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)

Abstract This study had the following aims: (i) to translate the Spiritual Health and Life-Orientation Measure (SHALOM) into Brazilian Portuguese and adapt it to ensure the semantic/conceptual equivalence and content validity of the Brazilian version and (ii) to analyse the psychometric properties—reliability, convergent validity, discriminant validity and factorial validity—of the lived experience component, also called the Spiritual Well-Being Questionnaire (SWBQ), in a calibration sample and in a validation sample of Brazilian adults. The calibration sample comprised 436 subjects, 159 men and 277 women, aged between 18 and 79 years (mean age = 32.20 years; SD = 11.46); the validation study sample comprised 388 subjects, 253 women and 135 men, aged between 18 and 59 years (mean age = 30.59 years; SD = 9.44). All subjects completed a sociodemographic questionnaire, the Brazilian SWBQ and the Psychological Well-being Scale (PWBS). The results provide evidence of the reliability and factorial validity of an oblique four-factor model of a reduced 17-item version but revealed some problems with the convergent validity of the communal and personal factors (average variance extracted < .50). Nonetheless, these results provide evidence that the Brazilian version of the lived experience component of SHALOM (or SWBQb) has good psychometric properties and is a valid method of evaluating the spiritual health of Brazilian adults. Further research is required to establish the convergent and discriminant validity of this reduced version