#1: Codon Usage Bias in Phylogenetic Systematics: A review
Authors
Justin Miller
Michael Whiting
Perry Ridge
Novelty of Approach
-Describes phylogenetic approaches using codon usage
-Proposes future avenues of research
Causes of Codon Usage Bias
-The ramp sequence consists of rare, slowly translated codons that increase ribosomal spacing, reduce mRNA secondary structure, and slow initial translation.
-tRNA are recharged with amino acids for synonymous codon translation when synonymous codons are in close proximity to each other. Recharging allows the tRNA to stay attached to the ribosome and significantly increases translation efficiency.
-tRNA are recharged with amino acids for identical codon translation when identical codons are in close proximity to each other. Recharging allows the tRNA to stay attached to the ribosome and significantly increases translation efficiency.
-Cognate, near-cognate, and non-cognate tRNA may attempt to bind to an mRNA codon. If relatively few cognate tRNA are available, translation will slow because other tRNA attempt to bind to the same codon. This process is essential for translation elongation, efficiency, and accuracy.
-Overall GC content in a gene is highly correlated with GC content at the third codon position. GC content influences over two-thirds of codon variation.
#2: Codon Pairs are Phylogenetically Conserved: Codon pairing as a novel phylogenetic character state for parsimony and alignment-free methods
Authors
Justin Miller
Lauren McKinnon
Michael Whiting
Perry Ridge
Novelty of Approach
-Recovers phylogenies using codon pairing under both alignment-free and parsimony frameworks
-Analyzes the extent of codon pairing across 23,423
Results
-Co-tRNA and identical codon pairing are prevalent in all domains of life.
-The optimal window size for codon pairs is typically smaller than the length of a ribosome.
-Combined, the alignment-free and parsimony-based approaches recover the most congruent trees compared with the established phylogenies in six out of ten taxonomic groups and ties maximum likelihood in another taxonomic group.
-Codon pairing should be considered as a novel character state in future phylogenomic studies.
Implications
-Novel character state in phylogenomic studies
-Faster and more accurate than maximum likelihood in some instances
-Another avenue of phylogenomic research
Comparisons with the Open Tree of Life
Comparisons with the NCBI Taxonomy
#3: Arabidopsis Twinkle and DNA Polymerase Interactions
Authors
Stewart Morley
Antolin Peralta
Luis Brieba
Justin Miller
Perry Ridge
Amanda Oliphant
Stephen Aldous
Brent Nielsen
Novelty of Approach
-Used Direct Coupling Analysis to identify potential interactions between Twinkle and DNA polymerase
Results
-8 out of 10 top potential interaction sites were verified in the wet lab.
Implications
-Identified new interaction sites in Arabidopsis
-Shows that DCA can accurately predict potential protein-protein interaction domains.
Ramp Sequences in Various Species Partitions