SNP-VISTA: An interactive SNP visualization tool

BACKGROUND: Recent advances in sequencing technologies promise to provide a better understanding of the genetics of human disease as well as the evolution of microbial populations. Single Nucleotide Polymorphisms (SNPs) are established genetic markers that aid in the identification of loci affecting quantitative traits and/or disease in a wide variety of eukaryotic species. With today's technological capabilities, it has become possible to re-sequence a large set of appropriate candidate genes in individuals with a given disease in an attempt to identify causative mutations. In addition, SNPs have been used extensively in efforts to study the evolution of microbial populations, and the recent application of random shotgun sequencing to environmental samples enables more extensive SNP analysis of co-occurring and co-evolving microbial populations. The program is available at [1]. RESULTS: We have developed and present two modifications of an interactive visualization tool, SNP-VISTA, to aid in the analyses of the following types of data: A. Large-scale re-sequence data of disease-related genes for discovery of associated and/or causative alleles (GeneSNP-VISTA). B. Massive amounts of ecogenomics data for studying homologous recombination in microbial populations (EcoSNP-VISTA). The main features and capabilities of SNP-VISTA are: 1) mapping of SNPs to gene structure; 2) classification of SNPs, based on their location in the gene, frequency of occurrence in samples and allele composition; 3) clustering, based on user-defined subsets of SNPs, highlighting haplotypes as well as recombinant sequences; 4) integration of protein evolutionary conservation visualization; and 5) display of automatically calculated recombination points that are user-editable. CONCLUSION: The main strength of SNP-VISTA is its graphical interface and use of visual representations, which support interactive exploration and hence better understanding of large-scale SNP data by the user

SB-224289 Antagonizes the Antifungal Mechanism of the Marine Depsipeptide Papuamide A

In order to expand the repertoire of antifungal compounds a novel, high-throughput phenotypic drug screen targeting fungal phosphatidylserine (PS) synthase (Cho1p) was developed based on antagonism of the toxin papuamide A (Pap-A). Pap-A is a cyclic depsipeptide that binds to PS in the membrane of wild-type Candida albicans, and permeabilizes its plasma membrane, ultimately causing cell death. Organisms with a homozygous deletion of the CHO1 gene (cho1ΔΔ) do not produce PS and are able to survive in the presence of Pap-A. Using this phenotype (i.e. resistance to Pap-A) as an indicator of Cho1p inhibition, we screened over 5,600 small molecules for Pap-A resistance and identified SB-224289 as a positive hit. SB-224289, previously reported as a selective human 5-HT1B receptor antagonist, also confers resistance to the similar toxin theopapuamide (TPap-A), but not to other cytotoxic depsipeptides tested. Structurally similar molecules and truncated variants of SB-224289 do not confer resistance to Pap-A, suggesting that the toxin-blocking ability of SB-224289 is very specific. Further biochemical characterization revealed that SB-224289 does not inhibit Cho1p, indicating that Pap-A resistance is conferred by another undetermined mechanism. Although the mode of resistance is unclear, interaction between SB-224289 and Pap-A or TPap-A suggests this screening assay could be adapted for discovering other compounds which could antagonize the effects of other environmentally- or medically-relevant depsipeptide toxins

Sharing the Rewards, Dividing the Costs? The Electoral Consequences of Social Pacts and Legislative Reform in Western Europe

Research suggests that electoral pressures may provide an explanation for why governments offer pacts to unions and employers rather than acting through legislation when faced with the need to pass potentially unpopular reforms to welfare policies, wages, and labour markets. Here, we analyse whether governments’ pursuit of pacts affects their vote share and increases the probability that they gain re-election for 16 West European countries between 1980 and 2012. We find that the presence of social pacts has a significant and positive effect on incumbents’ vote shares at the next election and also results in a higher probability of re-election. While all types of governments benefit electorally from pacts, the electoral penalties from the pursuit of unilateral legislation on policy reforms harm single-party majorities the most, minority governments moderately, and coalition majorities the least

Reactivity in ELISA with DNA-loaded nucleosomes in patients with proliferative lupus nephritis

