RESUMEN

A benzo[6]annulene, 4-(tert-butyl)-N-(3-methoxy-5,6,7,8-tetrahydronaphthalen-2-yl) benzamide (1a), was identified as an inhibitor against Chikungunya virus (CHIKV) with antiviral activity EC90 = 1.45 µM and viral titer reduction (VTR) of 2.5 log at 10 µM with no observed cytotoxicity (CC50 = 169 µM) in normal human dermal fibroblast cells. Chemistry efforts to improve potency, efficacy, and drug-like properties of 1a resulted in a novel lead compound 8q, which possessed excellent cellular antiviral activity (EC90 = 270 nM and VTR of 4.5 log at 10 µM) and improved liver microsomal stability. CHIKV resistance to an analog of 1a, compound 1c, tracked to a mutation in the nsP3 macrodomain. Further mechanism of action studies showed compounds working through inhibition of human dihydroorotate dehydrogenase in addition to CHIKV nsP3 macrodomain. Moderate efficacy was observed in an in vivo CHIKV challenge mouse model for compound 8q as viral replication was rescued from the pyrimidine salvage pathway.

Asunto(s)

Antivirales/farmacología , Derivados del Benceno/química , Virus Chikungunya/fisiología , Replicación Viral/efectos de los fármacos , Animales , Antivirales/química , Antivirales/farmacocinética , Antivirales/uso terapéutico , Derivados del Benceno/metabolismo , Derivados del Benceno/farmacología , Derivados del Benceno/uso terapéutico , Sitios de Unión , Línea Celular , Supervivencia Celular/efectos de los fármacos , Fiebre Chikungunya/tratamiento farmacológico , Dihidroorotato Deshidrogenasa , Modelos Animales de Enfermedad , Femenino , Semivida , Humanos , Masculino , Ratones , Ratones Endogámicos C57BL , Microsomas Hepáticos/metabolismo , Simulación del Acoplamiento Molecular , Oxidorreductasas actuantes sobre Donantes de Grupo CH-CH/antagonistas & inhibidores , Oxidorreductasas actuantes sobre Donantes de Grupo CH-CH/metabolismo , Relación Estructura-Actividad

RESUMEN

Chikungunya virus (CHIKV) is a mosquito-borne alphavirus associated with debilitating arthralgia in humans. RNA secondary structure in the viral genome plays an important role in the lifecycle of alphaviruses; however, the specific role of RNA structure in regulating CHIKV replication is poorly understood. Our previous studies found little conservation in RNA secondary structure between alphaviruses, and this structural divergence creates unique functional structures in specific alphavirus genomes. Therefore, to understand the impact of RNA structure on CHIKV biology, we used SHAPE-MaP to inform the modeling of RNA secondary structure throughout the genome of a CHIKV isolate from the 2013 Caribbean outbreak. We then analyzed regions of the genome with high levels of structural specificity to identify potentially functional RNA secondary structures and identified 23 regions within the CHIKV genome with higher than average structural stability, including four previously identified, functionally important CHIKV RNA structures. We also analyzed the RNA flexibility and secondary structures of multiple 3'UTR variants of CHIKV that are known to affect virus replication in mosquito cells. This analysis found several novel RNA structures within these 3'UTR variants. A duplication in the 3'UTR that enhances viral replication in mosquito cells led to an overall increase in the amount of unstructured RNA in the 3'UTR. This analysis demonstrates that the CHIKV genome contains a number of unique, specific RNA secondary structures and provides a strategy for testing these secondary structures for functional importance in CHIKV replication and pathogenesis.IMPORTANCE Chikungunya virus (CHIKV) is a mosquito-borne RNA virus that causes febrile illness and debilitating arthralgia in humans. CHIKV causes explosive outbreaks but there are no approved therapies to treat or prevent CHIKV infection. The CHIKV genome contains functional RNA secondary structures that are essential for proper virus replication. Since RNA secondary structures have only been defined for a small portion of the CHIKV genome, we used a chemical probing method to define the RNA secondary structures of CHIKV genomic RNA. We identified 23 highly specific structured regions of the genome, and confirmed the functional importance of one structure using mutagenesis. Furthermore, we defined the RNA secondary structure of three CHIKV 3'UTR variants that differ in their ability to replicate in mosquito cells. Our study highlights the complexity of the CHIKV genome and describes new systems for designing compensatory mutations to test the functional relevance of viral RNA secondary structures.

