April 4

URSA Scholars Week Poster Presentations (4/1/19-4/3/19)

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Rationale:

Practiced presenting and presented poster and viewed other URSA posters and abstracts to fully experience USRA’s Scholars Week. From these experiences, ways to improve class poster/presentation will be taken into consideration.

Procedure:

  1. Performed a mock poster presentation in front of the class.
  2. Visited a poster and filled out survey.
  3. Read and critiqued the abstract that correlated to the poster.
  4. Presented poster.

Results:

The following poster was presented.

The following image below shows the poster viewed.

The following image below shows the abstract critiqued.

Conclusion:

The URSA Scholars Week posters/presentations were very good.  However, in my opinion, the BEARS in the SEA poster was my favorite. The poster had the perfect amount of text and figures. When presenting to the judge, I was able to expand upon the poster. When asked “Why NapoleonB was selected?,” the two distinct lytic plaque sizes from the Wet Lab Results along with the supportive graph, Phamerator, and pham analysis from the In-Silico Results allowed the conversation to move towards discussing my holin and endolysin findings from my individual research project. Also, when the gel electrophoresis methods were questioned, I was prepared and was able to explain the last-minute reference paper from Stu Mair’s research.

Future Work:

Use literature to find as much information about holin and Peptidase_M23 endolysin proteins’ chemical mechanisms, metabolic pathways, and specific structures that could possible help in identification of these proteins in other phages.

March 28

In the Literature (3/27/19)

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Rationale:

Create a procedure to perform to test research question.

Procedure:

  1. Brainstormed procedure in groups.
  2. Performed NCBI BLASTp.
  3. Started reading in the literature about the mechanisms of holin and endolysin.

Results:

The following images below show the NCBI BLASTp.

 

The following articles were of interest.

https://pubs.acs.org/doi/10.1021/acschembio.5b00875

https://onlinelibrary.wiley.com/doi/full/10.1111/mmi.13448

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6116005/

https://www.sciencedirect.com/science/article/pii/S0065352718300563?via%3Dihub

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4012431/

Conclusion:

The NCBI BLASTp revealed that both the holin and endolysin genes shared CDD meaning that enough similarity exists between these genes among phages for it to be a legimate research question. Also, many articles found on holin and endolysin, showed the research question purposed was legitimate.

Future Work:

Further research into the mechanisms of holin and endolysin will be performed to achieve a thorough understanding before starting protein analysis.

March 27

Developing a Question (3/25/19)

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Rationale:

In groups, develop a specific question about Arthrobacter that can be tested with bioinformatic tools.

Procedure:

  1. Brainstormed ideas within groups.
  2. Sought approval from Coach.

Results:

After ideas for doing possible research into NapoleonB’s only reverse gene and tail proteins, it was decided that the research performed should attempt to thoroughly answer the question: Using bioinformatic tools, can phage holin’s and endolysin’s structures and functions be compared across Arthrobacter phages?

Conclusion:

Although comparing the structures and functions of holin and endolysin will require a great amount of biochemistry knowledge, this research question interests all group members and has motived them to understand topics that seem somewhat foreign.

Future Work:

Brainstorm and start an experiment to answer this research question.

March 21

Final Poster Touches and Starting Individual Project (3/20/19)

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Rationale:

Finish figures for the poster so it can be sent off to print. Start researching a possible research question relating to the in-silico aspects of the lab that can be investigate for individual project.

Procedure:

  1. Changed colors on Phamerator.
  2. Modified supportive function graph.
  3. Re-created predicted function pie.
  4. Started researching topics.

Results:

The image below shows the Phamerator.

The image below shows the modified supportive function graph.

The image below shows the predicted function pie.

Conclusion:

It is hard to create a visual when people cannot communicate what they want.

Future Work:

Go to open lab to confirm that the figures created are acceptable. On Monday, decide and brainstorm with group what topics should be considered for the projects.

