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Sample records for novos povoamentos florestais

  1. SR&GIS: ferramentas de análise e modelagem de povoamentos florestais / SR&GIS: tools of the analysis and modeling forest stands

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    Attilio Antonio Disperati

    2010-10-01

    Full Text Available Para um planejamento de preservação e uso em regime sustentável há necessidade de manter atualizada uma base da cartografia dos recursos florestais existentes, em níveis local, regional e global. Dessa forma, pode-se: determinar o potencial volumétrico ou de biomassa a ser explorado; determinar as condições da fragmentação de habitat e a perda da diversidade; determinar o impacto da degradação florestal e seus efeitos nas condições hidrológica, edáfica e climática. A tecnologia que envolve as ferramentas de SR&GIS tem demonstrado significativa contribuição com seus produtos aerotransportados ou orbitais e suas técnicas de extração de informações, nas tarefas de mapeamento, inventário, monitoramento e modelagem florestal. Com objetivo de compor a abertura desse número especial da Revista Ambiência, o presente artigo mostra os novos rumos das pesquisas e aplicações nesse campo tecnológico, capazes de subsidiar a avaliação e modelagem dos recursos florestais.

  2. The integration of the terrestrial and airborne laser scanning technologies in the semi-automated process of retrieving selected trees and forest stand parameters Integração das tecnologias terrestre e aerotransportada de scanner laser no processo semi-automático de recuperação de árvores selecionadas e de parâmetros de povoamentos florestais

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    Piotr Wezyk

    2012-10-01

    Full Text Available The traditional forest inventory based usually on thousands of the circle plots (radius = 12.62m; area 500 sq m set in regular network. On every inventory plot, the basic tree and forest stand parameters have to be collected using calliper and hypsometer or even human eye (i.e. crown closure as well. The modern multifunctional forestry models requires more and more: dens and accurate data to deliver as fast as possible the precise information on the amount of wood stock or other selected forest stand and tree parameters. One of the promising remote sensing technologies is LiDAR collecting the 3D point cloud data. The TLS technology is very precise and fast but is limited to relatively small areas like forest inventory plot. The ALS is more focused on wide-area data collection. Both technologies are complementary, therefore it is a need for the fusion of those two sources of information to enhance the accuracy of tree parameters and enlarge the results for the wide forest areas with statistical models. Paper presents a method of the TLS and ALS point cloud registration and transformation to one coordinate system. The goal of the data fusion was the semi-automatic extraction of the trees selected parameter (height, DBH, basal area, crown closure, base of crown, 2D and 3D tree crown surface of the TR2 transect in Niepolomice Forest (Krakow, Poland. The results showed that the big potential of the enhancement of height and crown closure or base of the crown exists.ResumoO inventário florestal tradicional baseia-se normalmente em milhares de parcelas circulares (raio = 12,62 m, área 500 m² dispostas em uma malha regular. Em cada parcela do inventário, os parâmetros básicos da árvore e do povoamento devem sercoletados usando suta e hipsômetro ou até mesmo o olho humano (densidade de copa. Os modernos modelos florestais multifuncionais requerem cada vez mais: dados densos e acurados para gerar o mais rápido possível a informação precisa da

  3. Estudo do banco de sementes em povoamentos florestais puros e em uma capoeira de Floresta Ombrófila Aberta, no município de Areia, PB, Brasil Study of a seed bank in a pure forest population and a ombrophylous secondary forest in Areia Municipal district, PB, Brazil