Asunto(s)

Regiones no Traducidas 3'/genética , Virus Chikungunya/genética , ARN Viral/química , ARN Viral/genética , Animales , Línea Celular , Fiebre Chikungunya/virología , Chlorocebus aethiops , Culicidae , Efecto Citopatogénico Viral , Genoma Viral , Mutación , Conformación de Ácido Nucleico , Análisis de Secuencia , Células Vero , Replicación Viral/genética

RESUMEN

Host genetic factors play a fundamental role in regulating humoral immunity to viral infection, including influenza A virus (IAV). Here, we utilize the Collaborative Cross (CC), a mouse genetic reference population, to study genetic regulation of variation in antibody response following IAV infection. CC mice show significant heritable variation in the magnitude, kinetics, and composition of IAV-specific antibody response. We map 23 genetic loci associated with this variation. Analysis of a subset of these loci finds that they broadly affect the antibody response to IAV as well as other viruses. Candidate genes are identified based on predicted variant consequences and haplotype-specific expression patterns, and several show overlap with genes identified in human mapping studies. These findings demonstrate that the host antibody response to IAV infection is under complex genetic control and highlight the utility of the CC in modeling and identifying genetic factors with translational relevance to human health and disease.

Asunto(s)

Interacciones Huésped-Patógeno/genética , Gripe Humana/genética , Replicación Viral/genética , Humanos

RESUMEN

BACKGROUND: Virus infections result in a range of clinical outcomes for the host, from asymptomatic to severe or even lethal disease. Despite global efforts to prevent and treat virus infections to limit morbidity and mortality, the continued emergence and re-emergence of new outbreaks as well as common infections such as influenza persist as a health threat. Challenges to the prevention of severe disease after virus infection include both a paucity of protective vaccines as well as the early identification of individuals with the highest risk that may require supportive treatment. METHODS: We completed a screen of mice from the Collaborative Cross (CC) that we infected with influenza, severe acute respiratory syndrome-coronavirus, and West Nile virus. RESULTS: The CC mice exhibited a range of disease manifestations upon infections, and we used this natural variation to identify strains with mortality after infection and strains exhibiting no mortality. We then used comprehensive preinfection immunophenotyping to identify global baseline immune correlates of protection from mortality to virus infection. CONCLUSIONS: These data suggest that immune phenotypes might be leveraged to identify humans at highest risk of adverse clinical outcomes upon infection, who may most benefit from intensive clinical interventions, in addition to providing insight for rational vaccine design.

Asunto(s)

Mortalidad , Infecciones por Virus ARN/inmunología , Infecciones por Virus ARN/mortalidad , Animales , Ratones de Colaboración Cruzada , Citocinas/metabolismo , Modelos Animales de Enfermedad , Femenino , Humanos , Virus de la Influenza A/inmunología , Gripe Humana , Masculino , Ratones , Infecciones por Orthomyxoviridae/inmunología , Infecciones por Orthomyxoviridae/mortalidad , ARN , Infecciones por Virus ARN/virología , Coronavirus Relacionado al Síndrome Respiratorio Agudo Severo/inmunología , Síndrome Respiratorio Agudo Grave/inmunología , Síndrome Respiratorio Agudo Grave/mortalidad , Linfocitos T/inmunología , Linfocitos T/metabolismo , Vacunas Virales/inmunología , Fiebre del Nilo Occidental/inmunología , Fiebre del Nilo Occidental/mortalidad , Virus del Nilo Occidental/inmunología

RESUMEN

We present an analysis of the problem of identifying biological context and associating it with biochemical events described in biomedical texts. This constitutes a non-trivial, inter-sentential relation extraction task. We focus on biological context as descriptions of the species, tissue type, and cell type that are associated with biochemical events. We present a new corpus of open access biomedical texts that have been annotated by biology subject matter experts to highlight context-event relations. Using this corpus, we evaluate several classifiers for context-event association along with a detailed analysis of the impact of a variety of linguistic features on classifier performance. We find that gradient tree boosting performs by far the best, achieving an F1 of 0.865 in a cross-validation study.

Asunto(s)

Biología Computacional/métodos , Minería de Datos/métodos , Procesamiento de Lenguaje Natural , Animales , Investigación Biomédica , Bases de Datos Factuales , Humanos , Ratones

RESUMEN

PubMed, a repository and search engine for biomedical literature, now indexes >1 million articles each year. This exceeds the processing capacity of human domain experts, limiting our ability to truly understand many diseases. We present Reach, a system for automated, large-scale machine reading of biomedical papers that can extract mechanistic descriptions of biological processes with relatively high precision at high throughput. We demonstrate that combining the extracted pathway fragments with existing biological data analysis algorithms that rely on curated models helps identify and explain a large number of previously unidentified mutually exclusive altered signaling pathways in seven different cancer types. This work shows that combining human-curated 'big mechanisms' with extracted 'big data' can lead to a causal, predictive understanding of cellular processes and unlock important downstream applications.

