Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 20
Filtrar
1.
Development ; 151(3)2024 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-38230566

RESUMO

Research in model organisms is central to the characterization of signaling pathways in multicellular organisms. Here, we present the comprehensive and systematic curation of 17 Drosophila signaling pathways using the Gene Ontology framework to establish a dynamic resource that has been incorporated into FlyBase, providing visualization and data integration tools to aid research projects. By restricting to experimental evidence reported in the research literature and quantifying the amount of such evidence for each gene in a pathway, we captured the landscape of empirical knowledge of signaling pathways in Drosophila.


Assuntos
Bases de Dados Genéticas , Drosophila , Animais , Drosophila/genética , Ontologia Genética , Transdução de Sinais , Drosophila melanogaster/genética
2.
Nucleic Acids Res ; 49(D1): D899-D907, 2021 01 08.
Artigo em Inglês | MEDLINE | ID: mdl-33219682

RESUMO

FlyBase (flybase.org) is an essential online database for researchers using Drosophila melanogaster as a model organism, facilitating access to a diverse array of information that includes genetic, molecular, genomic and reagent resources. Here, we describe the introduction of several new features at FlyBase, including Pathway Reports, paralog information, disease models based on orthology, customizable tables within reports and overview displays ('ribbons') of expression and disease data. We also describe a variety of recent important updates, including incorporation of a developmental proteome, upgrades to the GAL4 search tab, additional Experimental Tool Reports, migration to JBrowse for genome browsing and improvements to batch queries/downloads and the Fast-Track Your Paper tool.


Assuntos
Biologia Computacional/métodos , Bases de Dados Genéticas , Drosophila melanogaster/genética , Genoma de Inseto/genética , Genômica/métodos , Animais , Genes de Insetos/genética , Bases de Conhecimento , Anotação de Sequência Molecular/métodos , Ferramenta de Busca/métodos , Navegador
3.
Nucleic Acids Res ; 47(D1): D759-D765, 2019 01 08.
Artigo em Inglês | MEDLINE | ID: mdl-30364959

RESUMO

FlyBase (flybase.org) is a knowledge base that supports the community of researchers that use the fruit fly, Drosophila melanogaster, as a model organism. The FlyBase team curates and organizes a diverse array of genetic, molecular, genomic, and developmental information about Drosophila. At the beginning of 2018, 'FlyBase 2.0' was released with a significantly improved user interface and new tools. Among these important changes are a new organization of search results into interactive lists or tables (hitlists), enhanced reference lists, and new protein domain graphics. An important new data class called 'experimental tools' consolidates information on useful fly strains and other resources related to a specific gene, which significantly enhances the ability of the Drosophila researcher to design and carry out experiments. With the release of FlyBase 2.0, there has also been a restructuring of backend architecture and a continued development of application programming interfaces (APIs) for programmatic access to FlyBase data. In this review, we describe these major new features and functionalities of the FlyBase 2.0 site and how they support the use of Drosophila as a model organism for biological discovery and translational research.


Assuntos
Bases de Dados Genéticas , Drosophila melanogaster/genética , Genoma de Inseto/genética , Genômica , Animais , Domínios Proteicos/genética , Software
4.
Nucleic Acids Res ; 45(D1): D663-D671, 2017 01 04.
Artigo em Inglês | MEDLINE | ID: mdl-27799470

RESUMO

Since 1992, FlyBase (flybase.org) has been an essential online resource for the Drosophila research community. Concentrating on the most extensively studied species, Drosophila melanogaster, FlyBase includes information on genes (molecular and genetic), transgenic constructs, phenotypes, genetic and physical interactions, and reagents such as stocks and cDNAs. Access to data is provided through a number of tools, reports, and bulk-data downloads. Looking to the future, FlyBase is expanding its focus to serve a broader scientific community. In this update, we describe new features, datasets, reagent collections, and data presentations that address this goal, including enhanced orthology data, Human Disease Model Reports, protein domain search and visualization, concise gene summaries, a portal for external resources, video tutorials and the FlyBase Community Advisory Group.


