1. Did any of the Options appeal to you more than the others?
   • I thought that the relocation of communities was an interesting option. I didn’t think that relocation would be considered an option as it is view unrealistic for me. Mainly because as much as I understand why certain location should change, it wouldn’t be ideal for people in low income families. A lot of the options listed had financial/social issues involved with it. Although all of the options would help climate change, it is unrealistic when thinking about people from low income.
2. Did you hear or think of any new way of addressing the issues associated with the warming of the climate?
   • From one of the discussions heard from the group, one member talked about the use of solar panels, which I thought was interesting because I didn’t correlate solar panel with climate change before.
3. 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 think that PBI is great to help bring out ideas and discuss and counter argue some of the ideas that are already “planned out.” As many people already have their own options, its better for people that has a neutral aspective to give in some inquiry about the options for climate change. Although all of the options are great ideas despite having a few counter arguments and whether if its ideal or not, it all depends on the people’s motivation of wanting to help stop climate change.

Rationale

Fixed abstract from comments made by coach. Continued working on the presentation slides and also fix other parts of the research

Procedure

1. took comments from coach and applied them to the final abstract
2. fixed background and conclusion on presentation slides

Conclusion/Next Steps

We fixed our conclusion/discussion for our research and since my group and I have finished faster than our schedule we made, all we have to do next time in lab is to go over the powerpoint and practice presenting

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?

Many experiments has been performed in the past through other animals to see the effectiveness of phage therapy. In The Forgotten Cure,  Kuchment presented two examples of testing that was done to combat salmonella and e. coli. In 2002, Perdue headquarters began testing phages on salmonella. Salmonella began a huge problem that was found in uncooked chicken meat. They took the eggs, baby chicken, and adult chickens and treated them with phages. With the eggs, they injected bacteriophages and sprayed phages on the baby/adult chickens. As a result so far, they found that phage therapy was more effective compared to other methods for reducing salmonella in chickens.  GangaGen also tested out phages to see how well it would help e. coli in the cow’s stomachs. Their findings showed that the phages helped kill the bacteria and the viruses were flushed out of the cow’s intestines. According to The Forgotten Cure, the only FDA approved medical use of phage therapy were for patients with AIDS.

If phage therapy were to come back within later this year or in the future, I believe it would be better for human trails to start with other diseases other than AIDS. Other diseases, such as meningococcal meningitis, can be treated with vaccines, but the vaccines doesn’t work for all types of meningococcal disease, just a few. Although AIDS is a serious health concern, but phage therapy can help diseases that are rare or more serious compared to AIDS. Meningococcal disease affects the brain and spinal cord, which is arguably one of the most important parts for humans to live. Once FDA approves phage therapy for all diseases on humans, I would expect to see experiments first done through other animals that have a certain type of disease, and test out different forms of treatment (oral, injections, sprays). The treatments can be given at a certain time interval and results can be recorded until the animals are free from the disease. How long the treatment takes can be recorded and compared with other types of treatments. Once plenty of experiment done through other animals, human trails can start.

There are lots of risks that can happen during a human trail. There is a chance that even though the trails done by other species worked out well doesn’t necessarily mean that it would work for humans. For example, thalidomide is a drug that was used to help pregnant women relieve nausea. Through testing on rats, it showed no negative effects on the pregnant rat. FDA approved it to use on humans, but sadly, the babies born had physical defects such as missing limbs. FDA took back the approval and stated no pregnant women should take thalidomide. Since there are evidence that not all testing on animals would mean the same result for humans, but there has been a few experiments of phage therapy done on humans mentioned in The Forgotten Cure, when the dysentery patients were treated with phages and showed improvement in health.

Rationale

Create an abstract to inform the purpose, methods, and discussions from the research. Also had to form a background information/introduction and started a presentation slides to get work done faster.

Procedure

1. Fixed background information and cite sources
2. fixed abstract and upload as a qtm
3. finished collecting all data and forms final figures and tables to help write conclusion
4. shared powerpoint slides with other group mates and started to work on it to save some time in the future

Conclusion/Next Steps

Still had trouble making the tree but we had to put the best tree we can get out of. Clearly shows that the AM clusters as tight knit compared to other clusters. Abstract and background information is so far correct and the best we can make at the moment. Presentation slides are almost done, just need to work on the conclusion slides and fix any minor detailing such as color scheme or design. Next steps is to finish writing the conclusion, meet up with our TA to update with our results and fix any mistakes on the abstract.

Rationale

Find resources through primary literature, form and revise guiding question, and start making results and analyze them.

