April 24

Independent Research 4/24

Rationale: Analyze the hard data of the tape measure proteins, and to finish final abstract.

Procedure: DNA Master, google slides, Phagesdb, and google docs were used to gather information from the analyzation of tape measure proteins. Jmol was used to help construct models for the proteins.

Results:

Clusters

  • AY 6 phages
    • Alone AY has ⅖ UUG start
  • FE 3 phages (we have 2)
    • Idaho UUG start 1827bP. GC content 63.6
    • Corgi and Noely 1672bP average. GC content 67.9
  • Singleton 7 (we have 1 all others were drafts/not sequenced)
    • UUG start
  • AM
    • 4478bP
    • Pham 45114
    • Start AUG

NapoleonB GUG

NapoleonB AUG

NapoleonB UUG

Arcadia AUG

Arcadia GUG

Arcadia UUG

Conclusions: AM cluster phages tape measure protein share lots of unique features, but yet when start sites for these phages were altered, the structures were different. Six models are represented in the results, both are from the AM cluster. AUG and GUG are very similar, but compared to UUG, you can see differences.

Future work: Literature is needed to support why different structure and how this structure may have an affect on the proteins tail assembly, tail length determination, connection of capsid and distal tail regions, or genome delivery upon infection.

April 24

Independent Research Projects 4.24.19

Rationale:

To understand more about phage, the class was divided into several small groups to generate research questions that utilize bioinformatic tools to learn more about questions about NapoleonB and/or related phages.

Materials:
  • Laptop
  • Canvas Bio-Lab info page
  • DNA Master
  • NCBI & Phagesdb Database
  • Phamerator
Procedure & Results:
  1. The abstract was revised with the comments from the last abstract submission.
  2. Primary literature that provides insights to the project was found.
  3. Presentation powerpoint outline and graphs were compiled.

The hypothesis was supported by the new literature found in the lab. The final abstract version was revised and submitted.

The Next Step:

The next lab would be to try to complete the powerpoint and practice the presentation.

April 24

Preparing for CURES in BIO Symposium (4/24/19)

Rationale:

Rewrite abstract and work on PowerPoint for CURES Symposium.

Procedure:

  1. Made corrections to the abstract.
  2. Worked on PowerPoint presentation.
  3. Created structures using Jmol.

Results:

The following abstract was submitted for the CURES Symposium.

The following image is of the Gly-Gly structure created.

Conclusion:

The Phage Symposium PowerPoint and the modified abstract was used to create a rough draft for the PowerPoint presentation for the CURES in BIO Symposium. Jmol can be used to create 3D molecules.

Future Work:

Finish CURES in BIO Symposium PowerPoint and endolysin-holin interaction film.

April 24

April 24 2019 Independent Research Project and Abstract Updates

Purpose: The purpose of this lab is to continue working on the presentation for the final project, and update the abstract.

Tools/Procedures:

Tools:

  • NCBI BLAST
  • Google Docs

Procedures:

  1. More work was done to find other hosts and species that matched with AM specific genes from NapoleonB.
  2. The abstract was edited and corrected. Suggested changes were made, and the abstract was updated to reflect the current evidence found by the project.
  3. Work was begun on the presentation slides for the final presentation.

Results:
The results of this lab include finishing the research and data collection for the presentation, as well as finishing the abstract for the project. The results of the BLAST search found that 12/51 of the AM-specific genes of NapoleonB matched with genes from low %GC hosts and other species, such as roundworms and viruses.

Conclusions:
From this lab, it was concluded that a potential reason for the lower %GC of AM phages from their host is horizontal gene transfer, and this was reflected in the abstract.

Future Work: 
Future work will include creating the final project presentation. The presentation will also need to be rehearsed with the other group members.

April 24

4.24.19 Finalizing Independent Projects

4.24.19 Finalizing Independent Projects

Rationale: Since the due date for the project is approaching, today was used to consolidate the information that had been gathered and produce a final, complete abstract.

