Enrichment analysis of Alu elements with different spatial chromatin proximity in the human genome

Transposable elements (TEs) have no longer been totally considered as “junk DNA” for quite a time since the continual discoveries of their multifunctional roles in eukaryote genomes. As one of the most important and abundant TEs that still active in human genome, Alu, a SINE family, has demonstrated its indispensable regulatory functions at sequence level, but its spatial roles are still unclear. Technologies based on 3C(chromosomeconformation capture) have revealed the mysterious three-dimensional structure of chromatin, and make it possible to study the distal chromatin interaction in the genome. To find the role TE playing in distal regulation in human genome, we compiled the new released Hi-C data, TE annotation, histone marker annotations, and the genome-wide methylation data to operate correlation analysis, and found that the density of Alu elements showed a strong positive correlation with the level of chromatin interactions (hESC: r=0.9, P<2.2×1016; IMR90 fibroblasts: r = 0.94, P < 2.2 × 1016) and also have a significant positive correlation withsomeremote functional DNA elements like enhancers and promoters (Enhancer: hESC: r=0.997, P=2.3×10−4; IMR90: r=0.934, P=2×10−2; Promoter: hESC: r = 0.995, P = 3.8 × 10−4; IMR90: r = 0.996, P = 3.2 × 10−4). Further investigation involving GC content and methylation status showed the GC content of Alu covered sequences shared a similar pattern with that of the overall sequence, suggesting that Alu elements also function as the GC nucleotide and CpG site provider. In all, our results suggest that the Alu elements may act as an alternative parameter to evaluate the Hi-C data, which is confirmed by the correlation analysis of Alu elements and histone markers. Moreover, the GC-rich Alu sequence can bring high GC content and methylation flexibility to the regions with more distal chromatin contact, regulating the transcription of tissue-specific genes

Reversal of aberrant cancer methylome and transcriptome upon direct reprogramming of lung cancer cells

10.1038/srep00592Scientific Reports2

Income Attainment among Victims of Violence: Results From a Preliminary Study

Violent victimisation may have many short-term psychological and physical outcomes. Occasionally, the negative aftermath of violence persists over time or induces other and more far-reaching consequences. Income attainment after victimisation is one of these outcomes. To date, previous studies have focussed on the income effects of violent victimisation during childhood and adolescence. Violence exposure during the early stages of the life course may frustrate processes of educational and occupational attainment and consequentially result in lower income levels. However, in addition or alternatively, many other and age-independent pathways between violent victimisation and income may be suggested. Prior studies appear to have paid little attention to this issue. Therefore, the purpose of the current study was to explore whether violent victimisation is associated with income levels several years after victimisation, irrespective of the age at which victimisation occurs. Victims of violence were recruited through the Dutch Victim Compensation Fund. To preliminary estimate the effect of violent victimisation on income, a comparable control group of non-victims was composed. The study sample contained 206 victims and 173 non-victims. Both bivariate correlational and multivariate statistical techniques suggested that violent victimisation is a significant predictor of income. Implications of the presented results were discussed with regard to future research and policy practice

Geographic and Racial Variation in Premature Mortality in the U.S.: Analyzing the Disparities

Life expectancy at birth, estimated from United States period life tables, has been shown to vary systematically and widely by region and race. We use the same tables to estimate the probability of survival from birth to age 70 (S70), a measure of mortality more sensitive to disparities and more reliably calculated for small populations, to describe the variation and identify its sources in greater detail to assess the patterns of this variation. Examination of the unadjusted probability of S70 for each US county with a sufficient population of whites and blacks reveals large geographic differences for each race-sex group. For example, white males born in the ten percent healthiest counties have a 77 percent probability of survival to age 70, but only a 61 percent chance if born in the ten percent least healthy counties. Similar geographical disparities face white women and blacks of each sex. Moreover, within each county, large differences in S70 prevail between blacks and whites, on average 17 percentage points for men and 12 percentage points for women. In linear regressions for each race-sex group, nearly all of the geographic variation is accounted for by a common set of 22 socio-economic and environmental variables, selected for previously suspected impact on mortality; R2 ranges from 0.86 for white males to 0.72 for black females. Analysis of black-white survival chances within each county reveals that the same variables account for most of the race gap in S70 as well. When actual white male values for each explanatory variable are substituted for black in the black male prediction equation to assess the role explanatory variables play in the black-white survival difference, residual black-white differences at the county level shrink markedly to a mean of −2.4% (+/−2.4); for women the mean difference is −3.7% (+/−2.3)

