Tuesday, April 1, 2008

Systems Biology seminar TODAY!

We have the following seminar in systems computational biology this afternoon - try to attend if you can!

When & where: April 1, 2008, @ 3:00 PM in Alice Peters Auditorium.

What: Open Reading Frame Composition and Organization as Indicators of Phenotypic Diversity in Bacteria and Archaea.

Who: Scott Harrison, Ph.D., NIH Postdoctoral Fellow, Indiana University Purdue University Indianapolis.


Phenotypically, intragenomic recombination enables prokaryotic organisms to respond to dramatic changes in environmental conditions by restructuring the genome. The relationship between adaptation and alterations to genome structure over time impacts phylogeny and relates to factors regarding the optimal physiological configuration of genome structure. This study provides a quantitative treatment of open reading frame (ORF) organization based on aspects of functional conservation and DNA mobility. An analytical software system was built to facilitate randomizations, subsamplings, and comparative treatments of calculated and organized measures of open reading frame (ORF) attributes encompassing 447,551 annotated ORFs from 155 fully sequenced prokaryotic genomes. An operational subset of ORFs (O-ORFs) of putative phenotypic importance was selected based on a simple heuristic of similar length and content in comparison to five or more other ORFs. The proportion of total, annotated ORFs represented by O-ORFs strongly correlated with a predicted 3:1 signal-to-noise ratio of O-ORFs, likely associated with some phenotype, to putatively silent ORFs (S-ORFs) of unknown and undefined phenotype. The O-ORF subset had a significant degree of clustered chromosomal organization across a broad phylogenetic range. Additional study of ORF organization was conducted by developing quantitative measures of ORF clustering based on segmentation of the chromosomal sequence into consecutive regions of specified scalings. Properties associated with performance of non-parametric measures were partly characterized by simulation using an extended model of an abstract expansion modification system. Measures of ORF organization were evaluated as potential signatures of the recombinational history of an organism. As predicted by a postulated relationship between genomic organization and phylogenetic relatedness, the measurements had significant correspondence with times of divergence from last common ancestors. The presence of mobile elements predictably correlated with greater deviations from organizational symmetries of ORFs.



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