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

The implementation of zoning and other building restrictions appealed to me much more than forcing the relocation of people, however, this may be necessary for the future if the risk to life living in those areas proves to be too great. The option of relocation also has significant social and economic effects on people, but again this will have to be taken into consideration of the social and economic effects of certain areas where people live becoming uninhabitable for a safe and reliable living if climate change continues on its course.

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

The idea of a social awareness campaign that focuses on basically peer pressuring people into adopting climate change stopping practices based on revealing certain climate change causing practices of people. However, this poses privacy concerns if it were to be used to help curtail climate change, even still I believe it would prove effective and eventually we may need to resort to measures like this.

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 really enjoyed this public deliberation and thought it was an effective way to present new ideas and foster conversation over issues that impact us all. I could see myself facilitating one if it was over a topic I was passionate about.

Rationale:

To practice presenting the presentation.

Procedures:

1. Presented presentation in groups.
2. Listened to other presentations.

Conclusions/Next-Steps:

We got good presentation practice and received comments for last-minute fixes. We will address these concerns and present on Friday.

Rationale:

To finalize the presentation.

Procedures:

1. Continued working on the presentation and took into consideration comments for finalization.

Conclusions/Next-Steps:

We fixed the presentation/project according to the recommended fixes and we will continue working on the presentation in order to present the findings of our project. We will practice presenting on Wednesday.

Rationale:

To fix the abstract and to continue working on the presentation.

Procedures:

1. Looked at the abstract comments and revised the current abstract.
2. Continued working on the presentation.

Conclusions/Next-Steps:

We fixed the abstract according to the recommended fixes and we will continue working on the presentation in order to present the findings of our project.

1. 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 a scientist, I would like to see an experiment looking at the effect of endotoxins released from bacteria as a result of phage therapy usage and as a result the potential for septic shock to occur in a patient. As The Forgotten Cure states that phage therapy can act rapidly, something that was described by d’Herelle when he saw the rapid curing of dysentery patients during the first world war. Ramachandran additionally stated that this endotoxin release is a perceived limitation of phage therapy, as the threat of septic shock is not one to be trifled with.  In addition to endotoxins, allergic reactions to the phages and other aspects of the lysate solution would also have to be looked at in order to ensure its safety. But overall the threat of endotoxins and septic from the rapidly killed bacteria is what concerns me most as a scientist, thus I believe there should be several trials in order to ascertain the effect of relatively mass endotoxin release, of various types, on the body. This could potentially be done by injecting endotoxins into animals at an expected level of what would be released, or by infecting animals with bacterial diseases and then curing them with phage therapy and observing the effect of endotoxins that way. However, there is a way to mitigate, maybe even eliminate, the threat of septic shock as a result of phage therapy use. As Ramachandran determined that by blocking the endolysin gene in bacteria, toxins could not be released from the bacteria since it would not have the ability to lyse. The blocking of the endolysin gene also has the added bonus of limiting horizontal gene transfer between phages and bacteria as well as certain commercial benefits. Overall there is always a risk when foreign contaminants enter the body, either from the phage therapy itself or the byproduct of the phage therapy fulfilling its purpose. However, with appropriate testing and the blocking of the endolysin gene the threat of septic shock should be mitigated, making phage therapy much safer humans, thus encouraging its approval by governing bodies like the FDA.

Rationale:

To create an abstract and to work on the background information of the presentation.

Procedure:

1. I worked on finishing the results figures.
2. I also worked on creating the background information and introduction slides of the powerpoint.
3. I assisted in creating the abstract for the project.

Conclusions/Next Steps:

We can conclude that the NMT is apart of the NADH metabolic pathway. We also finished with the creation of the abstract. The next step will be to finish creating our presentation. We will also attempt to improve our phylogenetic tree, as it currently shows little more than the relation between the phages in the AM cluster.

Rationale:

Our goal was to work on figures for the results and to acquire further background information.

Procedures:

1. I looked at the MSA data and created a figure to show the alignment of the amino acids from other organisms and phages that matched with NapoleonB.
2. I looked at background information for NMT and NMN in order to begin working on the background part of our project.

Data:

This is the graphic that was created to show the alignment between amino acids.

Conclusions/Next Steps:

From the graphic I created, it can be seen that there are certain amino acids and amino acid sequences that are conserved throughout most of the genomes analyzed. The background information also served to provide a greater understanding of what NMT is actually for. The next step will be to continue working on the aspects required for the presentation and the abstract.

Rationale:

To continue working on our IRP, by further looking at background research, protein structure, and multiple sequence alignments.

Procedure:

1. The structure of gene 93 was looked at on TMHMM, in roder to provide evidence that it is a transmembrane transporter protein.
2. MSA’s were run in order to show phylogenetic relationships.
3. Further research was done into the pham changes.

Results/Data:

According to TMHMM gene 93 is indeed a transmembrane protein. The pham we were looking at on Monday was split, eliminating a lot of the confusion that was present on Monday. The new MSAs conducted show much more similarity between the different phages/bacteria.

Conclusions/Next Steps:

We can conclude that gene 93 is an NMT. We can also conclude that there was an apparent error in the pham system, as it is now fixed and makes a lot more sense. We can also start creating a phylogenetic tree based on our MSA data. The next step will be to continue investigating NMTs and NMN, along with conducting more MSA’s on more phages and bacteria in order to increase our understanding of the phylogenetic relationships and origins of the NMT gene in NapoleonB.

Rationale:

To continue working on our IRP by looking into the NMN pathway and NMT related proteins in other organisms and phages, we will also run MSA’s in order to determine phylogenetic relationships.

Procedure:

1. I conducted further background research into NMT and NMN.
2. We looked at other phages in the gene 93 pham.
3. We investigated the differences in NMT, NRT, and NRTransferase, using both literature and HHPred.
4. We ran multiple sequence alignments.

Data/Results:

We found that there may be apparent errors in either the pham organization or gene calling of other phages in regards to NMT, NRT, NRTransferase. We also found some relations between the various phages and bacteria compared via MSA but some error may have been involved, but it does appear that there are relations.

Conclusions/Next Steps:

We can conclude that there are relations between gene 93 in NapoleonB and similar genes in other organisms/phages, which will ultimately allow us to find phylogenetic relationships and help us to determine the origin of gene 93. We can also conclude that something weird/incorrect is happening with the pham organization and the gene calling of other phages. Our next step will be to continue investigating phylogenetic relationships and running MSAs, while also looking at protein structures in order to provide evidence/support.

Rationale:

To further look into the presence and possible origin source of the NMT gene in NapoleonB by creating a phylogenetic tree.

Procedures:

1. We looked at research articles regarding NMT related genes in bacteriophages and bacteria.
2. We looked at other phages that had the NMT genes.
3. We ran multiple sequence alignments and protein analysis on the found proteins to determine relations.

Conclusions/Next Steps:

We can conclude that there are other phages that do contain NMT related genes outside of the AM cluster. The next step will be to continue trying to assemble relations between NMT genes and where they came from.