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

Options 3 was the most appealing to me because rather than adopting a very aggressive cutdown or building our defenses against disasters,  Option 3 looks for an actual solution to the problem and encourages innovation that would solve the problem rather than just prolong the the lifespan of the planet.

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

The one thing that stuck with me was that any solution that we can come up with, we have to consider the opinions of the public and consider if it will be acceptable to them because the problem does not only need and idealistic solution, it needs a practical one that the public can accept and support rather than just a small proportion of the population that is willing to sacrifice some freedom and comfort. The bigger the proportion of the human population that is involved, the better the chances for success.

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

The use of public deliberation would be great in the classroom and the community. it would allow for a safe space for healthy discussion in the classroom and prepare an individual for participating in the community. This will train students in the art of peaceful communication and discussion, allowing for the exchange of ideas in an environment where one can free share their ideas, which can evolve into viable solutions for many of the problems in the world. this is definitely be something i would like to facilitate.

04/25/19

Rationale:

to learn to conduct individual research, from the process of making a research question, to designing the methods and concluding from the acquired results.

Procedure:

1. The individual research was worked on.
2. group members used jmol and raptor x to start structure analysis
3. the final abstract for the presentation was submitted
4. The group worked until the end of lab.

Results

based on the analysis of protein structures, there is a significant difference in the structure when the start codon is changed for the tape measure protein of phage cheesy, elsa and napoleon b.

example, AUG, GUG and UUG in order for phage Elsa

final abstract:

AUG, UUG and GUG are the three start codons that initiate gene translation in all bacteria. Different start codons produce different amino acids, which interact differently with other amino acids to form different structure. Genes in arthrobacter phage genomes were used to explore whether changing the start codon of the gene causes a significant difference in the structure of the product protein which could explain why the original start codon was preferred..The start codons for tape measure proteins, major tail proteins, and minor tail proteins in the annotated genome of known, sequenced arthrobacter phage were collected using the Phages DB Database and DNA Master. The gene length, genome length, cluster ,%GC, and direction of the genes were also recorded to determine possible factors that make one start codon preferable to another in the phage genome. Raptor X and Jmol were used to determine the most probable structure of the product protein based on the amino acid sequence and compare the structures. The protein structures were drastically different even though the gene length, pham, and preferred start codon were the same. Overall, many factors that were noted in the quantitative data for the AM Tape Measure were the same or very similar, while the qualitative data produced varying protein structures. Knowledge of how certain start codon may result in a more preferable protein structure may help future research for designing  phages to be more effective by simply changing the start codon.

Conclusion:

currently, from our qualitative data, all we can conclude is that the protein structure changes. quantitative data is still currently being analyzed.

Future steps

Look into primary literature and find information to understand the difference in structures.

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 approval process for any drug or treatment is extremely tedious and complex. The FDA approval process has a structure so complicated that one needs experts to be able to complete this process. Besides that, the FDA also has a high standard for evidence and definitive results, which is extremely difficult to meet due to the limitations on time and resources. It requires years and millions of dollars to get through the approval process of the FDA to even begin human trials and is even worse for approval for the market. In terms of phage therapy, increasing the awareness of this treatment among scientist and doctors would help improve the process. This will allow the FDA to have pool of experts to consult with on the topic, which decrease the amount of miscommunication that may exist between the companies and the FDA. Increase of funding from the government would also help these companies as it will give them more resources, which will allow them to sustain themselves while they wait during the approval process.

03/27/19

Rationale:

to learn to conduct individual research, from the process of making a research question, to designing the methods and concluding from the acquired results.

Procedure:

1. The individual research has now begun
2. the group members have started finding the start codons for their assigned proteins using phages db for the fasta file and dna master for the sequence
3. there are approximately 230 arthrobacter phages that can be used.
4. The grouped worked until the end of lab.

Results

so far. no real results. a lot of  the data collection has been performed.

Conclusion

this research will require a great deal of data collection as there are a little more than 200 sequenced arthrobacter phages. enough data can be collected for the research in the given time.