Health status and quality of life among older adults in rural Tanzania

BACKGROUND\ud \ud Increasingly, human populations throughout the world are living longer and this trend is developing in sub-Saharan Africa. In developing African countries such as Tanzania, this demographic phenomenon is taking place against a background of poverty and poor health conditions. There has been limited research on how this process of ageing impacts upon the health of older people within such low-income settings.\ud \ud OBJECTIVE\ud \ud The objective of this study is to describe the impacts of ageing on the health status, quality of life and well-being of older people in a rural population of Tanzania.\ud \ud DESIGN\ud \ud A short version of the WHO Survey on Adult Health and Global Ageing questionnaire was used to collect information on the health status, quality of life and well-being of older adults living in Ifakara Health and Demographic Surveillance System, Tanzania, during early 2007. Questionnaires were administered through this framework to 8,206 people aged 50 and over.\ud \ud RESULTS\ud \ud Among people aged 50 and over, having good quality of life and health status was significantly associated with being male, married and not being among the oldest old. Functional ability assessment was associated with age, with people reporting more difficulty in performing routine activities as age increased, particularly among women. Reports of good quality of life and well-being decreased with increasing age. Women were significantly more likely to report poor quality of life (odds ratio 1.31; p<0.001, 95% CI 1.15-1.50).\ud \ud CONCLUSIONS\ud \ud Older people within this rural Tanzanian setting reported that the ageing process had significant impacts on their health status, quality of life and physical ability. Poor quality of life and well-being, and poor health status in older people were significantly associated with marital status, sex, age and level of education. The process of ageing in this setting is challenging and raises public health concerns

Historical Research Approaches to the Analysis of Internationalisation

Historical research methods and approaches can improve understanding of the most appropriate techniques to confront data and test theories in internationalisation research. A critical analysis of all “texts” (sources), time series analyses, comparative methods across time periods and space, counterfactual analysis and the examination of outliers are shown to have the potential to improve research practices. Examples and applications are shown in these key areas of research with special reference to internationalisation processes. Examination of these methods allows us to see internationalisation processes as a sequenced set of decisions in time and space, path dependent to some extent but subject to managerial discretion. Internationalisation process research can benefit from the use of historical research methods in analysis of sources, production of time-lines, using comparative evidence across time and space and in the examination of feasible alternative choices

The comparative osmoregulatory ability of two water beetle genera whose species span the fresh-hypersaline gradient in inland waters (Coleoptera: Dytiscidae, Hydrophilidae).

A better knowledge of the physiological basis of salinity tolerance is essential to understanding the ecology and evolutionary history of organisms that have colonized inland saline waters. Coleoptera are amongst the most diverse macroinvertebrates in inland waters, including saline habitats; however, the osmoregulatory strategies they employ to deal with osmotic stress remain unexplored. Survival and haemolymph osmotic concentration at different salinities were examined in adults of eight aquatic beetle species which inhabit different parts of the fresh-hypersaline gradient. Studied species belong to two unrelated genera which have invaded saline waters independently from freshwater ancestors; Nebrioporus (Dytiscidae) and Enochrus (Hydrophilidae). Their osmoregulatory strategy (osmoconformity or osmoregulation) was identified and osmotic capacity (the osmotic gradient between the animal's haemolymph and the external medium) was compared between species pairs co-habiting similar salinities in nature. We show that osmoregulatory capacity, rather than osmoconformity, has evolved independently in these different lineages. All species hyperegulated their haemolymph osmotic concentration in diluted waters; those living in fresh or low-salinity waters were unable to hyporegulate and survive in hyperosmotic media (> 340 mosmol kg(-1)). In contrast, the species which inhabit the hypo-hypersaline habitats were effective hyporegulators, maintaining their haemolymph osmolality within narrow limits (ca. 300 mosmol kg(-1)) across a wide range of external concentrations. The hypersaline species N. ceresyi and E. jesusarribasi tolerated conductivities up to 140 and 180 mS cm(-1), respectively, and maintained osmotic gradients over 3500 mosmol kg(-1), comparable to those of the most effective insect osmoregulators known to date. Syntopic species of both genera showed similar osmotic capacities and in general, osmotic responses correlated well with upper salinity levels occupied by individual species in nature. Therefore, osmoregulatory capacity may mediate habitat segregation amongst congeners across the salinity gradient