Shepard Saabye

5 May 2019

1. Blog on the reflection concerning the Climate Choices Deliberation.
2. Did any of the Options appeal to you more than the others?
3. Did you hear or think of any new way of addressing the issues associated with the warming of the climate?
4. What are your thoughts on the use of Public Deliberation in the classroom or the community? Is this something you would like to facilitate?

1. To me, none of the options were really that great. I guess I was more or less looking for a magic answer, and outside of taking personal responsibility for your own products and wastes, I hadn’t thought much further. There are some major issues with all three options, but personally I believe privacy and the defense of the rights of the people is the most important issue in modern politics.

2. Climate change policy must be constructed in a way to most minimally interfere with the rights of the citizens. With that said, there are parts of option three that make sense to me, like economic incentives for innovation and for finding a cost-effective solution to the problem. As soon as a true solution is viable, it will be quickly implemented in the US and every other western country.

3. There are several problems with addressing climate change. First, it’s not localized to just one area. The symptoms aren’t just the ice caps melting, but also a change in the amount of precipitation across the globe, weather patterns, etc. All of these issues can be explained as man made or otherwise, but again there are more sources of the problem than even a million reasons could explain. While the US and Western countries are motivated to address the obvious problem, other parts of the world may not follow suit. Therefore, an all-encompassing strict legal reform would not be effective. While this idea isn’t exactly new to some people, its something that is often not mentioned, and gradually forgotten. Therefore, a better solution must be found for the world to adjust its efforts, and that’s where the incentives of economics will play a major part in correcting the issue.

4. Public deliberation is an interesting method for the discussion of these problems. It’s a very important topic, and may help further spread awareness, but the actual usefulness of the public deliberation format doesn’t seem to be particularly high to me. I enjoyed the deliberation, but until the deliberation can be conducted with people who have both a say in, and an understanding of, the problems affecting the community, state, country, and globe, these deliberations will not be the most effective, personal, or efficient way in addressing the problem.

The climate change discussion that occurred in class today was informative, influential, and a new experience. The three opinions that were put forth struck the right balance of giving new information and allowing individuals to be able to elaborate and share information that others in the group may not have heard. I feel that I was able to both listen and contribute to information and discussions of the group while learning more perspectives about climate change and facts that I may not have encountered otherwise. Due to the style of discussion, it was easy to learn without feeling any pressure to develop a counterpoint or feeling attacked about a point that I contributed. I feel the discussion was influential, as my perspective on how climate change should be addressed was changed by the discussion today. For example, Gabe happened to suggest a more advanced type of roof shingle that could harness the power of the sun and provide an alternate source of energy for the home. This was particularly interesting to me, as I had never considered such devices being widely viable or common. Another instance of this occurring was the second perspective that was listed on the placemat. Although it was more reactive than I believe our approach on climate change should be, I thought that it was interesting, and I realized that if I were to make a plan for combating climate change, I would need to consider fixes that would also protect communities in this moment in time until the other changes could take effect. Finally, I appreciated the style of discussion that was presented. Often, class debates become centered on two people while the rest of the class becomes the audience. While this can be entertaining, the development of new ideas is generally limited to those two individuals. Therefore, it was nice to experience a discussion where everyone’s ideas were heard at some point, as I feel that my knowledge about climate change was improved and expanded by today’s conversation. To summarize, today’s climate change discussion was interesting and productive because of how it was informational, influential, and open for everyone to participate.

Purpose: Finish our Abstract and conclude the research.

Procedure:

• Reviewed Lathan’s Comments on Abstract draft
• Corrected issues sequentially
• Reviewed new abstract
• Worked on our powerpoint project
• Figured out sources from various bioinformatic tools
• Reviewed other slides until the end of class

Results:
Finished the abstract, and have found all of our sources.

Future Plans: Finish the power point and begin practicing our presentation for next Friday.

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.

Abstract Rough Draft and Continued Research 4/17/19

Rationale

The rationale behind today in lab was to create a project outline to help guide the rest of our research and to help us begin to prepare for our final presentations. In addition, when we were done with our presentation outline, we continued working on sequencing and protein folding in order to collect the necessary data.

Tools/Procedure

1. Presentation outline was submitted
2. MEME Motif was used to find repeating motifs in the TMPs of selected proteins from each usable cluster

Results

The results above were generated using the MEME software to find motifs. The logo above represents a motif that was found in all 43 selected TMPs suggesting an area of conservation. In addition, when searching for other common motifs 2 appeared with much less frequency but much more similarity, which will require further research. This motif shows that there is less similarity in the actual amino acid sequences, but the color coding suggests that structure is more likely to be conserved as many of the amino acids at a location are color-coded the same, suggesting that the amino acids will behave very similarly.

