DNA Methylation: A Timeline of Methods and Applications

DNA methylation is a biochemical process where a DNA base, usually cytosine, is enzymatically methylated at the 5-carbon position. An epigenetic modification associated with gene regulation, DNA methylation is of paramount importance to biological health and disease. Recently, the quest to unravel the Human Epigenome commenced, calling for a modernization of previous DNA methylation profiling techniques. Here, we describe the major developments in the methodologies used over the past three decades to examine the elusive epigenome (or methylome). The earliest techniques were based on the separation of methylated and unmethylated cytosines via chromatography. The following years would see molecular techniques being employed to indirectly examine DNA methylation levels at both a genome-wide and locus-specific context, notably immunoprecipitation via anti-5′methylcytosine and selective digestion with methylation-sensitive restriction endonucleases. With the advent of sodium bisulfite treatment of DNA, a deamination reaction that converts cytosine to uracil only when unmethylated, the epigenetic modification can now be identified in the same manner as a DNA base-pair change. More recently, these three techniques have been applied to more technically advanced systems such as DNA microarrays and next-generation sequencing platforms, bringing us closer to unveiling a complete human epigenetic profile

Fusaproliferin production and its effects on two lepidopteran pests of maize

Species of fungi in the genus Fusarium infect a variety of commercially important crops, including maize. Many of these species also produce a variety of secondary metabolites (mycotoxins), which have been implicated in numerous human and livestock illnesses. Fusaproliferin is one such compound that has this potential because it is produced by F. proliferatum and F subglutinans, species that commonly infect maize. To identify optimal conditions for fusaproliferin production and to elucidate the relationship between fusaproliferin and deacetyl fusaproliferin, another secondary metabolite produced by F. subglutinans, three strains of F subglutinans were cultured for 6 weeks at 200C and 250C on solid maize kernels. Fusaproliferin production and the ratio of fusaproliferin to deacetyl fusaproliferin were both dependent on temperature and fungal strain. Fusaproliferin production was greatest at 250C, with ITEM 2404(4342 [Mu]g/g) and ISU93277 (3898[Mu]g/g) exhibiting the greatest production. Deacetyl fusaproliferin production was higher at 200C (mean concentration = 3614 [Mu]g/g), but its concentration did not substantially increase until after week 3. The ratio of fusaproliferin to deacetyl fusaproliferin decreased over time but was always \u3e1 at 250C for ITEM 2404 and ISU93277, a trend not seen at 200C. Therefore, 250C was a superior incubation temperature in terms of overall fusaproliferin production and the ratio of fusaproliferin to deacetyl fusaproliferin. Fusaproliferin and beauvericin were incorporated into artificial diets to study the developmental effects of two lepidopteran pests of maize, the European corn borer, Ostrinia nubilalis and fall armyworm, Spodoptera frugiperda, from the larval to adult stages. The use of methanol as the solvent affected the larval and pupal development of S. frugiperda but not 0. nubilalis. Neither mycotoxin affected the overall development of 0. nubilalis. The development of S. frugiperda was also not affected by consumption of either mycotoxin, although some non-dose related developmental effects were seen. Larval and pupal mortality of either insect were not significantly affected by treatment. The lack of oral toxicity of beauvericin to the two insect species, combined with previous data, suggests that beauvericin is not a potent insect toxin. This is the first report regarding the potential activity of fusaproliferin as an insect toxin and helped to further characterize its toxic nature

Critical thinking, peer-writing, and the importance of feedback.

Critical thinking is one of the key competencies listed by OECD (Organisation for Economic Co-operation and Development) [1], a central European Community organization, and is also mentioned as a learning outcome for higher education by international organizations, such as ABET, ACM, and IEEE, as well as in numerous national and university legislations regarding higher education degrees. The ability to communicate, not least in writing, is another important competence our students are supposed to gain during their education. There is thus high agreement regarding the importance of these competencies, but it is not clear how to achieve this

Replication and exploratory analysis of 24 candidate risk polymorphisms for neural tube defects.

