FlyBase: genes and gene models

FlyBase (http://flybase.org) is the primary repository of genetic and molecular data of the insect family Drosophilidae. For the most extensively studied species, Drosophila melanogaster, a wide range of data are presented in integrated formats. Data types include mutant phenotypes, molecular characterization of mutant alleles and aberrations, cytological maps, wild-type expression patterns, anatomical images, transgenic constructs and insertions, sequence-level gene models and molecular classification of gene product functions. There is a growing body of data for other Drosophila species; this is expected to increase dramatically over the next year, with the completion of draft-quality genomic sequences of an additional 11 Drosphila species

Natural language processing in aid of FlyBase curators.

BACKGROUND: Despite increasing interest in applying Natural Language Processing (NLP) to biomedical text, whether this technology can facilitate tasks such as database curation remains unclear. RESULTS: PaperBrowser is the first NLP-powered interface that was developed under a user-centered approach to improve the way in which FlyBase curators navigate an article. In this paper, we first discuss how observing curators at work informed the design and evaluation of PaperBrowser. Then, we present how we appraise PaperBrowser's navigational functionalities in a user-based study using a text highlighting task and evaluation criteria of Human-Computer Interaction. Our results show that PaperBrowser reduces the amount of interactions between two highlighting events and therefore improves navigational efficiency by about 58% compared to the navigational mechanism that was previously available to the curators. Moreover, PaperBrowser is shown to provide curators with enhanced navigational utility by over 74% irrespective of the different ways in which they highlight text in the article. CONCLUSION: We show that state-of-the-art performance in certain NLP tasks such as Named Entity Recognition and Anaphora Resolution can be combined with the navigational functionalities of PaperBrowser to support curation quite successfully.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Sources of non-methane hydrocarbons in surface air in Delhi, India

Rapid economic growth and development have exacerbated air quality problems across India, driven by many poorly understood pollution sources and understanding their relative importance remains critical to characterising the key drivers of air pollution. A comprehensive suite of measurements of 90 non-methane hydrocarbons (NMHCs) (C2–C14), including 12 speciated monoterpenes and higher molecular weight monoaromatics, were made at an urban site in Old Delhi during the pre-monsoon (28-May to 05-Jun 2018) and post-monsoon (11 to 27-Oct 2018) seasons using dual-channel gas chromatography (DC-GC-FID) and two-dimensional gas chromatography (GC×GC-FID). Significantly higher mixing ratios of NMHCs were measured during the post-monsoon campaign, with a mean night-time enhancement of around 6. Like with NOx and CO, strong diurnal profiles were observed for all NMHCs, except isoprene, with very high NMHC mixing ratios between 35–1485 ppbv. The sum of mixing ratios of benzene, toluene, ethylbenzene and xylenes (BTEX) routinely exceeded 100 ppbv at night during the post-monsoon period, with a maximum measured mixing ratio of monoaromatic species of 370 ppbv. The mixing ratio of highly reactive monoterpenes peaked at around 6 ppbv in the post-monsoon campaign and correlated strongly with anthropogenic NMHCs, suggesting a strong non-biogenic source in Delhi. A detailed source apportionment study was conducted which included regression analysis to CO, acetylene and other NMHCs, hierarchical cluster analysis, EPA UNMIX 6.0, principal component analysis/absolute principal component scores (PCA/APCS) and comparison with NMHC ratios (benzene/toluene and i-/n-pentane) in ambient samples to liquid and solid fuels. These analyses suggested the primary source of anthropogenic NMHCs in Delhi was from traffic emissions (petrol and diesel), with average mixing ratio contributions from Unmix and PCA/APCS models of 38% from petrol, 14% from diesel and 32% from liquified petroleum gas (LPG) with a smaller contribution (16%) from solid fuel combustion. Detailed consideration of the underlying meteorology during the campaigns showed that the extreme night-time mixing ratios of NMHCs during the post-monsoon campaign were the result of emissions into a very shallow and stagnant boundary layer. The results of this study suggest that despite widespread open burning in India, traffic-related petrol and diesel emissions remain the key drivers of gas-phase urban air pollution in Delhi