Asunto(s)

Aprendizaje Automático , Neoplasias/genética , Algoritmos , Automatización , Humanos , Publicaciones

RESUMEN

Alphaviruses are mosquito-borne pathogens that cause human diseases ranging from debilitating arthritis to lethal encephalitis. Studies with Sindbis virus (SINV), which causes fever, rash, and arthralgia in humans, and Venezuelan equine encephalitis virus (VEEV), which causes encephalitis, have identified RNA structural elements that play key roles in replication and pathogenesis. However, a complete genomic structural profile has not been established for these viruses. We used the structural probing technique SHAPE-MaP to identify structured elements within the SINV and VEEV genomes. Our SHAPE-directed structural models recapitulate known RNA structures, while also identifying novel structural elements, including a new functional element in the nsP1 region of SINV whose disruption causes a defect in infectivity. Although RNA structural elements are important for multiple aspects of alphavirus biology, we found the majority of RNA structures were not conserved between SINV and VEEV. Our data suggest that alphavirus RNA genomes are highly divergent structurally despite similar genomic architecture and sequence conservation; still, RNA structural elements are critical to the viral life cycle. These findings reframe traditional assumptions about RNA structure and evolution: rather than structures being conserved, alphaviruses frequently evolve new structures that may shape interactions with host immune systems or co-evolve with viral proteins.

Asunto(s)

Virus de la Encefalitis Equina Venezolana/genética , ARN/genética , Virus Sindbis/genética , Replicación Viral/genética , Alphavirus/química , Alphavirus/genética , Alphavirus/patogenicidad , Animales , Encefalitis/genética , Encefalitis/virología , Virus de la Encefalitis Equina Venezolana/química , Virus de la Encefalitis Equina Venezolana/patogenicidad , Genoma Viral/genética , Caballos/virología , Humanos , Conformación de Ácido Nucleico , ARN/química , Virus Sindbis/química , Virus Sindbis/patogenicidad

RESUMEN

Influenza A virus (IAV) is a respiratory pathogen that causes substantial morbidity and mortality during both seasonal and pandemic outbreaks. Infection outcomes in unexposed populations are affected by host genetics, but the host genetic architecture is not well understood. Here, we obtain a broad view of how heritable factors affect a mouse model of response to IAV infection using an 8 × 8 diallel of the eight inbred founder strains of the Collaborative Cross (CC). Expanding on a prior statistical framework for modeling treatment response in diallels, we explore how a range of heritable effects modify acute host response to IAV through 4 d postinfection. Heritable effects in aggregate explained ∼57% of the variance in IAV-induced weight loss. Much of this was attributable to a pattern of additive effects that became more prominent through day 4 postinfection and was consistent with previous reports of antiinfluenza myxovirus resistance 1 (Mx1) polymorphisms segregating between these strains; these additive effects largely recapitulated haplotype effects observed at the Mx1 locus in a previous study of the incipient CC, and are also replicated here in a CC recombinant intercross population. Genetic dominance of protective Mx1 haplotypes was observed to differ by subspecies of origin: relative to the domesticus null Mx1 allele, musculus acts dominantly whereas castaneus acts additively. After controlling for Mx1, heritable effects, though less distinct, accounted for ∼34% of the phenotypic variance. Implications for future mapping studies are discussed.

Asunto(s)

Teorema de Bayes , Predisposición Genética a la Enfermedad/genética , Proteínas de Resistencia a Mixovirus/genética , Infecciones por Orthomyxoviridae/genética , Animales , Modelos Animales de Enfermedad , Haplotipos , Humanos , Virus de la Influenza A/fisiología , Ratones de la Cepa 129 , Ratones Endogámicos C57BL , Ratones Endogámicos NOD , Ratones Endogámicos , Infecciones por Orthomyxoviridae/virología , Fenotipo , Especificidad de la Especie