Assuntos
Biologia Computacional/métodos , Bases de Dados Genéticas , Drosophila/genética , Genômica/métodos , Animais , Modelos Animais de Doenças , Estudos de Associação Genética , Humanos , Navegador
5.
Nucleic Acids Res ; 44(D1): D786-92, 2016 Jan 04.
Artigo em Inglês | MEDLINE | ID: mdl-26467478

RESUMO

Many publications describe sets of genes or gene products that share a common biology. For example, genome-wide studies and phylogenetic analyses identify genes related in sequence; high-throughput genetic and molecular screens reveal functionally related gene products; and advanced proteomic methods can determine the subunit composition of multi-protein complexes. It is useful for such gene collections to be presented as discrete lists within the appropriate Model Organism Database (MOD) so that researchers can readily access these data alongside other relevant information. To this end, FlyBase (flybase.org), the MOD for Drosophila melanogaster, has established a 'Gene Group' resource: high-quality sets of genes derived from the published literature and organized into individual report pages. To facilitate further analyses, Gene Group Reports also include convenient download and analysis options, together with links to equivalent gene groups at other databases. This new resource will enable researchers with diverse backgrounds and interests to easily view and analyse acknowledged D. melanogaster gene sets and compare them with those of other species.


Assuntos
Bases de Dados Genéticas , Drosophila melanogaster/genética , Genes de Insetos , Animais , Proteínas de Drosophila/genética
6.
Nucleic Acids Res ; 43(Database issue): D690-7, 2015 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-25398896

RESUMO

Release 6, the latest reference genome assembly of the fruit fly Drosophila melanogaster, was released by the Berkeley Drosophila Genome Project in 2014; it replaces their previous Release 5 genome assembly, which had been the reference genome assembly for over 7 years. With the enormous amount of information now attached to the D. melanogaster genome in public repositories and individual laboratories, the replacement of the previous assembly by the new one is a major event requiring careful migration of annotations and genome-anchored data to the new, improved assembly. In this report, we describe the attributes of the new Release 6 reference genome assembly, the migration of FlyBase genome annotations to this new assembly, how genome features on this new assembly can be viewed in FlyBase (http://flybase.org) and how users can convert coordinates for their own data to the corresponding Release 6 coordinates.


Assuntos
Bases de Dados Genéticas , Drosophila melanogaster/genética , Genoma de Inseto , Anotação de Sequência Molecular , Animais , Genômica/normas , Sequenciamento de Nucleotídeos em Larga Escala , Internet , Modelos Genéticos , Dados de Sequência Molecular , Padrões de Referência , Alinhamento de Sequência , Software
7.
Nucleic Acids Res ; 41(Database issue): D751-7, 2013 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-23125371

RESUMO

An accurate, comprehensive, non-redundant and up-to-date bibliography is a crucial component of any Model Organism Database (MOD). Principally, the bibliography provides a set of references that are specific to the field served by the MOD. Moreover, it serves as a backbone to which all curated biological data can be attributed. Here, we describe the organization and main features of the bibliography in FlyBase (flybase.org), the MOD for Drosophila melanogaster. We present an overview of the current content of the bibliography, the pipeline for identifying and adding new references, the presentation of data within Reference Reports and effective methods for searching and retrieving bibliographic data. We highlight recent improvements in these areas and describe the advantages of using the FlyBase bibliography over alternative literature resources. Although this article is focused on bibliographic data, many of the features and tools described are applicable to browsing and querying other datasets in FlyBase.


Assuntos
Bibliografias como Assunto , Bases de Dados Genéticas , Drosophila melanogaster/genética , Animais , Drosophila/genética , Internet
8.
bioRxiv ; 2023 Sep 15.
Artigo em Inglês | MEDLINE | ID: mdl-37645956

RESUMO

Research in model organisms is central to the characterization of signaling pathways in multicellular organisms. Here, we present the systematic curation of 17 Drosophila signaling pathways using the Gene Ontology framework to establish a comprehensive and dynamic resource that has been incorporated into FlyBase, providing visualization and data integration tools to aid research projects. By restricting to experimental evidence reported in the research literature and quantifying the amount of such evidence for each gene in a pathway, we captured the landscape of empirical knowledge of signaling pathways in Drosophila . Summary statement: Comprehensive curation of Drosophila signaling pathways and new visual displays of the pathways provides a new FlyBase resource for researchers, and new insights into signaling pathway architecture.

9.
Genetics ; 220(4)2022 04 04.
Artigo em Inglês | MEDLINE | ID: mdl-35266522

RESUMO

FlyBase provides a centralized resource for the genetic and genomic data of Drosophila melanogaster. As FlyBase enters our fourth decade of service to the research community, we reflect on our unique aspects and look forward to our continued collaboration with the larger research and model organism communities. In this study, we emphasize the dedicated reports and tools we have constructed to meet the specialized needs of fly researchers but also to facilitate use by other research communities. We also highlight ways that we support the fly community, including an external resources page, help resources, and multiple avenues by which researchers can interact with FlyBase.


