April
19
APRIL 15TH AND 17TH- LABS
- APRIL 15TH 2019
- OBJECTIVE:
- Create a document with all the sequences that need to be run through data bases
- Create a background for project
- PROCEDURE:
- A document was created and the gene for the terminase of a phage belonging to each of the following clusters was created:
- AU1 AU2 AU3 AW BI1(bing) BI2 BI3 BI4 CC DJ EL
- A background was written for the project
- RESULT:
- Introduction (Background Information)
- Horizontal gene transfer (HGT) is the transfer of genes from organism to another in- the gene is being passed along horizontally across a generation
- Occurs between bacteria and bacteria, or virus and bacteria
- Is a crucial part in antibiotic resistance
- Can be used to show ancestry between viruses, to look at genetic similarities
- Phamerator is a map of the genomes of phages, and lines are drawn across the gene in order to show synteny, or similarities between phages
- https://www.nature.com/articles/445369a
- CONCLUSION:
- Document was created
- FUTURE STEPS:
- Finish abstract
- –APRIL 17TH 2019
- OBJECTIVE:
- Write parts of presentation for project (abstract, methods used, results etc.)
- PROCEDURE:
- A document on google docs was shared with group members
- RESULT:
- Title
- Evidence for Supercluster 46041 and others.
- Guiding Question
- Our objective is to compare pham 46041 DNA polymerase and observe the patterns that can be derived from cross-analysis.
- Abstract
- The Horizontal gene transfer is an evolutionary method that promotes genetic diversity through the passing of genes. A result of the mosaic model within populations of bacteriophage cells is the common appearance of conserved domain groups that are present across different clusters. The smaller size of bacteriophage genome allows the presentation of modules, a group of specialized genes that are localized within the same region. The analysis of a conserved modules in clusters that are associated with the DNA polymerases was conducted in the experiment. Through the tool Phamerator, we observed the phage genome map to determine the range of modules and identify the clusters needed to detect the sequence similarity. We also used RaptorX to observe the protein-protein interaction similarity between the gene modules and constructed phylogenetic trees that visually compares the multiple clusters of actionobacteriophages and demonstrate the shared evolutionary relationship with the DNA Polymerase gene. We have discovered evidence of common modules existing across multiple seemingly dissimilar clusters. This leads us to believe that these clusters all belong to a larger group.
- Phage genome have a typically smaller genome that can be analyzed after isolation and characterization through bioinformatic tools such as Phamerator, the construction of a phylogenetic tree based sequence similarity for a specific protein product, and the structure analysis of analogous sequences of the same pham.
- List of tools used: Tmhmm, raptor X Structure Prediction, Raptor X Deep Align, Jmol,Dendroscope,, HGTree, Phamerator
- Introduction (Background Information)
- Horizontal gene transfer (HGT) is the transfer of genes from organism to another in- the gene is being passed along horizontally across a generation
- Occurs between bacteria and bacteria, or virus and bacteria
- Is a crucial part in antibiotic resistance
- Can be used to show ancestry between viruses, to look at genetic similarities
- Phamerator is a map of the genomes of phages, and lines are drawn across the gene in order to show synteny, or similarities between phages
- https://www.nature.com/articles/445369a
- Types of Data Collected
- Protein structure comparison, protein and dna sequences from different clusters, Phylogenetic tree,
- Results (to date)
- Supercluster 46041: AM, AW, AU, BI, CC, DJ, EL
- Supercluster 45806: AZ, BB, BJ, BL, EB, EH
- Conclusions (if any have been drawn)
- For gene 60, TMHMM results show it is a transmembrane protein. There also shows evidence for synteny in transmembrane call in EL phage. Each transmembrane protein is structurally very different, but is made out of a group of alpha helices then a chain of amino acids then a beta pleated sheets.
- For gene 61, there also seems to have a G5 domain. Blasted against actinobacteria and resulted in a streptomyces hit with a decent e value. The hit contained 3 conserved domains one of which aligned with the amino acid sequence hit. When comparing visual structures the predicted protein structure matches a typical g5 protein structure.
- CONCLUSION:
- Document was created
- FUTURE STEPS:
- Create phylogenetic tree and continue collecting data