RESUMEN

Chikungunya virus (CHIKV) is a mosquito-borne alphavirus responsible for several significant outbreaks of debilitating acute and chronic arthritis and arthralgia over the past decade. These include a recent outbreak in the Caribbean islands and the Americas that caused more than 1 million cases of viral arthralgia. Despite the major impact of CHIKV on global health, viral determinants that promote CHIKV-induced disease are incompletely understood. Most CHIKV strains contain a conserved opal stop codon at the end of the viral nsP3 gene. However, CHIKV strains that encode an arginine codon in place of the opal stop codon have been described, and deep-sequencing analysis of a CHIKV isolate from the Caribbean identified both arginine and opal variants within this strain. Therefore, we hypothesized that the introduction of the arginine mutation in place of the opal termination codon may influence CHIKV virulence. We tested this by introducing the arginine mutation into a well-characterized infectious clone of a CHIKV strain from Sri Lanka and designated this virus Opal524R. This mutation did not impair viral replication kinetics in vitro or in vivo Despite this, the Opal524R virus induced significantly less swelling, inflammation, and damage within the feet and ankles of infected mice. Further, we observed delayed induction of proinflammatory cytokines and chemokines, as well as reduced CD4+ T cell and NK cell recruitment compared to those in the parental strain. Therefore, the opal termination codon plays an important role in CHIKV pathogenesis, independently of effects on viral replication.IMPORTANCE Chikungunya virus (CHIKV) is a mosquito-borne alphavirus that causes significant outbreaks of viral arthralgia. Studies with CHIKV and other alphaviruses demonstrated that the opal termination codon within nsP3 is highly conserved. However, some strains of CHIKV and other alphaviruses contain mutations in the opal termination codon. These mutations alter the virulence of related alphaviruses in mammalian and mosquito hosts. Here, we report that a clinical isolate of a CHIKV strain from the recent outbreak in the Caribbean islands contains a mixture of viruses encoding either the opal termination codon or an arginine mutation. Mutating the opal stop codon to an arginine residue attenuates CHIKV-induced disease in a mouse model. Compared to infection with the opal-containing parental virus, infection with the arginine mutant causes limited swelling and inflammation, as well as dampened recruitment of immune mediators of pathology, including CD4+ T cells and NK cells. We propose that the opal termination codon plays an essential role in the induction of severe CHIKV disease.

Asunto(s)

Artritis/patología , Fiebre Chikungunya/patología , Virus Chikungunya/patogenicidad , Codón de Terminación , Mutación , Proteínas no Estructurales Virales/genética , Factores de Virulencia/genética , Animales , Arginina/genética , Artritis/virología , Fiebre Chikungunya/virología , Virus Chikungunya/fisiología , Modelos Animales de Enfermedad , Ratones , Replicación Viral

RESUMEN

Chikungunya virus (CHIKV) is a mosquito-borne alphavirus in the family Togaviridae that causes outbreaks of debilitating acute and chronic arthralgia in humans. Although historically associated with localized outbreaks in Africa and Asia, recent epidemics in the Indian Ocean region and the Americas have led to the recognition that CHIKV is capable of moving into previously unaffected areas and causing significant levels of human suffering. The severity of CHIKV rheumatic disease, which can severely impact life quality of infected individuals for weeks, months, or even years, combined with the explosive nature of CHIKV outbreaks and its demonstrated ability to quickly spread into new regions, has led to renewed interest in developing strategies for the prevention or treatment of CHIKV-induced disease. Therefore, this chapter briefly discusses the biology of CHIKV and the factors contributing to CHIKV dissemination, while also discussing the pathogenesis of CHIKV-induced disease and summarizing the status of efforts to develop safe and effective therapies and vaccines against CHIKV and related viruses.

Asunto(s)

Fiebre Chikungunya/epidemiología , Fiebre Chikungunya/patología , Enfermedades Transmisibles Emergentes/epidemiología , Enfermedades Transmisibles Emergentes/patología , Brotes de Enfermedades , Animales , Fiebre Chikungunya/prevención & control , Fiebre Chikungunya/terapia , Control de Enfermedades Transmisibles/métodos , Enfermedades Transmisibles Emergentes/prevención & control , Enfermedades Transmisibles Emergentes/terapia , Salud Global , Humanos , Vacunas Virales/inmunología , Vacunas Virales/aislamiento & purificación

RESUMEN

Host response to RNA virus infection is sensed by RNA sensors such as RIG-I, which induces MAVS-mediated NF-κB and IRF3 activation to promote inflammatory and antiviral responses, respectively. Here, we have found that CARMA3, a scaffold protein previously shown to mediate NF-κB activation induced by GPCR and EGFR, positively regulates MAVS-induced NF-κB activation. However, our data suggest that CARMA3 sequesters MAVS from forming high-molecular-weight aggregates, thereby suppressing TBK1/IRF3 activation. Interestingly, following NF-κB activation upon virus infection, CARMA3 is targeted for proteasome-dependent degradation, which releases MAVS to activate IRF3. When challenged with vesicular stomatitis virus or influenza A virus, CARMA3-deficient mice showed reduced disease symptoms compared to those of wild-type mice as a result of less inflammation and a stronger ability to clear infected virus. Altogether, our results reveal the role of CARMA3 in regulating the balance of host antiviral and pro-inflammatory responses against RNA virus infection.

