March 29

Beginning Individual Projects 3/25/19

Rationale: Start brainstorming ideas for different bioinformatics projects

Process:

  • Looked through different bioinformatic software and find topics of interest
  • Designed 4 different research questions

Results:

Questions:

  1. Are there repeats in NapoleonB? Are these segments specific to NapoleonB or found in other phage? Can we find meaning in this information (we hope so)?
  2. Are there sections of NapolonB’s genome that have significantly different %GC composition than the genome as a whole? Do these parts match other phage or bacteria (new acquisitions?)? How common is this for Arthrobacter phage?
  3. How conserved are phage genes? What genes do NapoleonB and most other AM cluster phage have in common? What about all Arthrobacter phage? How similar are the DNA sequences?
  4. Does NapoleonB have any Rho terminators and can we use protein folding software to predict their structure? Are these structures common in other Rho terminators for Arthrobacter phage?

Lathan liked question 3 so we did some refining:

  • To refine maybe find several conserved genes for each cluster (or a couple clusters) and compare these
  • Also look for areas within clusters where genomes vary significantly
  • Does genome length effect similarity
  • Will phamerator allow us to compare cross cluster
    • Rachel says we can edit the code so that we can do this
  • We can also look and see if any of the known function gene hits didn’t hit to an AM cluster or had other good hits to phage outside the cluster

Next Steps:
Get question approved my Leo and develop research methods

 

Category: Rachel Melone | LEAVE A COMMENT
March 29

03/27/19 Literature Review of Holin and Endolysin Proteins

Rationale:

The purpose of today’s lab was to discuss the proposed research questions with our research leaders and begin reading through the literature to inform us about this project.

Tools:

  • NCBI BLASTp
  • PhagesDB
  • PUBMED

Procedure:

  • The group discussed with our research leader the potential of our proposed research question, and the methods concerning it.
  • Once completed, the group began with BLASTp queries of both the holin and endolysin protein to determine any conserved domains that could be found in the proteins.
  • After that, literature regarding the biochemical mechanisms of these proteins was sought after and read.

Results:

Both the holin and endolysin contain conserved domains

Few recent articles were found regarding the biochemical mechanisms behind the holin protein, but there was information that suggested the overall mechanism of interacting with the bacterial cell to promote lysis.

Conclusions:

The discovery of conserved domains can suggest that the mechanisms in which holins and endolysins interact with bacterial cell is conserved or highly similar across bacteriophages, so there must be some research regarding those mechanisms. It was discovered that holins initially begin as alpha helices and somehow manage to oligomerize into beta sheets to stop the proton motive force causing bacterial cell death.

Next Steps: 

The next steps for this experiment are to continue with researching the literature and fold the proteins to try and determine any similar characteristics across the holins and endolysins of different phages.

Category: Gabriel Andino | LEAVE A COMMENT
March 29

DNA Day 18

27 March 2019 ✷ Independent Research Project Topics

Rationale:  Potential questions for research were generated and refined to produce a question that will lead to meaningful research.

Procedure

  • The questions created in the previous class were discussed with Dr Adair
  • Ultimately, it was decided to combine the first two questions to make a question that is a bit broader and that can be expanded
  • tools to analyze repeats and % GC were researched and some bumps in using DNA Master were worked out

Results

Conclusion

The question we created is more substantial and will allow for in-depth research of NapoleonB.

Future plans

Research into NapoleonB’s genome will begin.

Category: Lily Goodman | LEAVE A COMMENT
March 29

DNA Day 17

25 March 2019 ✷ Independent Research Project Topics

Rationale:  Potential questions for research were generated and discussed to ensure quality research.

Procedure

  • The class discussed the qualities of a “good” research question and then groups worked to craft research questions
  • The idea of % CG composition was looked upon favorably and thus most of the 4 questions revolved around that idea
  • 4 questions were created and discussed
  • the questions were submitted

Results

The group came up with the following questions:

Questions:
1. Is there a correlation within NapoleonB between the %GC of genes and the %GC of gaps with no
coding potential?
2. In NapoleonB’s genome, are there many repeated sequences within the gaps between genes, as
opposed to within the genes?
3. Is there a correlation within NapoleonB between the %GC of genes with known functions and
genes with no known function?
4. Can the amount of repeated sequences in phage genomes from different clusters indicate
evolutionary relationships?

Conclusion

The questions generated will need some refinement, but they should lead to some meaningful research.

Future plans

The questions will be looked over by Dr Adair to ensure the question is “good.” Then, research will begin.

Category: Lily Goodman | LEAVE A COMMENT
March 29

03/25/19 Independent Project Questions

Rationale: 

The purpose of today’s lab was to come up with 4 testable scientific questions that could be tested for our independent projects.

Tools:

  • Canvas Module with phage genomics research topics
  • Laptop

Procedure:

  • Group met up and began discussing several project ideas and different research possibilities.
  • Asked research mentor for thoughts on different project ideas, and which would possibly offer the best research.
  • Ranked each question 1-4, 1 being the best question, 4 being the least preferred question.

