Purpose: Continue Individual Research

Procedure:

• Searched for Phages containing an NMT in their genome to compare to the NMT found in NapoleonB and other AM cluster phages
• Found three AU cluster phages for future research
• Found three EG cluster phages with NMT genes
• Added all the fasta files for the NMT genes from the new phages, AM cluster, and bacteria to a splitstree diagram
• Fought splitstree for almost a half hour to get it to work
• Eventually manipulated the program to do its job
• Found that with the present data we couldn’t put together a map to truly represent the genealogy of the gene

Results: Found that the splitstree graph will be harder to create than previously imagined. Will need more samples.

Future Plans: Continue finding more NMT fasta files to make into a coherent phylogenetic tree

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. 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.

Purpose: Continue research into NMT

Procedure:

• Found Fasta AA files for all 14 AM phages
• Isolated NMT gene in all of them
• Also found a phage from very different cluster with NMT to compare
• Submitted files to RaptorX for analysis
• Got a splitting headache and couldn’t think
• Packed up and limped home

Results: We now have the protein models for 14 potential and 1 confirmed NMT

Future Steps: Continue investigating the protein structure and attempt to confirm the function of gene 93

Purpose: Prepare for poster presentation

Procedure:

• Critique other groups practicing their presentations for URSA
• Asked TAs clarifying questions for the presentation
• Practiced with Justin
• Refined our specific areas of focus

Results: Though nervous, I am now more prepared to present.

Future Steps: Present, and continue with individual projects

04/01/19

Rationale:

to prepare for presentation of poster board at URSA.

Procedure:

1. each presentation group presented the poster board.
2. the presentation was then critiqued and improvements were suggested

Results

learned about flaws in the presentation and acquired a better understanding of how the research should be presented

Conclusion

with the help of these critiques and improvements, the class is now ready to professionally present the poster board

Future steps

present poster board during assigned time

Poster Presentation Practice 4/1/19

Rationale

The rationale behind these procedures is to ensure that each member of the class can present the poster in a coherent way and to ensure that all of us know what information is on the poster and being presented. We also practiced answering questions so that we can better communicate our poster.

Tools/Procedure

1. Presentation groups were picked based on poster signup times
2. Each group gave a presentation and was critiqued
3. General points of confusion were clarified and poster presentation etiquette was explained

Results

There is no picture of what we did today in lab because it was just practice, but it helped us learn what to say and how to say it for scholar’s day.

Conclusion

There is not much that can be said as a conclusion as this was a practice day, but I can say that I feel more confident in my ability to present during my timeslot on Wednesday.

Future Plans

In the future, we will use what we learned to present during Scholar’s Week.

Title: Comparing Base Pair Repeats

Date: 3 April 2019

Rationale:  To begin the major research project, the group will be examining a 51-base pair repeated sequence in NapoleonB’s genome.

Tools: 

• DNA Master
• Gepard Alignment
• PhagesDB
• NCBI BLASTn

Procedure: The 51 bp sequence was BLAST’ed and the results compared using a phamerator map and DNA Master annotated FastA files to investigate the nature of the repeated sequence.

Results/Observations: It was observed that the 51 bp sequence repeated around 25,500 base pairs in the AM cluster after an NKF gene. However, the repeat was found after a minor tail protein in NapoleonB.

Conclusions/Next Steps: The sequence will continually be investigated to find if any more evidence can be found (perhaps in the predicted protein structure or conserved domain) to find out if the sequence has any meaning or if the NKF call can be reversed.