Conclusion

This motif demonstrates that there is at least one conserved motif for all of the randomly selected phage tested, answering our guiding question that, at least to a small degree, there are shared similarities between all TMPs.

Future Plans

In the future, we will continue to look for similarities and difference in the amino acid while continuing our folding of proteins to try to figure out if there are key conserved regions in TMPs. This motif needs to be further investigated, and I will see if I can find more motifs in all the proteins. I will also try to fold the amino acids found in just the motif to see if they are structurally similar to the sequences identified as the same motif.

04/17/19

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. two 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. one group member began to use jmol and raptor x to start structure analysis
4. the abstract for the presentation was drafted
5. The group worked until the end of lab.

Results

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

abstract draft:

ATG, TTG and GTG are the three start codons that initiate gene translation in all bacteria. When ribosomes detects these start codons, they begin to synthesize proteins according to the sequence of the codons. Each start codons produce different amino acids, which interact differently with other amino acids to form different structure i.e. leads to a different function. Genes in arthrobacter phage genomes are used to explore whether this change is significant and affects the preference for the start codons in specific genes based on the change or lack thereof. The start codons for tape measure protein, major tail proteins, and minor tail proteins in the annotated genome of known sequenced arthrobacter phage were collected using DNA Master and the PhagesDB database to determine the start codons of the genes that produce these proteins. 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. i.e. ribosomal binding and initiation of translation, in the phage genome. Raptor X and Jmol are used to determine the most probable structure of the product protein based on the amino acid sequence. Protein models are produced for each type of protein using different start codons and the structures are then compared.

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.

04/17/19

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. the group members found the start codons for their assigned proteins using phages db for the fasta file and dna master for the sequence.
3. group made the project outline
4. The grouped worked until the end of lab.

Results

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

project outline:

Title:

Analysis of start codons and change in structure due to start codons in proteins from arthrobacter phages

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?

Abstract:

ATG, TTG and GTG are the three start codons that initiate gene translation. But there is no known correlation between the start codons and the genes. Is there a factor that makes one start site preferable to another?. To answer this question, the start codons for tape measure protein, major tail protein and minor tail proteins were collected to find possible correlations. To analyze the structure of the product protein, predicted models were produced for the same protein using different start codons to see if there was a significant change in structure due to the change in start codons.

List of tools used

Phages DB, DNA Master, raptor x and jmol

Introduction (Background Information)

The standard genetic code table has one start codon, ATG. Over the years, however, many studies have demonstrated that alternative start codons, such as GTG and TTG, could be utilized for translation initiation. In accord of ranking of the start codons, genes starting with ATG are, on average, expressed at significantly higher levels than genes that start with GTG, and the very few genes that contain the start TTG. This is generally the case for genes in other bacteria as well, with ATG being the predominant start codon.

The AUG starts are replaced by GUG and especially UUG significantly less frequently than expected under the neutral expectation derived from the frequencies of the respective nucleotide triplet substitutions in non-coding regions and in 4-fold degenerate sites. Thus, AUG is the optimal start start codon that is actively maintained sites

Types of Data Collected

All the start codons of sequenced and annotated phages

Predicted protein structure of tape measure proteins with different start codons

Results (to date)

All start codons have been determined for tape measure proteins and major tail proteins.

Structures are still to be modelled and collected.

Conclusions (if any have been drawn)

As data is still being collected, we do not have any conclusions as of now

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.

Presentation Outline and Continued Research 4/15/19

Rationale

The rationale behind today in lab was to create a project outline to help guide the rest of our research and to help us begin to prepare for our final presentations. In addition, when we were done with our presentation outline, we continued working on sequencing and protein folding in order to collect the necessary data.

Tools/Procedure

1. Presentation outline was submitted
2. MEME Motif was used to find repeating motifs in the TMPs of selected proteins from each usable cluster

Results

The results above were generated using the MEME software to find motifs. The logo above represents a motif that was found in all selected TMPs except one, suggesting an area of conservation. When all of the TMPs have been folded, we will see if we can use the protein folding information to support this motif being conserved structurally as well.

Conclusion

While there is not enough data to make extensive conclusions yet, our data so far suggests that while there are significant differences among TMPs outside of their clusters, there do appear to be at least some similarities, which answers our guiding question.

Future Plans

In the future, we will continue to look for similarities and difference in the amino acid while continuing our folding of proteins to try to figure out if there are key conserved regions in TMPs. I will compare all 43 selected TMPs to ensure that the above-identified motif is as universal as it appears.