Made by: Special , Awesome, and Precious (Sandra, Morella, and Tal)

1. Reflection About Whether or Not the A3 Subcluster Should be Split into Two Groups Based on PCR Results Made by: Special, Awesome, and Precious (Sandra, Morella, and Tal) Conclusions/Discussion Based on the results, it is easy to state that the phages in the A3 subcluster seem to follow two different patterns. The photos of the gels support the fact that the A3 subcluster could be split into two distinct groups. JHC117 deviated from the two distinct groups with BamHI cutting the DNA along with EcoRI; however, it matches Bxz2’s gel otherwise, so it could be categorized in the same group. Data Abstract We set out to determine whether or not the A3 subcluster should be split into two groups or not. We used Case It! (1) to generate virtual DNA gels of each A3 phage and compared them. Our results supported the idea that the A3 subcluster could be split into two groups, even though JHC117 deviated from both groups by being cut by BamHI. 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 Figure 2: Popcicle (Group 1) Figure 1: Bxz2 (Group 2) Figure 3: JHC117 (Group 2) Key 1=1-kb Ladder 2=Undigested DNA 3=BamHI Enzyme 4=ClaI Enzyme 5=EcoRI Enzyme 6=HindIII Enzyme Introduction We are trying to determine whether the A3 subcluster should be split into two groups. There has been evidence from previous research that the A3 subcluster should be split, and we are further investigating that theory. Our previous class research compared the nucleotide sequences and Phamerator maps, which showed there was support for the A3 subcluster to be split into two groups (2). References Bergland, M, et. al. 2012. Case It!. http://www.caseitproject.org/credits/. Hatfull, G, et. al. 11 Jan 2010. Comparative Genomic Analysis of 60 MycobacteriophageGenomes: Genome Clustering, Gene Acquisition, and Gene Size. Science Direct, 397: 119-143. Group 1 Phages: Norbert, Phantastic, Popcicle, Veracruz,HelDan, Rockstar Group 2 Phages: Misomonster, JHC117, EpicPhail, Mainiac, MarQuardt, Methuselah, Phoxy, Microwolf, Vix, Bxz2, Spike509, Jobu08 Summary of results All of the phages in the group 1 have not been cut by any of the restriction enzymes. Figure 2, which shows a photo of the PCR of the phage Popcicle, is a representative of what all the gels of the phages in this group look like. Practically all of the gels that we generated in group 2 look like figure 1, which shows the gel of Bxz2. Only EcoRI cut the DNA. The phage JHC117, though, is special because it has been cut by both EcoRIand BamHI. Methods We used the Case It! (1) software to generate virtual gels of all the A3 phages. We downloaded the fasta files of each A3 phage and used it in Case It! (1) to generate the gels. Then, we took pictures of each gel and compared them. Virtual gels are the same as gels generated in the lab, but they are more efficient and run faster. Acknowledgements We would like to thank Dr. Klyczek, Dr. Mogen and Dr. Bonilla for being there to answer any questions or to clear out any confusions that we had. We would also like to thank Stephen, our Teacher Assistant for being available at anytime. Last but not least, we thank HHMI for making this experience possible.