Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution

August 1, 2010Bisulfite sequencing measures absolute levels of DNA methylation at single-nucleotide resolution, providing a robust platform for molecular diagnostics. Here, we optimize bisulfite sequencing for genome-scale analysis of clinical samples. Specifically, we outline how restriction digestion targets bisulfite sequencing to hotspots of epigenetic regulation; we show that 30ng of DNA are sufficient for genome-scale analysis; we demonstrate that our protocol works well on formalinfixed, paraffin-embedded (FFPE) samples; and we describe a statistical method for assessing significance of altered DNA methylation patterns.National Institutes of Health (U.S.) (Grant R01HG004401)National Institutes of Health (U.S.) (Grant U54HG03067)National Institutes of Health (U.S.) (Grant U01ES017155

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.

Analysis of DNA methylation patterns relies increasingly on sequencing-based profiling methods. The four most frequently used sequencing-based technologies are the bisulfite-based methods MethylC-seq and reduced representation bisulfite sequencing (RRBS), and the enrichment-based techniques methylated DNA immunoprecipitation sequencing (MeDIP-seq) and methylated DNA binding domain sequencing (MBD-seq). We applied all four methods to biological replicates of human embryonic stem cells to assess their genome-wide CpG coverage, resolution, cost, concordance and the influence of CpG density and genomic context. The methylation levels assessed by the two bisulfite methods were concordant (their difference did not exceed a given threshold) for 82% for CpGs and 99% of the non-CpG cytosines. Using binary methylation calls, the two enrichment methods were 99% concordant and regions assessed by all four methods were 97% concordant. We combined MeDIP-seq with methylation-sensitive restriction enzyme (MRE-seq) sequencing for comprehensive methylome coverage at lower cost. This, along with RNA-seq and ChIP-seq of the ES cells enabled us to detect regions with allele-specific epigenetic states, identifying most known imprinted regions and new loci with monoallelic epigenetic marks and monoallelic expression

The Perceptions on Male Circumcision as a Preventive Measure Against HIV Infection and Considerations in Scaling up of the Services: A Qualitative Study Among Police Officers in Dar es Salaam, Tanzania.

\ud In recent randomized controlled trials, male circumcision has been proven to complement the available biomedical interventions in decreasing HIV transmission from infected women to uninfected men. Consequently, Tanzania is striving to scale-up safe medical male circumcision to reduce HIV transmission. However, there is a need to investigate the perceptions of male circumcision in Tanzania using specific populations. The purpose of the present study was to assess the perceptions of male circumcision in a cohort of police officers that also served as a source of volunteers for a phase I/II HIV vaccine (HIVIS-03) trial in Dar es Salaam, Tanzania. In-depth interviews with 24 men and 10 women were conducted. Content analysis informed by the socio-ecological model was used to analyze the data. Informants perceived male circumcision as a health-promoting practice that may prevent HIV transmission and other sexually transmitted infections. They reported male circumcision promotes sexual pleasure, confidence and hygiene or sexual cleanliness. They added that it is a religious ritual and a cultural practice that enhances the recognition of manhood in the community. However, informants were concerned about the cost involved in male circumcision and cleanliness of instruments used in medical and traditional male circumcision. They also expressed confusion about the shame of undergoing circumcision at an advanced age and pain that could emanate after circumcision. The participants advocated for health policies that promote medical male circumcision at childhood, specifically along with the vaccination program. The perceived benefit of male circumcision as a preventive strategy to HIV and other sexually transmitted infections is important. However, there is a need to ensure that male circumcision is conducted under hygienic conditions. Integrating male circumcision service in the routine childhood vaccination program may increase its coverage at early childhood. The findings from this investigation provide contextual understanding that may assist in scaling-up male circumcision in Tanzania.\u

Rapid, sensitive, type specific PCR detection of the E7 region of human papillomavirus type 16 and 18 from paraffin embedded sections of cervical carcinoma

Human papillomavirus (HPV) infection, and in particularly infection with HPVs 16 and 18, is a central carcinogenic factor in the uterine cervix. We established and optimized a PCR assay for the detection and discrimination of HPV types 16 and 18 in archival formaldehyde fixed and paraffin embedded (FFPE) sections of cervical cancer

Increasing uptake of colorectal cancer screening in Korea: a population-based study

