previous lab on PowerPoint.
  • Procedure
    1. A second poster group was merged with ours in order to combine our work and finalize the first round of drafts.
    2. The PowerPoint presentation was shared with the new poster group.
    3. More diagrams and pictures explaining lab procedures were added to the poster. Formatting of the boxes, shapes, and colors were changed.
    4. A third, final rough draft of a poster created.
  • Results
    • A poster design was created on PowerPoint.

  • Future Plans
    • The next step is to compare this group’s poster with posters from other groups in order to decide which features from each should be included in the final poster.
March 1

2-27-19 — Second Draft Poster Design

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Second Draft Poster Design

Date: 2-27-19

  • Rational
    • The rational for this lab is to continue working on the poster design from the previous lab on PowerPoint.
  • Procedure
    1. A PowerPoint presentation was created and shared with the poster group.
    2. Diagrams and pictures explaining lab procedures were added to the poster.
    3. A second, more refined rough draft of a poster created.
  • Results
    • A poster design was created on PowerPoint.

 

  • Future Plans
    • The next step is to add more information and refine the poster design in order to work towards a completed design.
March 1

2-25-19 — Poster Design Planning

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Poster Design Planning

Date: 2-25-19

  • Rational
    • The rational for this lab is to brainstorm ideas for a potential poster design for Scholars Week.
  • Procedure
    1. Poster examples from previous were studied and favorable components were noted so they could be added to the new posters.
    2. Groups were assigned. 
    3. A rough sketch of a poster created.
  • Results
    • A poster design was drafted.

  • Future Plans
    • The next step is to produce a more finalized version of the poster design on PowerPoint.
February 22

2-20-19 — Gene Annotation Final Revision

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Gene Annotation Final Revision

Date: 2-20-19

  • Rational
    • The rational for this lab is to revise the annotations for the entire genome of NapoleonB before submission.
  • Procedure
    1. The class as a whole looked over the entirety of NapoleonB’s genome.
    2. Gaps were evaluated to see if new potential genes could be added with support from databases instead of being left blank.
    3. Overlaps that were too large were evaluated as a class to determine if they were accurately called or not.
    4. The class evaluated whether or not data had been correctly entered from student notes to the collective class google sheets page.
  • Results
    • NapoleonB’s genome was evaluated as a class and determined to be accurate as a whole.
  • Future Plans
    • The next step is to submit the annotations and to finalize an abstract. A poster needs to be planned and finished in order to present the research done. The next step is also to begin working on an individual research project.
February 22

2-18-19 — Abstract Refinement and Assigned Gene Corrections

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Abstract Refinement and Assigned Gene Corrections

Date: 2-18-19

  • Rational
    • The rational for this lab is to work on refining our abstract drafts as well as to correct genes with questionable calls for NapoleonB.
  • Procedure
    1. Groups were formed and abstracts between each member were compared.
    2. A consolidated version of the abstracts was created and submitted for further critique.
    3. The group was tasked with analyzing the calls made for gene 44.
    4. Phamerator, NCBI BLAST, and starterator, as well as the upstream gene – gene 43 – were studied to see whether gene 44 could be edited and called at a later start codon
    5. The gene was moved from a start codon at bp 30318 to a start codon at bp 30372.
  • Results
    • NapoleonB gene 44 was shortened to a new start codon to avoid an overlap of 86 bp, which is too much of an overlap to be accurate according to data on previously annotated genomes.
  • Future Plans
    • The next step is check the rest of the annotations to make sure they are accurate before submission. Also a final class abstract must be constructed from each group.