Title: Presentation Practice

Date: 1 April 2019

Rationale: The purpose of this lab is to practice the presentation for URSA Scholars Week.

Procedure: Each group took turns practicing a presentation of the class poster in preparation for Scholars Week judging.

Results/Observations: Each group received feedback from the class and found areas to improve upon.

Conclusions/Next Steps: Each group will continue to work on their independent project.

4.3.19 Next Steps of Independent Research Project

Rationale: After the brief intermission to practice presentations, the class returned to our independent research projects. Therefore, my group spent time furthering our understanding of repeats and making an outline to organize our group project.

Tools/Procedure: Gepard, DNA Master, Clustal Omega, Phamerator, NCBI BLAST

I focused my attention on browsing through literature, Gepard, and DNA Master to find repeats that could potentially be of significance. I took sequences from different genes, converted them to FASTA files, and used Gepard to visualize a dot plot that would reveal any potential repeated sequences that could have been of interest.

Results: One long repeat of 51 base pairs was found to be intriguing and effort and time was spent to find the significance. We have concluded that it is conserved across members of the AM cluster and it is close to tail proteins, but more investigating needs to be done to fully determine the purpose of this long repeat.

Conclusions: The problem of finding repeats has proved to be mostly solvable, so our topic for the project appears to be intact. More investigation will be needed to figure out whether this conjecture is true or false.

Next Steps: Members of the group will be investigating the repeat independently to gain knowledge and to investigate potential reasoning for why it is there before the next lab period.

Purpose: Investigate what affects the presence of multiple plaque morphologies in NapoleonB and other AM Cluster Phages

Procedure:

• Downloaded Fasta files for all AM Phages
• searched for phylogenetic tree generators
• Settled on program called splitstree
• Plugged in Fasta Files
• Generated Phylogenetic tree

• Determined the tree was not populated with enough data to find any correlation between phage evolution and the presence of multiple morphologies
• Revised question to begin research into Nicotinamide Mononucleotide transporters, specifically the one coded for in NapoleonB

Results: We have a revised question and a new simple procedure to find our nicotinamide mononucleotide transporter (NMT)  in other phages, to determine its origin.

Future Plans: Investigate the NMT in NapoleonB and associate it with other phages with similar proteins or nucleotide sequences.

Purpose: Determine a question to begin developing our research project

Procedure:

• With understanding of prior module, begun brainstorming ideas for questions
• Changed goal from researching repeats in NapoleonB to finding the importance of G/C content
• Wrote 4 different possibilities to research
• Refined our favorite question with help from Lathan
• Published as QTM

Results: We now have a research question to work on for our individual project.

Next Steps: We will begin research that will help us answer our question.

Individual Projects, Topic Generation 3/27/19

Rationale

The rationale behind these procedures is to ensure that Rachel and I can refine our research topic into something that is testable in the correct amount of time and to have us find tools that we can use to assist in our research in addition to mapping out a basic method/plan.

Tools/Procedure

1. Previously created groups refined a research question based on previously created possibilities
2. Groups consulted with their assigned coaches in order to further develop their research questions and understand what elements must be present in their research questions
3. Changes were made as necessary
4. Tools for research were researched and recorded
5. A basic method outline was created
6. Research project topic was approved

Results

The image above shows the evolution of our research question with our listed bioinformatics tools and basic methods outline. We are planning to compare Tape Measure proteins between the Podoviridae, Siphoviridae, and Myoviridae tail families.

Conclusion

There is not much that can be said as a conclusion as this was a brainstorming day. I can say that Rachel and I will likely be utilizing many bioinformatics tools that will allow us to compare protein structures and genes looking for important similarities or areas of conserved genetic code.

Future Plans

In the future, we will begin researching our question and see what conclusions we can draw from the data.

03/20/19

Rationale:

To learn how to conduct research , from forming a question to forming and performing a your own experiment.

Procedure:

1. The edits to be made for the final poster were discussed and are due on Friday
2. Assigned groups were then allowed to explore the various tools and topics to explore for questions for individual research.
3. All the tools available were explored.
4. all proposed topics to discover were also discussed.
5. Two topics that seemed interesting were stoperators and start site preferences.

Results:

these were the tools that were proposed. we were encouraged to find and use more.

Conclusion:

Individual research is going to be very difficult but also very interesting. it will require a great deal of productivity to finish it on time.

Future steps:

come up with a research question and begin planning the experiment.

Final Poster and Individual Projects 3/20/19

Rationale

The rationale behind these procedures is to ensure that poster creations for Scholar’s day follow the correct format and that basic poster requirements are understood. The procedures were also done to finish the poster for Scholar’s Day. In addition, the rubric and groups for the individual projects were introduced so that work can begin on the projects.

Tools/Procedure

1. Final edits were made to the poster in order to have it ready by Friday
   • 2 edits were made to the discussion section of the poster to reflect changes in the genome annotations
2. Groups for individual projects were introduced and rubric was discussed
3. Groups brainstormed about what individual questions to pursue and consulted with the coaches

Results

The image above shows the 2 small changes made to the discussion section to reflect new annotations. There are no other results to report as group brainstorming is currently a work in progress.

Conclusion

There is not much that can be said as a conclusion as this was a poster making and brainstorming day. I can say that Rachel and I may pursue research into comparing NapoleonB to the Arthobacter host that it came from to see if it acquired any bacterial DNA.

Future Plans

In the future, we will continue working as a class to create a poster for Scholar’s day and Rachel and I will begin research for our individual projects.

Purpose: Finish Final Poster and begin narrowing down a testable research question for us to look at next month

Procedure:

• Got into assigned groups
• Read through module and different genomic tools
• Decided to research Repeats in NapoleonB and compare to other phages in the AM cluster
• Completed QTM and reviewed final poster

Future Research: Search for repeats using instructions from the module. Identify the most common/interesting repeat, and investigate further.

Class Poster Creation 3/18/19

Rationale

The rationale behind these procedures is to ensure that poster creations for Scholar’s day follow the correct format and that basic poster requirements are understood. The procedures were also done to finish the poster for Scholar’s Day.

Tools/Procedure

1. The previously chosen design was critiqued and groups were assigned to fix each problem
2. The discussion section was rewritten and graphics were created for it
3. The layout of the poster was modified until it was deemed acceptable
4. Other small groups collaborated to address other aspects of the poster

Results

The results of both the total class collaboration and my small group collaboration on the discussion are shown in the images above. As can be seen, the class poster is almost complete with the exception of the In Silico results section that was not completed enough to be added to the final poster by the end of the lab. The discussion section is broken up into the wet lab and In Silico sections that wrap up the presentation.

Conclusion

There is not much that can be said as a conclusion as this was a poster making day; however, based on the class poster that is underway I fee that I and the class demonstrate an understanding of poster making that will lead to an effective Scholar’s Day poster.

Future Plans

In the future, we will continue working as a class to create a poster for Scholar’s day.