Procedure

1. found 5 sources and revised question
2. NCBI blasted NapoleonB’s gene 93 sequence
3. Found 6 bacteria and 6 non AM (3 AU and 3 EG) clusters that HHPred called as NMT
4. multiple sequence alignment with all 18 sequences, 6 AM, 6 non AM, 6 bacteria, 3 AU, and 3 EG.
5. Saved pdf filed for all 6 multiple sequence alignment results

Conclusion/Next Steps

We found that when we blasted NapoleonB, we found that it had some hits from bacteria. So that raised a hypothesis that NMT from NapoleonB might have come from or evolved from bacteria. From the MSA results from all 18 sequences, we found that bacteria and AM/AU cluster had more similarity and the EG cluster was pretty different compared to everything else. At one point, we found that there might have been a mistake in the pham results that some were called as a nicotinamide riboside transporter/transferase. The next day, our phage were put into a different pham from that other clusters. We doubled checked through raptorx and TMHMM that our phage’s sequence is indeed a NMT. In the next time, my group and I will make a phylogenetic tree and a figure to show which part of the sequences were similar from which cluster/bacteria

Rationale

Practice presentations for URSA and make sure as a class, we know every detail about NapoleonB. Also to start researching and working on project outlines for the independent research project

Procedure

1. practiced presentations in front of class and helped critiqued classmates
2. created a project outline for independent research
3. performed multiple sequence alignment with 20 sequences (6 from AM cluster and 14 from non AM cluster)
4. recorded results in the same doc.

Conclusions/Next Steps

URSA presentation went well and was able to be prepared for questions. Results from multiple sequence alignment are shown in pic below. Next lab day, my group and I will use RaptorX to see the protein model of the nicotinamide mononucleotide transporter

Rationale

Create a independent research question that is related to the findings of Napoleon, be able to test it and analyze results.

Procedure

1. Created 4 questions
2. Choose one question that was approved by coach
3. Used NPS for multiple sequence alignment of different nicotinamide mononucleotide transporters
4. Use HHPred to analyze hits of the transporters that were not in AM cluster

Conclusion/Next Steps

Due to limited time, I was only able to analyze the sequence alignment from 6 genomes. Founded out the families and superfamily that the transporter was in (PnuC, SWEET, and TOG.) In the future, I would have to find more phages in the AM cluster and phages outside of the cluster that contain this transporter, take the genome sequence, analyze the alignment, and use HHpred to analyze the hits of those genomes.

Rationale

Create a final poster to present at URSA. Correct any format issues and add any missing information into the poster.

Procedure

1. Got assigned into groups based on sections of the poster
2. Fixed any mistakes in regards to which section
3. Updated poster with final edits

Conclusion/Next Steps

The discussion was fixed with other group member. We had to change the format and had small issues along the way in terms of how to insert it into the poster. We had another classmate to help take the discussion and transfer it to another program. Formating is fixed. In the future, we will continue to work and try to find any other small mistakes and perfect it as much as possible.

1. In 1940s-50s Russia, phage therapy was more popular to use rather than antibiotics since it was cheaper to use. Due to state health system in Russia, this impacted on phage therapy. Most of the issues were due to lack of funding. Dr. Pokrovskaya’s reports hinted that phage therapy yielded such conflicting results was because it was hard to store and complex to use. Advanced technology wasn’t developed and needed funding for it, the lack of funding prevented that to happen.
2. Hirszfeld Institute had gone through tragic events with the Russians. After Hirszfeld’s daughter passed away, he settled in Wroclaw and petitioned the Polish Academy of Sciences to set up an institute. However, the request was possibly slowed by a series of events taking place in the Soviet Union at the time. Hirszfeld fell victim to Lysenkoisa and he designated Milgrom as his successor of his institute. Throughout the years, his institute was involved in phage typing and other institutes came to be. Two of them are the Eliava institute and Phage therapy center. Eliava institute has goals that are more toward research of bacteriophages and their potential uses in therapy while Phage therapy center focuses more on the treatment of patients. Both institute have common goals, but do have their differences.
3. Merril injected infected blood with bacteriophage, have it harvested in the mice for 7 hours, and repeated for a few times until a large amount of bacteriophage strains were present. The phages were named Argo1 and Argo2. Merril and his team found out that those strains could stay in the mices’ stomach at large amounts and rate than the control. According to PNAS, the control would go down by nearly half the amount as the staring titer. Argo1 and Argo2 only went down by a small amount. Through this, Merril and his team saw that the mice that were treated with phage therapy improved their conditions than mice without phage therapy.
4. GangaGen was created by Ramachandran who decided to set it up in India due to advantage of cost and plenty of people to recruit. There were plenty of high tech companies around them to help them. He had the same mindset of to “follow D’Herelle’s principal that in a hospital there is always somebody natural recovering and therefore there is a chance they’ve been exposed to the phage in the environment. In fact, that proved to be true.” (pg 85) Nowadays, GangaGen is focused on developing novel therapeutic proteins targeting infectious diseases in areas of high unmet need such as MRSA and other drug resistant bacteria. Using a proprietary platform, GangaGen is developing highly-specific therapeutic proteins called ectolysins to target clinically meaningful types of bacteria. Ectolysins act very rapidly to lyse bacteria and therefore have low potential for developing resistance. Each ectolysin is specific to the type of bacteria for which it is developed and leaves other beneficial bacteria unaffected. This means that ectolysins can work on drug resistant bacteria or when the bacteria are not active, such as in hard-to-treat biofilms. It would be interesting to see experiments to how ectolysins can affect different strains of bacteriophages or strains that are not yet identified or annotated as well as the rate of the ectolysins activity.

Rationale

Discuss as a class which poster can best tell the experiment for Scholars Week

Procedure

1. made poster within small groups
2. combined poster ideas with large group
3. discussed the final 4 poster ideas with the class

Conclusion

We decided to take Group 4’s poster layout and suggested changes or addition from other groups to that poster.