An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations

The number of significant genetic associations with common complex traits is constantly increasing. However, most of these associations have not been understood at molecular level. One of the mechanisms mediating the effect of DNA variants on phenotypes is gene expression, which has been shown to be particularly relevant for complex traits1

Factores que inciden en el proceso de la revitalización de la lengua Sumu-Ulwa en la comunidad de Karawala Desembocadura de Río Grande de Matagalpa

This research was made with the aim of contributing to strengthening identity of the Ulwa, through the analysis of the linguistic situation of the people and the aspects influencing the process of revitalization. It was important to carry out this investigative work to verify the incident features that hinder or encourage the process of revitalization of the Ulwa language. In this work, the selection and inclusive participation of Karawala community leaders including men and women, Ulwa speakers and non Ulwa speakers, male and female teachers, students, teenagers and children Ulwa speakers and non Ulwa speakers of this community. Through the mentioned actors, or key informants we managed to collect the necessary information about aspects that affect the process of revitalization of the Ulwa language successfully. It is important to note that the main performers in this work: a) The majority of youth recognize Ulwa language as their mother language, this identification with the language is the same for those who say speak and understand very well the Ulwa language and those who speak or understand only a little of the language. In their own words some young people manifest, “I only understand a little... but it is the language of my people... my tongue.” Also young people recognize the multi-ethnicity of Karawala, giving rise to a situation of multilingualism, but even in these circumstances there is an acceptance of the language, for example, some manifest that even if their mother is of Miskito origin, their language is Ulwa. Some stated that they do not speak, but understand, others just speak, but with pride, some who have Miskitu mother and Ulwa father respect the language and others expressed remorse for not being able to speak the language. But there are also young people who do not understand the linguistic situation of the community, and are unable to formulate an opinion on the language or do not have information about the revitalization process. b) Adult speakers also show that the situation has improved, always as a result of the new appraisal of the language, but still, although most adult speakers practice their language among members of his same generation and in environments, places and specific circumstances, there also are a considerable percentage of adult speakers who do not practice the language under any circumstances. This is really an obstacle for the revitalization and this phenomenon should be corrected. On the other hand, adult non-speakers, whom historically merged into the life of the Ulwa people establishing families, respect and value the language. This new attitude of adults not speakers must become a stronghold, urging them to support everything relating to the process of revitalization of the language beginning from the heart of households and with the promotion of the use of the Ulwa amongst the family Among the most relevant positive practice affecting the revitalization we have: The massive publicity in the community where the research on Ulwa language was done, educating all residents to the acceptance of the Ulwa language. Teachers teach to read and write in the Ulwa language

Characterisation of the global transcriptional response to heat shock and the impact of individual genetic variation

Abstract Background The heat shock transcriptional response is essential to effective cellular function under stress. This is a highly heritable trait but the nature and extent of inter-individual variation in heat shock response remains unresolved. Methods We determined global transcription profiles of the heat shock response for a panel of lymphoblastoid cell lines established from 60 founder individuals in the Yoruba HapMap population. We explore the observed differentially expressed gene sets following heat shock, establishing functional annotations, underlying networks and nodal genes involving heat shock factor 1 recruitment. We define a multivariate phenotype for the global transcriptional response to heat shock using partial least squares regression and map this quantitative trait to associated genetic variation in search of the major genomic modulators. Results A comprehensive dataset of differentially expressed genes following heat shock in humans is presented. We identify nodal genes downstream of heat shock factor 1 in this gene set, notably involving ubiquitin C and small ubiquitin-like modifiers together with transcription factors. We dissect a multivariate phenotype for the global heat shock response which reveals distinct clustering of individuals in terms of variance of the heat shock response and involves differential expression of genes involved in DNA replication and cell division in some individuals. We find evidence of genetic associations for this multivariate response phenotype that involves trans effects modulating expression of genes following heat shock, including HSF1 and UBQLN1. Conclusion This study defines gene expression following heat shock for a cohort of individuals, establishing insights into the biology of the heat shock response and hypotheses for how variation in this may be modulated by underlying genetic diversity

A common variant associated with dyslexia reduces expression of the KIAA0319 gene