Annotation of the Drosophila melanogaster euchromatic genome: a systematic review

BACKGROUND: The recent completion of the Drosophila melanogaster genomic sequence to high quality and the availability of a greatly expanded set of Drosophila cDNA sequences, aligning to 78% of the predicted euchromatic genes, afforded FlyBase the opportunity to significantly improve genomic annotations. We made the annotation process more rigorous by inspecting each gene visually, utilizing a comprehensive set of curation rules, requiring traceable evidence for each gene model, and comparing each predicted peptide to SWISS-PROT and TrEMBL sequences. RESULTS: Although the number of predicted protein-coding genes in Drosophila remains essentially unchanged, the revised annotation significantly improves gene models, resulting in structural changes to 85% of the transcripts and 45% of the predicted proteins. We annotated transposable elements and non-protein-coding RNAs as new features, and extended the annotation of untranslated (UTR) sequences and alternative transcripts to include more than 70% and 20% of genes, respectively. Finally, cDNA sequence provided evidence for dicistronic transcripts, neighboring genes with overlapping UTRs on the same DNA sequence strand, alternatively spliced genes that encode distinct, non-overlapping peptides, and numerous nested genes. CONCLUSIONS: Identification of so many unusual gene models not only suggests that some mechanisms for gene regulation are more prevalent than previously believed, but also underscores the complex challenges of eukaryotic gene prediction. At present, experimental data and human curation remain essential to generate high-quality genome annotations

Low-NO atmospheric oxidation pathways in a polluted megacity

The impact of emissions of volatile organic compounds (VOCs) to the atmosphere on the production of secondary pollutants, such as ozone and secondary organic aerosol (SOA), is mediated by the concentration of nitric oxide (NO). Polluted urban atmospheres are typically considered to be “high-NO” environments, while remote regions such as rainforests, with minimal anthropogenic influences, are considered to be “low NO”. However, our observations from central Beijing show that this simplistic separation of regimes is flawed. Despite being in one of the largest megacities in the world, we observe formation of gas- and aerosol-phase oxidation products usually associated with low-NO “rainforest-like” atmospheric oxidation pathways during the afternoon, caused by extreme suppression of NO concentrations at this time. Box model calculations suggest that during the morning high-NO chemistry predominates (95 %) but in the afternoon low-NO chemistry plays a greater role (30 %). Current emissions inventories are applied in the GEOS-Chem model which shows that such models, when run at the regional scale, fail to accurately predict such an extreme diurnal cycle in the NO concentration. With increasing global emphasis on reducing air pollution, it is crucial for the modelling tools used to develop urban air quality policy to be able to accurately represent such extreme diurnal variations in NO to accurately predict the formation of pollutants such as SOA and ozone

An intrinsically disordered proteins community for ELIXIR.

Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) are now recognised as major determinants in cellular regulation. This white paper presents a roadmap for future e-infrastructure developments in the field of IDP research within the ELIXIR framework. The goal of these developments is to drive the creation of high-quality tools and resources to support the identification, analysis and functional characterisation of IDPs. The roadmap is the result of a workshop titled "An intrinsically disordered protein user community proposal for ELIXIR" held at the University of Padua. The workshop, and further consultation with the members of the wider IDP community, identified the key priority areas for the roadmap including the development of standards for data annotation, storage and dissemination; integration of IDP data into the ELIXIR Core Data Resources; and the creation of benchmarking criteria for IDP-related software. Here, we discuss these areas of priority, how they can be implemented in cooperation with the ELIXIR platforms, and their connections to existing ELIXIR Communities and international consortia. The article provides a preliminary blueprint for an IDP Community in ELIXIR and is an appeal to identify and involve new stakeholders

The microtubule catastrophe promoter Sentin delays stable kinetochore-microtubule attachment in oocytes

