Vitamin D binding protein isoforms as candidate predictors of disease extension in childhood arthritis

Introduction: Juvenile idiopathic arthritis (JIA) comprises a poorly understood group of chronic autoimmune diseases with variable clinical outcomes. We investigated whether the synovial fluid (SF) proteome could distinguish a subset of patients in whom disease extends to affect a large number of joints.

Methods: SF samples from 57 patients were obtained around time of initial diagnosis of JIA, labeled with Cy dyes and separated by two-dimensional electrophoresis. Multivariate analyses were used to isolate a panel of proteins which distinguish patient subgroups. Proteins were identified using MALDI-TOF mass spectrometry with expression verified by immunochemical methods. Protein glycosylation status was confirmed by hydrophilic interaction liquid chromatography.

Results: A truncated isoform of vitamin D binding protein (VDBP) is present at significantly reduced levels in the SF of oligoarticular patients at risk of disease extension, relative to other subgroups (p < 0.05). Furthermore, sialylated forms of immunopurified synovial VDBP were significantly reduced in extended oligoarticular patients (p < 0.005).

Conclusion: Reduced conversion of VDBP to a macrophage activation factor may be used to stratify patients to determine risk of disease extension in JIA patients.

Resolving candidate genes of mouse skeletal muscle QTL via RNA-Seq and expression network analyses

BACKGROUND:

We have recently identified a number of Quantitative Trait Loci (QTL) contributing to the 2-fold muscle weight difference between the LG/J and SM/J mouse strains and refined their confidence intervals. To facilitate nomination of the candidate genes responsible for these differences we examined the transcriptome of the tibialis anterior (TA) muscle of each strain by RNA-Seq.

13,726 genes were expressed in mouse skeletal muscle. Intersection of a set of 1061 differentially expressed transcripts with a mouse muscle Bayesian Network identified a coherent set of differentially expressed genes that we term the LG/J and SM/J Regulatory Network (LSRN). The integration of the QTL, transcriptome and the network analyses identified eight key drivers of the LSRN (Kdr, Plbd1, Mgp, Fah, Prss23, 2310014F06Rik, Grtp1, Stk10) residing within five QTL regions, which were either polymorphic or differentially expressed between the two strains and are strong candidates for quantitative trait genes (QTGs) underlying muscle mass. The insight gained from network analysis including the ability to make testable predictions is illustrated by annotating the LSRN with knowledge-based signatures and showing that the SM/J state of the network corresponds to a more oxidative state. We validated this prediction by NADH tetrazolium reductase staining in the TA muscle revealing higher oxidative potential of the SM/J compared to the LG/J strain (p<0.03).

Thus, integration of fine resolution QTL mapping, RNA-Seq transcriptome information and mouse muscle Bayesian Network analysis provides a novel and unbiased strategy for nomination of muscle QTGs.

RanGTPase: A Candidate for Myc-Mediated Cancer Progression

BackgroundRas-related nuclear protein (Ran) is required for cancer cell survival in vitro and human cancer progression, but the molecular mechanisms are largely unknown.MethodsWe investigated the effect of the v-myc myelocytomatosis viral oncogene homolog (Myc) on Ran expression by Western blot, chromatin immunoprecipitation, and luciferase reporter assays and the effects of Myc and Ran expression in cancer cells by soft-agar, cell adhesion, and invasion assays. The correlation between Myc and Ran and the association with patient survival were investigated in 14 independent patient cohorts (n = 2430) and analyzed with Spearman's rank correlation and Kaplan-Meier plots coupled with Wilcoxon-Gehan tests, respectively. All statistical tests were two-sided.ResultsMyc binds to the upstream sequence of Ran and transactivates Ran promoter activity. Overexpression of Myc upregulates Ran expression, whereas knockdown of Myc downregulates Ran expression. Myc or Ran overexpression in breast cancer cells is associated with cancer progression and metastasis. Knockdown of Ran reverses the effect induced by Myc overexpression in breast cancer cells. In clinical data, a positive association between Myc and Ran expression was revealed in 288 breast cancer and 102 lung cancer specimens. Moreover, Ran expression levels differentiate better or poorer survival in Myc overexpressing breast (?(2) = 24.1; relative risk [RR] = 9.1, 95% confidence interval [CI] = 3.3 to 24.7, P <.001) and lung (?(2) = 6.04; RR = 2.8, 95% CI = 1.2 to 6.3; P = .01) cancer cohorts.ConclusionsOur results suggest that Ran is required for and is a potential therapeutic target of Myc-driven cancer progression in both breast and lung cancers.

