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?
- The following questions were developed by the group/group members:
- 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
- Research Questions
- CONCLUSION:
- Possible methods were developed to test research question
- FUTURE STEPS:
- Refine research method and make more specific methods