March 29

Research Question Discussion & Preliminary Research 3.27.19

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
Procedure & Results:

After looking for repeats in the NapoleonB genome, an outline of the question is generated,

Outline:

  1.      Locate and identify and significant repeats in NapleonB’s genome
  2.      Cross-check those repeats with other AM cluster phages
  3.      BLASTn any significant repeats to check for similarity with NCBI database
  4.      Check if any conclusions can be made with non-coding regions, protein similarity, NKF genes, etc.*

Tools*: Gepard, NCBI BLAST, DNA Master, Clustal Omega

*will be expanded

The Next Step:

The next step would be looking for initial points of interest in the NapoleonB genome, to find a incision point for the research to begin.

Category: Yang-En Yu | LEAVE A COMMENT
March 29

Research Question Discussion 3.25.19

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
Procedure & Results:

Different aspects of possible research directions were explored and four questions were generated. The Gepard dot plot software was used to find repeats in the NapoleonB genome. The leading question for the group is:

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?

The Next Step:

The next step would be trying to refine the question and have a clear and specific objective.

Category: Yang-En Yu | LEAVE A COMMENT
March 28

3.27.19 Other Questions for IRP

Rationale:

To continue working on our previous question and developing alternatives.

Procedures:

  1. We continued to research the background behind our plaque morphology question and ascertain its feasibility.
  2. . After determining its infeasibility we began looking at other questions, settling on a question about Nicotinamide Mononucleotide Transporters and how that gene appeared in NapoleonB.
  3. We created a basic plan for ascertaining how to proceed with the NMT question.

Conclusions/Next Steps:

After consulting with Lathan we determined our plaque morphology question was infeasible to pursue for our IRP, we then settled on a question about the appearance of NMT in NapoleonB. The next step will be to continue working on this question and researching it as it is our IRP question, we will also practice the presentation of our poster for NapoleonB.

Category: Nathan Newton | LEAVE A COMMENT
March 28

3.25.19 Creating a Question for the Independent Research Project

Rationale:

To create four possible questions for the independent research project and do minor research into the feasibility of each one.

Procedure:

  1. We looked at Canvas and using our knowledge created four questions relating to NapoleonB.
  2. We did research into the feasibility of each and ranked them from 1-4.
  3. Lathan was consulted about the questions.

Conclusions/Next Steps:

We concluded that a question about the reason for the dual plaque morphologies would be the most interesting to pursue. We will continue to look into this question and its feasibility, while also investigating other possible questions.

Category: Nathan Newton | LEAVE A COMMENT
March 28

Individual Projects, Topic Approval 3/27/19

Individual Projects, Topic Generation 3/27/19

Rationale

The rationale behind these procedures is to ensure that Rachel and I can refine our research topic into something that is testable in the correct amount of time and to have us find tools that we can use to assist in our research in addition to mapping out a basic method/plan.

Tools/Procedure

  1. Previously created groups refined a research question based on previously created possibilities
  2. Groups consulted with their assigned coaches in order to further develop their research questions and understand what elements must be present in their research questions
  3. Changes were made as necessary
  4. Tools for research were researched and recorded
  5. A basic method outline was created
  6. Research project topic was approved

Results

The image above shows the evolution of our research question with our listed bioinformatics tools and basic methods outline. We are planning to compare Tape Measure proteins between the Podoviridae, Siphoviridae, and Myoviridae tail families.

Conclusion

There is not much that can be said as a conclusion as this was a brainstorming day. I can say that Rachel and I will likely be utilizing many bioinformatics tools that will allow us to compare protein structures and genes looking for important similarities or areas of conserved genetic code.

Future Plans

In the future, we will begin researching our question and see what conclusions we can draw from the data.

Category: Uncategorized | LEAVE A COMMENT
March 28

Individual Projects, Topic Generation 3/26/19

Individual Projects, Topic Generation 3/26/19

Rationale

The rationale behind these procedures is to ensure that Rachel and I can come up with research topics for our individual project that can actually be answered in the time available while also providing a valuable amount of information.