Future steps

do more research, look into primary literature and find more tools that can be used.

03/27/19

Rationale:

to learn to conduct individual research, from the process of making a research question, to designing the methods and concluding from the acquired results.

Procedure:

1. Coaches were consulted for a final verification and the research began
2. Group researched and compiled more information on the topic of Start site preferences, exploring two research papers for reference
3. question was edited and finalized
4. tools to be used were listed in the QTM and a schedule was made
5. the group began acquiring data on start site preferences

Results

Title: Analysis of start site preferences among Arthrobacter Phage clusters and the effects of different start sites on resultant protein structures

Background: there are three possible start codons that initiate translation. Each codon produces three different proteins. The possible protein products are methionine, valine and leucine. Each has a different structure. We attempt to see if the structure of the product protein of a gene sequence changes if a different start codon is used, as intermolecular forces between the proteins forms the structure. If the structure is different, further research can be done to see why one structure is preferred over another. If the structure is the same, why would that start codon be preferable than the other.

Guiding Question:

Can a different start site affect the translation of the gene sequence? Will it change the structure of the product protein? If the structure does not change, is there a possible reason to prefer a certain start codon over another?

Bioinformatic tools: SwissModel , NCBI BLAST, PhagesDB,

Research Articles:

http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC509299&blobtype=pdf

https://www.ncbi.nlm.nih.gov/pubmed/9299334

Conclusion

this research will require a great deal of data collection as there are a little more than 200 sequenced arthrobacter phages. enough data can be collected for the research in the given time.

Future steps

do more research, look into primary literature and find more tools that can be used.

03/27/19

Rationale:

to learn to conduct individual research, from the process of making a research question, to designing the methods and concluding from the acquired results.

Procedure:

1. Coaches were consulted for the validity of each questions and for approval of question
2. Group researched and compiled more information on the topic of Start site preferences,
3. After some misconceptions were cleared, a question based on start site preferences was refined and approved by the coach
4. the group decided to look into the start site preferences of genes in different genomes of arthrobacter phages of CLuster AM and other phage clusters. after hard data is compiled on the start site preferences, the group will derive conclusions based on the acquired data.
5. the group will then use modeling software to see how different start sites will affect the structure of the protein produced by the gene. these will be the theoretical results.
6. possible tools that can be used were compiled.

Results

the research question for individual research

1. What are similarities and differences in the start codons for the nucleotide sequences coding for tape measure, major and minor tail proteins? is there a prefered start codon based on the cluster? How is the structure of the produced protein affected if a different start codon is used?

Tools: NCBI. PhagesDB, HHpred, SWISS Model Workspace, Openstructure and SWISS Pdb viewer.

Conclusion

this research will require a great deal of data collection as there are a little more than 200 sequenced arthrobacter phages. it may answer some questions about the phage genomes and possibly provide another attribute that can be used for gene annotation.

Future steps

do more research, look into primary literature and find more tools that can be used.

03/25/19

Rationale:

to learn to conduct individual research, from the process of making a research question, to designing the methods and concluding from the acquired results.

Procedure:

1. The possible topics were researched
2.  The tools available for use were researched.
3. based on the known information, possible topics and available tools, 4 possible research questions were formed
4. Coaches were consulted for advice on questions.

Results

the following questions are the possible research questions to be looked at

1. Is there a similarity in start site preferences for certain protein between the Napoleon B and other phages in cluster AM? If so, is there a similarity between other clusters? What is the importance of identifying these start site preferences? Can it be an identifier or supporting evidence for the existence of the specific gene? Can a different start site affect the transcription of the protein?
2. Is there a relation between the transposons in the genome of Napoleon B and other phages in the AM clusters?
3. Are there any similarities between the stoperators for Napoleon B and known stoperators for mycobacteriophage L5?
4. Can slight differences in nucleotide sequences lead to different protein structures within the AM cluster and other, similar clusters?

Conclusion

the first question is likely to be the one which will be researched. currently, more consultation will be required to refine the question and come up with a possible method to answer the question.