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    Kilson Pinheiro Lopes

    2006-03-01

    Full Text Available Em amostragem realizada na estação seca (outubro/2002 em três povoamentos florestais puros constituídos por: sabiá (Mimosa caesalpiniaefolia, sombreiro (Clitoria fairchildiana e pinus (Pinus sp. e em uma área em estágio inicial de sucessão ecológica "capoeira", foram coletadas 25 amostras de solos por área em duas profundidades: 0-5 cm e 5-10 cm para determinação da densidade e a composição florística do banco de sementes do solo nas diferentes áreas. A área estudada localiza-se no Balneário Ecológico "O Quebra", Município de Areia, PB. A maior densidade de sementes ocorreu sempre na profundidade de 0-5 cm, independente do ambiente estudado, havendo, contudo, destaque da área povoada com sombreiro, verificando-se 1.012 e 405 sementes germinadas/m² nas profundidades 0-5 cm e 5-10 cm, respectivamente. A composição florística do banco de sementes foi dominada por espécies da família Urticaceae com mais de 40% nas duas profundidades estudadas. A forma de vida mais abundante foi a herbácea, independente da profundidade, seguida da arbustiva e arbórea, nos demais ambientes, exceto no sombreiro, onde predominaram arbustos, seguido de ervas e árvores. Excetuando-se o povoamento de sombreiro, os demais ambientes estudados, mesmo apresentando diferentes densidades do banco de sementes do solo, revelaram-se floristicamente similares.In sampling accomplished in the drought station of 2002 in three pure forest populations constituted by: sabiá (Mimosa caesalpiniaefolia, sombreiro (Clitoria fairchildiana and pinus (Pinus sp. and, an area in initial process of ecological succession, 25 samples of soils were collected by area in two depths: 0-5 cm and 5-10 cm. The studied universe is located at the Balneary "O Quebra", Areia Municipal district, PB. The biggest seeds density always happened in the 0-5 cm depth, independent of the studied environment. The population of sombreiro showed the biggest stock of seeds, being verified 1

  4. Precipitação efetiva em diferentes formações florestais na floresta nacional de ipanema

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    Kelly Cristina Tonello

    2014-04-01

    Full Text Available O presente trabalho foi conduzido na Floresta Nacional de Ipanema, unidade de conservação de uso sustentável localizada no município de Iperó-SP, com o objetivo de quantificar e comparar as frações de precipitação efetiva e interceptação da chuva em três povoamentos florestais distintos, sendo eles: Eucalyptus cloeziana, Pinus caribea var. hondurensis e Floresta Estacional Semidecidual. Para tanto, realizou-se o monitoramento das variáveis precipitação interna, escoamento pelo tronco, interceptação e precipitação em aberto em cada formação florestal, ao longo do período de novembro de 2009 à maio de 2010. O estudo revelou a precipitação efetiva de 86,2%, 85,0% e 77,2%; interceptação de 13,8%, 15,0% e 22,8% em relação à precipitação em aberto em Eucalyptus cloeziana, Pinus caribea var. hondurensis e Floresta Estacional Semidecidual, respectivamente. A influência dos povoamentos na distribuição da chuva apresentou diferença significativa somente para o processo de interceptação entre Floresta Estacional Semidecidual e os demais.

  5. Os Fungos no Funcionamento dos Ecossistemas Florestais

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    Santos-Silva, Celeste; Machado, Helena

    2011-01-01

    Os fungos no funcionamento dos ecossistemas Florestais: Papel dos fungos sapróbios na degradação da matériaorgânica Papel dos fungos micorrízicos na nutrição e saúde das árvores Diversidade fúngica e estabilidade das florestas Relações entre os fungos e os animais Doenças radiculares associadas ao declínio do montado de sobro e azinho

  6. Quantificação e modelagem dos macronutrientes em povoamentos de bracatinga Quantification and modeling of macronutrients in bracatinga stands

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    Andressa Ribeiro

    2012-03-01

    Full Text Available

    quantificação dos nutrientes em ecossistemas florestais é fundamental para verificação da manutenção do fluxo contínuo entre o que é depositado no solo e o que é assimilado novamente pelas plantas. O uso da área basal como ferramenta prática na medição dos povoamentos florestais, faz com que a modelagem no âmbito dos povoamentos seja facilmente aplicável à quantificação de nutrientes. Assim, o presente trabalho teve como objetivo quantificar e modelar o peso de macronutrientes por hectare nos diferentes compartimentos aéreos. Os dados utilizados foram coletados em 304 parcelas temporárias com diferentes idades em povoamentos de bracatinga (Mimosa scabrella Bentham., localizados na região metropolitana de Curitiba. Foram avaliados 23 modelos matemáticos para cada compartimento aéreo, dos quais, apenas um modelo por compartimento para todos os macronutrientes foi selecionado e validado, se mostrando apropriado para estimativa dos nutrientes por hectare. Em ordem decrescente, os valores de macronutrientes encontrados na parte aérea dos bracatingais seguiram a sequência de N > Ca > K > Mg > P. Após a exploração da lenha, restaram na área os resíduos contendo 25% de Ca, 32% de Mg, 37% de N, 45% de P e 18% de K.

