Did any of the Options appeal to you more than the others?

The option that appeals to me the most is the one concerning acceleration of innovation, as there are steps currently being taken to ensure the harmful effects of climate change are being slowed down. Within this group, a specific option that seemed more workable is to ease regulatory processes to bring new environmentally friendly technologies to the market. Currently, more people are purchasing these technologies which indicates that there is an increase in awareness of the harmful effects of climate change.

Did you hear or think of any new way of addressing the issues associated with the warming of the climate?

During the discussion, there were ideas about what can be done to ease in these technologies. Someone offered the viewpoint that not many people will follow when being told what to do, the same idea can also be understood in terms of telling people to switch to more “green” technologies. With this problem in mind, someone offered the idea of beginning small such as producing a light bulb which can be environmentally friendly as it is changed out so often.

What are your thoughts on the use of Public Deliberation in the classroom or the community? Is this something you would like to facilitate?

I believe that public deliberation opens the minds of those participating in the deliberation to new ideas and concepts, and that new, unthought of ideas can be discussed and refined. In the classroom, this exercise would be a good way to expose students to how to fix real world situations through discussion and thought.  

Rationale:

• In lab, the abstract was corrected and more information such as results and future plans were added. Along with abstract correction, comparisons were made with the qualitative data to the quantitative data to find significant results.

Tools:

• Personal Computational Device
• JMol
• Raptor X
• Google Excel Sheet
• Phamerator
• PhagesDB
• NCBI

Above, the protein structures of Elsa and Nason are compared. The top row are the protein structures of Elsa with AUG (preferred start codon), GUG as the changed start codon, then UUG as the other changed start codon. What we found interesting is that both tape measure proteins from phages that are within the same cluster, same preferred start codon, and from the same pham, so we wondered why there is a drastic protein structure change.

Results:

• First, the data was checked with Phamerator to make sure that no updates have been made with the gene that is to be studied.
• Protein structures were made based on similarities that were found in the quantitative data.
• With the differences in the protein structures, primary literature was used to understand the reason for the drastic differences in protein structures.
• For the abstract, corrections were made based on the comments posted.
• Additionally, a results portion was added as the group found more significant correlations and a conclusion was also added.

Conclusion:

• Corrections were made to the abstract as was submitted as the final abstract. Also, significant results were found and assumptions were made. To rule out which reasoning was unimportant for the change in protein structure, primary literature was used.

Future Plans:

• For the last work day in lab, most of the results will be organized and the powerpoint will be completed.

Describe the differences between Intralytics and GangaGen. Can you locate their “best selling products”? What are the main struggles these companies have to deal with? Look at their current web page. What changes have taken place since the writing of The Forgotten Cure?

Although both of these companies deal with locating phages and creating remedies, the approach, purpose, and usage of the phages are on opposite sides of the spectrum. The greatest difference between the two companies is the location in which they were founded: the United States and India. This demonstrates that despite the large distance between centers or institutions, the building of knowledge within science is not an individual activity but rather a massive group project that requires the participation of many scientists all around the world. Along with location, the circumstances led Intralytix to stop the projects concerning human-resisting bacteriophages and to lean more towards phages resistant to contaminating-bacteria found in meat, poultry, fruits, and vegetables as these were suggestions made by the FDA. This led to the creation of a phage cocktail that is resistant to listeria monocytogenes. GangaGen, on the other hand, remained on their goal to find human bacteria-resistant phages which they did and produced StaphTame which became their “best-selling” product.

Intralytix struggled with a lack of funds and long-term partners as there were many cases in which this occurred. Intralytix were also losing their collaborations with other institutions thereby making it difficult for them to find revenue to fund the projects. In the spring of 2002, Intralytix began the process of gaining approval from the FDA to launch trials of phage therapy against VRE. In this process, they had help from their team of experts along with Marissa Miller, a program officer of the NIH’s National Institute for Allergies and Infectious Diseases. After some time, Sulakvelidze got a call from the FDA to set a conference call to report their decision. During the conference, the experts working with the FDA asked numerous questions to lay their confusion to rest. One of their main concerns was of lytic phages and that it may be used in the final products of Intralytix. Along with this, the government also recommended that Intralytix moves to another model which would more closely resemble the patients that would be candidates for phage therapy usage. Sulakvelidze took all their points and recommendations into consideration when writing another report for the FDA following the meeting. After the company was denied a much-needed grant, they decided to turn their focus away from human use and towards phages in agriculture, meat, and poultry. They received bad news such as their main partner, Ecolab, dropped out, they remained hopeful as they received news that a British company was interested in their product. However, they soon let go of the deal was they claimed that the economy was bad which led to other companies dropping their deals with Intralytix. GangaGen did not face as many struggles; however, they did face the problem of lack of funding along with an inability to receive timely approval from the FDA.