Asunto(s)

Proteínas Adaptadoras de Señalización CARD/inmunología , Inflamación , Infecciones por Virus ARN/inmunología , Vesiculovirus/inmunología , Proteínas Adaptadoras Transductoras de Señales/genética , Proteínas Adaptadoras Transductoras de Señales/metabolismo , Animales , Proteína 10 de la LLC-Linfoma de Células B , Proteínas Adaptadoras de Señalización CARD/antagonistas & inhibidores , Proteínas Adaptadoras de Señalización CARD/genética , Línea Celular , Citocinas/genética , Citocinas/metabolismo , Proteína 58 DEAD Box/genética , Proteína 58 DEAD Box/metabolismo , Modelos Animales de Enfermedad , Células HEK293 , Humanos , Factor 3 Regulador del Interferón/metabolismo , Ratones , Ratones Endogámicos BALB C , FN-kappa B/metabolismo , Complejo de la Endopetidasa Proteasomal/metabolismo , Proteínas Serina-Treonina Quinasas/metabolismo , Interferencia de ARN , Infecciones por Virus ARN/metabolismo , Infecciones por Virus ARN/patología , Transducción de Señal , Vesiculovirus/genética , Vesiculovirus/fisiología , Carga Viral

RESUMEN

West Nile virus (WNV) employs several different strategies to escape the innate immune response. We have previously demonstrated that the WNV NS1 protein interferes with signal transduction from Toll-like receptor 3 (TLR3). NS1 is a glycoprotein that can be found intracellularly or associated with the plasma membrane. In addition, NS1 is secreted to high levels during flavivirus infections. We investigated whether the secreted form of NS1 inhibits innate immune signaling pathways in uninfected cells. Secreted NS1 (sNS1) was purified from supernatants of cells engineered to express the protein. Purified sNS1 associated with and repressed TLR3-induced cytokine production by HeLa cells, and inhibited signaling from TLR3 and other TLRs in bone marrow-derived macrophages and dendritic cells. Footpad administration of sNS1 showed the protein associated predominantly with macrophages and dendritic cells in the draining lymph node. Additionally, sNS1 significantly reduced TLR3 signaling and WNV replicon particle-mediated cytokine transcription in popliteal lymph nodes.

Asunto(s)

Inmunidad Innata , Transducción de Señal/inmunología , Proteínas no Estructurales Virales/inmunología , Virus del Nilo Occidental/inmunología , Animales , Células HeLa , Humanos , Luciferasas/metabolismo , Macrófagos/inmunología , Macrófagos/metabolismo , Ratones , Ratones Endogámicos C57BL , Células Mieloides/inmunología , Células Mieloides/metabolismo , Poli I-C/farmacología , Organismos Libres de Patógenos Específicos , Receptor Toll-Like 3/antagonistas & inhibidores , Proteínas no Estructurales Virales/fisiología , Virus del Nilo Occidental/metabolismo

RESUMEN

West Nile virus (WNV) is a mosquito-transmitted pathogen, which causes significant disease in humans. The innate immune system is a first-line defense against invading microorganism and many flaviviruses, including WNV, have evolved multifunctional proteins, which actively suppress its activation and antiviral actions. The WNV non-structural protein 1 (NS1) inhibits signal transduction originating from Toll-like receptor 3 (TLR3) and also critically contributes to virus genome replication. In this study we developed a novel FACS-based screen to attempt to separate these two functions. The individual amino acid changes P320S and M333V in NS1 restored TLR3 signaling in virus-infected HeLa cells. However, virus replication was also attenuated, suggesting that the two functions are not easily separated and may be contained within overlapping domains. The residues we identified are completely conserved among several mosquito- and tick-borne flaviviruses, indicating that they are of biological importance to the virus.

Asunto(s)

Interacciones Huésped-Patógeno , Evasión Inmune , Receptor Toll-Like 3/inmunología , Proteínas no Estructurales Virales/inmunología , Replicación Viral , Virus del Nilo Occidental/inmunología , Virus del Nilo Occidental/fisiología , Sustitución de Aminoácidos , Análisis Mutacional de ADN , Células HeLa , Humanos , Proteínas Mutantes/genética , Proteínas Mutantes/inmunología , Receptor Toll-Like 3/antagonistas & inhibidores , Proteínas no Estructurales Virales/genética , Virus del Nilo Occidental/genética

RESUMEN

In Drosophila, the Gal4-UAS system is used to drive ectopic gene expression in a tissue-specific manner. In this system, transgenic flies expressing tissue specific Gal4 are crossed to a line in which the gene to be expressed is under the control of a Gal4-responsive UAS sequence. The resulting progeny express the gene of interest in the pattern of the particular Gal4 line. Since a given UAS-transgene can be driven by any Gal4 line, this system is predominantly limited by available Gal4 lines. Here we report the characterization of a novel line, DE-Gal4, which in the eye is expressed in the dorsal compartment for the majority of development. Furthermore, we use functional tests to show that the DE-Gal4 line is a useful tool with which to manipulate gene expression in half of the developing eye.