<p>Abstract</p> <p>Background</p> <p>Colorectal cancer (CRC) screening rates are low in most Asian countries and remain largely unknown. This study examined trends in CRC screening rates after the introduction of the Korean National Cancer Screening Programme (NCSP) and determined the factors associated with uptake of CRC screening by test modality over time.</p> <p>Methods</p> <p>An annual population-based survey conducted through nationally representative random sampling from 2005-2008. In total, 3,699 participants from the 2005-2008 surveys were selected as study subjects. Face-to-face interviews were performed to assess the utilization rate of CRC screening by each screening modality.</p> <p>Results</p> <p>Overall, CRC screening within the recommended time interval increased significantly from 22.9% in 2005 to 36.6% in 2008 (<it>p </it>< 0.001). The proportion of subjects receiving a fecal occult blood test (FOBT) test within the previous year increased significantly from 7.2% in 2005 to 21.3% in 2008 (<it>p </it>< 0.001). Increases in FOBT testing were highest among those who had a lower income status (relative difference = 511.9%) and women (relative difference = 266.1%). Endoscopy use also increased from 18.0% in 2005 to 20.5% in 2008, albeit not significant. Overall, those who were male, non-smokers, 60-69 years old, and had a higher income status were more likely to have undergone up-to-date endoscopy and CRC screening.</p> <p>Conclusions</p> <p>This study revealed a substantial increase in up-to-date CRC screening in the general population from 2005 to 2008. However, more than half of adults in Korea are still not up-to-date with their CRC tests. It will be important to continue to investigate factors associated with up-to-date CRC screening by each modality.</p

Activity in perceptual classification networks as a basis for human subjective time perception

Despite being a fundamental dimension of experience, how the human brain generates the perception of time remains unknown. Here, we provide a novel explanation for how human time perception might be accomplished, based on non-temporal perceptual classification processes. To demonstrate this proposal, we build an artificial neural system centred on a feed-forward image classification network, functionally similar to human visual processing. In this system, input videos of natural scenes drive changes in network activation, and accumulation of salient changes in activation are used to estimate duration. Estimates produced by this system match human reports made about the same videos, replicating key qualitative biases, including differentiating between scenes of walking around a busy city or sitting in a cafe or office. Our approach provides a working model of duration perception from stimulus to estimation and presents a new direction for examining the foundations of this central aspect of human experience

Quantum Gravity in Everyday Life: General Relativity as an Effective Field Theory

This article is meant as a summary and introduction to the ideas of effective field theory as applied to gravitational systems. Contents: 1. Introduction 2. Effective Field Theories 3. Low-Energy Quantum Gravity 4. Explicit Quantum Calculations 5. ConclusionsComment: 56 pages, 2 figures, JHEP style, Invited review to appear in Living Reviews of Relativit

Isolated and dynamical horizons and their applications

Over the past three decades, black holes have played an important role in quantum gravity, mathematical physics, numerical relativity and gravitational wave phenomenology. However, conceptual settings and mathematical models used to discuss them have varied considerably from one area to another. Over the last five years a new, quasi-local framework was introduced to analyze diverse facets of black holes in a unified manner. In this framework, evolving black holes are modeled by dynamical horizons and black holes in equilibrium by isolated horizons. We review basic properties of these horizons and summarize applications to mathematical physics, numerical relativity and quantum gravity. This paradigm has led to significant generalizations of several results in black hole physics. Specifically, it has introduced a more physical setting for black hole thermodynamics and for black hole entropy calculations in quantum gravity; suggested a phenomenological model for hairy black holes; provided novel techniques to extract physics from numerical simulations; and led to new laws governing the dynamics of black holes in exact general relativity.Comment: 77 pages, 12 figures. Typos and references correcte

The feasibility of using electromagnetic waves in determining membrane failure through concrete

Concrete flat roof defects such as water leakage present a significant and common problem in large buildings, particularly in tropical countries, where rainfall is high. To monitor this condition, effective non-destructive test methods are required to detect problems at an early stage, especially hidden defects within the concrete roof, which are critical. This paper presents the potential use of electromagnetic (EM) waves for determining possible leakage of the concrete flat roof as a result of failure of the waterproof membrane layer. This study was assessed, experimentally by investigation of the propagation of EM waves through the roof and their interaction with water. Novel Microwave sensors described in the paper operate in the 6 GHz to 12 GHz frequency range using a Marconi 6200A microwave test set. A range of existing methods was reviewed and analysed. Results of experimental tests confirmed that microwaves could be used as an alternative non-destructive method for identifying water ingress caused by membrane failure into the concrete roof surface

Culture Shapes Efficiency of Facial Age Judgments

Background: Cultural differences in socialization can lead to characteristic differences in how we perceive the world. Consistent with this influence of differential experience, our perception of faces (e.g., preference, recognition ability) is shaped by our previous experience with different groups of individuals. Methodology/Principal Findings: Here, we examined whether cultural differences in social practices influence our perception of faces. Japanese, Chinese, and Asian-Canadian young adults made relative age judgments (i.e., which of these two faces is older?) for East Asian faces. Cross-cultural differences in the emphasis on respect for older individuals was reflected in participants ’ latency in facial age judgments for middle-age adult faces—with the Japanese young adults performing the fastest, followed by the Chinese, then the Asian-Canadians. In addition, consistent with the differential behavioural and linguistic markers used in the Japanese culture when interacting with individuals younger than oneself, only the Japanese young adults showed an advantage in judging the relative age of children’s faces. Conclusions/Significance: Our results show that different sociocultural practices shape our efficiency in processing facia