Modelling the H Lyman lines in evolved late-type stars

The importance of partial redistribution (PRD) in the modelling of the Lyman a and Lyman ß emission lines of hydrogen in stellar atmospheres is examined using simple atmospheric models of a range of late-type stars. These models represent the subgiant Procyon (F5 IV-V), and the two giants ß Gem (K0 III) and a Tau (K5 III). These stars are selected to span a wide range of surface gravities: 1.25 <log g <4.00. The calculations are performed using the computer code MULTI with the modifications made by Hubeny & Lites. It is found that PRD effects are highly significant, both in the direct prediction of the Lyman line profiles and in the application of hydrostatic equilibrium to calculate the atmospheric electron density in static atmospheric models.

Mass-loss rates for hot luminous stars:The influence of line branching

The effect of photon frequency redistribution by line branching on mass-loss rates for hot luminous stars is investigated. Monte Carlo simulations are carried out for a range of OB star models which show that previous mass-loss calculations which neglect non-resonance line scattering overestimate mass-loss rates for luminous O stars by ~20 per cent. For luminous B stars the effect is somewhat larger, typically ~50 per cent. A Wolf-Rayet star model is used to investigate line branching in the strong wind limit. In this case the effect of line branching is much greater, giving mass-loss rates that are smaller by a factor ~3 from computations which neglect branching.

X-shooting Herbig Ae/Be stars: Accretion probed by near-infrared He I emission

The Herbig Ae/Be stars are intermediate mass pre-main sequence stars that bridge the gap between the low mass T Tauri stars and the Massive Young Stellar Objects. In this mass range, the acting star forming mechanism switches from magnetically controlled accretion to an as yet unknown mechanism, but which is likely to be direct disk accretion onto the star. We observed a large sample of Herbig Ae/Be stars with X-shooter to address this issue from a multi-wavelength perspective. It is the largest such study to date, not only because of the number of objects involved, but also because of the large wavelength coverage from the blue to the near-infrared. This allows many accretion diagnostics to be studied simultaneously. By correlating the various properties with mass, temperature and age, we aim to determine where and whether the magnetically controlled mass accretion mechanism halts and the proposed direct disk accretion takes over. Here, we will give an overview of the background, present some observations and discuss our initial results. We will introduce a new accretion diagnostic for the research of Herbig Ae/Be stars, the HeI 1.083 µm line. © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Connectivity Mapping for Candidate Therapeutics Identification Using Next Generation Sequencing RNA-Seq Data

The advent of next generation sequencing technologies (NGS) has expanded the area of genomic research, offering high coverage and increased sensitivity over older microarray platforms. Although the current cost of next generation sequencing is still exceeding that of microarray approaches, the rapid advances in NGS will likely make it the platform of choice for future research in differential gene expression. Connectivity mapping is a procedure for examining the connections among diseases, genes and drugs by differential gene expression initially based on microarray technology, with which a large collection of compound-induced reference gene expression profiles have been accumulated. In this work, we aim to test the feasibility of incorporating NGS RNA-Seq data into the current connectivity mapping framework by utilizing the microarray based reference profiles and the construction of a differentially expressed gene signature from a NGS dataset. This would allow for the establishment of connections between the NGS gene signature and those microarray reference profiles, alleviating the associated incurring cost of re-creating drug profiles with NGS technology. We examined the connectivity mapping approach on a publicly available NGS dataset with androgen stimulation of LNCaP cells in order to extract candidate compounds that could inhibit the proliferative phenotype of LNCaP cells and to elucidate their potential in a laboratory setting. In addition, we also analyzed an independent microarray dataset of similar experimental settings. We found a high level of concordance between the top compounds identified using the gene signatures from the two datasets. The nicotine derivative cotinine was returned as the top candidate among the overlapping compounds with potential to suppress this proliferative phenotype. Subsequent lab experiments validated this connectivity mapping hit, showing that cotinine inhibits cell proliferation in an androgen dependent manner. Thus the results in this study suggest a promising prospect of integrating NGS data with connectivity mapping. © 2013 McArt et al.