Asunto(s)

Proteínas de Unión al ADN/genética , Drosophila/genética , Ojo/metabolismo , Proteínas de Saccharomyces cerevisiae/genética , Factores de Transcripción/genética , Animales , Animales Modificados Genéticamente , Proteínas de Unión al ADN/metabolismo , Drosophila/embriología , Drosophila/crecimiento & desarrollo , Proteínas de Drosophila/genética , Proteínas de Drosophila/metabolismo , Embrión no Mamífero/embriología , Embrión no Mamífero/metabolismo , Ojo/embriología , Ojo/crecimiento & desarrollo , Proteínas del Ojo/genética , Proteínas del Ojo/metabolismo , Femenino , Regulación del Desarrollo de la Expresión Génica , Proteínas Fluorescentes Verdes/genética , Proteínas Fluorescentes Verdes/metabolismo , Inmunohistoquímica , Operón Lac/genética , Larva/genética , Masculino , Interferencia de ARN , Proteínas de Saccharomyces cerevisiae/metabolismo , Factores de Transcripción/metabolismo , Transgenes/genética , beta-Galactosidasa/genética , beta-Galactosidasa/metabolismo

RESUMEN

The Hippo tumor-suppressor pathway controls tissue growth in Drosophila and mammals by regulating cell proliferation and apoptosis. The Hippo pathway includes the Fat cadherin, a transmembrane protein, which acts upstream of several other components that form a kinase cascade that culminates in the regulation of gene expression through the transcriptional coactivator Yorkie (Yki). Our previous work in Drosophila indicated that Merlin (Mer) and Expanded (Ex) are members of the Hippo pathway and act upstream of the Hippo kinase. In contrast to this model, it was suggested that Mer and Ex primarily regulate membrane dynamics and receptor trafficking, thereby affecting Hippo pathway activity only indirectly. Here, we examined the effects of Mer, Ex and the Hippo pathway on the size of the apical membrane and on apical-basal polarity complexes. We found that mer;ex double mutant imaginal disc cells have significantly increased levels of apical membrane determinants, such as Crb, aPKC and Patj. These phenotypes were shared with mutations in other Hippo pathway components and required Yki, indicating that Mer and Ex signal through the Hippo pathway. Interestingly, however, whereas Crb was required for the accumulation of other apical proteins and for the expansion of the apical domain observed in Hippo pathway mutants, its elimination did not significantly reverse the overgrowth phenotype of warts mutant cells. Therefore, Hippo signaling regulates cell polarity complexes in addition to and independently of its growth control function in imaginal disc cells.

Asunto(s)

Proliferación Celular , Proteínas de Drosophila/metabolismo , Drosophila/metabolismo , Péptidos y Proteínas de Señalización Intracelular/metabolismo , Proteínas de la Membrana/metabolismo , Neurofibromina 2/metabolismo , Proteínas Serina-Treonina Quinasas/metabolismo , Transducción de Señal , Proteínas Supresoras de Tumor/metabolismo , Animales , Apoptosis , Cadherinas/metabolismo , Membrana Celular/metabolismo , Polaridad Celular , Drosophila/genética , Drosophila/crecimiento & desarrollo , Drosophila/ultraestructura , Proteínas de Drosophila/genética , Ojo/metabolismo , Proteínas del Ojo/metabolismo , Regulación del Desarrollo de la Expresión Génica , Genotipo , Péptidos y Proteínas de Señalización Intracelular/genética , Proteínas de la Membrana/genética , Mutación , Neurofibromina 2/genética , Proteínas Nucleares/metabolismo , Fenotipo , Proteína Quinasa C/metabolismo , Proteínas Serina-Treonina Quinasas/genética , Transducción de Señal/genética , Transactivadores/metabolismo , Proteínas Supresoras de Tumor/genética , Alas de Animales/metabolismo , Proteínas Señalizadoras YAP

RESUMEN

We report a streamlined procedure to efficiently carry samples from chromatin to qPCR-compatible DNA in as little as 4 h. We use this streamlined ChIP to quantify histone H3 modifications at active (cad) and repressed (T early alpha) promoters in a Rag1-deficient pro-T cell line after 1-2 h IP. We further show that the protocol readily quantified histone modifications in chromatin from 10(4) Rag-deficient DN thymocytes. Taken together, these data outline a simple, cost-effective procedure for efficient ChIP analysis.