The critical step in meiosis is to attach homologous chromosomes to the opposite poles. In mouse oocytes, stable microtubule end-on attachments to kinetochores are not established until hours after spindle assembly, and phosphorylation of kinetochore proteins by Aurora B/C is responsible for the delay. Here we demonstrated that microtubule ends are actively prevented from stable attachment to kinetochores until well after spindle formation in Drosophila melanogaster oocytes. We identified the microtubule catastrophe-promoting complex Sentin-EB1 as a major factor responsible for this delay. Without this activity, microtubule ends precociously form robust attachments to kinetochores in oocytes, leading to a high proportion of homologous kinetochores stably attached to the same pole. Therefore, regulation of microtubule ends provides an alternative novel mechanism to delay stable kinetochore–microtubule attachment in oocytes

Detection of Respiratory Viruses and Subtype Identification of Influenza A Viruses by GreeneChipResp Oligonucleotide Microarray

Acute respiratory infections are significant causes of morbidity, mortality, and economic burden worldwide. An accurate, early differential diagnosis may alter individual clinical management as well as facilitate the recognition of outbreaks that have implications for public health. Here we report on the establishment and validation of a comprehensive and sensitive microarray system for detection of respiratory viruses and subtyping of influenza viruses in clinical materials. Implementation of a set of influenza virus enrichment primers facilitated subtyping of influenza A viruses through the differential recognition of hemagglutinins 1 through 16 and neuraminidases 1 through 9. Twenty-one different respiratory virus species were accurately characterized, including a recently identified novel genetic clade of rhinovirus.Fil: Quan, Phenix-Lan. Columbia University. Jerome L. and Dawn Greene Infectious Disease Laboratory; Estados Unidos.Fil: Palacios, Gustavo. Columbia University. Jerome L. and Dawn Greene Infectious Disease Laboratory; Estados Unidos.Fil: Jabado, Omar J. Columbia University. Jerome L. and Dawn Greene Infectious Disease Laboratory; Estados Unidos.Fil: Conlan, Sean. Columbia University. Jerome L. and Dawn Greene Infectious Disease Laboratory; Estados Unidos.Fil: Hirschberg, David L. Stanford School of Medicine; Estados Unidos.Fil: Pozo, Francisco. Instituto de Salud Carlos III. Centro Nacional de Microbiología; España.Fil: Jack, Philippa J. M. Australian Animal Health Laboratory. CSIRO Livestock Industries; Australia.Fil: Cisterna, Daniel. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Enfermedades Infecciosas; Argentina.Fil: Renwick, Neil. Columbia University. Jerome L. and Dawn Greene Infectious Disease Laboratory; Estados Unidos.Fil: Hui, Jeffrey. Columbia University. Jerome L. and Dawn Greene Infectious Disease Laboratory; Estados Unidos.Fil: Drysdale, Andrew. Columbia University. Jerome L. and Dawn Greene Infectious Disease Laboratory; Estados Unidos.Fil: Amos-Ritchie, Rachel. Australian Animal Health Laboratory. CSIRO Livestock Industries; Australia.Fil: Baumeister, Elsa. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Enfermedades Infecciosas; Argentina.Fil: Savy, Vilma. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Enfermedades Infecciosas; Argentina.Fil: Lager, Kelly M. USDA. National Animal Disease Center; Estados Unidos.Fil: Richt, Jürgen A. USDA. National Animal Disease Center; Estados Unidos.Fil: Boyle, David B. Australian Animal Health Laboratory. CSIRO Livestock Industries; Australia.Fil: García-Sastre, Adolfo. Mount Sinai School of Medicine. Department of Microbiology and Emerging Pathogens Institute; Estados Unidos.Fil: Casas, Inmaculada. Instituto de Salud Carlos III. Centro Nacional de Microbiología; España.Fil: Perez-Breña, Pilar. Instituto de Salud Carlos III. Centro Nacional de Microbiología; España.Fil: Briese, Thomas. Columbia University. Jerome L. and Dawn Greene Infectious Disease Laboratory; Estados Unidos.Fil: Lipkin, W. Ian. Columbia University. Jerome L. and Dawn Greene Infectious Disease Laboratory; Estados Unidos

Detection of Respiratory Viruses and Subtype Identification of Influenza A Viruses by GreeneChipResp Oligonucleotide Microarray

