May 4

Public Deliberation

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Today’s discussion about climate change was an insightful one filled with meaningful observations and viewpoints. Pertaining to the course of action(s) we talked about, I believe that a mix between preparing for the worst as well as taking drastic measures will be the choices we will be facing in the near future. As is, we are already noticing the effects of global warming not in our own environments but in the ecosystems and habitats of many animals around the world. Due to the effects of the Industrial Revolution and technological innovations ever since, we’ve gained much innovation at an irreplaceable cost. I believe that we will need to start taking drastic measures to save the environment which will be more than just switching to reusable bags and refillable water bottles. In our group today, we discussed how many won’t like the idea of our rights being infringed upon by protocols that may help save the environment. I think one question we need to ask ourselves is, “How much more can the Earth take and are we willing to push those boundaries until they break?”. Evident in alternate energy source technology such as Tesla and hybrid cars, we are still looking for ways to minimize the footprint we are permanently imprinting on Earth rather than stop creating those large footprints.

April 26

4/24 ~ Final Abstract

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Rationale: Work on the final abstract for the independent research project and continue searching for data

 

Materials:

  • Google Drive
  • DNA Master
  • Laptop

 

Procedure:

  • Worked together in the research groups to refine the rough draft of the abstract
  • Submitted the final abstract draft as the QTM

 

Observations:

  • The final abstract

     

    Conclusion/Next Steps: Will continue to work on gathering data for one more workday and then will work on drawing conclusions and discussion.

April 22

The Forgotten Cure 3

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Prompt: As a scientist, describe the main experiment you would like to see performed before phage therapy is approved for human use. What are the risks involved with using phage therapy?

 

As mentioned in The Forgotten Cure, phage therapy has hit many roadblocks in the process of becoming approved for medical use in the United States. Some of the major risks involved with using phage therapy are septic shock, bacterial transduction, as well as the concern of bacteriophage being lysogenic. With septic shock, many bacteria house endotoxins within themselves which can be released into the patient’s body when lysed by the bacteriophage, which can lead to dangerously low blood pressure. In bacterial transduction, the phage has the possibility of exchanging genes with the bacterium and “turning” the bacterial cell into a deadly and pathogenic one. An example is the strains of E. coli 0,157. The main experiment I would like to see performed before phage therapy is approved is decreasing the likelihood that any of these mentioned risks from happening.

In the book, Ramachandran had the idea that if they would be able to block the gene that codes for endolysin, then they could create a phage that kills its prey but never lyse the cell, therefor solving the problem of septic shock in patients. He partnered with Sriram and Bharati Padmanabhan to test his hypothesis using a plasmid to inactivate the endolysin. His hypothesis was successful in that no plaques were formed, but the E. coli bacteria were inactive. This discovery also led Ramachandran to hypothesize that this process could be used to create more effective vaccines. In current vaccinations, the bacteria are killed using intense heat or formaldehyde solution which can denature or destroy many of the antigens on the surfaces of the bacteria. In the study conducted by Bharathi, the vaccinated group all survived, while 80% of the mice not vaccinated died. Such discoveries and research is slowly moving bacteriophage therapy towards medical use, but is not yet a 90-100% success rate.

I believe that bacteriophage research is approaching the threshold of being approved by the FDA for commercial use, but there are still many limitations or “grey areas” in which we have no research to back our hypothesis. Such a grey area is that how will the FDA and general public react to the bacteriophages being left in the patients body after treatment? As of right now, there is no procedure to remove the bacteriophage from the body after administration. Will the FDA approve bacteriophage even though they’re harmless to other “helpful” bacteria found throughout the body and will be degraded after some time? I believe that although there are still many questions that need to be answered, we need to be able to realize that the use of antibiotics have created superbugs that are more deadly than ever and bacteriophage therapy provides a possible solution to these bacterium.

