efam: an expanded, metaproteome-supported HMM profile database of viral protein families

Motivation: Viruses infect, reprogram and kill microbes, leading to profound ecosystem consequences, from elemental cycling in oceans and soils to microbiome-modulated diseases in plants and animals. Although metagenomic datasets are increasingly available, identifying viruses in them is challenging due to poor representation and annotation of viral sequences in databases. Results: Here, we establish efam, an expanded collection of Hidden Markov Model (HMM) profiles that represent viral protein families conservatively identified from the Global Ocean Virome 2.0 dataset. This resulted in 240 311 HMM profiles, each with at least 2 protein sequences, making efam >7-fold larger than the next largest, panecosystem viral HMM profile database. Adjusting the criteria for viral contig confidence from 'conservative' to 'eXtremely Conservative' resulted in 37 841 HMM profiles in our efam-XC database. To assess the value of this resource, we integrated efam-XC into VirSorter viral discovery software to discover viruses from less-studied, ecologically distinct oxygen minimum zone (OMZ) marine habitats. This expanded database led to an increase in viruses recovered from every tested OMZ virome by similar to 24% on average (up to similar to 42%) and especially improved the recovery of often-missed shorter contigs (<5 kb). Additionally, to help elucidate lesser-known viral protein functions, we annotated the profiles using multiple databases from the DRAM pipeline and virion-associated metaproteomic data, which doubled the number of annotations obtainable by standard, single-database annotation approaches. Together, these marine resources (efam and efam-XC) are provided as searchable, compressed HMM databases that will be updated bi-annually to help maximize viral sequence discovery and study from any ecosystem

Evaluating the Effectiveness of an Autism-Specific Workplace Tool for Employers: A Randomised Controlled Trial

A randomised controlled trial evaluated the effectiveness of the Integrated Employment Success Tool (IEST™) in improving employers’ self-efficacy in modifying the workplace for individuals on the autism spectrum. Employers (N = 84) were randomised to the IEST™ or support as usual groups. Measurements of self-efficacy, knowledge and attitudes towards disability in the workplace were obtained at baseline and post-test. Results revealed a significant improvement in self-efficacy within the IEST™ group between baseline and post-test (p = 0.016). At post-test, there were no significant differences between groups in relation to self-efficacy in implementing autism-specific workplace modifications and employer attitudes towards disability in the workplace. Given the lack of significant outcomes, further research is needed to determine the effectiveness of the IEST™ for employers

SUPREMATISMO Y REVOLUCIÓN. ARTE MODERNO Y POLÍTICA CONTEMPORÁNEA

RESUMEN Este artículo examina la estética suprematista en relación con teorías políticas contemporáneas sobre la revolución y la transformación social. El punto de partida del suprematismo es la destrucción de la realidad objetiva como acto liberador. Aunque diversos autores contemporáneos del campo de la teoría política conciben el arte tcomo producción de sentimientos que actúan como puntos de partida de la acción y el compromiso. Ambas perspectivas se entrelazan en el concepto de 'revolución': la liberación de la representación totalitaria y la creación de una nueva sociedad

Progress towards a public chemogenomic set for protein kinases and a call for contributions

Protein kinases are highly tractable targets for drug discovery. However, the biological function and therapeutic potential of the majority of the 500+ human protein kinases remains unknown. We have developed physical and virtual collections of small molecule inhibitors, which we call chemogenomic sets, that are designed to inhibit the catalytic function of almost half the human protein kinases. In this manuscript we share our progress towards generation of a comprehensive kinase chemogenomic set (KCGS), release kinome profiling data of a large inhibitor set (Published Kinase Inhibitor Set 2 (PKIS2)), and outline a process through which the community can openly collaborate to create a KCGS that probes the full complement of human protein kinases

Polymorphisms in the receptor for GDNF (RET) are not associated with Parkinson's disease in Southern Germany

The aetiology of the selective neurodegeneration in Parkinson's disease (PD) is still unknown. Neurotrophic factors, e.g. glial cell line-derived neurotrophic factor (GDNF), have been shown to promote-survival of dopaminergic neurons. Interestingly, aged mice lacking GDNF-receptor (RET) in their dopaminergic neurons show a phenotype similar to presymptomatic PD. We therefore were interested whether polymorphisms in the RET gene were associated with increased PD risk. Analyzing 25 SNPs in the RET region in 340 Southern German PD patients and 340 age- and sex-matched controls from Southern Germany (KORA S4), we did not find any significant association with PD, suggesting that the equilibrium of trophic factors in PD might be disturbed on other levels than the genomic encoding. (C) 2008 Elsevier Inc. All rights reserved