Procedure:

  • Abstract was revised using the tips that Lathan left for us
  • Primary literature was used to give additional weight to our findings, and the literature found today was positive for supporting the notion that our sequence was a regulatory sequence
  • PowerPoint graphics were created and consolidated
  • Information and an outline were made for the PowerPoint
  • Slides were created, not finished.

Results:

  • Hypothesis that the sequence is a regulatory sequence is supported by primary literature, which also gave steps for continuing research to prove this.
  • Abstract was successfully edited and submitted
  • Powerpoint was created and distributed to group members.

Conclusions:

  • Since many other logical options have been eliminated, the last remaining option that would be a regulatory sequence. This was supported by primary literature, which provides enough of a basis to present this as relevant findings.

Next Steps: Finalize PowerPoint and present to the class.

 

April 24

Finalizing Data Representations and Writing and Abstract 4/24/19

Rationale: Now that data has been gathered for the independent research, I need to find a good way to visually and numerically display this data. On top of that my group worked on making an abstract  to submit to CURES in bio.

Tools: MEGA, Google Drive, Jmol

Procedure:

1. Using  Jmol and MEGA to visually demonstrate the protein structures of different phages in the supercluster and show the differences from each and created a phylogenetic tree to display that data.

2. Worked on the rough draft of the abstract from before and made sure that the tense was correct, as it was active voice before.

Results: Data showed that the AM cluster is very closely related to the EL cluster and the phylogenetic tree showed the closeness in the DNA sequence of the members of the supercluster as to other arthrobacter phages.

Conclusions and Future Work: I now need to complete putting my data in a presentable format and prepare for CURES in bio.

April 24

4-24-19 — The Forgotten Cure Part 3

Question:

One of the biggest problems in phage therapy has been in the approval process. Describe the trouble surrounding FDA approval and recommend some suggestions to improve the process of phage therapy approval.

One of the hardest parts about FDA approval or approval from any government agency for that matter is that they are all very picky when it comes to funding. This is understandably because there is only so much money to go around; however, they don’t make it easy to prove oneself to these agencies in order to receive funding. Since agencies like the FDA want to see results before deciding to throw money at a concept, groups like Intralytix and GangaGen were forced to cater to unreasonable requests without funding to begin with or give up on phage therapy for humans. Also understandably, this pushes groups like these two to the latter option, since in the world we live in there isn’t a very easy way up without monetary support. Given that the FDA doesn’t understand precisely the nature of phage (something that none of us fully understand yet, but something that some see more of than others) and asks for unreasonable results, combined with the fact that they won’t provide funding without these results, and lastly the fact that government agencies are basically comprised of red tape, the FDA has proven to be a fairly immovable roadblock.

Honestly, the only thing that I can think of that will help raise the understanding of phage usage and push for FDA approval is to continue what these companies are doing already and making products and testing on things other than humans. The more tests that are performed and the more basic knowledge that is accumulated, the more likely results will appear that give agencies like the FDA faith in this concept. All things take time. For example, funding wasn’t focused on renewable energy sources for a long time since faith and understanding was in coal. Obviously, the world has started to change its stance on that issue, and something like this will follow when the world is more ready to embrace it. The more data these groups can accumulate and the farther they can spread this information, the sooner it will be funded and the positive feedback loop occurring from this will provide Intralytix, GangaGen, and any other company like them the support they need to make real breakthroughs on phage therapy in humans.

April 24

Forgotten Cure #3

Question #2

Intralytix tried and failed to pass phage therapy through the FDA in 2002. The process of passing a drug through the FDA is challenging for any small startup company because it is typically very expensive and time consuming. In addition to expenses in time and money, Intralytix had to battle the country’s general aversion to phage treatment. At the time, American scientists had tunnel vision for antibiotics and drugs creating added resistance to the emergence of phage therapy. When the FDA was reviewing the product they found a lot of problems including the accuracy of separating lytic and lysogenic phages, a less than desirable animal model that had been used, and unknown rated at which the phages within a cocktail would mutate and affect the experimental animal. Finally, there was not sufficient evidence showing that the results of phage therapy would be different from the results of antibiotics. Intralytix  concluded that testing and revaluating each of these issues would be much too costly and time consuming so the project was put on hold.

