75 research outputs found
Genome Dynamics of Short Oligonucleotides: The Example of Bacterial DNA Uptake Enhancing Sequences
Among the many bacteria naturally competent for transformation by DNA uptake—a phenomenon with significant clinical and financial implications— Pasteurellaceae and Neisseriaceae species preferentially take up DNA containing specific short sequences. The genomic overrepresentation of these DNA uptake enhancing sequences (DUES) causes preferential uptake of conspecific DNA, but the function(s) behind this overrepresentation and its evolution are still a matter for discovery. Here I analyze DUES genome dynamics and evolution and test the validity of the results to other selectively constrained oligonucleotides. I use statistical methods and computer simulations to examine DUESs accumulation in Haemophilus influenzae and Neisseria gonorrhoeae genomes. I analyze DUESs sequence and nucleotide frequencies, as well as those of all their mismatched forms, and prove the dependence of DUESs genomic overrepresentation on their preferential uptake by quantifying and correlating both characteristics. I then argue that mutation, uptake bias, and weak selection against DUESs in less constrained parts of the genome combined are sufficient enough to cause DUESs accumulation in susceptible parts of the genome with no need for other DUES function. The distribution of overrepresentation values across sequences with different mismatch loads compared to the DUES suggests a gradual yet not linear molecular drive of DNA sequences depending on their similarity to the DUES. Other genomically overrepresented sequences, both pro- and eukaryotic, show similar distribution of frequencies suggesting that the molecular drive reported above applies to other frequent oligonucleotides. Rare oligonucleotides, however, seem to be gradually drawn to genomic underrepresentation, thus, suggesting a molecular drag. To my knowledge this work provides the first clear evidence of the gradual evolution of selectively constrained oligonucleotides, including repeated, palindromic and protein/transcription factor-binding DNAs
Psychometric properties of the Brazilian version of the lived experience component of the Spiritual Health And Life-Orientation Measure (SHALOM)
Continued Development and Unconditioned Stimulus Characterization of Selectively Bred Lines of Taste Aversion Prone and Resistant Rats
Subpopulations of T Cells in the Rat that Mediate Graft-Versus-Host Reactions and Lethal Graft-Versus-Host Disease
Specific Systemic Graft-Versus-Host Resistance: Failure to Induce in Adult F1 Rats Tolerized at Birth to Anti-MHC Receptors on Parental T Cells
H-2-Restriction of T Cells Mediating Lethal Graft-Versus-Host-Disease to Minor Histocompatibility Determinants
Immunohistology of graft-versus-host disease mediated skin lesions and its correlation to a large granular lymphocyte surface phenotype and function
A minor transplantation antigen detected by MHC-restricted cytotoxic T lymphocytes during graft-versus-host disease
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