April 5

Practice Poster Presentation

4/1/19

Rational:

To practice our poster presentation for when we present during URSA

Procedure:

  • Each group of two presented
  • The class, the TAs, and Dr. Adair asked questions throughout
  • The group had to answer any question to the best of their ability
  • The groups and class listened to critiques of the presentation

Observations:

  • One critique given was to spend more time on the results and figures than on anything else
  • Another thing was to mae sure that all of the terms and procedures on the poster were understood clearly

Conclusion:

We presented watched groups present the poster and lstened to the ways that the presentation could be improved.  When my group presented we used the earlier critiques to improve it and looked for specific ways we needed to improve. Next lab we will contnue working on the indvdual research poster.

Category: Emily Balint | LEAVE A COMMENT
April 5

April 3, 2019

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

 

Category: Uncategorized | LEAVE A COMMENT
April 5

Monday, April 1

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

Category: Uncategorized | LEAVE A COMMENT
April 5

Individual Project Final Outline 4/3/19

Individual Project Final Outline 4/3/19

Rationale

The rationale behind today in lab was to create a final outline of our final project so that we have a good basis of information moving forward. This outline also served as a plan that we can use to accomplish our goals.

Tools/Procedure

  1. A final outline was created and submitted
  2. All 23 clusters of Arthrobacter phage were classified
  3. A random number generator was used to pick 3 phages from each cluster for further examination

Results

Our final outline can be seen above, it is on this that we will base the rest of our research. We also began the process of randomly picking the phage whose proteins we will analyze, and I will further detail that in future reports.

Conclusion

There is not much that can be said as a conclusion as this was a planning session, but we did discover that of the 4 podovirade phages that are on phages DB not one calls a tape measure proteins. This may be something interesting to look into in the future,

Future Plans

In the future, we will continue our research based on the plan we laid out above.

Category: Lucy FIsher | LEAVE A COMMENT
April 5

4-3-19 — Independent Research

Independent Research

Date: 4-3-19

  • Rationale
    • The rational for this lab is to gather data to use for our independent research project.
  • Procedure
    1. A Microsoft excel document was created and shared with independent research project groups.
    2. PhagesDB and DNAMaster were used in order to gather information about the start codons used by phages that infect Arthrobacter.
  • Results
    • Above is a screenshot of  Mudcat, an arthrobacter phage in the AM cluster, and its start codon choices for various genes.
  • Future Plans
    • The next step is to continue gathering this data before attempting to further subcluster phages based on start codon preference.
Category: Brandon Reider, Uncategorized | LEAVE A COMMENT
April 5

4-1-19 — URSA Scholars Week

URSA Scholars Week

Date: 4-1-19

  • Rationale
    • The rational for this lab is to practice poster presentations and test understanding of our research poster.
  • Procedure
    1. Presentation groups took turns practicing poster presentations.
    2. The class critiqued each group and gave tips for presenting.
  • Results
    • The poster above was learned and ready to be presented over.
  • Future Plans
    • The next step is to focus on independent research projects.
Category: Brandon Reider | LEAVE A COMMENT
April 5

Minor tail proteins 4/5

Procedure: Continue research on start site preferences for minor tail proteins.

Procedure: Met with the group to continue independent research. Data were obtained by using PhagesDB and DNA Master. Obtained FASTA file, and checked start site preferences on known minor tail proteins. Data was recorded onto a google spreadsheet so group members have access to data.

Results: 

Conclusions/Future work: Finish up data on google sheets and start structure analysis along with the manipulation of start sites for these tail proteins.

Category: Michael Lum | LEAVE A COMMENT
April 5

Independent Research Project Layout (4/3/19)

Rationale: After presentations were made, a final layout of the project was made to make sure the group was on track. Several primary works of literature were found to provide evidence of the findings and the scientific question was refined. Towards the end, the group began to collect hard data for the theoretical data.

 

Tools:

  • OneSearch
  • Personal Computational Device
  • Google Excel
  • PhagesDB

 

 

Results:

  • First, the group began to search for primary literature related to the research begin done.
  • Then, the question was specified more in order to be finalized later.
  • At the end of the lab, hard data was being noted in Google Excel along with the usage of PhagesDB to later be used for the theoretical data.

 

Conclusion:

Primary literature was found, then the question was refined. The group began to collect hard data to later be used for theoretical data.

 

Future Plans:

Using the hard data, protein structures will be made using a database along with changing the start site to see if the protein structure changed.

Category: Sabin Patel | LEAVE A COMMENT
April 5

Presentation Practice (4/1/19)

Rationale: To practice poster presentations and to locate mistakes in order to be fixed before the actual presentations were to be made

 

Tools:

  • Poster

 

Results:

  • The poster was presented by each group.
  • Each time, mistakes were found and corrected in order to be avoided on the actual presentation day.
  • Questions were asked by the others to make sure the presenters were ready.

 

Conclusion:

Each group practiced presentations to find mistakes and correct them before they were made on the actual presentation day.

 

Future Plans:

After presentations, begin to work on independent research projects.

 

 

Category: Sabin Patel | LEAVE A COMMENT
April 5

APRIL 1ST AND 2ND-LABS

  • APRIL 1ST 2019
  • OBJECTIVE: 
    • To make sure all are prepared for poster presentations, and can answer questions on the poster
  • PROCEDURE: 
    • Students went up to the poster and presented to the class in their groups
    • People asked questions and proper answers were generated 
  • RESULTS:
    • N/A
  • CONCLUSION: 
    • Students were prepared to present and answer questions on the poster 
  • FUTURE STEPS:
    • Formally present the poster at URSA scholars week, and continue working on in depend project
  • APRIL 3RD 2019 
  • OBJECTIVE:
    • To create a timeline for independent projects 
  • PROCEDURE:
    • A google docs was shared where group members added information to create a timeline of project 
    • Phamerator was looked at to determine what specific genes the group wanted to look into 
  • RESULTS: 
    • 4/8 : Determine protein structure of gene 62, and see how it interacts with upstream gene 59
    • 4/10: look at synteny and try to come up with a method of representation for synteny of other clusters for gene 62
    • 4/15: Have evidence to show the types of modules in Napoleon/AM cluster. Make setup for presentation, have background rough draft. 
    • 4/17, 19: Start constructing basic outline presentation, look into evidence for gene function in the different types of module. Start on Methods and figures. 
    • 4/22: Organize database of collected evidence for each gene in each module. Began constructing Results. Ensure phylogenetic tree is accurate and well made.  
    • 4/24 Continue collection of evidence for module 1, 2, 
    • 4/29 Finish final touches on presentation, and be able to flawlessly run through the presentation 
    • 5/1- Practice Presentations
      • 59 gene interaction: using raptor x, no correlation 
      • Bing, clustered in BI1: 
      • 60: transmembrane protein matches own cluster, BI 
      • Newly identified, used to calculate it can fit inside the membrane
      • Used synteny phage Camille, and other EL phages that have the same membrane protein.  
  • CONCLUSION: 
    • A timeline was made and there will be further investigation into gene 59 of Napoleon B
  • FUTURE STEPS: 
    • To analyze proteins made by gene 59 in AM cluster
    • Continue to read primary literature 
Category: Lauren Foley | LEAVE A COMMENT