April 1

April 1 2019 Practice Poster Presentations

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Purpose: The purpose of this lab is to become comfortable presenting and explaining the class poster for Scholar’s week.

Tools/Procedures:

Tools:

  • Poster

Procedures:

  1. Groups for Scholar’s week practiced presenting the poster to the class.
  2. The class participated in asking questions about the poster to help those who were presenting prepare for the presentation.

Results: The class learned and practiced how to present a poster.

Conclusions: 
In conclusion, in this lab the class accomplished poster presentations. The class members helped each other to know more about the poster, and asked questions to stimulate understanding.

Future Work:
Future work will include presenting the poster for Scholar’s Week. Also, work will begin again on individual projects.

March 27

March 27 2019 Independent Project

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Purpose: The purpose of this lab is to finalize the independent research question and create a plan for the project and data collection.

Tools/Procedures:

Tools:

  • Canvas
  • DNA Master
  • Online Bioinformatics Resources

Procedures:

  1. A new question was formed from the list of questions created in the last lab. The new question focuses on characterization of the gaps of AM phages with %GC and repeated sequences, in comparison to coding regions.
  2. Research was done to find the best ways to calculate %GC for each gene and gap.
  3. Research was begun to look for ways to find repeated sequences in NapoleonB.
  4. Work was saved.

Results: The results of this lab include creating a new research question and beginning the process of planning the project and data collection.

Picture: %GC

Conclusions:
In conclusion, the research question was created, centering around the characterization of AM phage gaps. Work was done to find the best way to collect the data and analyze the results.

Future Work:
Future work will include collecting the data for the research project and finding repeated sequences. Once data has been collected, the results will be analyzed.

March 25

March 25 2019 Independent Project Questions

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Purpose: The purpose of this lab is to develop questions for the final project.

Tools/Procedures:

Tools:

  • Provided Canvas resources
  • Microsoft Word

Procedures:

  1. Ideas were generated for question topics, and it was decided that the areas of most interest to the group were %GC and repeats in NapoleonB.
  2. Four questions were generated, relating to %GC or repeats.
  3. Questions were submitted to Canvas.

Results:
The results of this lab were four potential questions. This will help the group to begin the independent project.

Conclusion:
In conclusion, four potential questions were written, but it was not decided which question would be researched.

Future Work:
Future work will include choosing a question from the four created and beginning the research process to answer the question.

 

March 20

March 20 2019 Posters and Final Projects

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Purpose: The purpose of this lab is to make final edits to the poster, as well as begin learning about the final project and ways to conduct the research.

Tools/Procedures:

Tools:

  • Poster
  • Canvas Resources

Procedures:

  1. The parts of the poster that need to be fixed were outlined.
  2. Groups learned about the final project and the different tools that could be used for different research topics.
  3. The QTM was completed.
  4. Groups worked on fixing the elements of the poster.
  5. Work was saved.

Results:
The poster finalizations were analyzed. Work was begun on the final project.

Conclusions:
The poster was not finished, but a plan was made for its completion. Ideas were generated for the group final project, but a final question was not created.

Future Work:
Future work will include finalizing all figures for the poster and adding them, as well as finalizing the poster. Also, a question will need to be made for the final project, and then work on the final project will be started.

March 18

March 18 2019 Poster Editing

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Purpose: The purpose of this lab is to edit the poster for Scholars Week.

Tools/Procedures:

Tools:

  • Poster
  • DNA Master
  • Phage Notes
  • Excel

Procedures:

  1. Groups were created to work on different elements of the poster.
  2. Figures were designed to display the In Silico Results, such as gene function.
  3. Work was started to collect the data for the figures. Not all figures were completed.

Results:
The figures for the In Silico results were started,  but not all of them are finished. Other elements of the posters were also edited by other groups.

Conclusions:
In conclusion, the poster was not finished, but many elements of the poster were edited. The In Silico figures will need to be finished and added to the poster.

Future Work:
Future work will include finalizing all figures for the poster. Also, once all of the elements of the poster are added, the poster will need to be edited to ensure it has the proper layout.

March 9

The Forgotten Cure 2

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Bacteriophage research, like all research, relies on interested scientists and funding for its success. Not only does it rely on this, but also the state of the government and the government systems. In Russia, phage therapy was cheaper than antibiotics and because of this, was more prominent during the 1940s-50s. The phage came from the environment and did not cost the government like antibiotics did. Also, the Russians liked to use non-conventional medicines and treatments like herbs. Bacteriophage were not considered standard medications, and because of this, the Russians naturally fell to using phages in place of antibiotics when possible. However, one difficulty in the spreading of phage research in the 1940s and 1950s in Russia was the state health system. Because of lack of funding, scientists were not paid well. Institutes like Eliava did not always have electricity, which made keeping phages alive difficult with no refrigeration. Some doctors even took their phage home with them. So while the Russian systems influenced the spread of phage, other areas of the government kept them from becoming more widespread.

Many different phage institutes in Russia made discoveries in bacteriophage research. The institutes all had their own difficulties, and many of them fought against wars such as World War II. Hirszfeld and his family suffered from the war and Stalin’s reign in Russia. Because of the wars and other difficulties, many of the phage institutes struggled to continue. The Eliava Institute is still functioning today and has grown much larger, expanding to include many spin-off companies. The Phage Therapy Center in Wroclaw focuses more on providing therapies and treatments to patients than new research like the Eliava Institute does. They treat many different infections such as acne, colitis, laryngitis, and burns. The different institutes all play an important role in the spread of bacteriophage research and therapy.

