Phenotypic and transcriptional response to selection for alcohol sensitivity in Drosophila melanogaster

Gene-expression profiling combined with selection for genetically divergent Drosophila lines either highly sensitive or resistant to ethanol exposure has been used to identify candidate genes that affect alcohol sensitivity, including 23 novel genes that have human orthologs

Maternal gene expression in Atlantic halibut (Hippoglossus hippoglossus L.) and its relation to egg quality

<p>Abstract</p> <p>Background</p> <p>The commercial production of Atlantic halibut (<it>Hippoglossus hippoglossus </it>L.) suffers from a major bottleneck due to the low success of producing juveniles for on-growing. Atlantic halibut females are routinely hand-stripped and incorrect timing of stripping can result in low quality eggs due to post-ovulatory aging. Post-ovulatory aging leads to compositional changes in eggs that include maternally provided proteins and RNAs. There have been few studies of the maternally provided mRNA transcripts that control early development in commercially important fish species. The present study aimed to study maternal gene expression in Atlantic halibut and its relation to egg quality parameters including blastomere symmetry and hatching success.</p> <p>Results</p> <p>A maternal EST library containing 2341 sequences was constructed by suppressive subtractive hybridisation. Thirty genes were selected for expression studies; 23 novel genes and 7 genes with documented roles in early development. The expressions of twenty-one selected genes were measured by qPCR from fertilization to the 10-somite stage. Three genes were identified as strictly maternal genes that were expressed until the start of gastrulation; <it>askopos </it>(<it>kop</it>), <it>si:dkey-30j22.9 </it>(Tudor family member), and <it>Tudor 5 protein </it>(<it>Tdrd5</it>). The expressions of 18 genes at the 8-cell stage were correlated with egg quality parameters. The majority of genes showed either no or very minor correlations with egg quality parameter. However, two genes correlated positively with hatching success (<it>r</it>> 0.50, HHC00353: <it>r </it>= 0.58, <it>p </it>< 0.01; HHC01517: <it>r </it>= 0.56, <it>p </it>< 0.01) and one gene (HHC00255) was negatively correlated with the percentage of normal blastomeres (<it>r </it>= -0.62, <it>p </it>< 0.05).</p> <p>Conclusions</p> <p>During this study we have related maternal levels of gene expression to hatching success in fish. Poor hatching success was not correlated with a general decrease in transcript abundance but with low transcript levels of some specific genes. Thus, the molecular mechanisms leading to low Atlantic halibut egg quality cannot be entirely explained by post-ovulatory aging.</p

The histone-like protein HupB influences biofilm formation and virulence in Xanthomonas citri ssp. citri through the regulation of flagellar biosynthesis

Citrus canker is an important disease of citrus, whose causal agent is the bacterium Xanthomonas citri ssp. citri (Xcc). In previous studies, we found a group of Xcc mutants, generated by the insertion of the Tn5 transposon, which showed impaired ability to attach to an abiotic substrate. One of these mutants carries the Tn5 insertion in hupB, a gene encoding a bacterial histone-like protein, homologue to the β-subunit of the Heat-Unstable (HU) nucleoid protein of Escherichia coli. These types of protein are necessary to maintain the bacterial nucleoid organization and the global regulation of gene expression. Here, we characterized the influence of the mutation in hupB regarding Xcc biofilm formation and virulence. The mutant strain hupB was incapable of swimming in soft agar, whereas its complemented strain partially recovered this phenotype. Electron microscope imaging revealed that impaired motility of hupB was a consequence of the absence of the flagellum. Comparison of the expression of flagellar genes between the wild-type strain and hupB showed that the mutant exhibited decreased expression of fliC (encoding flagellin). The hupB mutant also displayed reduced virulence compared with the wild-type strain when they were used to infect Citrus lemon plants using different infection methods. Our results therefore show that the histone-like protein HupB plays an essential role in the pathogenesis of Xcc through the regulation of biofilm formation and biosynthesis of the flagellum.Fil: Conforte, Valeria Paola. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Ciencia y Tecnología "Dr. César Milstein". Fundación Pablo Cassará. Instituto de Ciencia y Tecnología "Dr. César Milstein"; ArgentinaFil: Malamud, Florencia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; ArgentinaFil: Yaryura, Pablo Marcelo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Centro de Investigaciones y Transferencia de Villa María. Universidad Nacional de Villa María. Centro de Investigaciones y Transferencia de Villa María; ArgentinaFil: Toum, Laila. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Instituto de Tecnología Agroindustrial del Noroeste Argentino. Provincia de Tucumán. Ministerio de Desarrollo Productivo. Estación Experimental Agroindustrial "Obispo Colombres" (p). Instituto de Tecnología Agroindustrial del Noroeste Argentino; ArgentinaFil: Torres, Pablo Sebastian. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Ciencia y Tecnología "Dr. César Milstein". Fundación Pablo Cassará. Instituto de Ciencia y Tecnología "Dr. César Milstein"; ArgentinaFil: de Pino, Veronica. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Ciencia y Tecnología "Dr. César Milstein". Fundación Pablo Cassará. Instituto de Ciencia y Tecnología "Dr. César Milstein"; ArgentinaFil: Chazarreta, Cristian Nicolás. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Ciencia y Tecnología "Dr. César Milstein". Fundación Pablo Cassará. Instituto de Ciencia y Tecnología "Dr. César Milstein"; ArgentinaFil: Gudesblat, Gustavo Eduardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Biodiversidad y Biología Experimental y Aplicada. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Biodiversidad y Biología Experimental y Aplicada; ArgentinaFil: Castagnaro, Atilio Pedro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Instituto de Tecnología Agroindustrial del Noroeste Argentino. Provincia de Tucumán. Ministerio de Desarrollo Productivo. Estación Experimental Agroindustrial "Obispo Colombres" (p). Instituto de Tecnología Agroindustrial del Noroeste Argentino; ArgentinaFil: Marano Roude, María de Los Milagros. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; ArgentinaFil: Vojnov, Adrián Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Ciencia y Tecnología "Dr. César Milstein". Fundación Pablo Cassará. Instituto de Ciencia y Tecnología "Dr. César Milstein"; Argentin

