AURKA mRNA expression is an independent predictor of poor prognosis in patients with non-small cell lung cancer

Deregulation of mitotic spindle genes has been reported to contribute to the development and progression of malignant tumours. The aim of the present study was to explore the association between the expression profiles of Aurora kinases (AURKA, AURKB and AURKC), cytoskeleton-associated protein 5 (CKAP5), discs large-associated protein 5 (DLGAP5), kinesin-like protein 11 (KIF11), microtubule nucleation factor (TPX2), monopolar spindle 1 kinase (TTK), and β-tubulins (TUBB) and (TUBB3) genes and clinicopathological characteristics in human non-small cell lung carcinoma (NSCLC). Reverse transcription-quantitative polymerase chain reaction-based RNA gene expression profiles of 132 NSCLC and 44 adjacent wild-type tissues were generated, and Cox's proportional hazard regression was used to examine associations. With the exception of AURKC, all genes exhibited increased expression in NSCLC tissues. Of the 10 genes examined, only AURKA was significantly associated with prognosis in NSCLC. Multivariate Cox's regression analysis demonstrated that AURKA mRNA expression [hazard ratio (HR), 1.81; 95% confidence interval (CI), 1.16-2.84; P=0.009], age (HR, 1.03; 95% CI, 1.00-1.06; P=0.020), pathological tumour stage 2 (HR, 2.43; 95% CI, 1.16-5.10; P=0.019) and involvement of distal nodes (pathological node stage 2) (HR, 3.14; 95% CI, 1.24-7.99; P=0.016) were independent predictors of poor prognosis in patients with NSCLC. Poor prognosis of patients with increased AURKA expression suggests that those patients may benefit from surrogate therapy with AURKA inhibitors

The resurrection initiative: Storing ancestral genotypes to capture evolution in action

In rare circumstances, scientists have been able to revive dormant propagules from ancestral populations and rear them with their descendants to make inferences about evolutionary responses to environmental change. Although this is a powerful approach to directly assess microevolution, it has previously depended entirely upon fortuitous conditions to preserve ancestral material. We propose a coordinated effort to collect, preserve, and archive genetic materials today for future studies of evolutionary change - a "resurrection paradigm." The availability of ancestral material that is systematically collected and intentionally stored using best practices will greatly expand our ability to illuminate microevolutionary patterns and processes and to predict ongoing responses of species to global change. In the workshop "Project Baseline," evolutionary biologists and seed storage experts met to discuss establishing a coordinated effort to implement the resurrection paradigm. © 2008 American Institute of Biological Sciences

Persistent T Cell Repertoire Perturbation and T Cell Activation in HIV After Long Term Treatment

Objective: In people living with HIV (PLHIV), we sought to test the hypothesis that long term anti-retroviral therapy restores the normal T cell repertoire, and investigate the functional relationship of residual repertoire abnormalities to persistent immune system dysregulation. Methods: We conducted a case-control study in PLHIV and HIV-negative volunteers, of circulating T cell receptor repertoires and whole blood transcriptomes by RNA sequencing, complemented by metadata from routinely collected health care records. Results: T cell receptor sequencing revealed persistent abnormalities in the clonal T cell repertoire of PLHIV, characterized by reduced repertoire diversity and oligoclonal T cell expansion correlated with elevated CD8 T cell counts. We found no evidence that these expansions were driven by cytomegalovirus or another common antigen. Increased frequency of long CDR3 sequences and reduced frequency of public sequences among the expanded clones implicated abnormal thymic selection as a contributing factor. These abnormalities in the repertoire correlated with systems level evidence of persistent T cell activation in genome-wide blood transcriptomes. Conclusions: The diversity of T cell receptor repertoires in PLHIV on long term anti-retroviral therapy remains significantly depleted, and skewed by idiosyncratic clones, partly attributable to altered thymic output and associated with T cell mediated chronic immune activation. Further investigation of thymic function and the antigenic drivers of T cell clonal selection in PLHIV are critical to efforts to fully re-establish normal immune function

Not just another genome

Sequence analysis of the Daphnia pulex genome holds some surprises that could not have been anticipated from what was learned so far from other arthropod genomes. It establishes Daphnia as an eco-genetical model organism par excellence

Turbulent thermal diffusion in a multi-fan turbulence generator with the imposed mean temperature gradient