     

    doi: 10.4336/2012.pfb.32.69.29

    Quantification of nutrients in forest ecosystems is fundamental for the verification of the maintenance of continuous flow between what is deposited in the soil and what is re-assimilated by the plants. Using basal area as a practical tool in the measurement of forest stands makes modeling easy at stand level for nutrient quantification. Thus, the present work had as objective to quantify and fit the weight of macronutrients per hectare in different compartments of above ground biomass. The data used in this research came from 304 temporary plots with different ages in Mimosa scabrella Bentham. (bracatinga stands located in the metropolitan region of Curitiba

  7. Enraizamento de estacas lenhosas de espécies florestais

    OpenAIRE

    Santos,Juliano de Paulo dos; Davide,Antonio Claudio; Teixeira,Luis Antonio Fonseca; Melo,Ana Julia Santos; Melo,Lucas Amaral de

    2011-01-01

    Neste estudo, objetivou-se estudar o potencial de enraizamento de estacas lenhosas de 20 espécies florestais nativas. Dois experimentos distintos foram conduzidos. Em ambos, as estacas caulinares apresentavam em média de 15 a 20 cm de comprimento. No primeiro, estacas de nove espécies foram selecionadas em quatro classes de diâmetro, com média de 5,0; 9,0; 14,5 e 24 mm. No segundo, estacas de 20 espécies foram tratadas com ácido indolbutirico (AIB). Cada tratamento foi avaliado em quatro repe...

  8. Variáveis Condicionantes na Susceptibilidade de Incêndios Florestais no Parque Nacional do Itatiaia

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    Marlon Thiago de Oliveira Nunes

    2015-01-01

    Full Text Available O grande número de incêndios florestais que atingem o Parque Nacional do Itatiaia (PNI é motivo de preocupação, pois eles modificam a paisagem e acarretam perda de flora e fauna. Desta forma, torna-se importante a criação de metodologia que ajude na identificação de fatores que influenciam a susceptibilidade a incêndios. Este trabalho tem como objetivo avaliar variáveis geomorfológicas (forma da encosta, radiação solar global, declividade e altitude e meteorológicas (chuva na ocorrência de incêndios. Para atingir o objetivo foi utilizado o Modelo Digital de Elevação (MDE gerado a partir de cartas topográficas e dados pluviométricos de três estações presentes no PNI e arredores. Este MDE possibilitou a criação das variáveis geomorfológicas, e os dados pluviométricos possibilitaram o cálculo do Standardized Precipitation Index (SPI. As variáveis obtidas foram comparadas com os Relatórios de Ocorrência de Incêndio (ROI, e os resultados mostram que as variáveis geomorfológicas mais significativas foram a forma da encosta e a radiação solar global. O índice SPI introduziu novos indicativos temporais para o melhor entendimento do comportamento da ocorrência dos incêndios florestais no PNI.

  9. Aplicação do método de análise do tronco a povoamentos de Pinus pinaster na Zona do Pinhal

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    Grácio, C.

    1992-01-01

    Apresenta um estudo dendrométrico baseado na aplicação do método de análise do tronco em povoamentos de Pinus pinaster pertencentes a alguns concelhos do distrito de Castelo Branco. É uma abordagem preliminar integrada num projeto em curso na ESA-IPCB sobre "Estudos de Crescimento de e Produção em Povoamentos de Pinus pinaster na Região da Beira Interior".