When bacteriophage research spread to the US, many changes had to be made to accommodate the regulations in the US. For instance, scientists and the FDA wanted proof that the phage actually helped in the healing process and did not just activate the immune response. Carl Merril and his team helped to prove this by using heat-killed phages to show that while they did activate the immune response, the phages would do more by lysing the bacterial cells. Merril, Carlton, and Adhya, in their PNAS paper, provided a way to select for bacteriophages that would stay in their patient longer and therefore help in the immune response. Using lambda phage and E. coli, Merril and his team created the passaging technique to select for phages that could survive longer in the stomachs of their patients. They would isolate phages still present in the stomach of their mice patients 7 hours after infection, propagate them, and then reinject the phages into the mice. The scientists would do this multiple times, and in the end, they created strains of lambda phage that could survive in the stomach conditions for longer than the wild types. The phages, names Argo1 and Argo2, were able to stay in the stomach in much higher amounts than the wild type. In their PNAS paper, the figures show how at 24 hours, the titers of the wild type would have been reduced by about half of their original titer, while Argo1 and Argo2 would have only gone down a small amount. Also, the scientists were able to see that mice treated with the phage improved much more than mice without treatment and that those treated with Argo1 had fewer symptoms than those treated with the wild type lambda phage.

While many still consider phage therapy an alternative to other treatments like antibiotics, there are many companies discussed in The Forgotten Cure that are researching to change this and make phage as prominent as antibiotics in bacterial treatments. GangaGen is one company that is attempting to make bacteriophage an alternative treatment to antibiotic-resistant bacteria. There are many experiments that need to be done in order to spread phage therapy in the US. Phage therapy has to go through clinical trials in order to be approved by the FDA and given as treatment to patients. Experiments need to be done to test more bacteriophage and find more that match specific bacterial strains in order to best fight these diseases. Also, experiments need to be done to test the best phage cocktails for different diseases, as well as the effect of combining them with different antibiotics. One example is the experiments at Exponential Biotherapies. They are working on phage therapy for acute kidney injury and irradiation damage from cancer therapies. Because of the FDA and other regulations, any new possible therapies will need to be tested with animals and then undergo strict human clinical trials. While each of these experiments will take time, it could lead to a new era of treatment in bacterial infections

March 6

March 6 2019 Poster Presentations and Critiques

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Purpose: The purpose of this lab is to present the four posters that were created in order to compare them and design a collective class poster.

Tools/Procedures:

Tools:

  • Posters
  • Critiques QTM

Procedures:

  1. The four posters were presented to the class, discussing why different choices were made for each poster.
  2. Each poster was critiqued, both positively and negatively, on its design, information, and details.
  3. As a class, it was decided that the class poster would be based off poster 4 and would include details from other posters as well as new figures and information.

Results:
The class poster layout was chosen and discussions were started to create the final product. Below is a picture of the poster chosen for layout.

Conclusions:
In conclusion, the layout for the poster was chosen. Ideas were shared for how the final poster should look and what it should include. Also, new ideas were shared for figures that could add more details to the poster that highlight NapoleonB more specifically.

Future Work:
Future work will include editing and designing the class poster, as well as designing new figures for NapoleonB.

March 4

March 4 2019 Poster Design

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Purpose: The purpose of this lab is to finish poster designs in large groups.

Tools/Procedures:

Tools:

  • Google Slides
  • Powerpoint

Procedures:

  1. Small groups met with large poster groups to compare posters.
  2. Posters were compared, and a layout was chosen.
  3. Information from both posters was combined into one poster. The design and layouts were chosen as a large group.
  4. The poster was saved and submitted.

Results:
The poster was completed.

Conclusions:
In conclusion, the poster was finished and submitted. The two group posters were consolidated into one poster as a team.

Future Work:
Future work will include fixing any formatting errors in the poster, and practicing presenting the poster. Also, the posters will then need to be made into one final class poster.

 

February 27

February 27 2019 Poster Creation

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Purpose: The purpose of this lab is to design and create a poster for Scholars Week.

Tools/Procedures:

Tools:

  • Microsoft Powerpoint
  • Lab Data
  • Abstract
  • Institutional Logos

Procedures:

  1. A powerpoint presentation was created and shared with the group.
  2. Powerpoint settings were created and an outline of the poster was made.
  3. Information was added to the poster.
  4. Figures were obtained or created and added to the poster.
  5. The poster was saved.

Results:
A rough draft of the final poster was created, and the data were inputted.

Conclusions:
The poster rough draft was finished, but the poster was not. The layout of the poster still needs to be adjusted and fixed. Also, the poster needs to be checked to see if more data from the lab needs to be added.

Future Work:
For future work, the poster needs to be finalized and all formatting issues need to be fixed. The final poster will be compared to other groups and used to create a final class poster presentation.

February 26

February 25 2019 Poster Design

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Purpose: The purpose of this lab is to begin designing posters for Scholars Week.

Tools/Procedures:

Tools:

  • Reference Posters
  • Paper, Pencil

Procedures:

  1. Previous SEA-PHAGE posters and other example posters were looked at and analyzed to gain insight into proper poster presentation and to see what makes a poster look good.
  2. The layout for the poster was designed.
  3. The most important figures to include on the poster were discussed.

Results:
The design for the poster was begun. It was decided that it was not necessary to include the full abstract on the poster, but to provide a summary abstract section with the introduction. The layout was created, and figures were chosen to be included on the poster.

Conclusion:
In conclusion, the poster design was not finished, but the process of designing was started. Discussions were begun about which figures would best represent the research done be visually pleasing to an audience.

Future Work:
Future work will include finishing the poster design and layout. The next step will to begin building the poster and adding the research.