Assuntos
Bases de Dados Genéticas , Drosophila melanogaster , Animais , Drosophila melanogaster/genética , Genoma , Genômica
10.
Nucleic Acids Res ; 36(Database issue): D588-93, 2008 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-18160408

RESUMO

FlyBase (http://flybase.org) is the primary resource for molecular and genetic information on the Drosophilidae. The database serves researchers of diverse backgrounds and interests, and offers several different query tools to provide efficient access to the data available and facilitate the discovery of significant relationships within the database. Recently, FlyBase has developed Interactions Browser and enhanced GBrowse, which are graphical query tools, and made improvements to the search tools QuickSearch and QueryBuilder. Furthermore, these search tools have been integrated with Batch Download and new analysis tools through a more flexible search results list, providing powerful ways of exploring the data in FlyBase.


Assuntos
Bases de Dados Genéticas , Drosophila melanogaster/genética , Drosophilidae/genética , Genes de Insetos , Animais , Gráficos por Computador , Genoma de Inseto , Internet , Software , Integração de Sistemas , Interface Usuário-Computador
11.
J Phys Chem A ; 113(29): 8182-6, 2009 Jul 23.
Artigo em Inglês | MEDLINE | ID: mdl-19569676

RESUMO

Solution-phase transient dc photoconductivity (TDCP) measurements are used to address the question of exciton localization/delocalization in strongly coupled oligomeric porphyrins and in well-defined, higher-order assemblies of oligomers (ladder and prism assemblies). The approach used is determination of the excited-state excess polarizability volume, Delta alpha(V)--a quantity known to report on exciton delocalization. The measurements reveal for the oligomers that singlet excitons are substantially delocalized but that triplet excitons are much more localized. For each of the two higher-order assemblies, the measurements reveal that excitons are transiently confined to individual oligomeric subunits rather than being delocalized over the entire assembly.

12.
Nucleic Acids Res ; 35(Database issue): D486-91, 2007 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-17099233

RESUMO

FlyBase (http://flybase.org/) is the primary database of genetic and genomic data for the insect family Drosophilidae. Historically, Drosophila melanogaster has been the most extensively studied species in this family, but recent determination of the genomic sequences of an additional 11 Drosophila species opens up new avenues of research for other Drosophila species. This extensive sequence resource, encompassing species with well-defined phylogenetic relationships, provides a model system for comparative genomic analyses. FlyBase has developed tools to facilitate access to and navigation through this invaluable new data collection.


Assuntos
Bases de Dados Genéticas , Drosophilidae/genética , Genoma de Inseto , Animais , Drosophila/classificação , Drosophila/genética , Drosophilidae/classificação , Genômica , Internet , Filogenia , Software , Interface Usuário-Computador
13.
Methods Mol Biol ; 1478: 1-31, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-27730573

RESUMO

For nearly 25 years, FlyBase (flybase.org) has provided a freely available online database of biological information about Drosophila species, focusing on the model organism D. melanogaster. The need for a centralized, integrated view of Drosophila research has never been greater as advances in genomic, proteomic, and high-throughput technologies add to the quantity and diversity of available data and resources.FlyBase has taken several approaches to respond to these changes in the research landscape. Novel report pages have been generated for new reagent types and physical interaction data; Drosophila models of human disease are now represented and showcased in dedicated Human Disease Model Reports; other integrated reports have been established that bring together related genes, datasets, or reagents; Gene Reports have been revised to improve access to new data types and to highlight functional data; links to external sites have been organized and expanded; and new tools have been developed to display and interrogate all these data, including improved batch processing and bulk file availability. In addition, several new community initiatives have served to enhance interactions between researchers and FlyBase, resulting in direct user contributions and improved feedback.This chapter provides an overview of the data content, organization, and available tools within FlyBase, focusing on recent improvements. We hope it serves as a guide for our diverse user base, enabling efficient and effective exploration of the database and thereby accelerating research discoveries.


