Functional analysis of the osteoarthritis susceptibility locus marked by the polymorphism rs10492367

https://nsuworks.nova.edu/nsudigital_harrison/3337/thumbnail.jp

A rapid method for assessing the RNA-binding potential of a protein

In recent years, evidence has emerged for the existence of many diverse types of RNA, which play roles in a wide range of biological processes in all kingdoms of life. These molecules generally do not, however, act in isolation, and identifying which proteins partner with RNA is a major challenge. Many methods, in vivo and in vitro, have been used to address this question, including combinatorial or high-throughput approaches, such as systematic evolution of ligands, cross-linking and immunoprecipitation and RNA immunoprecipitation combined with deep sequencing. However, most of these methods are not trivial to pursue and often require substantial optimization before results can be achieved. Here, we demonstrate a simple technique that allows one to screen proteins for RNA-binding properties in a gel-shift experiment and can be easily implemented in any laboratory. This assay should be a useful first-pass tool for assessing whether a protein has RNA- or DNA-binding properties, prior to committing resources to more complex procedure

Quantum Interference in the Kirkwood-Rihaczek representation

We discuss the Kirkwood-Rihaczek phase space distribution and analyze a whole new class of quasi-distributions connected with this function. All these functions have the correct marginals. We construct a coherent state representation of such functions, discuss which operator ordering corresponds to the Kirkwood-Rihaczek distribution and their generalizations, and show how such states are connected to squeezed states. Quantum interference in the Kirkwood-Rihaczek representation is discussed.Comment: 10 pages, 7 figure

Utilizing qualitative data from nominal groups: Exploring the influences on treatment outcome prioritization with rheumatoid arthritis patients

The nominal group technique generates quantitative data through a process of experts ranking items of interest. This article focuses on the additional collection of qualitative data from nominal groups with rheumatoid arthritis (RA) patients, used to explore the influences on prioritizing treatment outcomes. Across all groups, the top five outcomes with the highest importance scores were identified as: pain; joint damage; fatigue; activities of daily living; and mobility. Qualitative findings showed that the personal impact of RA influenced decisions on how to rank specific outcomes through four domains: disease impact; adaptation to illness; external resources and stressors; and social expectations. © The Author(s) 2011

Decoding the Regulatory Landscape of Ageing in Musculoskeletal Engineered Tissues Using Genome-Wide DNA Methylation and RNASeq

Mesenchymal stem cells (MSC) are capable of multipotent differentiation into connective tissues and as such are an attractive source for autologous cell-based regenerative medicine and tissue engineering. Epigenetic mechanisms, like DNA methylation, contribute to the changes in gene expression in ageing. However there was a lack of sufficient knowledge of the role that differential methylation plays during chondrogenic, osteogenic and tenogenic differentiation from ageing MSCs. This study undertook genome level determination of the effects of DNA methylation on expression in engineered tissues from chronologically aged MSCs. We compiled unique DNA methylation signatures from chondrogenic, osteogenic, and tenogenic engineered tissues derived from young; n = 4 (21.8 years ± 2.4 SD) and old; n = 4 (65.5 years±8.3SD) human MSCs donors using the Illumina HumanMethylation 450 Beadchip arrays and compared these to gene expression by RNA sequencing. Unique and common signatures of global DNA methylation were identified. There were 201, 67 and 32 chondrogenic, osteogenic and tenogenic age-related DE protein-coding genes respectively. Findings inferred the nature of the transcript networks was predominantly for ‘cell death and survival’, ‘cell morphology’, and ‘cell growth and proliferation’. Further studies are required to validate if this gene expression effect translates to cell events. Alternative splicing (AS) was dysregulated in ageing with 119, 21 and 9 differential splicing events identified in chondrogenic, osteogenic and tenogenic respectively, and enrichment in genes associated principally with metabolic processes. Gene ontology analysis of differentially methylated loci indicated age-related enrichment for all engineered tissue types in ‘skeletal system morphogenesis’, ‘regulation of cell proliferation’ and ‘regulation of transcription’ suggesting that dynamic epigenetic modifications may occur in genes associated with shared and distinct pathways dependent upon engineered tissue type. An altered phenotype in engineered tissues was observed with ageing at numerous levels. These changes represent novel insights into the ageing process, with implications for stem cell therapies in older patients. In addition we have identified a number of tissue-dependant pathways, which warrant further studies

Using the 'myVolcano' mobile phone app for citizen science in St. Vincent and the Grenadines : a pilot study