  10. Arranjos comunitários, sistemas produtivos e aportes de ciência e tecnologia no uso da terra e de recursos florestais na Amazônia

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    Wanderley Messias da Costa

    Full Text Available O foco principal deste trabalho é o exame de algumas das tendências atuais que estão promovendo mudanças significativas nos padrões de uso econômico dos produtos florestais amazônicos. Em termos gerais, essas novas tendências expressam, sob diversos modos, um amplo processo de modernização das atividades produtivas, no qual comunidades organizadas da região estão se estruturando segundo vetores desencadeados pelo impulso de cadeias produtivas complexas e suas respectivas redes. Por outro lado, elas também expressam a ampliação e a crescente sofisticação dos mercados de consumo para os produtos naturais em geral, os produtos florestais em particular e, especialmente, para aqueles da biodiversidade amazônica. Finalmente, esses sistemas produtivos emergentes passaram a contar com um aliado poderoso nos últimos anos, representado por sua crescente interação com as atividades de Ciência e Tecnologia (C&T e de Pesquisa e Desenvolvimento (P&D, cujos resultados já podem ser observados em diversas experiências em curso, tais como ganhos de qualidade, de produtividade, de escala, de competitividade e, como consequência principal, a conquista de novos mercados de consumo.

  11. DETERMINAÇÃO INDIRETA DO ESTOQUE DE BIOMASSA E CARBONO EM POVOAMENTOS DE ACÁCIA-NEGRA (Acacia mearnsii De Wild.

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    Paulo Sérgio Pigatto Schneider

    2005-12-01

    Full Text Available Este trabalho foi realizado com o objetivo de estimar o estoque de carbono em povoamentos equiâneos de Acacia mearnsii De Wild., na região da Encosta Inferior do Sudeste, no Rio Grande do Sul, com o método de derivação do volume em biomassa e carbono. As quantificações dos componentes da biomassa e do carbono foram feitas em povoamentos com idade entre 4 e 8 anos. O método de derivação do volume em biomassa e carbono mostrou-se eficiente na determinação do estoque de carbono, pois a diferença relativa média foi de apenas 4,4%, quando considerada toda a amostragem e independência da idade dos povoamentos. A densidade básica média da madeira foi de 0,6, independente da idade dos povoamentos. A proporção de biomassa média entre o volume com casca pelo volume de folhas, ramos, serrapilheira e raízes foram de 0,59, independente da idade dos povoamentos. A concentração média de carbono, independente da idade dos povoamentos, foi igual a 0,40. O estoque de carbono estimado pelo método de derivação de volume e carbono, em povoamentos de 7 anos de idade, foi de 99,46 t ha-1 no índice de sítio 20, 82,98 t ha-1 no índice de sítio 16, e 46,13 t ha-1 no índice de sítio 12.

  12. PRODUTIVIDADE E CUSTOS DO FELLER-BUNCHER E PROCESSADOR FLORESTAL EM POVOAMENTO DE EUCALIPTO DE PRIMEIRO CORTE

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    Danilo Simões

    2014-09-01

    Full Text Available http://dx.doi.org/10.5902/1980509815742A racionalização da colheita florestal e a minimização dos custos é uma busca constante por parte dos gestores envolvidos nesse processo, competindo a esses deliberar práticas economicamente viáveis para otimizar essa operação. O objetivo deste estudo foi avaliar técnica e economicamente a produtividade do feller-buncher e do processador florestal em povoamento de eucalipto em primeiro corte. A análise técnica englobou um estudo de tempos e movimentos, produtividade, eficiência operacional e disponibilidade mecânica. A análise econômica englobou os parâmetros do custo operacional, custo de colheita florestal e rendimento energético. Visando à otimização do custo de colheita florestal, o sistema composto pelo feller-buncher e processador florestal apresenta-se como uma alternativa viável tecnicamente e economicamente para a colheita em povoamentos de eucalipto de primeiro corte ou para povoamentos que não possuam árvores bifurcadas.