Assuntos
Bases de Dados Genéticas/estatística & dados numéricos , Drosophila melanogaster/genética , Genes de Insetos , Genoma de Inseto , Proteômica/métodos , Software , Animais , Linhagem Celular , Bases de Dados Genéticas/história , Conjuntos de Dados como Assunto , Modelos Animais de Doenças , Drosophila melanogaster/metabolismo , História do Século XX , História do Século XXI , Humanos , Internet , Pesquisa Translacional Biomédica
14.
Curr Protoc Bioinformatics ; 56: 1.31.1-1.31.23, 2016 12 08.
Artigo em Inglês | MEDLINE | ID: mdl-27930807

RESUMO

FlyBase (flybase.org) is the primary online database of genetic, genomic, and functional information about Drosophila species, with a major focus on the model organism Drosophila melanogaster. The long and rich history of Drosophila research, combined with recent surges in genomic-scale and high-throughput technologies, mean that FlyBase now houses a huge quantity of data. Researchers need to be able to rapidly and intuitively query these data, and the QuickSearch tool has been designed to meet these needs. This tool is conveniently located on the FlyBase homepage and is organized into a series of simple tabbed interfaces that cover the major data and annotation classes within the database. This unit describes the functionality of all aspects of the QuickSearch tool. With this knowledge, FlyBase users will be equipped to take full advantage of all QuickSearch features and thereby gain improved access to data relevant to their research. © 2016 by John Wiley & Sons, Inc.


Assuntos
Bases de Dados Genéticas , Genômica/métodos , Animais , Drosophila melanogaster/genética , Genoma/genética
15.
J Org Chem ; 64(5): 1640-1649, 1999 Mar 05.
Artigo em Inglês | MEDLINE | ID: mdl-11674231

RESUMO

Under the 9,10-dicyanoanthracene-sensitized photoinduced electron-transfer conditions, (Z,Z)-, (E,E)-, (E,Z)-3,6-diaryl-2,6-octadiene and (d,l),(meso)-2,5-diaryl-3,4-dimethyl-1,5-hexadiene stereospecifically undergo the Cope rearrangement to give a Cope photostationary mixture. Remarkably, the photoinduced electron-transfer Cope rearrangements of the 4-methylphenyl derivatives are concurrent with the formation of trans- or endo,cis-1,4-bis(4-methylphenyl)-2,3-dimethylbicyclo[2.2.0]hexane in a Cope photostationary mixture. Observed stereospecificity of the Cope rearrangement and the formation of the bicyclo[2.2.0]hexane derivatives demonstrate the intermediacies of both the chair and boat 1,4-diaryl-1,2-dimethylcyclohexane-1,4-diyl and cation radical intermediates in a Cope rearrangement cycle. Photoreactions of trans- and exo,cis-1,4-diaryl-5,6-dimethyl-2,3-diazabicyclo[2.2.2]oct-2-enes further support the interventions of the diyl intermediates in the Cope rearrangement cycle. By photoacoustic analysis, a cation radical cyclization-diradical cleavage mechanism is proposed for the photoinduced electron-transfer Cope rearrangement of the title dienes.

16.
Chemistry ; 13(33): 9207-15, 2007.
Artigo em Inglês | MEDLINE | ID: mdl-17768760

RESUMO

Photoinduced single-electron-transfer promoted oxidation of 2,5-diphenyl-1,5-hexadiene by using N-methylquinolinium tetrafluoroborate/biphenyl co-sensitization takes place with the formation of an intense electronic absorption band at 476 nm, which is attributed to the 1,4-diphenylcyclohexane-1,4-diyl radical cation. The absorption maximum (lambda(ob)) of this transient occurs at a longer wavelength than is expected for either the cumyl radical or the cumyl cation components. Substitution at the para positions of the phenyl groups in this radical cation by CH(3)O, CH(3), F, Cl, and Br leads to an increasingly larger redshift of lambda(ob). A comparison of the rho value, which was obtained from a Hammett plot of the electronic transition energies of the radical cations versus sigma(+), with that for the cumyl cation shows that the substituent effects on the transition energies for the 1,4-diarylcyclohexane-1,4-diyl radical cations are approximately one half of the substituent effects on the transition energies of the cumyl cation. The observed substituent-induced redshifts of lambda(ob) and the reduced sensitivity of lambda(ob) to substituent changes are in accordance with the proposal that significant through-space and -bond electronic interactions exist between the cumyl radical and the cumyl cation moieties of the 1,4-diphenylcyclohexane-1,4-diyl radical cation. This proposal gains strong support from the results of density functional theory (DFT) calculations. Moreover, the results of time-dependent DFT calculations indicate that the absorption band at 476 nm for the 1,4-diphenylcyclohexane-1,4-diyl radical cation corresponds to a SOMO-3 --> SOMO transition.

