March 29

Independent Research 3/27/19

Title: Independent Research

Date: 27 March 2019

Rationale: The four previous research topics will be reconsidered and one topic will be selected as the final project

Tools: 

  • DNA Master
  • Gepard
  • NCBI BLASTn

Procedure: After discussing as a group, the decided upon topic was repeat sequences in NapoleonB’s genome. Therefore, Gepard and DNA Master were used to locate sequences of interest that repeated throughout NapoleonB’s genome. Once a potential repeated sequence was identified, it was entered into DNA Master’s “Scan” feature to check if it repeated a significant number of times. Potential repeat sequences were also BLAST’ed by NCBI’s BLAST database to see if they appeared in other phage genomes.

Results/Observations: One 51-base pair sequence was shown to repeat twice in NapoleonB’s genome, as well as show BLAST results for many other AM cluster phages. No other found repeat sequences showed significance.

Conclusions/Next Steps: Gepard will be used continuously throughout the experiment in order to locate sequences of interest. The specific location of the repeat will also give clues as to why the repeat exists. The main point of the project is to investigate whether or not a repeat sequence can be used as a “tag” in order to reverse an “NKF” call made on the annotation of NapleonB.

Category: Cooper Johnson | LEAVE A COMMENT
March 29

Research Topics 3/25/19

Title: Research Topics

Date: 25 March 2019

Rationale:  A research topic will be discussed and eventually conferred upon

Procedure: With group members, the available information and tools were considered in order to formulate a research topic. Four different topics were decided upon that would be narrowed down at a later time.

Results/Observations: The four topics for research were: 1. Repeats in NapoleonB’s genome. 2. attP sites in NapoleonB’s genome. 3. Stoperator genes in NapoleonB’s genome. 4. GC% content and its phylogenetic connection to the AM cluster.

Conclusions/Next Steps: Since 4 topics have been determined, they will be investigated once more in order to decide upon one topic that will be pursued for future research

Category: Cooper Johnson | LEAVE A COMMENT
March 29

Research Topic

3/27/19

Rational:

To create a research question, to start looking at the literature relating to the question, and to look  into how to research the topic chosen.

Procedure:

  • BLASTed NapoleonB’s endolysin and holin genes in order to see if they are conserved
  • Searched for articles relating to holin proteins, endolysin proteins, and these protens in relation to phages
  • Refined the topic on holin and endolysins in phage into a research question

Observations:

  • The BLAST showed that both gene have a CDD and are conserved meaning that the genes will likely be similar to other phages
  • The final queston was Using bioinformatics can phage’s endolysin and holin structures and functions compare to other Arthrobacter phages?

Conclusion:

By the end of lab we discovered many articles to use in order start our research. We also created the final research question and confirmed that we would be able to with our resources research the topic. Next lab we will prepare for the poster presentation for our class poster.

Category: Emily Balint | LEAVE A COMMENT
March 29

Individual Projects 2

Purpose: Investigate what affects the presence of multiple plaque morphologies in NapoleonB and other AM Cluster Phages

Procedure:

  • Downloaded Fasta files for all AM Phages
  • searched for phylogenetic tree generators
  • Settled on program called splitstree
  • Plugged in Fasta Files
  • Generated Phylogenetic tree

  • Determined the tree was not populated with enough data to find any correlation between phage evolution and the presence of multiple morphologies
  • Revised question to begin research into Nicotinamide Mononucleotide transporters, specifically the one coded for in NapoleonB

Results: We have a revised question and a new simple procedure to find our nicotinamide mononucleotide transporter (NMT)  in other phages, to determine its origin.

Future Plans: Investigate the NMT in NapoleonB and associate it with other phages with similar proteins or nucleotide sequences.

Category: Uncategorized | LEAVE A COMMENT
March 29

Individual Projects

Purpose: Determine a question to begin developing our research project

Procedure:

  • With understanding of prior module, begun brainstorming ideas for questions
  • Changed goal from researching repeats in NapoleonB to finding the importance of G/C content
  • Wrote 4 different possibilities to research
  • Refined our favorite question with help from Lathan
  • Published as QTM

Results: We now have a research question to work on for our individual project.