When Forgotten Cure was written, Intralytix were focused on creating phage resistant sprays and cocktails aimed to destroy bacteria that were found to contaminate meats and poultry. Now, on the company’s website, Intralytix announced its recent collaboration with Ferring Pharmaceuticals to design bacteriophages that treat inflammatory bowel diseases. The company’s products shifted from solely producing agricultural products to also include projects involving human pathogens. Also, on February 8 of this year, Intralytix announced that their study concerning bacteriophage targets within patients with Crohn’s diseases has entered a Phase 1/2a stage of clinical trials. GangaGen, on the other hand, remained on their focus of creating bacteriophages for human pathogens. Based on the publications posted on their website, the company began looking at looking and testing other factors that can affect endolysin efficiency within Staphylococcus aureus.  

Rationale: Although some of the data points have not been entered for the tape measure protein, due to the time frame, protein structures for the major tail protein in the AM cluster were looked at.

Tools:

• Personal Computational Device
• Google Excel
• PhagesDB
• Swiss-Model

Results:

• With Google Excel, the major tape protein amino acid sequences in the AM cluster were each individually copied and pasted into the Swiss-Model program which then generated a model for the protein.
• These models were screenshotted and saved in separate files to ensure that the data remains organized.

Heisenberger Major Tail 15 AUG

Heisenberger Major Tail 15 GUG

Heisenberger Major Tail 15 UUG

Conclusion

• The protein structures from the AM cluster were looked at and organized to avoid confusion.

Future Plans:

• Protein structures will be continued to be observed and organized.

Rationale: The rest of the hard data was entered into the Google Excel sheet.

Tools:

• Personal Computational Device
• Google Excel
• Phages DB

Results:

• Data from PhagesDB was entered into the Google Excel sheet in groups separated into GC content, gene length, etc.

Conclusion:

The rest of the data was entered into the sheet.

Future Plans:

To begin looking at protein structures in the AM cluster

Rationale: After presentations were made, a final layout of the project was made to make sure the group was on track. Several primary works of literature were found to provide evidence of the findings and the scientific question was refined. Towards the end, the group began to collect hard data for the theoretical data.

Tools:

• OneSearch
• Personal Computational Device
• Google Excel
• PhagesDB

Results:

• First, the group began to search for primary literature related to the research begin done.
• Then, the question was specified more in order to be finalized later.
• At the end of the lab, hard data was being noted in Google Excel along with the usage of PhagesDB to later be used for the theoretical data.

Conclusion:

Primary literature was found, then the question was refined. The group began to collect hard data to later be used for theoretical data.

Future Plans:

Using the hard data, protein structures will be made using a database along with changing the start site to see if the protein structure changed.

Rationale: To practice poster presentations and to locate mistakes in order to be fixed before the actual presentations were to be made

Tools:

• Poster

Results:

• The poster was presented by each group.
• Each time, mistakes were found and corrected in order to be avoided on the actual presentation day.
• Questions were asked by the others to make sure the presenters were ready.

Conclusion:

Each group practiced presentations to find mistakes and correct them before they were made on the actual presentation day.

Future Plans:

After presentations, begin to work on independent research projects.

Rationale: One question was chosen of the four and additional research was done on the topic.

Tools:

• Personal Computational Device

Results:

• In this lab, the best question will be picked and refined with the guidance of the couch, Dr. Adair. To refine the question, additional research was completed to make sure that it was possible to test.

Conclusion:

The best question of the four was chosen and was refined with the help of Dr. Adair. More research was done to make sure that it was possible to obtain results from the question.

Future Plans:

Begin on the Independent Research Project.

Rationale: The group thought of research questions for the individual research projects with the guidance of the couch, Dr. Adair, and ideas posted in the Modules.

Tools:

• Personal Computational Device
• “Modules” in Canvas
• Required BioInformatic Tools

Results:

• Prior to class, research was done on additional topics to view other options for the questions which were to be used.
• With the additional information and ideas from the module, the group brainstormed on possible questions which can be tested bioinformatically and with the tools that are present.

Conclusion:

After more research was done on possible topics for questions, the group came together and formulated four questions which were testable bioinformatically and within the time that was given.

Future Plans:

With the four questions, one questions which the group collectively prefers will be researched even further to ensure that the question is feasible.

Rationale:

Each group was assigned certain parts of a poster to finalize the edits and texts.

Tools:

• Poster
• Groups
• Adobe Spark
• Google Slides
• Personal Computer

Results

• The groups were formed and each was assigned to a certain part of the poster to finalize.

Results:

Groups were made to edit and finalize the poster.

Future:

To begin the independent research project