From my experience working at a pharmaceutical company, the FDA can be used as a resource, not just a merciless judge. The best and fastest results are achieved by working directly with the FDA and approaching them in the beginning stages and asking for guidance instead of just viewing the FDA as an end location. With FDA guidance, phage therapy funds can be more focused and precise to test the most necessary components. I think it is also important to show how phage therapy has advantages over antibiotics.

April 24

THE FORGOTTEN CURE #3

One of the biggest problems in phage therapy has been in the approval process.   Describe the trouble surrounding FDA approval and recommend some suggestions to improve the process of phage therapy approval.

The trouble surrounding the approval process of the FDA is due to both, the fact that phages tend to have a more negative view in the United States, and the fact that there simply may not be enough research to determine the safety of commercial phage use. Due to the lack of phage use in the Unites States, I feel as if its seen as more of a safety risk because phages haven’t been extensively used, therefore the long term ramifications of commercial phage use have yet to be determined. Also there is also a lot of skepticism surrounding phage use, for example when the FDA responded to Sulakvelidze they had a request that seemed unreasonable: “What Sulakvelidze felt was a less reasonable request was that the FDA also asked him to determine the rate at which each of the six phages in Intralytix’s proposed VRE cocktail would mutate inside an experimental animal” (92). The amount of money and time that would be needed to prove the mutation rate is astronomical and borderline impossible, and it could be agued that it really isn’t even needed. 

Some ways that I feel the phage therapy approval process can be improved is if as a society we can readily adopt the idea of using phages as a from of treatment, and try to diminish the stigma surrounding phage therapy. Secondly, I think if we can approve some form of phage therapy that seems safe and effective, I feel as if that would could help diminish stigma and help us determine the long term ramifications of phages in a real world setting (if there even are any) 

April 24

Forgotten Cure 3

One of the biggest problems in phage therapy has been in the approval process. Describe the trouble surrounding FDA approval and recommend some suggestions to improve the process of phage therapy approval.

Despite the promise phage therapy has, it has yet to become a practice used in medicine due to the constant overwhelmingly large obstacle that is FDA approval. The approval process is riddled with problems that make approval for phage therapy an incredibly tedious process. The largest obstacle and issue with the FDA approval process is the fact that the FDA wishes to see promising results regarding the use of phages against bacterium, but require scientist to jump through hoops with little to no resources or funding. This can best be seen The Forgotten Cure, when the FDA made completely unreasonable request towards Sulakvelidze and Intralytix when they requested Intralytix to “determine the rate at which each of the phages in Intralytix’s proposed VRE cocktail would mutate inside an experimental animal”. This request was deemed unreasonable by Sulakvelidze, and noted that “if they [FDA] persist in this, it will be very difficult for us to carry on”. These roadblocks intentionally put in place by the FDA can hinder or completely prevent phage therapy companies from continuing on with their research. This can cause approval for phage therapy to take an incredibly long time, as it wasn’t until 2006 that phages were approved by the FDA just for food usage. Unfortunately, the FDA is a government agency, and for phage therapy to be approved it must meet and overcome every rule and regulation set in place.

I think the best way to improve the process of phage therapy is to loosen the reigns a little on the companies that are participating in this research. It is obvious that phage therapy, unfortunately, is relatively unknown and under-appreciated, meaning these companies have a hard enough time securing funding and the means necessary to do this type of research. In combination with reduced funding, the FDA putting up unnecessary roadblocks and obstacles can make it extremely difficult for these companies to succeed. This could be largely contributing to the lack of the fully achieved potential and promise phage therapy holds. I understand that the FDA is simply doing its duty, as it is trying to ensure phage therapy is completely free of any potential threats to public health, however the process of scientific inquiry is already a long and drawn out process as it is. The constant interference with the FDA and the lengthy approval process continues to slow down phage therapy to a crawl. With looser regulations, and increased support from the FDA and the public, I believe the process of phage therapy approval will not only go by much smoother, but also at an increased rate.