04/17/19

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 individual research was worked on.
2. two group members have started finding the start codons for their assigned proteins using phages db for the fasta file and dna master for the sequence
3. one group member began to use jmol and raptor x to start structure analysis
4. the abstract for the presentation was drafted
5. The group worked until the end of lab.

Results

so far. no real results. a lot of  the data collection has been performed.

abstract draft:

ATG, TTG and GTG are the three start codons that initiate gene translation in all bacteria. When ribosomes detects these start codons, they begin to synthesize proteins according to the sequence of the codons. Each start codons produce different amino acids, which interact differently with other amino acids to form different structure i.e. leads to a different function. Genes in arthrobacter phage genomes are used to explore whether this change is significant and affects the preference for the start codons in specific genes based on the change or lack thereof. The start codons for tape measure protein, major tail proteins, and minor tail proteins in the annotated genome of known sequenced arthrobacter phage were collected using DNA Master and the PhagesDB database to determine the start codons of the genes that produce these proteins. The gene length, genome length, cluster %GC, and direction of the genes were also recorded to determine possible factors that make one start codon preferable to another. i.e. ribosomal binding and initiation of translation, in the phage genome. Raptor X and Jmol are used to determine the most probable structure of the product protein based on the amino acid sequence. Protein models are produced for each type of protein using different start codons and the structures are then compared.

Conclusion

this research will require a great deal of data collection as there are a little more than 200 sequenced arthrobacter phages. enough data can be collected for the research in the given time.

Future steps

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