Asunto(s)

Inmunoprecipitación de Cromatina/métodos , Cromatina/aislamiento & purificación , Histonas/metabolismo , Animales , Aspartato Carbamoiltransferasa/genética , Aspartato Carbamoiltransferasa/metabolismo , Carbamoil-Fosfato Sintasa (Glutamina-Hidrolizante)/genética , Carbamoil-Fosfato Sintasa (Glutamina-Hidrolizante)/metabolismo , Línea Celular , Cromatina/genética , Cromatina/metabolismo , Proteínas de Unión al ADN/genética , Proteínas de Unión al ADN/metabolismo , Dihidroorotasa/genética , Dihidroorotasa/metabolismo , Técnicas de Silenciamiento del Gen , Histonas/genética , Ratones , Ratones Noqueados , ARN Polimerasa II/genética , ARN Polimerasa II/metabolismo , Linfocitos T/metabolismo

RESUMEN

Fecal pollution is a serious threat to the estuarine environment along the Georgia coast. Culture-dependant and molecular methodologies were utilized to compare and evaluate the abundance of fecal indicator bacteria in four Georgia estuaries (Darien River, Frederica River, Gulley Hole Creek, and St. Marys River). The functionality of enterococci and bifidobacteria as indicator organisms in marine environments was assessed, as well as Bifidobacterium adolescentis densities. At each study site, enterococci were enumerated as colony forming units (CFU) on mEI agar. For quantitative polymerase chain reaction (qPCR), genus- and species-specific primer sets were used to quantify bifidobacteria and B. adolescentis as 16S rRNA gene copies and enterococci as tuf gene copies. A high correlation (r=0.925) was observed between CFU and qPCR enumeration of enterococci. Enterococci densities in the estuarine rivers ranged from 3-449CFU/100ml on mEI plates and 4.58-5.39Log(10) gene copies/100ml by qPCR. Bifidobacteria densities ranged from 3.62-4.14Log(10) gene copies/100ml and suggested the Frederica River as least affected by fecal bacteria and the Darien River as most affected by fecal pollution. A correlation of 0.46 was observed among qPCR densities of enterococci and bifidobacteria at all sample sites. Quantitative polymerase chain reaction detection of B. adolescentis was a rapid (i.e., less than 2h) indicator of presumptive human fecal pollution and suggested that Gulley Hole Creek, the Darien River, and the St. Marys River were affected by fecal bacteria derived from a human source. Gulley Hole Creek and the Darien River had the highest levels of fecal pollution detected in the studied estuaries. Molecular quantification of bifidobacteria may be a more accurate method of determining immediate health risks associated with fecal pollution in estuarine water than traditional and contemporary assessments of enterococci.

Asunto(s)

Bifidobacterium/aislamiento & purificación , Enterococcus/aislamiento & purificación , Ríos/microbiología , Microbiología del Agua , Georgia , Océanos y Mares , Aguas del Alcantarillado/microbiología , Contaminantes del Agua

RESUMEN

BACKGROUND: With over 20 parapatric races differing in their warningly colored wing patterns, the butterfly Heliconius erato provides a fascinating example of an adaptive radiation. Together with matching races of its co-mimic Heliconius melpomene, H. erato also represents a textbook case of Müllerian mimicry, a phenomenon where common warning signals are shared amongst noxious organisms. It is of great interest to identify the specific genes that control the mimetic wing patterns of H. erato and H. melpomene. To this end we have undertaken comparative mapping and targeted genomic sequencing in both species. This paper reports on a comparative analysis of genomic sequences linked to color pattern mimicry genes in Heliconius. RESULTS: Scoring AFLP polymorphisms in H. erato broods allowed us to survey loci at approximately 362 kb intervals across the genome. With this strategy we were able to identify markers tightly linked to two color pattern genes: D and Cr, which were then used to screen H. erato BAC libraries in order to identify clones for sequencing. Gene density across 600 kb of BAC sequences appeared relatively low, although the number of predicted open reading frames was typical for an insect. We focused analyses on the D- and Cr-linked H. erato BAC sequences and on the Yb-linked H. melpomene BAC sequence. A comparative analysis between homologous regions of H. erato (Cr-linked BAC) and H. melpomene (Yb-linked BAC) revealed high levels of sequence conservation and microsynteny between the two species. We found that repeated elements constitute 26% and 20% of BAC sequences from H. erato and H. melpomene respectively. The majority of these repetitive sequences appear to be novel, as they showed no significant similarity to any other available insect sequences. We also observed signs of fine scale conservation of gene order between Heliconius and the moth Bombyx mori, suggesting that lepidopteran genome architecture may be conserved over very long evolutionary time scales. CONCLUSION: Here we have demonstrated the tractability of progressing from a genetic linkage map to genomic sequence data in Heliconius butterflies. We have also shown that fine-scale gene order is highly conserved between distantly related Heliconius species, and also between Heliconius and B. mori. Together, these findings suggest that genome structure in macrolepidoptera might be very conserved, and show that mapping and positional cloning efforts in different lepidopteran species can be reciprocally informative.