Host plant adaptation in the polyphagous whitefly, Trialeurodes vaporariorum, is associated with transcriptional plasticity and altered sensitivity to insecticides

This is the final version. Available from BMC via the DOI in this record. Background: The glasshouse whitefly, Trialeurodes vaporariorum, is a damaging crop pest and an invasive generalist capable of feeding on a broad range of host plants. As such this species has evolved mechanisms to circumvent the wide spectrum of anti-herbivore allelochemicals produced by its host range. T. vaporariorum has also demonstrated a remarkable ability to evolve resistance to many of the synthetic insecticides used for control. Results: To gain insight into the molecular mechanisms that underpin the polyphagy of T. vaporariorum and its resistance to natural and synthetic xenobiotics, we sequenced and assembled a reference genome for this species. Curation of genes putatively involved in the detoxification of natural and synthetic xenobiotics revealed a marked reduction in specific gene families between this species and another generalist whitefly, Bemisia tabaci. Transcriptome profiling of T. vaporariorum upon transfer to a range of different host plants revealed profound differences in the transcriptional response to more or less challenging hosts. Large scale changes in gene expression (> 20% of genes) were observed during adaptation to challenging hosts with a range of genes involved in gene regulation, signalling, and detoxification differentially expressed. Remarkably, these changes in gene expression were associated with significant shifts in the tolerance of host-adapted T. vaporariorum lines to natural and synthetic insecticides. Conclusions: Our findings provide further insights into the ability of polyphagous insects to extensively reprogram gene expression during host adaptation and illustrate the potential implications of this on their sensitivity to synthetic insecticides.ER

Systematic analysis of somatic mutations driving cancer: Uncovering functional protein regions in disease development

Background: Recent advances in sequencing technologies enable the large-scale identification of genes that are affected by various genetic alterations in cancer. However, understanding tumor development requires insights into how these changes cause altered protein function and impaired network regulation in general and/or in specific cancer types. Results: In this work we present a novel method called iSiMPRe that identifies regions that are significantly enriched in somatic mutations and short in-frame insertions or deletions (indels). Applying this unbiased method to the complete human proteome, by using data enriched through various cancer genome projects, we identified around 500 protein regions which could be linked to one or more of 27 distinct cancer types. These regions covered the majority of known cancer genes, surprisingly even tumor suppressors. Additionally, iSiMPRe also identified novel genes and regions that have not yet been associated with cancer. Conclusions: While local somatic mutations correspond to only a subset of genetic variations that can lead to cancer, our systematic analyses revealed that they represent an accompanying feature of most cancer driver genes regardless of the primary mechanism by which they are perturbed during tumorigenesis. These results indicate that the accumulation of local somatic mutations can be used to pinpoint genes responsible for cancer formation and can also help to understand the effect of cancer mutations at the level of functional modules in a broad range of cancer driver genes. Reviewers: This article was reviewed by Sándor Pongor, Michael Gromiha and Zoltán Gáspári. © 2016 Mészáros et al

Genomewide Expression Analysis in Zebrafish mind bomb Alleles with Pancreas Defects of Different Severity Identifies Putative Notch Responsive Genes

10.1371/journal.pone.0001479PLoS ONE3

Host plant adaptation in the polyphagous whitefly, Trialeurodes vaporariorum, is associated with transcriptional plasticity and altered sensitivity to insecticides