Acute respiratory infections are significant causes of morbidity, mortality, and economic burden worldwide. An accurate, early differential diagnosis may alter individual clinical management as well as facilitate the recognition of outbreaks that have implications for public health. Here we report on the establishment and validation of a comprehensive and sensitive microarray system for detection of respiratory viruses and subtyping of influenza viruses in clinical materials. Implementation of a set of influenza virus enrichment primers facilitated subtyping of influenza A viruses through the differential recognition of hemagglutinins 1 through 16 and neuraminidases 1 through 9. Twenty-one different respiratory virus species were accurately characterized, including a recently identified novel genetic clade of rhinovirus.Fil: Quan, Phenix-Lan. Columbia University. Jerome L. and Dawn Greene Infectious Disease Laboratory; Estados Unidos.Fil: Palacios, Gustavo. Columbia University. Jerome L. and Dawn Greene Infectious Disease Laboratory; Estados Unidos.Fil: Jabado, Omar J. Columbia University. Jerome L. and Dawn Greene Infectious Disease Laboratory; Estados Unidos.Fil: Conlan, Sean. Columbia University. Jerome L. and Dawn Greene Infectious Disease Laboratory; Estados Unidos.Fil: Hirschberg, David L. Stanford School of Medicine; Estados Unidos.Fil: Pozo, Francisco. Instituto de Salud Carlos III. Centro Nacional de Microbiología; España.Fil: Jack, Philippa J. M. Australian Animal Health Laboratory. CSIRO Livestock Industries; Australia.Fil: Cisterna, Daniel. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Enfermedades Infecciosas; Argentina.Fil: Renwick, Neil. Columbia University. Jerome L. and Dawn Greene Infectious Disease Laboratory; Estados Unidos.Fil: Hui, Jeffrey. Columbia University. Jerome L. and Dawn Greene Infectious Disease Laboratory; Estados Unidos.Fil: Drysdale, Andrew. Columbia University. Jerome L. and Dawn Greene Infectious Disease Laboratory; Estados Unidos.Fil: Amos-Ritchie, Rachel. Australian Animal Health Laboratory. CSIRO Livestock Industries; Australia.Fil: Baumeister, Elsa. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Enfermedades Infecciosas; Argentina.Fil: Savy, Vilma. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Enfermedades Infecciosas; Argentina.Fil: Lager, Kelly M. USDA. National Animal Disease Center; Estados Unidos.Fil: Richt, Jürgen A. USDA. National Animal Disease Center; Estados Unidos.Fil: Boyle, David B. Australian Animal Health Laboratory. CSIRO Livestock Industries; Australia.Fil: García-Sastre, Adolfo. Mount Sinai School of Medicine. Department of Microbiology and Emerging Pathogens Institute; Estados Unidos.Fil: Casas, Inmaculada. Instituto de Salud Carlos III. Centro Nacional de Microbiología; España.Fil: Perez-Breña, Pilar. Instituto de Salud Carlos III. Centro Nacional de Microbiología; España.Fil: Briese, Thomas. Columbia University. Jerome L. and Dawn Greene Infectious Disease Laboratory; Estados Unidos.Fil: Lipkin, W. Ian. Columbia University. Jerome L. and Dawn Greene Infectious Disease Laboratory; Estados Unidos

Evaluating the population impact of hepatitis C direct acting antiviral treatment as prevention for people who inject drugs (EPIToPe) – a natural experiment (protocol)

Hepatitis C virus (HCV) is the second largest contributor to liver disease in the UK, with injecting drug use as the main risk factor among the estimated 200 000 people currently infected. Despite effective prevention interventions, chronic HCV prevalence remains around 40% among people who inject drugs (PWID). New direct-acting antiviral (DAA) HCV therapies comine high cure rates (>90%) and short treatment duration (8 to 12 weeks). Theoretical mathematical modelling evidence suggests HCV treatment scale-up can prevent transmission and substantially reduce HCV prevalence/incidence among PWID. Our primary aim is to generate empirical evidence on the effectiveness of HCV ‘Treatment as Prevention’ (TasP) in PWID