March 28

Independent Research Project 3/27/19

Rationale

Today we will finalize our independent research question and explore the tools needed to answer the question.

Procedure

  • A final question was created using a mixture of the questions proposed on 3/25/19.
  • DNA Master and a variety of external tools were used to explore the %GC in NapoleonB.
  • DNA Master was also used to look for repeated sequences in NapoleonB.

Results

The new research question devised explores the characterization of the coding regions versus the non-coding regions of AM cluster phages by comparing the %GC and the number of repeated sequences present.

Shown below is a picture of DNA Master and the %GC data for gene 1.

Conclusion/Next Steps

Next, we will determine the %GC of the non-coding regions and the coding regions of NapoleonB. We will also look for repeated sequences in the genome. After analyzing NapoleonB, we will expand our research to more AM cluster phages.

Category: Emily Gaw | LEAVE A COMMENT
March 28

Individual Research Project and Question 3/25/19

Rationale

Today we will create 4 possible research questions for an Independent Research Project.

Procedure

  • The tools and ideas provided on Canvas were looked through to see if any generated interest
  • After consideration, %GC and repeats were found to be most interesting to the group and four research questions were created around the topic.

Results

The questions created are presented below.

  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 number of repeated sequences in phage genomes from different clusters indicate evolutionary relationships?

Conclusions/Next Steps

Next, we will narrow down the proposed questions to one final question for independent research. We will then begin research for the finalized topic.

Category: Emily Gaw | LEAVE A COMMENT
March 28

Lab Day 18-19: Independent Research

Rationale

Create a independent research question that is related to the findings of Napoleon, be able to test it and analyze results.

Procedure

  1. Created 4 questions
  2. Choose one question that was approved by coach
  3. Used NPS for multiple sequence alignment of different nicotinamide mononucleotide transporters
  4. Use HHPred to analyze hits of the transporters that were not in AM cluster

Conclusion/Next Steps

Due to limited time, I was only able to analyze the sequence alignment from 6 genomes. Founded out the families and superfamily that the transporter was in (PnuC, SWEET, and TOG.) In the future, I would have to find more phages in the AM cluster and phages outside of the cluster that contain this transporter, take the genome sequence, analyze the alignment, and use HHpred to analyze the hits of those genomes.

Category: Soo-Un Jeong | LEAVE A COMMENT
March 28

Start site preference of certian proteins 3/27

Rationale: Refine the question made on 3/25 and create a procedure to test the research question.

Procedure: Questions were refined and ideas were bounced from group members to coach. Performed NCBI BLASTp on a tape measure protein to see other know bacteria to have the same known protein, and the starts of AM cluster tape measure proteins were determined.

Results: The following images below show the NCBI BLASTp and confirmation that all AM cluster phages have methionine as the first amino acid sequence.

Conclusions: NCBI BLASTp showed many hits with many known bacteria to have the same protein meaning there are similarities between them.

Future work: Test to see if these hits have the same start sequences. Find a database that can allow the manipulation of the starts to see if the change of the start site of the tape measure protein has an effect on the shape of the protein. See if there is a correlation between the starts and why certain proteins prefer this start sequence rather than the other two start sequences.

Category: Michael Lum | LEAVE A COMMENT
March 28

In the Literature (3/27/19)

Rationale:

Create a procedure to perform to test research question.

Procedure:

  1. Brainstormed procedure in groups.
  2. Performed NCBI BLASTp.
  3. Started reading in the literature about the mechanisms of holin and endolysin.

Results:

The following images below show the NCBI BLASTp.

 

The following articles were of interest.

https://pubs.acs.org/doi/10.1021/acschembio.5b00875

https://onlinelibrary.wiley.com/doi/full/10.1111/mmi.13448

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6116005/

https://www.sciencedirect.com/science/article/pii/S0065352718300563?via%3Dihub

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4012431/

Conclusion:

The NCBI BLASTp revealed that both the holin and endolysin genes shared CDD meaning that enough similarity exists between these genes among phages for it to be a legimate research question. Also, many articles found on holin and endolysin, showed the research question purposed was legitimate.

Future Work:

Further research into the mechanisms of holin and endolysin will be performed to achieve a thorough understanding before starting protein analysis.

Category: Kathryn Adkins | LEAVE A COMMENT
March 27

Developing a Question (3/25/19)

Rationale:

In groups, develop a specific question about Arthrobacter that can be tested with bioinformatic tools.