Background: The glasshouse whitefly, Trialeurodes vaporariorum, is a damaging crop pest and an invasive generalist capable of feeding on a broad range of host plants. As such this species has evolved mechanisms to circumvent the wide spectrum of anti-herbivore allelochemicals produced by its host range. T. vaporariorum has also demonstrated a remarkable ability to evolve resistance to many of the synthetic insecticides used for control. Results: To gain insight into the molecular mechanisms that underpin the polyphagy of T. vaporariorum and its resistance to natural and synthetic xenobiotics, we sequenced and assembled a reference genome for this species. Curation of genes putatively involved in the detoxification of natural and synthetic xenobiotics revealed a marked reduction in specific gene families between this species and another generalist whitefly, Bemisia tabaci. Transcriptome profiling of T. vaporariorum upon transfer to a range of different host plants revealed profound differences in the transcriptional response to more or less challenging hosts. Large scale changes in gene expression (> 20% of genes) were observed during adaptation to challenging hosts with a range of genes involved in gene regulation, signalling, and detoxification differentially expressed.Remarkably, these changes in gene expression were associated with significant shifts in the tolerance of host-adapted T. vaporariorum lines to natural and synthetic insecticides. Conclusions: Our findings provide further insights into the ability of polyphagous insects to extensively reprogram gene expression during host adaptation and illustrate the potential implications of this on their sensitivity to synthetic insecticides

Respostas bioquímicas e moleculares em ostras do mangue, Crassostrea brasiliana, expostas a diferentes contaminantes ambientais

Tese (doutorado) - Universidade Federal de Santa Catarina, Centro de Ciências Biológicas. Programa de Pós-Graduação em BioquímicaA contaminação dos ambientes costeiros apresenta-se como uma realidade na extensa costa brasileira. Dejetos e subprodutos das mais variadas atividades antrópicas, como os provenientes da atuação da indústria do petróleo e da ineficiência na coleta e tratamento do esgoto doméstico, provocam danos variados aos organismos expostos. Esses compostos químicos podem causar alterações biológicas de caráter molecular, celular, fisiológico ou ecológico, resultando em efeitos negativos não apenas para as comunidades naturais, como para os organismos destinados ao consumo humano. Desta forma, a identificação dessas alterações pode ser usada como biomarcador de contaminação aquática. O presente estudo contribui fornecendo informações para o estabelecimento de ferramentas sensíveis e viáveis para estudos ecotoxicológicos, através da avaliação de repostas de biomarcadores bioquímicos clássicos e da identificação de novos genes potenciais candidatos a biomarcadores. Para tal, ostras do mangue, Crassostrea brasiliana, foram expostas a diferentes contaminantes ambientais. São apresentados os resultados de biomarcadores bioquímicos em brânquia e glândula digestiva de ostras expostas por 96 horas a quatro concentrações da fração de óleo diesel acomodada em água (FAA). As respostas das enzimas antioxidantes e de fase II do sistema de biotransformação de xenobióticos, em conjunto com aspectos químicos, demonstraram que a ostra é capaz de bioacumular hidrocarbonetos alifáticos e aromáticos, além de responder a essa bioacumulação de forma concentração-dependente. Esses dados indicam um papel promissor dessa espécie como bioindicadora em programas de biomonitoramento ambiental. Entretanto, como muito pouco é conhecido sobre a biologia molecular de C. brasiliana, bibliotecas subtrativas de cDNA foram construídas. Esta metodologia possibilitou a identificação de 23 novos genes nessa espécie, comparando ostras expostas à FAA de óleo diesel por 24 horas e o grupo controle. Destes genes, três (protease específica de ubiquitina 25 - USP25, precursor de dominina, nucleosídeo difosfato quinase B - NDPK-B) foram validados por PCR quantitativo em tempo real (qPCR), representando genes de interesse para estudos ecotoxicológicos em C. brasiliana. Ainda, com o intuito de aumentar as informações gênicas de C. brasiliana, a técnica de pirosequenciamento utilizando a plataforma 454 foi aplicada em ostras expostas à FAA de óleo diesel, ao fenantreno e ao esgoto doméstico. A partir desta abordagem metodológica de sequenciamento em grande escala, a montagem de novo das leituras geradas produziu o primeiro transcriptoma referência de C. brasiliana. Como resultado, 7.401 novos genes foram identificados, destacando-se os genes codificadores de proteínas possivelmente envolvidas no sistema de biotransformação de xenobióticos e no sistema de defesa antioxidante. Por fim, com o intuito de avaliar a utilidade dos dados gerados pelo banco de ESTs, o nível de transcrição de seis genes CYP-like e quatro GST-like, previamente identificados no transcriptoma referência, foram testados por qPCR, fornecendo subsídios para o entendimento dos mecanismos moleculares de toxicidade exercidos pelo fenantreno, um hidrocarboneto policíclico aromático (HPA) prioritário. Para tal, ostras foram expostas a duas concentrações de fenantreno (100 ?g.L-1 e 1000 ?g.L-1) por 24 horas. Os resultados obtidos indicam o papel de CYPs e GSTs no metabolismo de HPAs, uma vez que o tratamento induziu um aumento no nível dos transcritos. A maior resposta da brânquia, se comparada à glândula digestiva, sugere papéis diferenciados no metabolismo de xenobióticos destes tecidos, no qual o papel da brânquia é destacado. Os dados apresentados nessa tese demonstram a aplicabilidade do uso de biomarcadores bioquímicos e moleculares em estudos ecotoxicológicos utilizando a ostra C. brasiliana como bioindicador de contaminação aquática. Em última instância, os resultados constituem importantes fontes de informação para o biomonitoramento de águas contaminadas por derivados de petróleo e esgoto doméstico ao longo da costa brasileira