Asunto(s)

Mariposas Diurnas/genética , Orden Génico , Genes de Insecto , Ligamiento Genético , Secuencias Repetitivas de Ácidos Nucleicos , Análisis del Polimorfismo de Longitud de Fragmentos Amplificados , Animales , Secuencia de Bases , Paseo de Cromosoma , Cromosomas Artificiales Bacterianos , Secuencia Conservada , ADN/genética , Marcadores Genéticos , Fenotipo , Pigmentación/genética , Análisis de Secuencia , Sintenía , Alas de Animales

RESUMEN

BACKGROUND: The Hippo tumor-suppressor pathway has emerged as a key signaling pathway that controls tissue size in Drosophila. Hippo signaling restricts tissue size by promoting apoptosis and cell-cycle arrest, and animals carrying clones of cells mutant for hippo develop severely overgrown adult structures. The Hippo pathway is thought to exert its effects by modulating gene expression through the phosphorylation of the transcriptional coactivator Yorkie. However, how Yorkie regulates growth, and thus the identities of downstream target genes that mediate the effects of Hippo signaling, are largely unknown. RESULTS: Here, we report that the bantam microRNA is a downstream target of the Hippo signaling pathway. In common with Hippo signaling, the bantam microRNA controls tissue size by regulating cell proliferation and apoptosis. We found that hippo mutant cells had elevated levels of bantam activity and that bantam was required for Yorkie-driven overgrowth. Additionally, overexpression of bantam was sufficient to rescue growth defects of yorkie mutant cells and to suppress the cell death induced by Hippo hyperactivation. Hippo regulates bantam independently of cyclin E and diap1, two other Hippo targets, and overexpression of bantam mimics overgrowth phenotypes of hippo mutant cells. CONCLUSIONS: Our data indicate that bantam is an essential target of the Hippo signaling pathway to regulate cell proliferation, cell death, and thus tissue size.

Asunto(s)

Ciclinas/genética , Proteínas de Drosophila/genética , Proteínas de Drosophila/metabolismo , Drosophila/metabolismo , MicroARNs/metabolismo , Proteínas Serina-Treonina Quinasas/metabolismo , Animales , Apoptosis , Proliferación Celular , Ciclina E/genética , Ciclina E/metabolismo , Ciclinas/metabolismo , Drosophila/genética , Drosophila/crecimiento & desarrollo , Regulación de la Expresión Génica , Proteínas Inhibidoras de la Apoptosis/genética , Proteínas Inhibidoras de la Apoptosis/metabolismo , Péptidos y Proteínas de Señalización Intracelular , Mutación , Proteínas Nucleares/genética , Proteínas Nucleares/metabolismo , Fenotipo , Proteínas Serina-Treonina Quinasas/genética , Retina/metabolismo , Transducción de Señal , Transactivadores/genética , Transactivadores/metabolismo , Proteínas Supresoras de Tumor/metabolismo , Proteínas Señalizadoras YAP

RESUMEN

Guidance and patterning of axons are orchestrated by cell-surface receptors and ligands that provide directional cues. Interactions between the Robo receptor and Slit ligand families of proteins initiate signaling cascades that repel axonal outgrowth. Although the vascular and nervous systems grow as parallel networks, the mechanisms by which the vascular endothelial cells are guided to their appropriate positions remain obscure. We have identified a putative Robo homologue, Robo4, based on its differential expression in mutant mice with defects in vascular sprouting. In contrast to known neuronal Robo family members, the arrangement of the extracellular domains of Robo4 diverges significantly from that of all other Robo family members. Moreover, Robo4 is specifically expressed in the vascular endothelium during murine embryonic development. We show that Robo4 binds Slit and inhibits cellular migration in a heterologous expression system, analogous to the role of known Robo receptors in the nervous system. Immunoprecipitation studies indicate that Robo4 binds to Mena, a known effector of Robo-Slit signaling. Finally, we show that Robo4 is the only Robo family member expressed in primary endothelial cells and that application of Slit inhibits their migration. These data demonstrate that Robo4 is a bona fide member of the Robo family and may provide a repulsive cue to migrating endothelial cells during vascular development.

Asunto(s)

Endotelio Vascular/embriología , Receptores Inmunológicos/fisiología , Receptores de Activinas Tipo I/deficiencia , Receptores de Activinas Tipo I/genética , Receptores de Activinas Tipo I/fisiología , Receptores de Activinas Tipo II , Secuencia de Aminoácidos , Animales , Línea Celular , Movimiento Celular , Mapeo Cromosómico , Regulación del Desarrollo de la Expresión Génica , Humanos , Hibridación in Situ , Péptidos y Proteínas de Señalización Intercelular , Ligandos , Ratones , Ratones Noqueados , Datos de Secuencia Molecular , Proteínas del Tejido Nervioso/metabolismo , Filogenia , ARN Mensajero/genética , ARN Mensajero/metabolismo , Receptores Inmunológicos/química , Receptores Inmunológicos/genética , Homología de Secuencia de Aminoácido , Transducción de Señal , Pez Cebra , Proteínas Roundabout