Identification of a unique library of complex, but ordered, arrays of repetitive elements in the human genome and implication of their potential involvement in pathobiology

Approximately 2% of the human genome is reported to be occupied by genes. Various forms of repetitive elements (REs), both characterized and uncharacterized, are presumed to make up the vast majority of the rest of the genomes of human and other species. In conjunction with a comprehensive annotation of genes, information regarding components of genome biology, such as gene polymorphisms, non-coding RNAs, and certain REs, is found in human genome databases. However, the genome-wide profile of unique RE arrangements formed by different groups of REs has not been fully characterized yet. In this study, the entire human genome was subjected to an unbiased RE survey to establish a whole-genome profile of REs and their arrangements. Due to the limitation in query size within the bl2seq alignment program (National Center for Biotechnology Information [NCBI]) utilized for the RE survey, the entire NCBI reference human genome was fragmented into 6206 units of 0.5 M nucleotides. A number of RE arrangements with varying complexities and patterns were identified throughout the genome. Each chromosome had unique profiles of RE arrangements and density, and high levels of RE density were measured near the centromere regions. Subsequently, 175 complex RE arrangements, which were selected throughout the genome, were subjected to a comparison analysis using five different human genome sequences. Interestingly, three of the five human genome databases shared the exactly same arrangement patterns and sequences for all 175 RE arrangement regions (a total of 12,765,625 nucleotides). The findings from this study demonstrate that a substantial fraction of REs in the human genome are clustered into various forms of ordered structures. Further investigations are needed to examine whether some of these ordered RE arrangements contribute to the human pathobiology as a functional genome unit.     

Fidelity or flexibility: An ethnographic study of the implementation and use of the Patient Activation Measure

Objective

To evaluate the use of the PAM in the English National Health service. The PAM is a validated scale that measures ‘activation’ (people’s knowledge, skills, and confidence in managing their health) and assigns patients to four categories of activation (low-to-high). Some evidence suggests that higher activation levels correlate to better clinical outcomes and patient experiences, and lower healthcare costs. Empirical studies of implementing the PAM are scarce.

Simulation of damage in a porcine prosthetic heart valve

A model of a bioprosthetic porcine valve has been produced which simulates the non-linear elastic behaviour of the fixed tissue and the re-inforcement of the leaflets by collagen fibre bundles. The loading on the model is a spatially uniform but temporally varying distribution of pressure. Bending is allowed in the tissue of the leaflets and is shown to be significant in determining the behaviour and failure modes of the leaflets. The simulation of the undamaged valve is validated against in vitro pulse duplicator studies and a simple fluid-solid interaction simulation. Progressive damage is introduced into three models of the valve at a location where tears have been commonly found in vivo. It was found that during the opening and closing of the valve the tip of the tears were subject to mode III or tearing displacements, but that in the fully closed or diastolic state the tear tip was subject to mode I or opening displacements such that it would be expected to propagate parallel to the line of attachment to the stent. The tear tip stresses increased with the length of the tear so that the rate of tearing would be expected to increase with length.     

Myxoma virus M063R is a host range gene essential for virus replication in rabbit cells

The myxoma virus M063R gene product exhibits some sequence similarity to the poxvirus host range gene, C7L, of vaccinia virus. To address the potential host range function of the M063R gene product in rabbits, a deletion mutant of myxoma virus (vMyx63KO) was generated and characterized. vMyx63KO replicated to normal titre levels and produced foci that were indistinguishable from those produced by MV in vitro in a monkey kidney cell line (BGMK) that are permissive for wild type MV. However, vMyx63KO failed to replicate in all rabbit cell lines tested, including both primary and established cells lines, as well as cells derived from a variety of tissues. M063R expression was not required for myxoma virus binding, entry or early gene expression, whereas DNA replication was aborted and late genes were not expressed in vMyx63KO infected rabbit cells. Thus, the replication block for vMyx63KO in rabbit cells preceded the stage of late gene expression and DNA replication. Finally, an in vivo pathogenesis study indicated that vMyx63KO failed to cause any signs of classic myxomatosis in infected rabbits, but functioned as a non-replicating vaccine and provided protection for subsequent challenge by wild type myxoma virus. Altogether, these observations demonstrate that M063R plays a critical role in determining the host specificity of myxoma virus in rabbit cells.     

Linkage Disequilibrium Pattern in Asthma Candidate Genes from 5q31‐q33 in the Singapore Chinese Population

Studies have shown linkage between microsatellite markers from the chromosome 5q31‐q33 region with asthma, atopy and total IgE levels in the Singapore Chinese population. However, subsequent case‐control studies failed to show association between the polymorphisms in the candidate genes from this region and asthma or related phenotypes. In this study, we investigated 20 asthma candidate genes from this region for all possible informative polymorphisms within our population, linkage disequilibrium (LD) structure and tagging SNP transferability from HapMap populations. We re‐sequenced these genes and identified 267 polymorphisms including 26 insertion‐deletions, four microsatellite markers and 237 single nucleotide polymorphisms. The region contained 17 distinct LD blocks with the largest within the serine peptidase inhibitor kazal type 5 (SPINK5) gene spanning 23 kb. Of the 267 polymorphisms identified, 40% are represented in HapMap Han Chinese from Beijing and 29% in Han Chinese from Denver. 72% of the polymorphisms can be represented by tagged SNPs from the HapMap Beijing Han Chinese population and are highly correlated in terms of minor allele frequencies and LD structure. Our data suggest that although the HapMap Han Chinese population from Beijing is very similar to the Singapore Chinese population, this similarity is insufficient to account for up to 28% of the polymorphisms in the local population.     