  13. Chuva de sementes em remanescentes florestais de Campo Verde, MT

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    William Pietro-Souza

    2014-08-01

    Full Text Available O objetivo deste trabalho consistiu em avaliar sazonalmente a produção de sementes provenientes de fragmentos florestais presentes na zona rural de Campo Verde, MT. Essa caracterização ocorreu em termos de produção de sementes e riqueza de espécies vegetais. Foram selecionados três fragmentos florestais caracterizados como Floresta Estacional Semidecidual. Em cada fragmento, cinco coletores foram instalados e confeccionados com canos de PVC (1 m²; malha de náilon de 0,001 m e 0,15 m de profundidade do bojo. O material foi coletado mensalmente, cujas sementes foram quantificadas e separadas conforme a síndrome de dispersão, etapa sucessional e forma de vida. Houve a determinação da densidade, frequência absoluta, índice de diversidade e equitabilidade. Ao todo, foram obtidas 3.622 sementes, pertencentes a 74 táxons. Maiores densidades de sementes foram observadas durante os meses de setembro, outubro e novembro. As lianas Gouania sp., Fridericia speciosa, Heteropterys sp. e Distictella sp. responderam com 55,95% do total de sementes aportadas. Das espécies que compuseram a chuva de sementes, 74% não são dispersas pelo vento. Todavia, quando se verificou a quantidade de diásporos coletados, formas dispersas pelo vento foram predominantes, representando 76% do total. Citam-se como táxons arbóreos importantes para a recomposição florestal na região de Campo Verde, situada no Sudeste de Mato Grosso: Tachigali rubiginosa, Siparuna guianensis, Nectandra sp., Cordia alliodora, Alibertia sp., Terminalia brasiliensis e Myrcia sp. Essas espécies devem ser alvo de estudos mais específicos relacionados ao seu potencial para recuperação de ambientes degradados, considerando-se as Áreas de Preservação Permanente e Reservas Legais.

  14. Subsídios para o monitoramento de formigas cortadeiras em plantios florestais no Planalto Catarinense

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    Hoffer, Hadson

    2015-01-01

    O objetivo deste trabalho foi fornecer subsídios para o monitoramento de formigas cortadeiras em plantios florestais no Planalto Catarinense, conhecendo as espécies de formigas cortadeiras da região, sua associação com o tipo de solo e a distribuição espaço-temporal dos danos causados em Pinus taeda. Para isso foram percorridos plantios florestais em sete municípios do Planalto Catarinense na busca por ninhos de formigas cortadeiras. As coletas ocorreram em cinco diferentes tipos de solo com ...

  15. História do povoamento de Picote (HISTPP) : projecto de investigação (2012-2015)

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    Centeno, Rui; Barroca, Mário Jorge; Ferreira, Daniela Filipa de Freitas; Rodrigues, Sérgio Monteiro; Morais, Rui; Sanches, Maria de Jesus; Soeiro, Teresa; Vaz, Filipe M. Costa

    2014-01-01

    In a time of great decline of public funding in archaeological investigation, it was formed in 2012 the research project "História do Povoamento de Picote", proposed by Associação para o Desenvolvimento Integrado de Picote (Frauga) to the University of Porto (UP). This project was created with the main objective of carrying out excavations in the archaeological site of Puio, as well as the recovery of other information’s regarding the past human settlement of Picote village.

  16. Análise da trafegabilidade em estradas florestais utilizando métodos computacionais

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    Robson Jose de Oliveira

    2013-04-01

    Full Text Available As estradas florestais são o principal meio de integração entre as florestas e as empresas. A partir do exposto, percebe-se a necessidade não apenas da correta aplicação de atividades de manutenção, mas também de se determinar o tempo exato para tal intervenção. Partindo desse pressuposto, este trabalho apresenta os resultados da apreciação de dois métodos de classificação da qualidade de estradas não pavimentadas, com o intuito de se verificar a aplicabilidade dos mesmos na caracterização das estradas florestais brasileiras e servir como base para um sistema de gestão das operações de manutenção destas vias. Foram medidos os principais defeitos em estradas florestais seguindo um método denominado de Índice de Condição de Rodovia Não Pavimentada (ICRNP, que serviram de base para gerar um banco de dados para testar a eficiência do uso de redes neurais artificiais (RNA na administração das estradas florestais, minimizando custos e paralisações de tráfego. Concluiu-se que a utilização das redes neurais artificiais apresentou resultados superiores ao método do ICRNP.