Item does not contain fulltextAutoantibodies against nucleosomes are considered a hallmark of systemic lupus erythematosus (SLE). We compared in patients with proliferative lupus nephritis the diagnostic usefulness of a dsDNA-loaded nucleosome ELISA (anti-dsDNA-NcX) with ELISAs in which dsDNA or nucleosomes alone were coated. First, we analysed whether DNA loading on nucleosomes led to masking of epitopes by using defined monoclonal anti-DNA, anti-histone and nucleosome-specific autoantibodies to evaluate the accessibility of nucleosomal epitopes in the anti-dsDNA-NcX ELISA. Second, autoantibody levels were measured in these 3 ELISAs in 100 patients with proliferative lupus nephritis (LN) before immunosuppressive treatment and in 128 non-SLE disease controls. In patients with LN inter-assay comparisons and associations with clinical and serological parameters were analysed. The panel of monoclonal antibodies revealed that all epitopes were equally accessible in the anti-dsDNA-NcX ELISA as in the two other ELISAs. Patients with proliferative lupus nephritis were positive with dsDNA-loaded nucleosomes in 86%, with DNA in 66% and with nucleosomes in 85%. In the non-lupus disease control group these frequencies were 1.6% (2 out of 128) for both the anti-dsDNA-NcX and the anti-dsDNA ELISA and 0% in the anti-nucleosome ELISA. The levels in the anti-dsDNA-NcX ELISA were high in a group of patients with LN that showed absent reactivity in the anti-DNA or low levels in the anti-nucleosome ELISA. Anti-dsDNA-NcX positivity was associated with higher SLEDAI scores within this group. Within nucleosome-based ELISAs, we propose the anti-dsDNA-NcX ELISA as the preferred test system

Experimental quantum speed-up in reinforcement learning agents

Increasing demand for algorithms that can learn quickly and efficiently has led to a surge of development within the field of artificial intelligence (AI). An important paradigm within AI is reinforcement learning (RL), where agents interact with environments by exchanging signals via a communication channel. Agents can learn by updating their behaviour based on obtained feedback. The crucial question for practical applications is how fast agents can learn to respond correctly. An essential figure of merit is therefore the learning time. While various works have made use of quantum mechanics to speed up the agent's decision-making process, a reduction in learning time has not been demonstrated yet. Here we present a RL experiment where the learning of an agent is boosted by utilizing a quantum communication channel with the environment. We further show that the combination with classical communication enables the evaluation of such an improvement, and additionally allows for optimal control of the learning progress. This novel scenario is therefore demonstrated by considering hybrid agents, that alternate between rounds of quantum and classical communication. We implement this learning protocol on a compact and fully tunable integrated nanophotonic processor. The device interfaces with telecom-wavelength photons and features a fast active feedback mechanism, allowing us to demonstrate the agent's systematic quantum advantage in a setup that could be readily integrated within future large-scale quantum communication networks.Comment: 10 pages, 4 figure

Do mycorrhizal network benefits to survival and growth of interior Douglas-fir seedlings increase with soil moisture stress?

Facilitation of tree establishment by ectomycorrhizal (EM) networks (MNs) may become increasingly important as drought stress increases with climate change in some forested regions of North America. The objective of this study was to determine (1) whether temperature, CO2 concentration ([CO2]), soil moisture, and MNs interact to affect plant establishment success, such that MNs facilitate establishment when plants are the most water stressed, and (2) whether transfer of C and water between plants through MNs plays a role in this. We established interior Douglas-fir (Pseudotsuga menziesiivar.glauca) seedlings in root boxes with and without the potential to form MNs with nearby conspecific seedlings that had consistent access to water via their taproots. We varied temperature, [CO2], and soil moisture in growth chambers. Douglas-fir seedling survival increased when the potential existed to form an MN. Growth increased with MN potential under the driest soil conditions, but decreased with temperature at 800 ppm [CO2]. Transfer of 13C to receiver seedlings was unaffected by potential to form an MN with donor seedlings, but deuterated water (D2O) transfer increased with MN potential under ambient [CO2]. Chlorophyll fluorescence was reduced when seedlings had the potential to form an MN under high [CO2] and cool temperatures. We conclude that Douglas-fir seedling establishment in laboratory conditions is facilitated by MN potential where Douglas-fir seedlings have consistent access to water. Moreover, this facilitation appears to increase as water stress potential increases and water transfer via networks may play a role in this. These results suggest that conservation of MN potential may be important to forest regeneration where drought stress increases with climate change