April 5

Individual Project 4/3/19

Rationale: continue working on individual project. More specifically, select the specific phages from arthobacter clusters that we want to look at the tape measure protein of

Process:

  • went through and randomly chose ~3 phages per cluster that had an annotated tape measure protein
  • started to plug the amino acid sequences into I-Tasser

Observations/Results:

  • None of the podoviridae phages have an annotated tape measure protein
    • can we figure out what gene it is?
    • is it that different from the other types of phages?

Nest Steps:

Research podoviridae tape measure proteins

April 5

Poster Presentations 4/1/19

Rationale: Practice presenting the poster

Process:

take turns presenting the poster in pairs to the rest of the class

Results/What I learned:

  • Don’t go into too much detail
  • know how to describe the figures
  • make sure you aren’t talking too fast

Nest Steps:

Present poster at scholar’s day!!

April 5

Begin individual research

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.

April 5

presentation practice

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

April 5

4.3.19 Working on Our IRP

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.

April 5

Poster Presentation Practice 4/1/19

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.

April 5

Comparing Base Pair Repeats 4/3/2019

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.

April 5

Independent Research Projects 4/3/19

Rationale

Today we will finalize our independent research questions and begin looking more into the topics at hand.

Procedure

  • Topics were reviewed to determine if the would be fit for an independent research project.
  • A question was determined for use in the project
  • Scientific literature was investigated to find articles that included topics in the realm of our project.

Results

The question that we created stated: What is the relationship between the percent GC and GC3 in AM-specific genes and genes present in AM and non-AM phages?

We utilized the following links establish a background on our topic:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3923770/

https://www.omicsonline.org/open-access/the-gc-content-of-bacterial-genomes-2329-9002-2-e108.php?aid=26236

https://www.pnas.org/content/111/39/E4096

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4576692/

Conclusions/Next Steps

Next, we will begin collecting data regarding our scientific question and dive deeper into our independent research project.

April 5

Presentation Practice 4/1/2019

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.