Procedure:

  1. Brainstormed ideas within groups.
  2. Sought approval from Coach.

Results:

After ideas for doing possible research into NapoleonB’s only reverse gene and tail proteins, it was decided that the research performed should attempt to thoroughly answer the question: Using bioinformatic tools, can phage holin’s and endolysin’s structures and functions be compared across Arthrobacter phages?

Conclusion:

Although comparing the structures and functions of holin and endolysin will require a great amount of biochemistry knowledge, this research question interests all group members and has motived them to understand topics that seem somewhat foreign.

Future Work:

Brainstorm and start an experiment to answer this research question.

Category: Kathryn Adkins | LEAVE A COMMENT
March 27

March 27 2019 Independent Project

Purpose: The purpose of this lab is to finalize the independent research question and create a plan for the project and data collection.

Tools/Procedures:

Tools:

  • Canvas
  • DNA Master
  • Online Bioinformatics Resources

Procedures:

  1. A new question was formed from the list of questions created in the last lab. The new question focuses on characterization of the gaps of AM phages with %GC and repeated sequences, in comparison to coding regions.
  2. Research was done to find the best ways to calculate %GC for each gene and gap.
  3. Research was begun to look for ways to find repeated sequences in NapoleonB.
  4. Work was saved.

Results: The results of this lab include creating a new research question and beginning the process of planning the project and data collection.

Picture: %GC

Conclusions:
In conclusion, the research question was created, centering around the characterization of AM phage gaps. Work was done to find the best way to collect the data and analyze the results.

Future Work:
Future work will include collecting the data for the research project and finding repeated sequences. Once data has been collected, the results will be analyzed.

Category: Lucy Potts | LEAVE A COMMENT
March 27

Finalizing Research Question 3/27/19

Rationale: We are beginning to look in to the question and building a plan for moving forward with looking into this research question.

Tools: NCBI Blastp, Word, Phamerator

Procedure:

1. Explored more into the different clusters that contain the pham 19129, and found not all of the clusters infect arthrobacter.

2. Refined and reworded the research question.

3. Blasted the amino acid sequence for the DNA polymerase in NapoleonB’s genome against actinobacteria. Found it hit to Streptomyces.

4. Made a plan for conducting the research going forward.

Results:

Blast results for the DNA polymerase in NapoleonB’s genome against actinobacteria.

Conclusions and Future Work: Now that we can see some sort of start point with the streptomyces the plan is to analyze the differences between the hosts and blast the genes we found similarities in against the different hosts. From there we can compare the slight differences in amino acid sequence and nucleotide sequence in the cassette that contains the three shared genes.

 

Category: Sriram Avirneni | LEAVE A COMMENT
March 26

Independent research question 3/25

Rationale: Develop multiple questions that are testable for the final project.

Procedure: Got into groups and ideas were generated fro question topics. Everyone decided what topics the group had the most interest in. Four questions were generated and the questions were submitted to Canvas.

Results: Image shows the four questions that were generated.

Conclusions: Four questions were generated and three of the four could be potential research topics that could support the class poster.

Future work: Decide on the final question and start independent research.

Category: Michael Lum | LEAVE A COMMENT
March 26

3.25.19 Creating a Research Question

3.25.19 Creating a Research Question

Rationale: As the poster has been predominantly finished, the class will now move on to independent research projects. Therefore, it is necessary to develop a research question to guide our research moving forward.

Tools:

Our group narrowed down our search to focus mainly on repeats and how they may reveal functions about genes with no function. To find these repeats, we downloaded the Gepard dotplot software that will allow us to find areas of NapoleonB’s genome.

Results:

Four questions were successfully developed and submitted, and the Gepard software was successfully downloaded and usage was practiced to build confidence before research formally begins. The main question that our group would like to focus on is “Is it possible to use coding or noncoding repeats in the genomes of AM cluster Arthrobacter phages to predict the functions of genes with no known function?”. There are components of this question that will be refined as preliminary research is done, but this question seemed to our group to fit each component of a good research question.

Conclusion:

Research questions need to be specific, as initially looking at the immense genome of NapoleonB and all the options seemed a daunting task. By creating a specific question, results are likely to be focused and easier to process, which eliminates doing inefficient work that will result in less meaningful results.

Next Steps:

The Gepard software will be used to create a dot plot of NapoleonB’s genome and begin to reveal where there are repeats. These results will be analyzed and used to hone our research question.

Category: Henry Burns | LEAVE A COMMENT