Update of the Anopheles gambiae PEST genome assembly

BACKGROUND: The genome of Anopheles gambiae, the major vector of malaria, was sequenced and assembled in 2002. This initial genome assembly and analysis made available to the scientific community was complicated by the presence of assembly issues, such as scaffolds with no chromosomal location, no sequence data for the Y chromosome, haplotype polymorphisms resulting in two different genome assemblies in limited regions and contaminating bacterial DNA. RESULTS: Polytene chromosome in situ hybridization with cDNA clones was used to place 15 unmapped scaffolds (sizes totaling 5.34 Mbp) in the pericentromeric regions of the chromosomes and oriented a further 9 scaffolds. Additional analysis by in situ hybridization of bacterial artificial chromosome (BAC) clones placed 1.32 Mbp (5 scaffolds) in the physical gaps between scaffolds on euchromatic parts of the chromosomes. The Y chromosome sequence information (0.18 Mbp) remains highly incomplete and fragmented among 55 short scaffolds. Analysis of BAC end sequences showed that 22 inter-scaffold gaps were spanned by BAC clones. Unmapped scaffolds were also aligned to the chromosome assemblies in silico, identifying regions totaling 8.18 Mbp (144 scaffolds) that are probably represented in the genome project by two alternative assemblies. An additional 3.53 Mbp of alternative assembly was identified within mapped scaffolds. Scaffolds comprising 1.97 Mbp (679 small scaffolds) were identified as probably derived from contaminating bacterial DNA. In total, about 33% of previously unmapped sequences were placed on the chromosomes. CONCLUSION: This study has used new approaches to improve the physical map and assembly of the A. gambiae genome

GateFinder: projection-based gating strategy optimization for flow and mass cytometry

Motivation: High-parameter single-cell technologies can reveal novel cell populations of interest, but studying or validating these populations using lower-parameter methods remains challenging.Results: Here, we present GateFinder, an algorithm that enriches high-dimensional cell types with simple, stepwise polygon gates requiring only two markers at a time. A series of case studies of complex cell types illustrates how simplified enrichment strategies can enable more efficient assays, reveal novel biomarkers and clarify underlying biology

Testing for differential abundance in mass cytometry data.

When comparing biological conditions using mass cytometry data, a key challenge is to identify cellular populations that change in abundance. Here, we present a computational strategy for detecting 'differentially abundant' populations by assigning cells to hyperspheres, testing for significant differences between conditions and controlling the spatial false discovery rate. Our method (http://bioconductor.org/packages/cydar) outperforms other approaches in simulations and finds novel patterns of differential abundance in real data.This work was supported by Cancer Research UK (core funding to J.C.M., award no. A17197), the University of Cambridge and Hutchison Whampoa Limited. J.C.M. was also supported by core funding from EMBL

VectorBase: a home for invertebrate vectors of human pathogens

VectorBase () is a web-accessible data repository for information about invertebrate vectors of human pathogens. VectorBase annotates and maintains vector genomes providing an integrated resource for the research community. Currently, VectorBase contains genome information for two organisms: Anopheles gambiae, a vector for the Plasmodium protozoan agent causing malaria, and Aedes aegypti, a vector for the flaviviral agents causing Yellow fever and Dengue fever

VectorBase: a data resource for invertebrate vector genomics

VectorBase (http://www.vectorbase.org) is an NIAID-funded Bioinformatic Resource Center focused on invertebrate vectors of human pathogens. VectorBase annotates and curates vector genomes providing a web accessible integrated resource for the research community. Currently, VectorBase contains genome information for three mosquito species: Aedes aegypti, Anopheles gambiae and Culex quinquefasciatus, a body louse Pediculus humanus and a tick species Ixodes scapularis. Since our last report VectorBase has initiated a community annotation system, a microarray and gene expression repository and controlled vocabularies for anatomy and insecticide resistance. We have continued to develop both the software infrastructure and tools for interrogating the stored data

Single-cell analysis tools for drug discovery and development

The genetic, functional or compositional heterogeneity of healthy and diseased tissues presents major challenges in drug discovery and development. Such heterogeneity hinders the design of accurate disease models and can confound the interpretation of biomarker levels and of patient responses to specific therapies. The complex nature of virtually all tissues has motivated the development of tools for single-cell genomic, transcriptomic and multiplex proteomic analyses. Here, we review these tools and assess their advantages and limitations. Emerging applications of single cell analysis tools in drug discovery and development, particularly in the field of oncology, are discussed

A gamificação como recurso estratégico para interatividade entre mídias digitais e usuários

A rápida ascensão da tecnologia e a transição para as mídias digitais trazem consigo certas dificuldades de adaptação. Essa “corrida digital” pode criar produtos com design confuso e que muitas vezes não agradam seu público-alvo. Nesse contexto, novas estratégias estão surgindo com o intuito de auxiliar essas mídias a serem mais colaborativas, interativas, intuitivas e divertidas. Um dos recursos que tem ganhado destaque é a gamificação, que propõe o uso de elementos de jogos em contextos não jogos. Esse trabalho tem como objetivo analisar a relevância da gamificação como estratégia para facilitar a interatividade entre os usuários e as mídias digitais, observando aplicações e fazendo uma pesquisa exploratória para identificar se os usuários de mídias digitais podem se beneficiar com o uso da gamificação. Para isso são apresentados os conceitos desse método: como aplicar, quando aplicar, além de sua história e origem nas mídias digitais e educação. Por último, este trabalho estuda alguns casos para identificar as técnicas de game design utilizadas com o intuito de facilitar a aplicação da gamificação nas mídias digitais, para que designers, professores ou qualquer desenvolvedor que opte pela gamificação como estratégia, entenda como aplicá-la de forma eficiente.The fast rise of technology and the transition to digital media brings with it several adaptation difficulties. This "digital rush" generally creates products with confusing design which usually do not please the general public. So, new strategies are emerging in order to assist these media to be more collaborative, interactive, intuitive and fun. One of the features that have gained prominence is gamification, which suggests the use of game elements in non-gaming circumstances. This work aims to analyze the relevance of gamification as a strategy to facilitate interactivity between users and digital media, noting applications and making an exploratory study to identify whether users of digital media can take advantage of gamification or not. Therefore, the general concepts of this method are: how to apply, when to apply, as well as its history and origin in digital media and education. Finally, this paper studies some cases to identify game design techniques used in order to facilitate the application of gamification in digital media so that designers , teachers or any developer who opt for gamification as a strategy, understand how to apply it efficiently