Results:

Research Questions:

  • NapoleonB has both a holin and an endolysin gene, but other phages in the AM cluster do not have this (or people simply did not call it). Bioinformatic tools could be used to compare holin protein structure and the mechanism behind the interactions with the bacterial cell walls.
  • Random Reverse gene (no coding potential, was called)
    • Is gene 2 an actual gene even if it has no coding potential? If so, why?
    • Are there other random reverse genes in other phage genomes that were called and break the guiding principles of gene annotation? (maybe phylogenetic tree to suggest any relationships?)
  • Why does NapoleonB have multiple tail proteins? How does that compare to other phages?

Conclusions:

It was chosen to rank the question regarding the holin and endolysin proteins, mostly due to the fact that it was a question that posed both a level of difficulty that would challenge the group and it was different from the rest of the class. It also presented an opportunity to do a more in depth analysis of the essential functions of a lytic bacteriophage.

Next Steps:

The next steps for this project are to begin with researching the literature behind this question.

Category: Gabriel Andino | LEAVE A COMMENT
March 29

3.27.19 Preliminary Research

3.27.19 Preliminary Research

Rationale: Since Leo approved our preferred research question about repeats in NapoleonB, he encouraged us to begin finding information to answer our question. Therefore, we began looking for repeats in the genome of NapoleonB

Tools/Procedure:

Gepard dot plots and DNA Master.

I used the Gepard dot plot software updated with NapoleonB’s fasta file to begin to search for repeats within the genome. When a possible repeat was found, I used DNA Master’s scan feature to determine the quantity and location of the repeats in the genome.

Results:

Over the course of the lab hour, a few repeats were found to have relatively minor significance. There was one repeat of approximately 50 base pairs that showed two repeats, and other shorter repeats that were repeated a maximum of five times.

Conclusions:

Repeats are more difficult to find upon initial examination. A bigger challenge that was not as anticipated was a lack of immediate success with repeats. While I understood immediate success was unlikely, I had anticipated the process would involve weeding through many more significant repeats to find the most significant ones rather than weeding through many insignificant repeats to rare significant ones. With more time and effort, I think that we will eventually have more success – resilience!

Next Steps:

More time will be spent looking for and analyzing repeats.

Category: Henry Burns | LEAVE A COMMENT
March 29

3-27-19 — Final Research Question

Final Research Question

Date: 3-27-19

  • Rationale
    • The rational for this lab is to decide on a final idea for a research project over the genome of Arthrobacter ATCC 2102.
  • Procedure
    1. Groups met together to decide on which question was the best out of the four that were braingstormed during the previous lab.
    2. Group leaders were asked for direction and whether or not the final question was specific and testable.
  • Results
    • A final question was decided on.
  • Future Plans
    • The next step is to refine this question and work towards gathering data in order to answer it.
Category: Brandon Reider | LEAVE A COMMENT
March 29

3-25-19 — Project Question Ideas

Project Question Ideas

Date: 3-25-19

  • Rationale
    • The rational for this lab is to decide on four ideas for a research project over the genome of Arthrobacter ATCC 2102.
  • Procedure
    1. Groups met together to brainstorm ideas.
    2. Group leaders were asked for direction and whether or not a question was specific and testable.
  • Results
    • Four questions were formed.

      • The four questions that we came up with

  • Future Plans
    • The next step is to focus on one question and receive approval for a project based on one of the questions.
Category: Brandon Reider | LEAVE A COMMENT
March 29

Research Question for Independent Group Project (3/27/19)

Rationale:  

The purpose of the lab was to conduct research and finalize a question which could be tested using bioinformatic databases.  

Tools: 

  • PhagesDB 
  • Phamerator  
  • PhageNotes  
  • DNA Master 

Procedure: 

  1. Collaborated with group to choose a question to test. 
  2. Research was conducted for Question 1 and databases were used to test plaque morphologies and mechanisms which could control it.  
  3. Another question was chosen, and research was conducted using DNA Master, and PhagesDB .  
  4. Research question was decided upon.   

Result: 

Research Question:  

 

Conclusion: 

The first question, which compared plaque morphology and possible mechanisms which control it, was collectively decided by the group and coaches that it would be too hard to perform with the time and resources provided, and therefore the next question was chosen. 

Future Work: 

More research for the question will be conducted, and changes to the question will be made accordingly.  

Category: Sona Subramanian | LEAVE A COMMENT
March 29

Group Project Questions (3/25/19)

Rationale:

Ideas in small groups were generated to create four questions to answer and research on for the independent group project.  

Tools: 

  • NapoleonB’s PhageNotes 
  • DNA Master 

Procedure: 

  1. Group met and brainstormed ideas that seemed interesting.  
  2. Questions were formulated, and databases were used to come up with ideas.  
  3. Coaches reviewed the questions to make sure they were testable questions.  
  4. Final four questions were decided upon.  

Result: 

4 testable questions were produced:  

Conclusion: 

Questions were ordered depending on interest and feasibility. The questions were created to be testable depending on their ability to be answered using bioinformatic databases.  

Future Work:  

One question will be decided upon, and research will be conducted to answer the question bioinformatically .  

Category: Sona Subramanian | LEAVE A COMMENT