Association Study of 167 Candidate Genes for Schizophrenia Selected by a Multi-Domain Evidence-Based Prioritization Algorithm and Neurodevelopmental Hypothesis

Integrating evidence from multiple domains is useful in prioritizing disease candidate genes for subsequent testing. We ranked all known human genes (n = 3819) under linkage peaks in the Irish Study of High-Density Schizophrenia Families using three different evidence domains: 1) a meta-analysis of microarray gene expression results using the Stanley Brain collection, 2) a schizophrenia protein-protein interaction network, and 3) a systematic literature search. Each gene was assigned a domain-specific p-value and ranked after evaluating the evidence within each domain. For comparison to this
ranking process, a large-scale candidate gene hypothesis was also tested by including genes with Gene Ontology terms related to neurodevelopment. Subsequently, genotypes of 3725 SNPs in 167 genes from a custom Illumina iSelect array were used to evaluate the top ranked vs. hypothesis selected genes. Seventy-three genes were both highly ranked and involved in neurodevelopment (category 1) while 42 and 52 genes were exclusive to neurodevelopment (category 2) or highly ranked (category 3), respectively. The most significant associations were observed in genes PRKG1, PRKCE, and CNTN4 but no individual SNPs were significant after correction for multiple testing. Comparison of the approaches showed an excess of significant tests using the hypothesis-driven neurodevelopment category. Random selection of similar sized genes from two independent genome-wide association studies (GWAS) of schizophrenia showed the excess was unlikely by chance. In a further meta-analysis of three GWAS datasets, four candidate SNPs reached nominal significance. Although gene ranking using integrated sources of prior information did not enrich for significant results in the current experiment, gene selection using an a priori hypothesis (neurodevelopment) was superior to random selection. As such, further development of gene ranking strategies using more carefully selected sources of information is warranted.

DONUTS: A Science Frame Autoguiding Algorithm with Sub-Pixel Precision, Capable of Guiding on Defocused Stars

We present the DONUTS autoguiding algorithm, designed to fix stellar positions at the sub-pixel level for high-cadence time-series photometry, and also capable of autoguiding on defocused stars. DONUTS was designed to calculate guide corrections from a series of science images and recentre telescope pointing between each exposure. The algorithm has the unique ability of calculating guide corrections from undersampled to heavily defocused point spread functions. We present the case for why such an algorithm is important for high precision photometry and give our results from off and on-sky testing. We discuss the limitations of DONUTS and the facilities where it soon will be deployed.

Finding exoplanets orbiting young active stars - I. Technique

Stellar activity, such as starspots, can induce radial velocity (RV) variations that can mask or even mimic the RV signature of orbiting exoplanets. For this reason RV exoplanet surveys have been unsuccessful when searching for planets around young, active stars and are therefore failing to explore an important regime which can help to reveal how planets form and migrate. This paper describes a new technique to remove spot signatures from the stellar line-profiles of moderately rotating, active stars (v sin i ranging from 10 to 50 km s(-1)). By doing so it allows planetary RV signals to be uncovered. We used simulated models of a G5V type star with differing dark spots on its surface along with archive data of the known active star HD 49933 to validate our method. The results showed that starspots could be effectively cleaned from the line-profiles so that the stellar RV jitter was reduced by more than 80 per cent. Applying this procedure to the same models and HD 49933 data, but with fake planets injected, enabled the effective removal of starspots so that Jupiter mass planets on short orbital periods were successfully recovered. These results show that this approach can be useful in the search for hot-Jupiter planets that orbit around young, active stars with a v sin i of similar to 10-50 km/s.

