Rationale:

To understand more about phage, the class was divided into several small groups to generate research questions that utilize bioinformatic tools to learn more about questions about NapoleonB and/or related phages.

Materials:

• Laptop
• Canvas Bio-Lab info page
• Gepard dot plot software
• DNA Master

Procedure & Results:

1. Scientific literature that relates to the topic were found and treated as reference.
2. More repeats within the NapoleonB genome were found.
3. A new method for a more efficient way to scan for repeats may be needed.

QTM for lab was written:

Presentation Title (Can be changed): Discovery of repeats in Arthrobacter phages and examination of potential functions.

Two research articles discussing your area of research

• https://jb.asm.org/content/193/19/5300
  • Shows that tail protein areas should be examined to find potential repeats
• https://www.ncbi.nlm.nih.gov/pubmed/29204885
  • Discusses tail fiber domains (in relation to a repeat found after a minor tail protein)

Guiding Research Question (include any background information relevant to the question)

Is it possible to use repeats in coding or noncoding regions of the genomes within the AM phage cluster to predict the functions of genes with no known functions?

Three bioinformatic tools you plan to use in your research

• DNA Master Scan
• Gepard
• Phamerator
• Clustal Omega

You will be presenting your findings at the CURES in Biology Symposium on Friday, May 3. You will do a ‘practice presentation’ on May 1st to your coaches. There are 7 lab days before the May 3rd presentation. While most of your research can be completed during class, presentation practice and presentation design will need to be worked on outside of class. With this in mind, formulate a schedule with ‘check points’ for your group to make sure you stay on track during this busy time of the year. Dates of lab meetings have been provided, but if you plan to meet outside of class as well feel free to include those times.

4/8 – Look for repeats and deepen understanding of prospective repeats that are being investigated

4/10 – Select most promising repeats to focus on and find more information and research to give meaning to the sequences found

4/15 – Apply findings to other AM Cluster phages and begin to finalize data and observations

4/17 – (by the end of lab) Have concrete findings (positive/or negative) that can serve as an answer to the question

4/22 – Compile data and results & create graphics to display findings

4/24 – Organize findings and research into presentation form

4/29 – Finish and revise presentation

5/1- Practice Presentations

5/3- CURES in Biology Presentations 2-5 pm

The Next Step:

The next lab would be to look for repeats and deepen understanding of prospective repeats that are being investigated.