This work was supported by the Wellcome Trust (MYD, SP, TSS, JCK, RWM, PC, SB, and APM), the Intramural Research Programs of the National Human Genome Research Institute (MYD and EDG) and National Cancer Institute (MPO), and the NIH/Ox-Cam Graduate Partnership Program (MYD).Numerous genetic association studies have implicated the KIAA0319 gene on human chromosome 6p22 in dyslexia susceptibility. The causative variant(s) remains unknown but may modulate gene expression, given that (1) a dyslexia-associated haplotype has been implicated in the reduced expression of KIAA0319, and (2) the strongest association has been found for the region spanning exon 1 of KIAA0319. Here, we test the hypothesis that variant(s) responsible for reduced KIAA0319 expression resides on the risk haplotype close to the gene's transcription start site. We identified seven single-nucleotide polymorphisms on the risk haplotype immediately upstream of KIAA0319 and determined that three of these are strongly associated with multiple reading-related traits. Using luciferase-expressing constructs containing the KIAA0319 upstream region, we characterized the minimal promoter and additional putative transcriptional regulator regions. This revealed that the minor allele of rs9461045, which shows the strongest association with dyslexia in our sample (max p-value = 0.0001), confers reduced luciferase expression in both neuronal and non-neuronal cell lines. Additionally, we found that the presence of this rs9461045 dyslexia-associated allele creates a nuclear protein-binding site, likely for the transcriptional silencer OCT-1. Knocking down OCT-1 expression in the neuronal cell line SHSY5Y using an siRNA restores KIAA0319 expression from the risk haplotype to nearly that seen from the non-risk haplotype. Our study thus pinpoints a common variant as altering the function of a dyslexia candidate gene and provides an illustrative example of the strategic approach needed to dissect the molecular basis of complex genetic traits.PostprintPeer reviewe

Hybridising inorganic materials with fluorescent BOPHY dyes: A structural and optical comparative study

This study presents the design and characterization of new monochromatic light-harvesting systems based on inorganic porous materials hybridized with organic dye molecules within their structure. A new fluorescent BOPHY dye was prepared, characterized optically and used as both reference and synthetic precursor for two alkoxysilane derivatives that were incorporated separately within a silica structure. The dyes, one bearing one alkoxysilane group and the other one two, were co-condensed with tetraethyl orthosilicate to form a hybrid organo-silica framework, where they are found at specific locations. The structure of the new materials was analysed by powder XRD and TEM, which confirmed the presence of the hexagonal pore arrangement typical of mesoporous MCM-41 silica particles. The steady-state and time-resolved analysis showed that the particles where the dyes are most dispersed within the framework retain the highest fluorescence quantum yield, up to 0.63, in the green-yellow region of the visible spectrum. On the other hand, increasing the content of BOPHY units in the solid matrix seem to favour non-radiative deactivation pathways and aggregation phenomena, which lower the efficiency of light emission. The materials also exhibit interesting properties, such as a dual excited-state decay and fluorescence anisotropy. The short fluorescence lifetime, about 2 ns, matches the typical singlet lifetime of BOPHY dyes, whereas the long component, up to 20 ns, is attributed to delayed fluorescence, which could take place via charge recombination. Optical anisotropy experiments revealed that all materials show polarised light emission to a significant extent and, for most samples, it was also possible to determine a polarisation transfer decay trace, from 400 to 800 ps This is ascribed to the occurrence of energy migration between neighbouring dye units within the silica structure

Investigating the Impact of a Musical Intervention on Preschool Children’s Executive Function

The impact of music interventions on the cognitive skills of young children has become the focus of a growing number of research studies in recent years. This study investigated the effect of weekly musicianship training on the executive function abilities of 3-to-4-year-old children at a London, United Kingdom preschool, using a two-phase experimental design. In Phase 1, 14 children (Group A) took part in eight weekly musicianship classes, provided by a specialist music teacher, while 25 children (Groups B and C combined) engaged in nursery free play. Results of this Phase showed Group A to have improved on two measures relating to planning and inhibition skills. During Phase 2, Group A continued with music classes, while Group B began music classes for the first time and Group C took part in an art intervention. Repeated measures ANOVA found no significant difference in performance improvement between the three participant groups during phase 2; however, the performance difference between groups was nearing significance for the peg tapping task (p = 0.06). The findings from this study contribute to current debates about the potential cognitive benefit of musical interventions, including important issues regarding intervention duration, experimental design, target age groups, executive function testing, and task novelty

Ex vivo mass cytometry analysis reveals a profound myeloid proinflammatory signature in psoriatic arthritis synovial fluid

