Rationale: Listen to the critiques of the TA’s as well as Dr. Adair to finish the final poster

Materials:

• Final Poster Google Document
• Computer

Procedure:

• Listened to the advice of the TA’s and Dr. Adair
• Opened the Google doc and worked with the group to finish/clean up the wet-lab results section of the poster

Observations:

The Final Poster

Conclusion/Next Steps: After finishing up the poster, the cohort will begin to work on individual group projects.

1. Having a state health system in the USSR during the 1940’s -1950’s caused the USSR physicians and researchers to research other alternatives of treatments rather than rely on antibiotics. During World War II, through Western funding and support, the USSR was able to rely on the United States and Great Britain for aid in advancements in antibiotics. However, with the end of World War II, the USSR was left alone with little resources to continue antibiotic research. Alternative medicine has always been an essential part of treatment in the USSR, so phage therapy was able to take root more easily in that culture than in others. In a culture where natural substances were trusted, phage therapy was readily accepted and used to treat infectious diseases.
2. The Hirszfeld Institute in Wroclaw and Eliava Institute in Tbilisis were two medical institutes established near/during the 2nd World War. However, only the Hirszfeld Institute found lasting support and success. I believe this is mostly credited to the strict emphasis placed on bacteriophage research and immunology at the institution. Such an example is in 1952, when Hirszfeld petitioned to devote an institution only to immunology within the Medical School’s Department of Microbiology, as well as the continued emphasis and research in phage typing throughout the years of 1950-1960. I also believe that the Hirszfeld Institute was able to flourish because of their joining of the EU in 2005, which connected them to other Western countries. The Eliava Institute was prosperous for a while, but lost most of it’s market after the dissociation of the USSR.
3. Merril and his team took blood samples from animals and isolated the phages present and re-injected them into the mice. This process was repeated multiple times to isolate lambda phages that were able to remain in the bloodstream for as long as 18 hours (Named Argo1 and Argo2). These phages, along with wild-type phages were used to treat mice injected with lethal doses of bacteria. Argo1 and Argo2 phage-treated mice had a milder illness before recuperating than those treated with the wild-type phage, showing results that supported Merril’s hypothesis.
4. Phage Therapy has immense potential in Western Medicine but in may cases, are stopped by government regulations and approvals that can only be given through studies which yield safe results. Particularly in the United States, the FDA has since recently allowed the establishment of the first phage therapy center at University of California, San Diego; however, phage companies yet have to conduct large studies with control groups to ensure credible results for approval. Companies, such as GangaGen, have devoted their resources and research towards discovering and developing ectolysins (high-specific therapeutic proteins) to target meaningful types of bacteria. Although first founded in India in 2000, it was incorporated into the US in 2001. Experiments run by phage companies should show the effectiveness of phage in treating infections, but also should emphasize the safety of the phages. One large misconception of phage therapy may be the notion perceived when individuals are told that scientists are using viruses to infect bacteria. The use of terms such as viruses may immediately be a red flag to patients or individuals. This misconception needs to be addressed and changed so we are more accepting of discoveries which are different from what we are used to.

Rationale: Present the group created posters and determine which one to use as a template

Materials:

• Group posters
• Opinion from classmates

Procedure:

• Each group went up to present their poster design
• Collaborated as a cohort on which design was to be used
• Determined which aspects of other poster was to be kept/transferred to the design

Observations:

• 

  The selected final poster

  ‘

• Conclusion/Next Steps: As a class, determined which poster to use as a template. In the upcoming labs, will be transferring and tweaking the aspects of the poster to the desired information to be displayed.

Rationale: In groups, finalize the poster layout with information

Materials:

• PowerPoint
• Laptop

Procedure:

• Got into large groups and brainstormed/formatted posters into a final poster to be presented
• Added in the rationale, methods, results, discussion, and acknowledgement sections of the poster

Observations:

• 

  The group created poster

   

  Conclusion/Next Steps: The poster is “finished” and will be presented in front of the class next lab so a final poster design can be determined and created

Rationale: After creating the rough layout last lab, will be creating the “first draft” of the poster with group members.

Materials:

• Computer
• Paint
• PowerPoint
• Office

Procedure:

• Got together in groups and discussed how to effectively create the poster
• Deliberated about which aspects/results should be displayed on the Results part of the poster
• Opened PowerPoint and created the individual sections of the poster, along with the specific headings
• Worked on the center circle graph representing the genes of NapoleonB
• Submitted the “first draft” poster as the QTM

Observations:

The “first draft” of the poster created by the group

Conclusion/Next Steps: The posters will be reviewed by the TA’s and Dr. Adair. After consideration, the lab will continue to work on and critique and posters until one, singular academic poster is created.

Rationale: Brainstorm ideas for the poster design with assigned group

Materials:

• Laptop
• Paper
• Writing Utensil

Procedure:

• Viewed examples of past posters with the lab
• Met group members and brainstormed ideas for the poster
• Drew a rough sketch of how the poster would look like

Observations;

The rough draft sketch of the poster design

Conclusion/Next Steps: Learned more about poster aspects and necessary parts of the poster. Next lab, will be completely creating the poster design(s) and information that goes in each respective section.

Rationale: Finish (As a class) looking at the annotations of NapoleonB, making sure any gaps are accounted for, as well as work on the abstract

Materials:

• DNA Mastering
• PhagesDB
• NCBI
• GeneMark
• Phamerator

Procedure:

• Opened DNA Mastering
• Opened NapoleonB file and opened frames
• Opened NapoleonB Phagenotes and followed along with the class, accounting for each gap in genes
• Assisted in fixing any genes that needed to be pulled back or up
• Looked at all submitted abstracts and determined an abstract that worked best

Observations:

The coding potential of gene 96, which was one of the genes deliberated about during lab

The frames view of gene 96, which has a large gap upstream

Conclusion/Next Steps: The annotations of NapoleonB are almost done. After the last few changes, NapoleonB will be checked once more by the TA’s and then confirmed. The abstract of the poster will continue to be worked on.

