The radial arrangement of the human chromosome 7 in the lymphocyte cell nucleus is associated with chromosomal band gene density

This is the author's accepted manuscript. The final published article is available from the link below. Copyright @ Springer-Verlag 2008.In the nuclei of human lymphocytes, chromosome territories are distributed according to the average gene density of each chromosome. However, chromosomes are very heterogeneous in size and base composition, and can contain both very gene-dense and very gene-poor regions. Thus, a precise analysis of chromosome organisation in the nuclei should consider also the distribution of DNA belonging to the chromosomal bands in each chromosome. To improve our understanding of the chromatin organisation, we localised chromosome 7 DNA regions, endowed with different gene densities, in the nuclei of human lymphocytes. Our results showed that this chromosome in cell nuclei is arranged radially with the gene-dense/GC-richest regions exposed towards the nuclear interior and the gene-poorest/GC-poorest ones located at the nuclear periphery. Moreover, we found that chromatin fibres from the 7p22.3 and the 7q22.1 bands are not confined to the territory of the bulk of this chromosome, protruding towards the inner part of the nucleus. Overall, our work demonstrates the radial arrangement of the territory of chromosome 7 in the lymphocyte nucleus and confirms that human genes occupy specific radial positions, presumably to enhance intra- and inter-chromosomal interaction among loci displaying a similar expression pattern, and/or similar replication timing

Dissecting the impact of environment, season and genotype on blackcurrant fruit quality traits.

This work aims to determine the effect of genotype x environment (GxE) interaction that influence blackcurrant (Ribes nigrum) fruit quality. We applied metabolomics-driven analysis on fruits from four cultivars grown in contrasting European-locations over two seasons. By integrating metabolomics and sensory analysis, we also defined specific metabolic signatures associated with consumer acceptance. Our results showed that rainfall is a crucial factor associated with accumulation of delphinidin- and cyanidin-3-O-glucoside, the two mayor blackcurrant pigments meanwhile temperature affects the main organic acid levels which can be decisive for fruit taste. Sensorial analysis showed that increases in terpenoid and acetate ester volatiles were strongly associated with higher appreciation score, while proacacipetalin, a cyanogenic-glycoside, was positively associated to bitter taste. Our results pave the way for the selection of high-quality cultivars and suitable production sites for blackcurrant cultivation.publishedVersio

Fast and Reliable Differentiation of Eight Trichinella Species Using a High Resolution Melting Assay

High resolution melting analysis (HRMA) is a single-tube method, which can be carried out rapidly as an additional step following real-time quantitative PCR (qPCR). The method enables the differentiation of genetic variation (down to single nucleotide polymorphisms) in amplified DNA fragments without sequencing. HRMA has previously been adopted to determine variability in the amplified genes of a number of organisms. However, only one work to date has focused on pathogenic parasites–nematodes from the genus Trichinella. In this study, we employed a qPCR-HRMA assay specifically targeting two sequential gene fragments–cytochrome c oxidase subunit I (COI) and expansion segment V (ESV), in order to differentiate 37 single L1 muscle larvae samples of eight Trichinella species. We prove that qPCR-HRMA based on the mitochondrial COI gene allows differentiation between the sequences of PCR products of the same length. This simple, rapid and reliable method can be used to identify at the species level single larvae of eight Trichinella taxa.High resolution melting analysis (HRMA) is a single-tube method, which can be carried out rapidly as an additional step following real-time quantitative PCR (qPCR). The method enables the differentiation of genetic variation (down to single nucleotide polymorphisms) in amplified DNA fragments without sequencing. HRMA has previously been adopted to determine variability in the amplified genes of a number of organisms. However, only one work to date has focused on pathogenic parasites–nematodes from the genus Trichinella. In this study, we employed a qPCR-HRMA assay specifically targeting two sequential gene fragments–cytochrome c oxidase subunit I (COI) and expansion segment V (ESV), in order to differentiate 37 single L1 muscle larvae samples of eight Trichinella species. We prove that qPCR-HRMA based on the mitochondrial COI gene allows differentiation between the sequences of PCR products of the same length. This simple, rapid and reliable method can be used to identify at the species level single larvae of eight Trichinella taxa

New materialist social inquiry: designs, methods and the research-assemblage

This paper discusses issues of research design and methods in new materialist social inquiry, an approach that is attracting increasing interest across the social sciences as an alternative to either realist or constructionist ontologies. New materialism de-privileges human agency, focusing instead upon how assemblages of the animate and inanimate together produce the world, with fundamental implications for social inquiry methodology and methods. Key to our exploration is the materialist notion of a ‘research-assemblage’ comprising researcher, data, methods and contexts. We use this understanding first to explore the micropolitics of the research process, and then – along with a review of 30 recent empirical studies – to establish a framework for materialist social inquiry methodology and methods. We discuss the epistemological consequences of adopting a materialist ontology

Delivering the WISE (Whole Systems Informing Self-Management Engagement) training package in primary care: learning from formative evaluation

Background: The WISE (Whole System Informing Self-management Engagement) approach encompasses creating, finding, and implementing appropriate self-care support for people with long-term conditions. A training package for primary care to introduce the approach was developed and underwent formative evaluation. This entailed exploring the acceptability of the WISE approach and its effectiveness in changing communication within consultations. The study aimed to refine the patient, practitioner, and patient level components of the WISE approach and translate the principles of WISE into an operational intervention deliverable through National Health Service training methods. Methods: Normalisation Process Theory provided a framework for development of the intervention. Practices were recruited from an inner city Primary Care Trust in NW England. All practice staff were expected to attend two afternoon training sessions. The training sessions were observed by members of the training team. Post-training audio recordings of consultations from each general practitioner and nurse in the practices were transcribed and read to provide a narrative overview of the incorporation of WISE skills and tools into consultations. Face-to-face semi-structured interviews were conducted with staff post-training. Results: Two practices out of 14 deemed eligible agreed to take part. Each practice attended two sessions, although a third session on consultation skills training was needed for one practice. Fifty-four post-training consultations were recorded from 15 clinicians. Two members of staff were interviewed at each practice. Significant elements of the training form and methods of delivery fitted contemporary practice. There were logistical problems in getting a whole practice to attend both sessions, and administrative staff founds some sections irrelevant. Clinicians reported problems incorporating some of the tools developed for WISE, and this was confirmed in the overview of consultations, with limited overt use of WISE tools and missed opportunities to address patients' self-management needs. Conclusions: The formative evaluation approach and attention to normalisation process theory allowed the training team to make adjustments to content and delivery and ensure appropriate staff attended each session. The content of the course was simplified and focussed more clearly on operationalising the WISE approach. The patient arm of the approach was strengthened by raising expectations of a change in approach to self-care support by their practice. <br/

RE: pedagogy – after neutrality

Within the UK and in many parts of the world, official accounts of what it is to make sense of religion are framed within a rhetorics of neutrality in which such study is premised upon the possibility of dispassionate engagement and analysis. This paper, which is largely theoretical in scope, explores both the affordances and the costs of such an approach which has become ‘black boxed’ on account of the work that it achieves. A series of new orientations within the academy that are broadly associated with post-structuralist philosophies, feminist and post-colonial studies, together with insights from Science and Technology Studies, question the plausibility of these claims for neutrality whilst in turn raising a series of new questions and priorities. It therefore becomes necessary to re-think and re-frame what it is to make sense of religious and cultural difference after neutrality. The gathering and co-ordination of new planes of sense-making that are responsive to an emergent series of epistemological, ontological, and ethical orientations are considered. Some of the distinctive pedagogical implications of such an approach that engages material practice, difference and uncertainty are then entertained