Objectives A number of immune populations have been implicated in psoriatic arthritis (PsA) pathogenesis. This study used mass cytometry (CyTOF) combined with transcriptomic analysis to generate a high-dimensional dataset of matched PsA synovial fluid (SF) and blood leucocytes, with the aim of identifying cytokine production ex vivo in unstimulated lymphoid and myeloid cells. Methods Fresh SF and paired blood were either fixed or incubated with protein transport inhibitors for 6 h. Samples were stained with two CyTOF panels: a phenotyping panel and an intracellular panel, including antibodies to both T cell and myeloid cell secreted proteins. Transcriptomic analysis by gene array of key expanded cell populations and single-cell RNA-seq, and ELISA and LEGENDplex analysis of PsA SF were also performed. Results We observed marked changes in the myeloid compartment of PsA SF relative to blood, with expansion of intermediate monocytes, macrophages and dendritic cell populations. Classical monocytes, intermediate monocytes and macrophages spontaneously produced significant levels of the proinflammatory mediators osteopontin and CCL2 in the absence of any in vitro stimulation. By contrast minimal spontaneous cytokine production by T cells was detected. Gene expression analysis showed the genes for osteopontin and CCL2 to be amongst those most highly upregulated by PsA monocytes/macrophages; and both proteins were elevated in PsA SF. Conclusions Using multiomic analyses we have generated a comprehensive cellular map of PsA SF and blood to reveal key expanded myeloid proinflammatory modules in PsA of potential pathogenic and therapeutic importance. Competing Interest Statement The authors have declared no competing interest

Ex vivo mass cytometry analysis reveals a profound myeloid proinflammatory signature in psoriatic arthritis synovial fluid

Objectives: A number of immune populations have been implicated in psoriatic arthritis (PsA) pathogenesis. This study used mass cytometry (CyTOF) combined with transcriptomic analysis to generate a high-dimensional dataset of matched PsA synovial fluid (SF) and blood leucocytes, with the aim of identifying cytokine production ex vivo in unstimulated lymphoid and myeloid cells. Methods: Fresh SF and paired blood were either fixed or incubated with protein transport inhibitors for 6 hours. Samples were stained with two CyTOF panels: a phenotyping panel and an intracellular panel, including antibodies to both T cell and myeloid cell secreted proteins. Transcriptomic analysis by gene array of key expanded cell populations, single-cell RNA-seq, ELISA and LEGENDplex analysis of PsA SF were also performed. Results: We observed marked changes in the myeloid compartment of PsA SF relative to blood, with expansion of intermediate monocytes, macrophages and dendritic cell populations. Classical monocytes, intermediate monocytes and macrophages spontaneously produced significant levels of the proinflammatory mediators osteopontin and CCL2 in the absence of any in vitro stimulation. By contrast minimal spontaneous cytokine production by T cells was detected. Gene expression analysis showed the genes for osteopontin and CCL2 to be among those most highly upregulated by PsA monocytes/macrophages in SF; and both proteins were elevated in PsA SF. Conclusions: Using multiomic analyses, we have generated a comprehensive cellular map of PsA SF and blood to reveal key expanded myeloid proinflammatory modules in PsA of potential pathogenic and therapeutic importance

Distinct Transcriptional and Anti-Mycobacterial Profiles of Peripheral Blood Monocytes Dependent on the Ratio of Monocytes: Lymphocytes.

The ratio of monocytes and lymphocytes (ML ratio) in peripheral blood is associated with tuberculosis and malaria disease risk and cancer and cardiovascular disease outcomes. We studied anti-mycobacterial function and the transcriptome of monocytes in relation to the ML ratio. Mycobacterial growth inhibition assays of whole or sorted blood were performed and mycobacteria were enumerated by liquid culture. Transcriptomes of unstimulated CD14 + monocytes isolated by magnetic bead sorting were characterised by microarray. Transcript expression was tested for association with ML ratio calculated from leucocyte differential counts by linear regression. The ML ratio was associated with mycobacterial growth in vitro (β = 2.23, SE 0.91, p = 0.02). Using sorted monocytes and lymphocytes, in vivo ML ratio (% variance explained R(2) = 11%, p = 0.02) dominated over in vitro ratios (R(2) = 5%, p = 0.10) in explaining mycobacterial growth. Expression of 906 genes was associated with the ML ratio and 53 with monocyte count alone. ML-ratio associated genes were enriched for type-I and -II interferon signalling (p = 1.2 × 10(− 8)), and for genes under transcriptional control of IRF1, IRF2, RUNX1, RELA and ESRRB. The ML-ratio-associated gene set was enriched in TB disease (3.11-fold, 95% CI: 2.28-4.19, p = 5.7 × 10(− 12)) and other inflammatory diseases including atopy, HIV, IBD and SLE. The ML ratio is associated with distinct transcriptional and anti-mycobacterial profiles of monocytes that may explain the disease associations of the ML ratio