March 21

In-Silico Results Figure Making (3/18/19)

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Rationale:

Work on the research poster for scholar’s week.

Procedure:

  1. Divided class into teamsto work on different sections.
  2. Brainstormed possible figures to be used for the “In-Silico Results” section.
  3. Collected and organization data from PhageNotes on which databases supported the predicted functions.
  4. Collected cluster data and formed graph.

Results:

The graph below shows brainstormed figures to show the Phamerator number and cluster that were created using not PhagesDB and Phamerator data.

 

The table below shows the supported predicted function data collected where 1 represents that the predicted function was supporting and 0 represents that the predicted function was not supported.

Gene # NCBI Hhpred PhagesDB CDD
3 1 1 1 0
4 1 1 1 1
7 1 1 1 1
9 1 0 1 1
10 0 1 0 0
11 1 0 0 0
14 1 1 1 0
16 1 1 1 1
17 1 0 1 0
18 1 0 1 1
19 1 0 1 1
20 1 1 1 1
21 1 1 1 1
22 1 1 1 1
25 1 1 1 1
39 1 1 1 1
45 1 1 1 0
62 1 1 1 1
77 1 1 1 1
81 1 1 1 0
85 1 1 1 0
87 1 1 1 1
93 0 1 0 0
96 1 0 1 0
98 1 0 1 1

Conclusion:

Since PhagesDB and Phamerator have not received the annotations for NapoleonB, the data used to create the figures to display phamerator numbers and cluster graph was not accurate.

Future Work:

Ram has offered to create his own Phamerator program to have access to the most accurate data for NapoleonB. He will focus on the cluster graph when the rest of the group will continue on the other figures such as the supportive function graph and the predicted function pie.

March 15

The Forgotten Cure Part 2

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Phage therapy’s influence has varied over time and across different countries such as Russia, Poland, India, and the United States. Politics and culture have both contributed to increases and limitations of the use of phage therapy.

In the 1940s–50s Russia, the state health system controlled the treatment of diseases due to its limited supplies. During World War II, Soviets received Western support and funding which allowed for antibiotic production. This support was removed after the war. Since Russia provided universal health care without charge, the Soviets did not have the resources to continue antibiotic production or buy from American pharmaceutical companies. The lack of resources caused phage therapy to regain popularity through government-supported propaganda which promoted patriotism.

World War II had differing influences on the phage research institutions including the Ludwik Hirszfeld Institute of Immunology and Experimental Therapy in Wroclaw and the Eliava Institute in Tbilisis. In Wroclaw, Poland, the Hirszfeld Institute was in fear of Stalin’s Lysenkoism since “more than 90% of Wroclaw’s Jewish population was killed” and both the founder, Ludwik Hirszfeld, and many staff members had Jewish heritage (Kuchment 65). After Stalin’s death, the Polish government provided support to the Hirszfeld institute. In contrast, the Eliava Institute had its peak during World War II since they received support from other countries to create phages to use for soldiers. After the war their funding was eliminated, they started to focus more on research than the production of phages. In 2003, two Eliava Institute scientists created the Phage Therapy Center in Tbilisi with goals of making phages more available for use. The outcomes of these centers can be contributed to political influences and differing priorities.

During the 1990s in the United States, an antibiotic resistance article led to a phage experiment performed by Merril, Carlton, and Adhya. Although other phage studies had already been performed in Russia and Poland, many Western scientists remained skeptical of how reliable the outcomes of these experiments were due to their poor study designs. In Merril’s experiment, the design considers various variables including: phage’s narrow host range, possible presence of phage lysate toxins, and the patient’s immune defense system. Mice were divided into four groups: a control group, a W60 (the “parent” lambda phage) treated group, an Argo1 treated group, and Argo2 treated group. Through serial-passage techniques, they were successfully able to isolate phages (Argo1 and Argo2) that could survive longer than the original lambda phage and eradicate the target bacteria.