Tools/Procedure

  1. Previously created groups brainstormed 4 potential research questions for the individual research projects
  2. Groups consulted with their assigned coaches in order to further develop their research questions and understand what elements must be present in their research questions
  3. Changes were made as necessary

Results

The image above shows the several questions Rachel and I generated as potential research topics and our responses to/ notes on coaching advice. These questions represent a rough draft of sorts that we will explore while trying to figure out what exactly we will be researching and how we will narrow down our topic further.

Conclusion

There is not much that can be said as a conclusion as this was a brainstorming day. I can say that Rachel and I will likely work with our potential question number three because Lathan and Dr. Adair seemed to like it most and think it was the most testable question that would still yield good information.

Future Plans

In the future, we will continue working to finalize a research topic and begin our individual research project once our topic has been fully determined.

Category: Lucy FIsher | LEAVE A COMMENT
March 28

3/27 ~ Independent Research Question

Rationale: Focus on one of the questions created last lab and research sources for the topic

 

Procedure:

  • Brainstormed with group members on which question to focus on
  • Used PhagesDB and Phamerator to research potential correlation between plaque morphologies and genes
  • Focused on another question when the group realized that evidence would be hard to find for the first question
  • Used DNA Mastering to looks at the start site preferences in terms of codons

Observations:

The refined question our group will focus the research on

 

Conclusion/Next Steps: With the next labs, will continue research on the question. If the question doesn’t show much promising results or an interesting discussion, will change questions.

Category: Justin Yu | LEAVE A COMMENT
March 28

3/25 ~ Independent Question(s) Brainstorm

Rationale: Work with assigned groups to create questions that would serve as the basis of the independent research project(s)

 

Procedure:

  • Met with group members to begin brainstorming questions
  • Consulted with “coaches” on the questions that were created
  • Decided on four “major” questions that could be focused on

 

Observations:

  • The four questions that we came up with

     

Conclusion/Next Steps: Next lab, will be choosing one question out of the four to research more on and look for sources

Category: Justin Yu | LEAVE A COMMENT
March 28

Final research Questions

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 the validity of each questions and for approval of question
  2. Group researched and compiled more information on the topic of Start site preferences,
  3. After some misconceptions were cleared, a question based on start site preferences was refined and approved by the coach
  4. the group decided to look into the start site preferences of genes in different genomes of arthrobacter phages of CLuster AM and other phage clusters. after hard data is compiled on the start site preferences, the group will derive conclusions based on the acquired data.
  5. the group will then use modeling software to see how different start sites will affect the structure of the protein produced by the gene. these will be the theoretical results.
  6. possible tools that can be used were compiled.

Results

the research question for individual research

  1. What are similarities and differences in the start codons for the nucleotide sequences coding for tape measure, major and minor tail proteins? is there a prefered start codon based on the cluster? How is the structure of the produced protein affected if a different start codon is used?

Tools: NCBI. PhagesDB, HHpred, SWISS Model Workspace, Openstructure and SWISS Pdb viewer.

Conclusion

this research will require a great deal of data collection as there are a little more than 200 sequenced arthrobacter phages. it may answer some questions about the phage genomes and possibly provide another attribute that can be used for gene annotation.

Future steps

do more research, look into primary literature and find more tools that can be used.

Category: Aman Patel, Dr. Adair | LEAVE A COMMENT
March 28

Research Question Drafts

03/25/19

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. The possible topics were researched
  2.  The tools available for use were researched.
  3. based on the known information, possible topics and available tools, 4 possible research questions were formed
  4. Coaches were consulted for advice on questions.

Results

the following questions are the possible research questions to be looked at

  1. Is there a similarity in start site preferences for certain protein between the Napoleon B and other phages in cluster AM? If so, is there a similarity between other clusters? What is the importance of identifying these start site preferences? Can it be an identifier or supporting evidence for the existence of the specific gene? Can a different start site affect the transcription of the protein?
  2. Is there a relation between the transposons in the genome of Napoleon B and other phages in the AM clusters?
  3. Are there any similarities between the stoperators for Napoleon B and known stoperators for mycobacteriophage L5?
  4. Can slight differences in nucleotide sequences lead to different protein structures within the AM cluster and other, similar clusters?

Conclusion

the first question is likely to be the one which will be researched. currently, more consultation will be required to refine the question and come up with a possible method to answer the question.

Future steps

do more research, look into primary literature and find more tools that can be used.

Category: Aman Patel, Dr. Adair | LEAVE A COMMENT