Cellular deconvolution of GTEx tissues powers discovery of disease and cell-type associated regulatory variants.

The Genotype-Tissue Expression (GTEx) resource has provided insights into the regulatory impact of genetic variation on gene expression across human tissues; however, thus far has not considered how variation acts at the resolution of the different cell types. Here, using gene expression signatures obtained from mouse cell types, we deconvolute bulk RNA-seq samples from 28 GTEx tissues to quantify cellular composition, which reveals striking heterogeneity across these samples. Conducting eQTL analyses for GTEx liver and skin samples using cell composition estimates as interaction terms, we identify thousands of genetic associations that are cell-type-associated. The skin cell-type associated eQTLs colocalize with skin diseases, indicating that variants which influence gene expression in distinct skin cell types play important roles in traits and disease. Our study provides a framework to estimate the cellular composition of GTEx tissues enabling the functional characterization of human genetic variation that impacts gene expression in cell-type-specific manners

Southern Cross Soloists Season 2016

Ensemble in Residence at the Queensland Performing Arts Centre, Southern Cross Soloists present three concerts: Forbidden Love (with Jack Liebeck, Violin)– 20th March 2016 at 3pm Visions of Earth (with William Barton, Didjeridu)– 19th June 2016 at 3pm Heavenly Voice (with Sara Macliver, Soprano)– 27th November 2016 at 3p

Allele-specific NKX2-5 binding underlies multiple genetic associations with human electrocardiographic traits.

The cardiac transcription factor (TF) gene NKX2-5 has been associated with electrocardiographic (EKG) traits through genome-wide association studies (GWASs), but the extent to which differential binding of NKX2-5 at common regulatory variants contributes to these traits has not yet been studied. We analyzed transcriptomic and epigenomic data from induced pluripotent stem cell-derived cardiomyocytes from seven related individuals, and identified ~2,000 single-nucleotide variants associated with allele-specific effects (ASE-SNVs) on NKX2-5 binding. NKX2-5 ASE-SNVs were enriched for altered TF motifs, for heart-specific expression quantitative trait loci and for EKG GWAS signals. Using fine-mapping combined with epigenomic data from induced pluripotent stem cell-derived cardiomyocytes, we prioritized candidate causal variants for EKG traits, many of which were NKX2-5 ASE-SNVs. Experimentally characterizing two NKX2-5 ASE-SNVs (rs3807989 and rs590041) showed that they modulate the expression of target genes via differential protein binding in cardiac cells, indicating that they are functional variants underlying EKG GWAS signals. Our results show that differential NKX2-5 binding at numerous regulatory variants across the genome contributes to EKG phenotypes

Mutations in topoisomerase IIβ result in a B cell immunodeficiency.

B cell development is a highly regulated process involving multiple differentiation steps, yet many details regarding this pathway remain unknown. Sequencing of patients with B cell-restricted immunodeficiency reveals autosomal dominant mutations in TOP2B. TOP2B encodes a type II topoisomerase, an essential gene required to alleviate topological stress during DNA replication and gene transcription, with no previously known role in B cell development. We use Saccharomyces cerevisiae, and knockin and knockout murine models, to demonstrate that patient mutations in TOP2B have a dominant negative effect on enzyme function, resulting in defective proliferation, survival of B-2 cells, causing a block in B cell development, and impair humoral function in response to immunization

Universal behavior of highly-confined heat flow in semiconductor nanosystems: from nanomeshes to metalattices

Nanostructuring on length scales corresponding to phonon mean free paths provides control over heat flow in semiconductors and makes it possible to engineer their thermal properties. However, the influence of boundaries limits the validity of bulk models, while first principles calculations are too computationally expensive to model real devices. Here we use extreme ultraviolet beams to study phonon transport dynamics in a 3D nanostructured silicon metalattice with deep nanoscale feature size, and observe dramatically reduced thermal conductivity relative to bulk. To explain this behavior, we develop a predictive theory wherein thermal conduction separates into a geometric permeability component and an intrinsic viscous contribution, arising from a new and universal effect of nanoscale confinement on phonon flow. Using both experiments and atomistic simulations, we show that our theory is valid for a general set of highly-confined silicon nanosystems, from metalattices, nanomeshes, porous nanowires to nanowire networks. This new analytical theory of thermal conduction can be used to predict and engineer phonon transport in boundary-dominated nanosystems, that are of great interest for next-generation energy-efficient devices

Defining the genetic susceptibility to cervical neoplasia - a genome-wide association study