April 12

4/10 ~ Continued research for Independent Research Projects

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Rationale: Continue to gather data to answer the scientific question regarding preferred start codons and the relationships that can be drawn between clusters and phages within clusters

 

Materials:

  • DNA Master
  • Google SpreadSheet
  • PhagesDB

 

Procedure:

  • Loaded up the FASTA files from PhagesDB of the AR phage and annotated them in DNA Master
  • Recorded the start codons of each gene and calculated the percentage of each start codon (ATG, GTG, TTG)

 

Observations:

  • The preferred start codons of phage KBurrousTX

    The preferred start codons of phage Linus

     

Conclusion/Next Steps: Similar to the AM cluster, there were patterns within the AR cluster which is unique to the phages found within the cluster. In the examples of phage KBurrousTX and Linus, the last five genes of the phages preferred an ATG-GTG-ATG-ATG-ATG pattern which was found throughout all the phages in the AR cluster. The next steps would be to calculate the preferred percentage of the start codons and observe if there is a correlation between clusters or phages in the clusters.

April 12

4/8 ~ Research for Independent Projects

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Rationale: Find date for independent research projects which support the scientific question

 

Materials:

  • DNA Master
  • PhagesDB
  • Google SpreadSheet

 

Procedure:

  • Opened DNA Master and opened FASTA files of phages in AM cluster
  • Recorded each start codon for each gene
  • Determined the preference percentage of each start codon (ATG, TTG, GTG)

 

Observations:

NapoleonB with the preferred percentages of each start codon

Mudcat with the preferred start codon of each gene

 

Results/Next Steps:

  • When observing the preferred start codons, there was a pattern in the last four genes of the phages in the AM cluster. They all preferred a GTG-GTG-ATG-ATG for their last 4 genes, which may show that they code for similar genes. This discovery can help other scientists help characterize and cluster their phage earlier in research. Will continue to find the preferred start codons of the AM cluster as well as the AR cluster
April 3

4/1 ~ Scholars Week

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Rationale: Practice in class giving the oral presentation with the poster

 

Procedure:

  • Examined and looked at printed poster
  • In presenting groups, practiced presenting an oral presentation in front of the class
  • Received feedback from the students, TA’s, and Doctor Adair

 

Observations:

  • Advice was given to cover results rather than the procedure/methods covered in the lab

 

Conclusion/Next Steps: Will be presenting on Wednesday from 12:46 – 1:00. After URSA Scholars Week is over, will continue to work on independent research projects.

April 3

4/3 ~ Independent Research Project Work

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Rationale: Continue to find data for the chosen question of the research group

 

Materials:

  • DNA Master
  • SpreadSheet
  • PhagesDB

 

Procedure:

  • Met with research group to discuss next steps and to create schedule of upcoming dates
  • Used PhagesDB to download FASTA files of bacteriophages within the AM cluster to auto-annotate
  • Used DNA Master to auto-annotate the files and recorded the start codon for each gene

 

Observations;

Tentative Schedule

Screenshot of the start codons of one of the phages in the AM cluster

 

Conclusion/Next Steps: Will continue to work with the FASTA files of bacteriophages and compare the preferred start codons.

March 28

3/27 ~ Independent Research Question

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Rationale: Focus on one of the questions created last lab and research sources for the topic

 

Procedure:

  • Brainstormed with group members on which question to focus on
  • Used PhagesDB and Phamerator to research potential correlation between plaque morphologies and genes
  • Focused on another question when the group realized that evidence would be hard to find for the first question
  • Used DNA Mastering to looks at the start site preferences in terms of codons

Observations:

The refined question our group will focus the research on

 

Conclusion/Next Steps: With the next labs, will continue research on the question. If the question doesn’t show much promising results or an interesting discussion, will change questions.

March 28

3/25 ~ Independent Question(s) Brainstorm

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Rationale: Work with assigned groups to create questions that would serve as the basis of the independent research project(s)

 

Procedure:

  • Met with group members to begin brainstorming questions
  • Consulted with “coaches” on the questions that were created
  • Decided on four “major” questions that could be focused on

 

Observations:

  • The four questions that we came up with

     

Conclusion/Next Steps: Next lab, will be choosing one question out of the four to research more on and look for sources

March 22

3/20 ~ Final Poster Reflection and Individual Research Projects

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Rationale: For the QTM, reflect on the final poster as well as choose a subject to focus the research project on

 

Materials:

  • Final Poster Google Document
  • Computer

 

Procedure:

  • Opened and completed QTM, which was a reflection of the final poster
  • Worked with group members to find a topic that was to be the focus of the research project (Creating phylogenetic tree of bacteriophage)

Conclusion/Next Steps:

  • Will be sending the proposed research idea to the group mentor (Aadil) and hopefully it will be approved. In the upcoming labs, will be working on the scientific question to be answered with the project.