Future steps

do more research, look into primary literature and find more tools that can be used.

03/18/19

Rationale:

To make a final draft of the poster board, which will later be combined with other poster boards in the group for a final poster for scholars day

Procedure:

1. The changes to be made to the first draft of the posters were discussed
2. responsibilities were assigned to groups for making certain edits
3. edits were to be made according to the prescription of the TA
4. the group made graphics for the poster and made edits to methods and materials.

Results:

current version of the edited poster is above.

Conclusion

the progress so far is great but some more content needs to be added to this poster. the poster will be easy to present when completed according to plan.

Future steps

More graphics will be added to the poster. more data will also be presented about the Napoleon B and its relation to other phages and clusters.

1. In the 1940s-50s, Russia had scant resources and knowledge when it came antibiotics. Even though there was collaboration with the western allies, the lack of proper funding held back the production and use of antibiotics in the USSR. The USSR attempted to implement a state healthcare system that provided treatment without cost with inadequate funding, which is why it failed to be effective. So, alternative medicine was promoted by the state. this is the biggest influence for the use of phage therapy at the time as it was considered as alternative medicine. It gained widespread use due to the influence of the state health system and became the primary way to treat infectious diseases at the time.
2. The two institutes and their founders suffered similar setbacks in terms of persecution and lack of cooperation of with leadership. But they both had different outcomes. The Eliva institute did not reap the same success as the phage therapy center. This is mainly due to how the death of Stalin favored the fate of the Phage Therapy Center in Wroclaw.  Both institutes suffered due to persecution from leadership but when Stalin died, the individual who was the main driving force for this persecution, the institute was revived with passing of the petition for the Institute of Immunology and Experimental Therapy, which helped it gain global connections and flourish in the scientific community whereas the Eliva Institute struggled.
3. The biggest challenge faced by phage therapy, which is what made many doctors skeptical of its effect, was to find phages that would not be immediately removed by the liver and the spleen. Merril accomplished this by using a phage called lambda. 7 hours after infecting the mice with phages , the surviving phages were extracted and reinjected into the mice. this process was called serial passage. After repeating the process was repeated eight times, the team acquired phages that lasted up to 18 hours in the bloodstream. the mice were also infected with multiple phages, which increased its effectiveness. the phages, named Argo 1 and Argo 2 were then used in another experiment to prove their effectiveness. four groups of mice were infected with a lethal dose of E.coli. three of the groups were treated, leaving one group as a control group. the untreated died but the treated survived. the phages also remained in circulatory system of the mice after recuperation, proving the effectiveness of the therapy.
4. Antibiotics have been the spearhead for the treatment of infectious diseases for the past few decade. It continues to be our primary tool for fighting against infections but its effectiveness continues to wane. Resistance to antibiotics increases among bacteria. Companies like Phage Biotics, GangaGen and Exponential Biotherapies offer another possible tool for fighting against bacterial infections. their research into phage therapy holds the potential to defeat the rising tide of resistance in bacteria. More experimentation is required in the effectiveness of antibiotics and phage therapy together. together, they may poses a greater threat to bacteria and may be a possible way improve the effectiveness of treatment for infectious diseases. But a better understanding of the dynamics of the two together is required to properly apply them for treatment.

02/27/19

rationale: to make a scientific poster board for presentation at scholars day

procedure:

1. google slide was used to start the first draft of the poster board for napoleon b.
2. dimensions were set as 48 in by 36 in, with the font size as 28
3. all data collected from wet lab and in silico lab was used
4. the introduction, methods and materials, references and acknowledgements were completed
5. multiple visuals from both labs were used for visual representation of the lab.

Results

the first draft of the poster board in development

Conclusion

the more skills you have with the computer, the better your performance. this process was quite slow and the visuals made are produced at our max potential, which is not much, but the visuals are easy to present and understand for the audience. the time at our disposal was also in inadequate for creating a proper, completed first draft.

Future steps

complete the first draft and create a better final draft through augmentation.