17.
J Am Chem Soc ; 127(6): 1620-1, 2005 Feb 16.
Artigo em Inglês | MEDLINE | ID: mdl-15700979

RESUMO

Photooxidation of 1,1,2,2-tetra-tert-butyl-1,2-diphenyldisilane, 1, by triplet sensitizers in CHCl3/CCl4 solutions yields chlorosilane, 2, in high chemical yield. The quantum yield for formation of 2 depends on the energy of the ion radical pair formed following initial electron transfer. Dissociative return electron transfer (DRET) is proposed as the mechanism for the highly efficient Si-Si bond cleavage in 1. DRET may be a useful strategy for the fragmentation of other such bonds in di-, oligo-, and polysilanes as well as other group 4A compounds using a variety of sensitizers with different spectral properties.

18.
J Gen Virol ; 85(Pt 11): 3249-3259, 2004 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-15483238

RESUMO

Influenza B virus is one of two types of influenza virus that cause substantial morbidity and mortality in humans, the other being influenza A virus. The inability to provide lasting protection to humans against influenza B virus infection is due, in part, to antigenic drift of the viral surface glycoprotein, haemagglutinin (HA). Studies of the antigenicity of the HA of influenza B virus have been hampered by lack of knowledge of its structure. To address this gap, two possible models have been inferred for this structure, based on two known structures of the homologous HA of the influenza A virus (subtypes H3 and H9). Statistical, structural and functional analyses of these models suggested that they matched important details of experimental observations and did not differ from each other in any substantive way. These models were used to investigate two HA sites at which viral variants appeared to carry a selective advantage. It was found that each of these sites coevolved with nearby sites to compensate for either size or charge changes.


Assuntos
Glicoproteínas de Hemaglutininação de Vírus da Influenza/genética , Hemaglutininas Virais/genética , Vírus da Influenza B/genética , Modelos Moleculares , Proteínas Virais/genética , Sequência de Aminoácidos , Variação Genética , Glicoproteínas/química , Glicoproteínas/genética , Glicoproteínas de Hemaglutininação de Vírus da Influenza/química , Hemaglutininas Virais/química , Vírus da Influenza B/química , Vírus da Influenza B/imunologia , Dados de Sequência Molecular , Alinhamento de Sequência , Homologia de Sequência de Aminoácidos , Proteínas Virais/química
19.
Photochem Photobiol Sci ; 2(11): 1169-76, 2003 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-14690230

RESUMO

The dynamics of the geminate radical-ion pairs formed by electron transfer to the excited states of cyanoanthracenes from 2-phenylcyclopropylamines are dominated by exothermic bond cleavage of the amine radical cations. Quantitative studies of product formation as a function of the energetics of the photochemical and corresponding thermal reactions provide support for a novel mechanism in which return electron transfer in the geminate pair occurs in concert with bond formation from the ring-opened radical cations. This bond-coupled electron transfer process is referred to as an associative return electron transfer reaction. The important features of the associative electron transfer process that explain the experimental observations are described in terms of potential energy surfaces and competition between adiabatic and non-adiabatic deactivation paths.

20.
J Am Chem Soc ; 125(30): 9147-57, 2003 Jul 30.
Artigo em Inglês | MEDLINE | ID: mdl-15369372

RESUMO

2-(dideuteriomethylene)-1,1-bis(4-methoxyphenyl)cyclopropane (d(2)-1) undergoes degenerate rearrangement in both singlet- and triplet-sensitized electron-transfer photoreactions. Nanosecond time-resolved absorption spectroscopy on laser flash photolysis of the unlabeled 1 with 9,10-dicyanoanthracene, 1,2,4,5-tetracyanobenzene, or N-methylquinolinium tetrafluoroborate as an electron-accepting photosensitizer gives rise to two transients with lambda(max) at 500 and 350 nm assigned to the dianisyl-substituted largely twisted trimethylenemethane cation radical (6.+) and the corresponding diradical (6..), respectively. These intermediates are also detected, respectively, by steady state and nanosecond time-resolved EPR with chloranil or anthraquinone as a sensitizer. The degenerate rearrangement of d(2)-1 thus proceeds via these two different types of intermediates in a cation radical cleavage-diradical cyclization mechanism. Energetics based on nanosecond time-resolved photoacoustic calorimetry support this mechanism. A comparison of the reactivities and the spectroscopic results of 1, 1,1-bis(4-methoxyphenyl)-2-methylenespiro[2.2]pentane (2), and 1-cyclopropylidene-2,2-bis(4-methoxyphenyl)cyclopropane (3) suggest that the reversible methylenecyclopropane rearrangement between 2 and 3 proceeds via a similar mechanism.

SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA