In order, the restriction enzymes we used were: BamHI, ClaI, EcoRI, HaeIII, HindIII, and SalI. The clusters are a way of sorting the phages based on similarity in their genome. For example, all C cluster phages may have a non-coding region unique only to the C cluster. And to my knowledge, the cluster does not matter in treatment.
First wanted to say how I really enjoyed how you named your phage “Squido.” In future directions you mentioned how you would like to sequence “Squido.” How would this be done?
The full genome would need to be isolated from the phage and then could be run using any variety of next-gen sequencing techniques (such as nanopore sequencing) to computer generate a copy of genome.
Great presentation! Why did you originally believe K cluster more likely? How would finding primer for the N cluster be beneficial to the bigger research?
When we ran the number of cuts through a software, it gave us a similarity value from 0-1 for each cluster (with 1 being the most similar) and the K cluster had a value of 0.66 compared to the N cluster value of 0.5. The similarity score is not definite however and only helps you form a hypothesis. The N cluster is rare so finding primers is difficult. More primers means more phage can be clustered and new phages can be found.
Do you know what type of restriction enzymes you used? Also, what do the different clusters mean- are some clusters better for treatment than others?
In order, the restriction enzymes we used were: BamHI, ClaI, EcoRI, HaeIII, HindIII, and SalI. The clusters are a way of sorting the phages based on similarity in their genome. For example, all C cluster phages may have a non-coding region unique only to the C cluster. And to my knowledge, the cluster does not matter in treatment.
Why was PCR the best method for analyzing your phage?
The goal of the “analysis” was to see what cluster the phage belonged in. PCR is what allowed us to visualize this.
First wanted to say how I really enjoyed how you named your phage “Squido.” In future directions you mentioned how you would like to sequence “Squido.” How would this be done?
The full genome would need to be isolated from the phage and then could be run using any variety of next-gen sequencing techniques (such as nanopore sequencing) to computer generate a copy of genome.
Great presentation! Why did you originally believe K cluster more likely? How would finding primer for the N cluster be beneficial to the bigger research?
When we ran the number of cuts through a software, it gave us a similarity value from 0-1 for each cluster (with 1 being the most similar) and the K cluster had a value of 0.66 compared to the N cluster value of 0.5. The similarity score is not definite however and only helps you form a hypothesis. The N cluster is rare so finding primers is difficult. More primers means more phage can be clustered and new phages can be found.