Dustborne and airborne fungal propagules represent a different spectrum of fungi with differing relations to home characteristics

BACKGROUND: Exposure to fungi is often assessed by culturing floor dust or air samples. Our objective was to evaluate the relationships between dustborne and airborne fungi and to identify factors that modify these relationships. METHODS: From November 1994 to September 1996 sequential duplicate 45-l air samples were collected in bedrooms of 496 homes in the Boston area, using a Burkard culture plate sampler. After air sampling, bedroom floors were sampled with a vacuum cleaner that was modified to collect dust in a cellulose extraction thimble. Dust was sieved, and the fine dust was dilution-plated onto DG-18 media. RESULTS: Concentrations of total culturable fungi per gram of bedroom-floor dust were correlated weakly, but significantly, with those of indoor air (r = 0.13, P < 0.05). Concentrations of some individual taxa in the dust and indoor air were also weakly associated. Adjusting for the concentrations of fungi in outdoor air, dustborne fungal concentrations were positively associated with those in indoor air for the taxa Cladosporium and Penicillium, but not for total fungi. The indoor air fungal levels were often predicted by different covariates to those predicting fungal levels in dust. The type of housing (house or apartment) and the presence of carpeting were often predictive factors for dust fungi. In contrast, outdoor fungal levels were often predictive of the indoor air fungal levels. CONCLUSIONS: Because our data do not indicate a strong overall relationship between culturable fungi in dust and indoor air, the results from these two methods (dust and air sampling) likely represent different types of potential fungal exposures to residents. It may be essential to collect both air and dust samples, as well as information on housing characteristics, as indicators for fungal exposure.     

Elevated peritoneal fluid luteinizing hormone and prolactin concentrations in infertile women with endometriosis

In this study, we compared (Mann-Whitney U-test) the peritoneal fluid FSH, LH and PRL levels, measured by RIA, at the follicular and luteal phases of the menstrual cycle in women with (n = 43; age 25-44 years) and with no evidence of endometriosis (n = 35; age 25-39 years) who were considered as controls. Both follicular and luteal phase FSH concentrations of women with endometriosis were not statistically different (n = 22 vs 18; 0.32-5.8 vs 0.50-8.2 IU/l, P = 0.247; n = 13 vs 14; 0.6-6.5 vs 0.66-6.7 IU/l, P = 0.604) compared to their respective controls. In contrast to FSH, the concentrations of LH at follicular (n = 19 vs 17; 3.1-34.2 vs 2.3-12.2 IU/l, P = 0.01) and luteal (n = 17 vs 15; 2.1-95.4 vs 1.3-17.9 IU/l, P = 0.02) phases of the test group was significantly elevated at both phases of the cycle. With respect to differences in PRL concentrations at follicular phase no significant change (n = 21 vs 16; 1030-5800 vs 1305-4650 mIU/l; P = 0.255) was observed. The greatest difference in luteal PRL concentrations (P = 0.007) was obtained between the women with endometriosis and controls (n = 17 vs 17; 1895-8600 vs 1041-5000 mIU/l). The results suggest that disordered synchronization of neuroendocrine mechanisms controlling LH and PRL may be the underlying abnormality causing infertility in our group of patients with endometriosis.     

Prospective Study of the Quality of Survival of Infants with Critical Fetal Reserve Detected by Antenatal Cardiotocography

From 1981 to 1986 antenatal cardiotocographic monitoring was performed on 9,992 high-risk pregnancies selected from a total obstetrical population of 31,518 patients (31.7%). A critical fetal reserve pattern was detected in 89 patients (0.9%) whose pregnancies resulted in 68 surviving infants, 19 perinatal deaths and 2 sudden infant deaths. Since 47.4% of the infants who died in the perinatal period did so because of a related congenital malformation, such a defect should be excluded in the fetus with critical fetal reserve, by ultrasonography, before delivery (there is usually insufficient time for fetal karyotyping). Sixty-three (92.6%) of the surviving children were assessed at our Growth and Developmental Clinic and disabilities were detected in 16 (25.4%); however, the disability was major in only 5, including 2 children with Down syndrome. The quality of survival of infants born from pregnancies complicated by critical fetal reserve was satisfactory as 60 of 63 children (95.2%) had neither a major disability related to intrauterine hypoxia identified by the cardiotocographic pattern, or had one likely to significantly interfere with their quality of life. Our results suggest that pregnancies can be continued until the cardiotocographic pattern becomes critical in order to gain fetal maturity, without compromise to the fetal brain.