BackgroundNeural tube defects (NTDs), which are among the most common congenital malformations, are influenced by environmental and genetic factors. Low maternal folate is the strongest known contributing factor, making variants in genes in the folate metabolic pathway attractive candidates for NTD risk. Multiple studies have identified nominally significant allelic associations with NTDs. We tested whether associations detected in a large Irish cohort could be replicated in an independent population.MethodsReplication tests of 24 nominally significant NTD associations were performed in racially/ethnically matched populations. Family-based tests of fifteen nominally significant single nucleotide polymorphisms (SNPs) were repeated in a cohort of NTD trios (530 cases and their parents) from the United Kingdom, and case-control tests of nine nominally significant SNPs were repeated in a cohort (190 cases, 941 controls) from New York State (NYS). Secondary hypotheses involved evaluating the latter set of nine SNPs for NTD association using alternate case-control models and NTD groupings in white, African American and Hispanic cohorts from NYS.ResultsOf the 24 SNPs tested for replication, ADA rs452159 and MTR rs10925260 were significantly associated with isolated NTDs. Of the secondary tests performed, ARID1A rs11247593 was associated with NTDs in whites, and ALDH1A2 rs7169289 was associated with isolated NTDs in African Americans.ConclusionsWe report a number of associations between SNP genotypes and neural tube defects. These associations were nominally significant before correction for multiple hypothesis testing. These corrections are highly conservative for association studies of untested hypotheses, and may be too conservative for replication studies. We therefore believe the true effect of these four nominally significant SNPs on NTD risk will be more definitively determined by further study in other populations, and eventual meta-analysis

Conceptions of patients and their roles in healthcare: insights from everyday practice and service improvement

Purpose: The purpose of this paper is two-fold. First, it sets the context for the special issue by considering conceptions of patients and their roles in service delivery and improvement. Second, it introduces the contributions to the special issue, and identifies thematic resonance. Design/Methodology/Approach: The paper utilises a literature synthesis and thematic analysis of the special issue submissions. These emanated from the 9th International Organisational Behaviour in Healthcare Conference, hosted by Copenhagen Business School on behalf of the Learned Society for Studies in Organizing Healthcare (SHOC). Findings: The articles evidence a range of perspectives on patients’ roles in healthcare. These range from their being subject to, a mobilising focus for, and active participants in service delivery and improvement. Building upon the potential patient roles identified, this editorial develops five ‘ideal type’ patient positions in healthcare delivery and improvement. These recognise that patients’ engagement with health care services is influenced both by personal characteristics and circumstances, which affect patients’ openness to engaging with health services, as well as the opportunities afforded to patients to engage, by organizations and their employees. Originality/Value: The paper explores the relationally embedded nature of patient involvement in healthcare, inherent in the interdependence between patient and providers’ roles. The typology aims to prompt discussion regarding the conceptualisation patients’ roles in healthcare organisations, and the individual, employee, organisational and contextual factors that may help and hinder their involvement in service delivery and improvement. We close by noting four areas meriting further research attention, and potentially useful theoretical lenses

Hospital doctors in Ireland and the struggle for work–life balance

Ireland has a high rate of doctor emigration. Challenging working conditions and poor work–life balance, particularly in the hospital sector, are often cited as a driver. The aim of this study was to obtain insight into hospital doctors’ experiences of work and of work–life balance. In late 2019, a stratified random sample of hospital doctors participated in an anonymous online survey, distributed via the national Medical Register (overall response rate 20%; n = 1070). This article presents a qualitative analysis of free-text questions relating to working conditions (n = 469) and work–life balance (n = 314). Results show that respondent hospital doctors, at all levels of seniority, were struggling to achieve balance between work and life, with work–life imbalance and work overload being the key issues arising. Work–life imbalance has become normalized within Irish hospital medicine. Drawing on insights from respondent hospital doctors, this study reflects on the sustainability of this way of working for the individual doctors, the medical workforce and the Irish health system. If health workforce planning is about getting the right staff with the right skills in the right place at the right time to deliver care, work–life balance is about maintaining doctor wellbeing and encouraging their retention

Indirect music therapy practice and skill-sharing in dementia care

Public interest in the benefits of music for people with dementia has rapidly increased in recent years. In addition to clinical work with clients, music therapists are often required to support and train staff, families, and volunteers and skill-share some music therapeutic skills. Six music therapy researchers from six countries agreed it was timely to organize a roundtable and share their indirect music therapy practice and examples of skill-sharing in dementia care. This article was developed following the roundtable at the World Congress of Music Therapy in 2017 and further discussion among the authors. This process highlighted the diversity and complexity of indirect music therapy practice and skill-sharing, but some common components emerged, including: 1) the importance of making clinical decisions about when direct music therapy is necessary and when indirect music therapy is appropriate, 2) supporting the transition from direct music therapy to indirect music therapy, 3) the value of music therapy skill-sharing in training care home staff, 4) the need for considering potential risks and burdens of indirect music therapy practice, and 5) expanding the role of music therapist and cultivating cross-professional dialogues to support organizational changes. In indirect music therapy practice, a therapist typically works with carers and supporters to strengthen their relationships with people with dementia and help them further develop their self-awareness and sense of competence. However, the ultimate goal of indirect music therapy practice in dementia care remains the wellbeing of people living with dementia