Funding: MAB was funded by a National Health and Medical Research Council (Australia) Senior Principal Research Fellowship. Support was also received from the Australian Cancer Research Foundation. JL holds a Tier 1 Canada Research Chair in Human Genome Epidemiology. The Seattle study was supported by the following grants: NIH, National Cancer Institute grants P01CA042792 and R01CA112512. Cervical Health Study (from which the NSW component was obtained) was funded by NHMRC Grant 387701, and CCNSW core grant. The Montreal study was funded by the Canadian Institutes of Health Research (grant MOP-42532) and sample processing was funded by the Reseau FRQS SIDA-MI. The Swedish Research Council, the Swedish Foundation for Strategic Research, the ALF/LUA research grant in Gothenburg and Umeå, the Lundberg Foundation, the Torsten and Ragnar Soderberg’s Foundation, the Novo Nordisk Foundation, and the European Commission grant HEALTH-F2-2008-201865-GEFOS, BBMRI.se, the Swedish Society of Medicine, the KempeFoundation (JCK-1021), the Medical Faculty of Umeå University, the County Council of Vasterbotten (Spjutspetsanslag VLL:159:33-2007). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscriptPeer reviewedPublisher PDFPublisher PD

A General and Predictive Understanding of Thermal Transport from 1D- and 2D-Confined Nanostructures : Theory and Experiment

Altres ajuts: Acord transformatiu CRUE-CSICHeat management is crucial in the design of nanoscale devices as the operating temperature determines their efficiency and lifetime. Past experimental and theoretical works exploring nanoscale heat transport in semiconductors addressed known deviations from Fourier's law modeling by including effective parameters, such as a size-dependent thermal conductivity. However, recent experiments have qualitatively shown behavior that cannot be modeled in this way. Here, we combine advanced experiment and theory to show that the cooling of 1D- and 2D-confined nanoscale hot spots on silicon can be described using a general hydrodynamic heat transport model, contrary to previous understanding of heat flow in bulk silicon. We use a comprehensive set of extreme ultraviolet scatterometry measurements of nondiffusive transport from transiently heated nanolines and nanodots to validate and generalize our ab initio model, that does not need any geometry-dependent fitting parameters. This allows us to uncover the existence of two distinct time scales and heat transport mechanisms: an interface resistance regime that dominates on short time scales and a hydrodynamic-like phonon transport regime that dominates on longer time scales. Moreover, our model can predict the full thermomechanical response on nanometer length scales and picosecond time scales for arbitrary geometries, providing an advanced practical tool for thermal management of nanoscale technologies. Furthermore, we derive analytical expressions for the transport time scales, valid for a subset of geometries, supplying a route for optimizing heat dissipation

Bella España

The Resonate concert series for 2015 brings art and music together in a highly original program featuring some of Australia’s best-loved performers. An internationally successful ensemble based at the Queensland Performing Arts Centre in Brisbane, the Southern Cross Soloists have helped set the benchmark for Australian chamber music since 1995. The Soloists have earned a well-deserved reputation for artistic excellence and continue to surprise and delight audiences with their constantly evolving repertoire and ever-changing annual programs. Their informal, up-close-and-personal performance style creates an intimate, inviting and deeply engaging experience. Acclaimed guitarist Slava Grigoryan joins the Southern Cross Soloists to present Bella España, a fiery program of Latin-influenced works celebrating dance and romance. Grigoryan, already a favourite with Gallery audiences, is one of Australia’s most renowned classical guitarists and a former Young Australian of the Year for the arts. In this program, works by Granados, De Falla and De Milan are paired with the flaming sounds of Villa-Lobos and Piazzolla, showcasing the beauty and intimacy of chamber music and the brilliance of the Spanish guitar

iPSCORE: A Resource of 222 iPSC Lines Enabling Functional Characterization of Genetic Variation across a Variety of Cell Types.

Large-scale collections of induced pluripotent stem cells (iPSCs) could serve as powerful model systems for examining how genetic variation affects biology and disease. Here we describe the iPSCORE resource: a collection of systematically derived and characterized iPSC lines from 222 ethnically diverse individuals that allows for both familial and association-based genetic studies. iPSCORE lines are pluripotent with high genomic integrity (no or low numbers of somatic copy-number variants) as determined using high-throughput RNA-sequencing and genotyping arrays, respectively. Using iPSCs from a family of individuals, we show that iPSC-derived cardiomyocytes demonstrate gene expression patterns that cluster by genetic background, and can be used to examine variants associated with physiological and disease phenotypes. The iPSCORE collection contains representative individuals for risk and non-risk alleles for 95% of SNPs associated with human phenotypes through genome-wide association studies. Our study demonstrates the utility of iPSCORE for examining how genetic variants influence molecular and physiological traits in iPSCs and derived cell lines