We studied experimentally the effect of turbulent thermal diffusion in a multi-fan turbulence generator which produces a nearly homogeneous and isotropic flow with a small mean velocity. Using Particle Image Velocimetry and Image Processing techniques we showed that in a turbulent flow with an imposed mean vertical temperature gradient (stably stratified flow) particles accumulate in the regions with the mean temperature minimum. These experiments detected the effect of turbulent thermal diffusion in a multi-fan turbulence generator for relatively high Reynolds numbers. The experimental results are in compliance with the results of the previous experimental studies of turbulent thermal diffusion in oscillating grids turbulence (Buchholz et al. 2004; Eidelman et al. 2004). We demonstrated that turbulent thermal diffusion is an universal phenomenon. It occurs independently of the method of turbulence generation, and the qualitative behavior of particle spatial distribution in these very different turbulent flows is similar. Competition between turbulent fluxes caused by turbulent thermal diffusion and turbulent diffusion determines the formation of particle inhomogeneities.Comment: 9 pages, 9 figure, REVTEX4, Experiments in Fluids, in pres

Preventing mental health problems in children : the families in mind population-based cluster randomised controlled trial.

BackgroundExternalising and internalising problems affect one in seven school-aged children and are the single strongest predictor of mental health problems into early adolescence. As the burden of mental health problems persists globally, childhood prevention of mental health problems is paramount. Prevention can be offered to all children (universal) or to children at risk of developing mental health problems (targeted). The relative effectiveness and costs of a targeted only versus combined universal and targeted approach are unknown. This study aims to the effectiveness, costs and uptake of two approaches to early childhood prevention of mental health problems ie: a Combined universal-targeted approach, versus a Targeted only approach, in comparison to current primary care services (Usual care).DesignThree armed, population-level cluster randomised trial (2010-2014) within the universal, well child Maternal Child Health system, attended by more than 80% of families in Victoria, Australia at infant age eight months. Participants: Families of eight month old children from nine participating local government areas. Randomised to one of three groups: Combined, Targeted or Usual care. Intervention: (a) the Combined universal and targeted program where all families are offered the universal Toddlers Without Tears group parenting program followed by the targeted Family Check-Up one-on-one program or (b) the Targeted Family Check-Up program. The Family Check-Up program is only offered to children at risk of behavioural problems. Analysis: Participants will be analysed according to the trial arm to which they were randomised, using logistic and linear regression models to compare primary and secondary outcomes. An economic evaluation (cost consequences analysis) will compare incremental costs to all incremental outcomes from a societal perspective.DiscussionThis trial will inform public health policy by making recommendations about the effectiveness and cost-effectiveness of these early prevention programs. If effective prevention programs can be implemented at the population level, the growing burden of mental health problems could be curbed.<br /

Association screening for genes with multiple potentially rare variants: an inverse-probability weighted clustering approach

Both common variants and rare variants are involved in the etiology of most complex diseases in humans. Developments in sequencing technology have led to the identification of a high density of rare variant single-nucleotide polymorphisms (SNPs) on the genome, each of which affects only at most 1% of the population. Genotypes derived from these SNPs allow one to study the involvement of rare variants in common human disorders. Here, we propose an association screening approach that treats genes as units of analysis. SNPs within a gene are used to create partitions of individuals, and inverse-probability weighting is used to overweight genotypic differences observed on rare variants. Association between a phenotype trait and the constructed partition is then evaluated. We consider three association tests (one-way ANOVA, chi-square test, and the partition retention method) and compare these strategies using the simulated data from the Genetic Analysis Workshop 17. Several genes that contain causal SNPs were identified by the proposed method as top genes

The novel mTOR inhibitor RAD001 (Everolimus) induces antiproliferative effects in human pancreatic neuroendocrine tumor cells

Background/Aim: Tumors exhibiting constitutively activated PI(3) K/Akt/mTOR signaling are hypersensitive to mTOR inhibitors such as RAD001 (everolimus) which is presently being investigated in clinical phase II trials in various tumor entities, including neuroendocrine tumors (NETs). However, no preclinical data about the effects of RAD001 on NET cells have been published. In this study, we aimed to evaluate the effects of RAD001 on BON cells, a human pancreatic NET cell line that exhibits constitutively activated PI(3) K/Akt/mTOR signaling. Methods: BON cells were treated with different concentrations of RAD001 to analyze its effect on cell growth using proliferation assays. Apoptosis was examined by Western blot analysis of caspase-3/PARP cleavage and by FACS analysis of DNA fragmentation. Results: RAD001 potently inhibited BON cell growth in a dose-dependent manner which was dependent on the serum concentration in the medium. RAD001-induced growth inhibition involved G0/G1-phase arrest as well as induction of apoptosis. Conclusion: In summary, our data demonstrate antiproliferative and apoptotic effects of RAD001 in NET cells in vitro supporting its clinical use in current phase II trials in NET patients. Copyright (c) 2007 S. Karger AG, Basel