With concerns for the antibiotic resistance problem, many companies are still looking into phage therapy as a possible alternative. In 1993 in the United States, Exponential Biotherapies emerged to commercialize phages to specifically target inflammatory responses. In 2000 in India, Dr. J Ramachandran founded GangaGen Inc. In recent publications, GangaGen has looked into using phage-derived lysins to break down biofilms which have high resistance to antibiotics. They are also working on a phage to target antibiotic resistant MRSA and VRSA infections.  Although more research is being performed, there are still some holes that research should fill before phage therapy can be applied to modern Western medicine. More experiments should use a design that considers variables and uses controls in order to show that phages are safe and beneficial. For instance, would the use of phages to treat minor infections significantly more beneficial or even necessary? Most doctors believe “draining puss from an infection is often enough to cure it – even without phages or antibiotics” (Kuchment 69). If phage therapy becomes approved in the United States for patients, it most likely will be used with antibiotics and probably will not replace them since it would be extremely rare for a bacterium to develop resistance to both phages and antibiotics.

By time traveling through different stages of phage therapy history, one can grasp a greater understanding of how the various political climates and cultural mindsets shaped the spread of phage therapy across different countries.

March 8

Poster Presentations (3/6/19)

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Rationale:

Groups presented their posters and the best poster was chosen for scholar’s week.

Procedure:

  1. Each group presented their poster to the class.
  2. Discussed in a group what was liked and disliked about each poster.
  3. Voted on a poster to use.
  4. Made a list of things to modify the poster selected.

Results:

The following poster was selected.

Conclusion:

All group posters lack interesting findings that made them stand out. It was decided that the Phamerator should stay on the poster, and the sunburst should not be used. The class was challenged to create a figure displaying the gene number, function, and related phages.

Future Work:

Modify this poster to make it stand out with interesting findings associated NapoleonB.

March 5

NapoleonB’s Genes 25 and 28 Corrections and Final Poster (3/4/19)

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Rationale:

Errors found in NapoleonB’s genome were corrected. The poster was completed.

Procedure:

  1. NapoleonB’s gene 25’s coding potential was checked using the GeneMark graph.
  2. NapoleonB’s gene 28’s start choice source was checked using DNA Master.
  3. Both genes were corrected on NapoleonB’s PhageNotes
  4. Completed poster through collaboration of ideas and with the addition information.

Results:

The following images show the updated NapoleonB genes 25 and 28.

The following image shows the final poster.

Conclusion:

NapoleonB’s gene 25’s coding potential error was fixed. NapoleonB’s gene 28’s start choice source error was corrected. However, the corrections for NapoleonB’s gene 25-28 are not complete since Starterator still needs to be checked.

The poster still needs a few images to be updated such as the TEM image of NapoleonB and NapoleonB’s leaf.

Future Work:

The Starterator will be checked for NapoleonB’s genes 25-28. A poster will also be selected to present for scholar’s week.

February 28

Digitally Designed Poster (2/27/19)

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Rationale:

Started designing using Microsoft PowerPoint a poster.

Procedure:

  1. Used Microsoft 365 PowerPoint to re-create the rough sketch previously brainstormed.

Results:

The following image shows what was completed.

Conclusion:

The poster still not finished. Figures and additional information still being completed.

Future Work:

Finish poster.

February 28

Poster Brainstroming (2/25/19)

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Rationale:

Looked at previous posters and started brainstorming.

Procedure:

  1. Viewed previous posters.
  2. Drew a rough sketch of an idea for the placement for the sections.

Results:

The following is an image of the rough sketch of my group’s ideas.

Conclusion:

Posters should include an introduction, methods, results, conclusions, reference, and acknowledgements sections. The introduction section should have the background information, objectives and the general research question stated. The way BEARS in the SEA 2017-2018 cohort used bullet points made it easy to read. Also, the figures they used made their posters stand out. The main goal in making the poster is to present the correct findings in a clear and concise way.

Future Work:

Start designing poster using Microsoft PowerPoint.