  17. Biomassa radicular, densidade do solo e análise química do solo de um povoamento de Pinus sp. / Root biomass, soil density and soil chemical analysis in a Pinus sp. plantition

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    Gerson Luiz Selle

    2010-04-01

    Full Text Available O sistema radicular é responsável direto pelo crescimento e sustentação das plantas, em especial das espécies florestais. As raízes finas (menor 2 mm, por sua vez, são as principais responsáveis pela absorção dos nutrientes necessários para o desenvolvimento e crescimento da planta. O gênero Pinus tem crescido em importância nos últimos anos em função de sua adaptabilidade a condições adversas do local, bem como sua grande versatilidade no que diz respeito à comercialização de sua madeira e demais produtos. O presente estudo teve como objetivo quantificar a biomassa de raízes finas e analisar alguns parâmetros edáficos em um povoamento de Pinus sp. plantado em Santa Maria (RS. A biomassa radicular e a densidade do solo foram avaliadas em seis profundidades de solo (0-10, 10-20, 20-30, 30-40, 40-50 e 50-60 cm e três posições: na linha de plantio; na entre linha de plantio; entre quatro plantas, em um povoamento de Pinus sp., com idade de sete anos, localizado em uma área pertencente à Universidade Federal de Santa Maria. A densidade do solo não apresentou diferença significativa ao longo do perfil do solo, não tendo, portanto, influência sobre os resultados de biomassa nas diferentes profundidades. A biomassa radicular encontrada no povoamento foi de 1606,3 kg ha-1 sendo que, 40,6% estavam nos primeiros dez centímetros do solo, diminuindo como o aumento da profundidade. Essa mesma tendência foi registrada para o teor de matéria orgânica, saturação por bases, bem como a quantidade de nutrientes, fatores estes que apresentaram estreita correlação com a quantidade de biomassa. Teor de alumínio e soma de bases aumentaram conforme o aumento da profundidade, mas apresentaram também uma estreita correlação com a biomassa. Os diferentes locais de coleta não diferiram estatisticamente entre si. AbstractThe root system is directly responsible for the growth and support of the plants, especially for the forests

  18. PRODUTIVIDADE E CUSTOS DO PROCESSADOR TRABALHANDO EM POVOAMENTOS DE Eucalyptus grandis Hill ex Maiden

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    Carlos Cardoso Machado

    1999-12-01

    Full Text Available No presente trabalho foi realizado um estudo de tempos com o objetivo de ajustar equações para estimar o tempo das atividades, a produtividade, o custo operacional e da produção do processador utilizado em um sistema de colheita de madeira de povoamentos de Eucalyptus grandis Hill ex Maiden, em topografia plana, no Estado da Bahia. O ciclo operacional do processador consistiu no tempo gasto para processar uma árvore e foi dividido em etapas as quais foram cronometradas, usando a metodologia dos tempos individuais. A unidade amostral foi constituída do ciclo operacional da máquina. A análise estatística baseou-se em estudo de regressão, sendo utilizado o procedimento de modelagem de regressão "stepwise". Com as equações ajustadas, foi possível estimar a produtividade da máquina em função do diâmetro das árvores. Nas condições do estudo, considerando uma eficiência operacional de 70%, a produtividade do processador foi de 25,8 m³cc/h, o custo operacional 47,90 US$/h e o custo de produção de 1,86 US$/m³cc. Com base nos resultados obtidos, pode-se concluir que: o tempo de processamento das árvores varia diretamente com o aumento do diâmetro; o tempo de preparação, ao contrário do tempo de processamento, possui uma baixa correlação com o diâmetro das árvores; a produtividade do processador é diretamente proporcional ao aumento do diâmetro das árvores, quando expressa em volume, e inversamente proporcional, quando expressa em número de árvores; o custo por metro cúbico de madeira processada com processador, varia numa relação inversa ao aumento do diâmetro; do custo operacional do processador, o custo fixo é o de maior proporção, seguido do custo variável, administrativo e da mão-de-obra; e, o custo de produção do processador diminui em forma exponencial com o aumento do diâmetro das árvores.

  19. Fauna do Solo como Indicadora em Fragmentos Florestais na Encosta de Morrotes

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    Rafael Nogueira Scoriza

    Full Text Available RESUMO A diferença sucessional entre os fragmentos florestais reflete-se na comunidade da fauna do solo, mostrando-se um bioindicador eficiente. A não diferenciação entre terços indica que a degradação antrópica ocorre de forma homogênea em toda a extensão da encosta florestal.