The British Geological Survey (BGS) has been working with Caribbean partners on the role of citizen science in increasing resilience to natural hazards. The work has largely focused on the potential use of the myVolcano smartphone app, which was developed by the BGS following the 2010 Eyafjallajökull and 2011 Grímsvötn eruptions in Iceland. During these eruptions the BGS asked the UK public to collect particle samples, subsequently analysing these for ash presence to map the distribution of ash fallout across the UK. These requests led to the development of the myVolcano app, which was designed to capture transboundary and distal observations of volcanic ash and emissions. The observations are made visible to other users via an interactive map built into the app. The map interface has global coverage and the data collection methods (free-text descriptions and photographs) are such that information about any natural hazard, anywhere in the world, can be captured. In 2015, BGS carried out an ESRC-DfID-NERC funded scoping study in collaboration with the University of the West Indies’ Seismic Research Centre (UWI SRC), to test the potential use of the app in environments affected by proximal volcanic hazards. The study focused on St. Vincent and the Grenadines and investigated the potential for capturing a wider variety of observations for use by the public, operational scientists and civil protection. The study, which included a combination of desk study and remote interviews, highlighted the potential for, and challenges of, using such an app for increasing resilience to natural hazards and the need for a follow-up study in St Vincent. In March 2017, a workshop and school activities were held in St. Vincent to collect feedback from potential users of myVolcano, hereafter referred to as the pilot study. Workshop participants came from across government, monitoring agencies, emergency response and telecommunications. As part of the workshop, a multi-hazard scenario was ‘played out’ to stimulate discussions on the usability of the app, data gathering and processing, and participants’ use of existing citizen science applications. Discussions developed around data validation and quality assurance, data sharing and presentation, local management of data by nominated scientists (e.g. to facilitate real-time decision making) and the associated need for a locally appropriate app (i.e. no one size fits all). This last point is particularly significant when considering the utility of an app in several countries – the user interface, at least, requires specific tailoring to the country’s needs. Using this feedback, the BGS Official Development Assistance (ODA) programme is currently funding collaborations with Caribbean partners in order to modify the app to meet the local requirements, including widening the multi-hazard application and enhancing two-way information sharing. Of particular importance is how best to share critical information with those making observations and how to make observations available to decision-makers and monitoring scientists in real-time (e.g. through local management of the app)

Nicotine-induced brain metabolism associated with anger provocation

Cortico-limbic brain activity associated with anger may be susceptible to nicotine and, thus, may contribute to smoking initiation and nicotine addiction. The purpose of the study was to identify the brain regions that are most reactive to nicotine and show the greatest association with anger task performance. Twenty adult nonsmokers (9 women, 11 men) participated in two laboratory sessions to assess brain metabolism with fluoro deoxy-glucose Positron Emission Topography (FDG-PET) in response to nicotine and placebo patches during an anger provocation task. Outcome variables for the anger provocation task were reaction time, intensity and length of retaliation. Reaction time was associated with nicotine-induced changes in the left thalamus. Length of retaliation was associated with a functionally linked set of cortical and subcortical structures such as right frontal lobe, right anterior cingulate (BA 24), right uncus, left parietal lobe, left BA 11, left cingulate, left BA 25, left amygdala, left BA 30, left BA 38 and BA 9. These findings reveal the underlying brain circuitry targeted by nicotine during anger provocation

Allelic expression analysis of the osteoarthritis susceptibility locus that maps to MICAL3

<p>Abstract</p> <p>Background</p> <p>A genome-wide association scan with subsequent replication study that involved over 67,000 individuals of European ancestry has produced evidence of association of single nucleotide polymorphism rs2277831 to primary osteoarthritis (OA) with a P-value of 2.9 × 10^-5. rs2277831, an A/G transition, is located in an intron of <it>MICAL3</it>. This gene is located on chromosome 22q11.21 and the association signal encompasses two additional genes, <it>BCL2L13 </it>and <it>BID</it>. It is becoming increasingly apparent that many common complex traits are mediated by <it>cis</it>-acting regulatory polymorphisms that influence, in a tissue-specific manner, gene expression or transcript stability.</p> <p>Methods</p> <p>We used total and allelic expression analysis to assess whether the OA association to rs2277831 is mediated by an influence on MICAL3, BCL2L13 or BID expression. Using RNA extracted from joint tissues of 60 patients who had undergone elective joint replacement surgery, we assessed whether rs2277831 correlated with allelic expression of either of the three genes by: 1) measuring the expression of each gene by quantitative PCR and then stratifying the data by genotype at rs2277831 and 2) accurately discriminating and quantifying the mRNA synthesised from the alleles of OA patients using allelic-quantitative PCR.</p> <p>Results</p> <p>We found no evidence for a correlation between gene expression and genotype at rs2277831, with P-values of 0.09 for <it>BCL2L13</it>, 0.07 for <it>BID </it>and 0.33 for <it>MICAL3</it>. In the allelic expression analysis we observed several examples of significant (p < 0.05) allelic imbalances, with an allelic expression ratio of 2.82 observed in <it>BCL2L13 </it>(P = 0.004), 2.09 at <it>BID </it>(P = 0.001) and the most extreme case being at <it>MICAL3</it>, with an allelic expression ratio of 5.47 (P = 0.001). However, there was no correlation observed between the pattern of allelic expression and the genotype at rs2277831.</p> <p>Conclusions</p> <p>In the tissues that we have studied, our data do not support our hypothesis that the association between rs2277831 and OA is due to the effect this SNP has on <it>MICAL3, BCL2L13 </it>or <it>BID </it>gene expression. Instead, our data point towards other functional effects accounting for the OA associated signal.</p