Biomedical subjects

Karen Oliver

Publications and source records attributed to Karen Oliver.

5 recordsLinked to original sources

PubMed2005

Dual polarization interferometry size and density characterisation of DNA immobilisation and hybridisation.

Investigation of nucleic acid interactions was performed using dual polarization interferometry, a novel approach to elucidating molecular interactions. This paper presents a preliminary study of adsorption of single stranded DNA onto functionalised silicon oxynitride, compared with covalent linkage, and avidin-biotin immobilisation. The effect of probe concentration on hybridisation efficiency was also examined. We found that increasing the electrolyte concentration resulted in a decrease of adsorbed DNA and that capture of a biotinylated duplex DNA on an adsorbed avidin layer resulted in four times fewer molecules per cm(2) than for duplex DNA covalently bound via an amine end terminal. The rate of thickness increase of a biotin probe layer on an adsorbed avidin capture layer increased 10-fold when the probe concentration was increased from 0.1 microM to 1 microM. The close grafting density of the higher concentration probe meant that the immobilised probes were unavailable for hybridisation.

Biosensing Techniques↗

PubMed2005

Evidence for widespread reticulate evolution within human duplicons.

Approximately 5% of the human genome consists of segmental duplications that can cause genomic mutations and may play a role in gene innovation. Reticulate evolutionary processes, such as unequal crossing-over and gene conversion, are known to occur within specific duplicon families, but the broader contribution of these processes to the evolution of human duplications remains poorly characterized. Here, we use phylogenetic profiling to analyze multiple alignments of 24 human duplicon families that span >8 Mb of DNA. Our results indicate that none of them are evolving independently, with all alignments showing sharp discontinuities in phylogenetic signal consistent with reticulation. To analyze these results in more detail, we have developed a quartet method that estimates the relative contribution of nucleotide substitution and reticulate processes to sequence evolution. Our data indicate that most of the duplications show a highly significant excess of sites consistent with reticulate evolution, compared with the number expected by nucleotide substitution alone, with 15 of 30 alignments showing a >20-fold excess over that expected. Using permutation tests, we also show that at least 5% of the total sequence shares 100% sequence identity because of reticulation, a figure that includes 74 independent tracts of perfect identity >2 kb in length. Furthermore, analysis of a subset of alignments indicates that the density of reticulation events is as high as 1 every 4 kb. These results indicate that phylogenetic relationships within recently duplicated human DNA can be rapidly disrupted by reticulate evolution. This finding has important implications for efforts to finish the human genome sequence, complicates comparative sequence analysis of duplicon families, and could profoundly influence the tempo of gene-family evolution.

Computational Biology↗

PubMed2005

The genome of the kinetoplastid parasite, Leishmania major.

Leishmania species cause a spectrum of human diseases in tropical and subtropical regions of the world. We have sequenced the 36 chromosomes of the 32.8-megabase haploid genome of Leishmania major (Friedlin strain) and predict 911 RNA genes, 39 pseudogenes, and 8272 protein-coding genes, of which 36% can be ascribed a putative function. These include genes involved in host-pathogen interactions, such as proteolytic enzymes, and extensive machinery for synthesis of complex surface glycoconjugates. The organization of protein-coding genes into long, strand-specific, polycistronic clusters and lack of general transcription factors in the L. major, Trypanosoma brucei, and Trypanosoma cruzi (Tritryp) genomes suggest that the mechanisms regulating RNA polymerase II-directed transcription are distinct from those operating in other eukaryotes, although the trypanosomatids appear capable of chromatin remodeling. Abundant RNA-binding proteins are encoded in the Tritryp genomes, consistent with active posttranscriptional regulation of gene expression.

Animals↗

PubMed2005

Correlates of physical activity among women with fibromyalgia syndrome.

BACKGROUND: Fibromyalgia (FMS) is a chronic pain syndrome of unknown origin that lacks standardized treatment. However, participation in physical activity (PA) benefits people with FMS. Despite the psychosocial and health benefits that can be gained through PA, the correlates of PA among people with FMS remain poorly understood. PURPOSE: The purpose of this study was to identify and compare the effects of cross-sectional and longitudinal correlates of PA among women with FMS. METHODS: Participants were 187 female members of a HMO with a confirmed diagnosis of FMS. They were administered a battery of questionnaires assessing potential correlates of PA. These correlates were suggested by social cognitive theory and the transtheoretical model, and have been repeatedly associated with PA among the general population. RESULTS: Multivariate analyses indicated that self-efficacy for PA and the behavioral processes of change were the strongest discriminators among PA adopters, maintainers, quitters, and those who were sedentary. Enjoyment of PA, barriers to PA, the impact of FMS, and the environment also significantly discriminated among these groups. Longitudinally, changes in self-efficacy were significantly associated with changes in PA. CONCLUSIONS: These findings suggest that self-efficacy may play a critical role in both the present and long-term PA of women with FMS. They also lend additional support to the role of social cognitive and transtheoretical variables in discriminating among levels of PA.

Aged↗

PubMed2002

Predictors of exercise behaviors among fibromyalgia patients.

BACKGROUND: Exercise improves the physical and psychological well being of patients with fibromyalgia syndrome (FMS). However, exercise interventions for patients with FMS have suffered from poor adherence. The purpose of this study was to examine predictors of exercise for people with FMS. METHODS: Participants were 444 patients with FMS who were part of a larger study. Hierarchical logistic regression analyses were conducted examining exercise behavior at multiple time points. Discriminant analyses were also used to identify predictor variables. RESULTS: Engaging in regular exercise and having higher exercise self-efficacy significantly predicted continued engagement in exercise behavior in people with FMS. Age, employment status, depression, education level, self-efficacy for managing FMS, and the size of one's social network also demonstrated predictive qualities. CONCLUSION: Exercise self-efficacy and continued participation in regular exercise most strongly predicted present and future exercise behavior in patients with FMS. Interventions designed to train FMS patients in initiating exercise programs while addressing exercise self-efficacy, depression, and social support are warranted.

Adult↗