Novel 5-aryloxypyrimidine SEN1576 as a candidate for the treatment of Alzheimer's disease

Prefibrillar assembly of amyloid-ß (Aß) is a major event underlying the development of neuropathology and dementia in Alzheimer's disease (AD). This study determined the neuroprotective properties of an orally bioavailable Aß synaptotoxicity inhibitor, SEN1576. Binding of SEN1576 to monomeric Aß 1–42 was measured using surface plasmon resonance. Thioflavin-T and MTT assays determined the ability of SEN1576 to block Aß 1–42-induced aggregation and reduction in cell viability, respectively. In vivo long-term potentiation (LTP) determined effects on synaptic toxicity induced by intracerebroventricular (i.c.v.) injection of cell-derived Aß oligomers. An operant behavioural schedule measured effects of oral administration following i.c.v. injection of Aß oligomers in normal rats. SEN1576 bound to monomeric Aß 1–42, protected neuronal cells exposed to Aß 1–42, reduced deficits in in vivo LTP and behaviour. SEN1576 exhibits the necessary features of a drug candidate for further development as a disease modifying treatment for the early stages of AD-like dementia.

High-contrast imaging search for planets and brown dwarfs around the most massive stars in the solar neighborhood

There has been a long-standing discussion in the literature as to whether core accretion or disk instability is the dominant mode of planet formation. Over the last decade, several lines of evidence have been presented showing that core accretion is most likely the dominant mechanism for the close-in population of planets probed by radial velocity and transits. However, this does not by itself prove that core accretion is the dominant mode for the total planet population, since disk instability might conceivably produce and retain large numbers of planets in the far-out regions of the disk. If this is a relevant scenario, then the outer massive disks of B-stars should be among the best places for massive planets and brown dwarfs to form and reside. In this study, we present high-contrast imaging of 18 nearby massive stars of which 15 are in the B2-A0 spectral-type range and provide excellent sensitivity to wide companions. By comparing our sensitivities to model predictions of disk instability based on physical criteria for fragmentation and cooling, and using Monte Carlo simulations for orbital distributions, we find that ~85% of such companions should have been detected in our images on average. Given this high degree of completeness, stringent statistical limits can be set from the null-detection result, even with the limited sample size. We find that

Roche Tomography of the Secondary Stars in CVS

The secondary stars in cataclysmic variables (CVs) are key to our understanding of the origin evolution and behaviour of this class of interacting binary. In seeking a fuller understanding of these objects the challenge for observers is to obtain images of the secondary star. This goal can be achieved through Roche tomography an indirect imaging technique that can be used to map the Roche-lobe-filling secondary star. The review begins with a description of the basic principles that underpin Roche tomography including methods for determining the binary system parameters. Noise propagation onto Roche tomograms is also covered. Finally the review concludes with a look at the main scientific highlights to date and the future prospects for Roche tomography

On the progenitor of the type IIP SN 2013ej in M74

We use natural seeing imaging of SN 2013ej in M74 to identify a progenitor candidate in archival Hubble Space Telescope (HST) + Advanced Camera for Survey images. We find a source coincident with the supernova (SN) in the F814W filter within the total 75 mas (~3 pc astrometric uncertainty; however, the position of the progenitor candidate in contemporaneous F435W and F555W filters is significantly offset. We conclude that the 'progenitor candidate' is in fact two physically unrelated sources; a blue source which is likely unrelated to the SN, and a red source which we suggest exploded as SN 2013ej. Deep images with the same instrument on board HST taken when the SN has faded (in approximately two year's time) will allow us to accurately characterize the unrelated neighbouring source and hence determine the intrinsic flux of the progenitor in three filters.We suggest that the F814W flux is dominated by the progenitor of SN 2013ej, and assuming a bolometric correction appropriate to an M-type supergiant, we estimate that the mass of the progenitor of SN 2013ej was between 8 and 15.5M⊙.