Next Steps: We will begin research that will help us answer our question.

Category: Uncategorized | LEAVE A COMMENT
March 29

Independent Research Project Question (3/27/19)

Rationale: One question was chosen of the four and additional research was done on the topic.

 

Tools:

  • Personal Computational Device

 

Results:

  • In this lab, the best question will be picked and refined with the guidance of the couch, Dr. Adair. To refine the question, additional research was completed to make sure that it was possible to test.

 

Conclusion:

The best question of the four was chosen and was refined with the help of Dr. Adair. More research was done to make sure that it was possible to obtain results from the question.

 

Future Plans:

Begin on the Independent Research Project.

Category: Sabin Patel | LEAVE A COMMENT
March 29

Research Question Ideas (3/25/19)

Rationale: The group thought of research questions for the individual research projects with the guidance of the couch, Dr. Adair, and ideas posted in the Modules.

 

Tools:

  • Personal Computational Device
  • “Modules” in Canvas
  • Required BioInformatic Tools

 

Results:

  • Prior to class, research was done on additional topics to view other options for the questions which were to be used.
  • With the additional information and ideas from the module, the group brainstormed on possible questions which can be tested bioinformatically and with the tools that are present.

Conclusion:

After more research was done on possible topics for questions, the group came together and formulated four questions which were testable bioinformatically and within the time that was given.

 

Future Plans:

With the four questions, one questions which the group collectively prefers will be researched even further to ensure that the question is feasible.

Category: Sabin Patel | LEAVE A COMMENT
March 29

Research Question

3/25/19

Rational:

To come up with several different ideas for a research question that can be used for the group poster.

Procedure:

  • Found parts of NapoleonB that were interesting (such as proteins, genes, or any other part of the genome)
  • Came up with a few questions relating to these interests
  • These interests included the holin gene whch was not found n many other phage in the cluster, gene 2 with defies the guiding principles for genes, and the reasoning behind the many tail proteins found in the genome
  • Ordered the questions in order to the best to worst

Observations:

  • The first and top question was about the holin gene’s structure and mechanism and comparing it to other Arthrobacter phage
  • The second queston was looking at whether gene two was an actual gene or not
  • The third was looking at whether there are other phage that have a reverse gene that also seems to break the guiding principles
  • The last was about the many tail proteins in NapoleonB and comparing it to other Arthrobacter phage

Conclusion:

Our group came up with four possible research questions and the question about the holin gene in NapoleonB’s genome was our group’s first choice. Next lab we will start to figure out how we are going to research this question or whatever question we choose.