Rationale: Finish up the final calls of NapoloenB and work on the abstract for the group poster

Materials:

• DNA Mastering
• PhagesDB
• NCBI
• Phamerator

Procedure:

• Opened the Document with the genes that need extra annotations
• Worked on the gene(s)
• Worked in groups to create an abstract
• Copy and pasted all the abstracts from everyone and created a new abstract
• Submitted abstract as a group

Observations:

The abstract our group came up with

Worked on Gene 78, which has a large overlap with Gene 77

Conclusion/Next Steps: This work is leading to the completed annotation of NapoloenB. After this week (or next week), the entire genome of NapoleonB should be completely annotated. The next steps would be to agree on an abstract for the scientific poster and work on the content of the poster.

1. Describe the role that locusts, dysentery, and war had in the discovery of bacteriophage

• Locusts, dysentery, and especially WWI played an essential role in the discovery of bacteriophage. Due to WWI, disease outbreaks and vaccines were among the most necessary problems that needed to be answered. Dysentery, an infection of the colon, was running rampant in the ranks of troops. Felix D’Herelle, a Montreal-born, Paris-raised scientist was asked to investigate the outbreak of dysentery and “fix” it if possible. Prior to the war, D’Herelle first discovered bacteriophage (meaning at the expense of bacteria) when studying sick locusts. There were clear plaques that appeared in his Petri dishes when growing bacteria, and then linked the same appearance of plaques when examining bacteria found in the feces of sick soldiers, D’Herelle then tested his hypothesis on a sick patient with dysentery by using the patient’s stool to extract the bacteria and bacteriophage from. The success of the experiment was applauded and D’Herelle published a paper on bacteriophages in 1917.

2. Discuss the characteristics of d’Herelle that led him to be a successful scientist. How did he compare to Georgi Eliava? What happened to the Eliava’s?

• As a self-taught scientist, d’Herelle was passionate about the field of science and would not give up on any idea that he would think of. Any problem or obstacle that he encountered, d’Herelle countered with scientific reasoning and experimentation. These characteristics ended up helping d’Herelle by opening up research opportunities for him, such as in the Soviet Union (USSR). Georgi Eliava was a bacteriologist from the Soviet Republic of Georgia that did research alongside d’Herelle. Eliava was described as charming and laid back, while d’Herelle was prickly and businesslike, seemingly counters of each other. Both came from privileged backgrounds and both invested their entire lives to science and the expansion of the known frontier. Eventually, the Eliava’s were executed by Stalin in labor camps.

3. Discuss the influence war and politics had on the spread of phage therapy

• War was one of the main driving forces that allowed for the discovery and usage of bacteriophage in medicine. If dysentery hadn’t run rampant during WWI, d’Herelle wouldn’t have been able to make the connection between his locus research and the plaques discovered when examining patients with dysentery. Due to this discovery, d’Herelle was able to publish papers and “start” the research on bacteriophage therapy (Not named that during the time period). Politics played a huge role in the spread of phage therapy in that the different countries all flocked to start research on bacteriophages, which resulted in the attraction and “migration” of many intellectual minds to different countries. In the specific example of the USSR, Stalin wanted to establish and accelerate the research of bacteriophage, which resulted in the establishment of the research facility in Georgia.

4. What are some of the reasons that the spread of phage therapy failed?

• One of the major reasons why phage therapy failed was the development and research of antibiotics. Sulfa pills and Penicillium developed and instantly took over the scientific world heading as they were “more simple in administration” and had promising results. Bacteriophage research was commonly tested without control groups and were tested on self-limiting conditions, which resulted in mixed results or results that had no comparison to. There was further research on the use of bacteriophage with penicillin, but did not catch on. A lack on complete understanding of bacteriophages also contributed to the failure of phage research.

5. How did the physicists Delbruck and Luria end up as part of the Phage Group? What contributions did they make to phage biology? Why did phage biology die out in the 70’s?

• Delbruck, an astronomy student living in Berlin, and Luria, an Italian-Jewish medical student living in Turin (At the time) were both scientists who ended up planting the seeds of what would become the Phage Group, which was a loose collection of scientists in diverse fields who believed that bacteriophages constituted he biological equivalent of hydrogen atoms; the smallest and simplest life forms. The group ended up finding the structure/physiology of bacteriophage, as well as determining it was DNA, not protein that was the genetic material. They also co-discovered the replication mechanism of bacteriophages. However in the 70’s, Phage Group and bacteriophage research died out due to research on human and animal cells that were easier to research (With the technology at that time).

Rationale: Continue annotating the genome of NapoleonB, specifically assigned genes 37-40.

Materials:

• DNA Mastering
• NapoleonB PhageNotes
• PhagesDB
• NCBI Database
• Phamerator
• GeneMark

Procedure:

• Booted up DNA Mastering on computer and opened NapoleonB file
• Continued annotating NapoleonB genes 37-40
• After completing, worked on the QTM due that lab day (Number 9)
• Utilized PhagesDB and NCBI to check protein sequences, and Phamerator to check predicted shape

Observations:

Complete annotated genes of 37-40 for NapoleonB

Questions I had on QTM 9, such as which genes I had problem with

Conclusion/Next Steps: After complete annotation, it’s expected that the genes will be reviewed and checked for correctness. After that process, will continue to work with NapoleonB and create scientific questions to be answered.