Category: Emily Balint | LEAVE A COMMENT
March 29

march 25th and 27th- brainstorm labs

  • MARCH 25TH, 2019
  • OBJECTIVE: 
    • Develop possible independent research question 
  • PROCEDURE: 
    • A google docs was created and shared among group members 
    • Phamerator map was used to compare clusters and look and possible synteny 
    • Questions were then typed into a document 
  • END RESULT: 
    • The following questions were developed by the group/group members:
      • By observing the conserved genes upstream and downstream of the DNA polymerase commonly identified in several clusters that are members of pham, can we show the point of divergence through a phylogenetic tree? What synteny is conserved is association with the extended DNA polymerase, involving also the helix-turn-helix protein). – Ram
      • Through GC analysis sequence, can we determine the possible source of helix-turn-helix DNA binding protein between phages within the same cluster and demonstrate through a phylogenetic analysis? – Melissa
      • How can attP sites be compared to other phages in the cluster in order to determine if there is a trend in the “aggressiveness” or lysogenic strength of the phages?- Lauren 
      • There are some genes that are unique to only certain phages in the AM cluster, but seem to be common in other clusters. How can we compare the sequences of these genes as well as the synteny of genes in members that contain the gene display differences within the AM cluster as well as similarities between the AM and AU clusters?
  • CONCLUSION: 
    • Questions were developed and submitted as a QTM 
  • FUTURE STEPS: 
    • Pick one questions and develop a way to use the methods available to answer that question
  • MARCH 27TH, 2019 
  • OBJECTIVE: 
    • Develop methods to be bale to answer a research question 
  • PROCEDURE: 
    • A google doc was created 
    • Phammerator was used to compare he presence of a DNA polymerase between different phages clusters
    • Brain stormed ideas on how to test question
  • END RESULT:
    • Research Questions
      • By observing the conserved genes upstream and downstream of the DNA polymerase commonly identified in several clusters that are members of pham, can we show the point of divergence through a phylogenetic tree? What synteny is conserved is association with the extended DNA polymerase, involving also the helix-turn-helix protein). – Ram
      • a look into the cassettes (can determine if its the same gene using promoter sequence even if it doesn’t have function)
      • look sequence promoter  (Can be done using DNA Master “DNA–>Promoter Prediction.” Make sure the settings are for sigma-70 promoters, and then click analyze)
      • compare protein structure through the nucleic acid 
      • Look into function of genes 
      • End goal: be able to create a phylogenetic tree 
      • Why does arthrobacter phage have DNA polymerase?
      • See if arthrobacter itself, has sequence for DNA polymerase….could theoretically be used by phage? Why have they co-evolved? Why don’t phages from other bacteria lack DNA polymerase? 
    • Topic questions: 
      • Question if a high percentage arthrobacter phage has this dna polymerase?
      • What other clusters are have the DNA Polymerase
      • Is there a significant difference with the presence of DNA polymerases in arthrobacter phage? 
      • Actinobacteria
      • Naked DNA? 
      • See if they cluster out?
    • Figure of host and see how those are all related then can see which one of them has DNA polymerases and see if they all branch out in Actinobacteria 
    • In order to get approved you must have a question that is specific and testable.
    • Our objective is to compare pham 19129 DNA polymerase and observe the patterns that can be derived from cross-analysis.
    • Are there some patterns that can be derived from analyzing the differences and similarities among phages that contain the pham 19129? Furthermore, could this insight help us determine the relationship between these phages such as a common ancestor, seeing as they all contain a similar gene despite some infecting different hosts?
    • In addition, you must show your coach that there is enough resources available for you to do your research
    • Protein-protein interaction DNA polymerase and upstream gene, (other biotech sources available on ExpasY) Phages DB, Phamerator, HHPred, and DNA Master. We must also come up with an organized system of data collection. Early evidence. 
    • You must propose a simple method outline for your research project. 
    • Compare host genome using NCBI blasts (must look into tools to compare bacterial genomes)
    • Need to specifically look in differences of DNA polymerases and nucleotide changes within that gene (using Phamerator, DNA master, HHPred)
    • Entire cassetete containing DNA polymerase can be analysed for similarities and differences as well 
    • Need to get rough understand of the DNA polymerase relation in order to find out where to continue further research 
  • CONCLUSION: 
    • Possible methods were developed to test research question 
  • FUTURE STEPS: 
    • Refine research method and make more specific methods
Category: Lauren Foley | LEAVE A COMMENT
March 29

Individual Project 3/27/19

Rationale: Begin a research outline for approved research question

Process:

  • Narrow down project to be more specific
  • Find software to help analyze research question
  • consolidate an outline

Result:

Goals of Project:

  • Compare Tape Measure proteins between the Podoviridae (with short noncontractile tails), Siphoviridae (with long noncontractile tails), and Myoviridae (with long contractile tails) tail family

Bioinformatics Tools:

  • FASTA searches
  • Phamerator
  • NCBI BLAST
  • PDB
  • Clustal Omega
  • I-tasser

Methods Outline

  • Look in literature to see if we can find any similar experiments from which we can draw data or info
  • Figure out what cluster corresponds to what tail type
  • Select a number X of phages from each family
  • Compare these tape measure proteins (amino acids) to other tape measure proteins in the family and then in comparison to other families
  • Use Protein folding software to simulate a tape measure protein (or several) for each family and then look for differences

Next Steps:

I will start experimenting with software and Lucy will search in literature

Category: Rachel Melone | LEAVE A COMMENT