  20. TRANSFORMAÇÃO GENÉTICA EM ESPÉCIES FLORESTAIS

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    Claudia Studart-Guimarães

    2003-01-01

    Full Text Available A transformação genética, que compreende a introdução de genes exógenos de forma controlada no genoma de uma célula vegetal e posterior regeneração da planta transgênica, tem contribuído com os programas de melhoramento genético de plantas pela obtenção de genótipos com novas características de interesse. O melhoramento de espécies florestais é limitado por características intrínsecas a tais espécies, como a altura dos indivíduos e o ciclo longo de vida. A transformação genética constitui, portanto, uma alternativa para a obtenção de espécies florestais com características desejáveis em um menor espaço de tempo. Plantas transgênicas com resistência a determinadas pragas, com melhor qualidade de madeira, maior produção de biomassa, tolerância a herbicidas, entre outras características de interesse, já foram obtidas para diferentes espécies florestais de importância econômica como álamo, eucalipto e pinheiros em geral. Este trabalho mostra a importância da transformação genética, associada a outras técnicas biotecnológicas no melhoramento de espécies florestais, as técnicas de transformação mais utilizadas e as características que já foram introduzidas nessas espécies pela transformação.

  1. Transformação genética em espécies florestais.

    Directory of Open Access Journals (Sweden)

    Claudia Studart-Guimarães

    2010-08-01

    Full Text Available A transformação genética, que compreende a introdução de genes exógenos de forma controlada no genoma de uma célula vegetal e posterior regeneração da planta transgênica, tem contribuído com os programas de melhoramento genético de plantas pela obtenção de genótipos com novas características de interesse. O melhoramento de espécies florestais é limitado por características intrínsecas a tais espécies, como a altura dos indivíduos e o ciclo longo de vida. A transformação genética constitui, portanto, uma alternativa para a obtenção de espécies florestais com características desejáveis em um menor espaço de tempo. Plantas transgênicas com resistência a determinadas pragas, com melhor qualidade de madeira, maior produção de biomassa, tolerância a herbicidas, entre outras características de interesse, já foram obtidas para diferentes espécies florestais de importância econômica como álamo, eucalipto e pinheiros em geral. Este trabalho mostra a importância da transformação genética, associada a outras técnicas biotecnológicas no melhoramento de espécies florestais, as técnicas de transformação mais utilizadas e as características que já foram introduzidas nessas espécies pela transformação.

  2. Medição e modelação da intercepção num povoamento de pinheiro bravo

    OpenAIRE

    Fernandes, Isabel Augusta Carvalho

    2008-01-01

    Esta dissertação tem como principal objectivo o aprofundamento do conhecimento e compreensão do fenómeno intercepção, como parte integrante e relevante do ciclo hidrológico. Esta análise é o prosseguimento dos estudos anteriormente realizados na Serra do Caramulo num povoamento de pinheiro bravo com cerca de 16 anos. Referente ao ano hidrológico de 2005, estimou-se a precipitação regional, a precipitação interna e o escoamento pelo tronco em 960, 748 e 49mm, respect...

  3. Utilização Potencial do Lenho de Acacia melanoxylon: a Crescer em Povoamentos Puros ou Mistos com Pinus pinaster - pela Indústria Florestal Portuguesa

    OpenAIRE

    Santos, António; Teixeira, Andreia; Anjos, Ofélia; Simões, Rogério; Nunes, Lina; Machado, José S.; Tavares, Mário

    2007-01-01

    A Acacia melanoxylon R. Br. (acácia-austrália ou austrália) cresce bem em Portugal, em povoamentos puros ou mistos com Pinus pinaster Aiton, ainda que apresente fortes constrangimentos ecológicos e legais. Apesar de algumas dificuldades, por exemplo na secagem, a madeira de austrália é usada em mobiliário e produtos manufacturados devido, principalmente, à sua textura e cor escura. Pode também ser usada para pasta, sendo plantada em muitos países com esse propósito juntamente com Acacia mangi...

  4. A complementary strategy for the conservation of native forest tree species: retrieval and conservation of threatened ecotypes Estratégia complementar para conservação de espécies florestais nativas: resgate e conservação de ecótipos ameaçados

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    Jarbas Yukio Shimizu

    2010-06-01

    conservação são fundamentais na conservação de ecossistemas naturais. No entanto, na conservação da variabilidade ecotípica de espécies florestais, sua eficácia se restringe aos limites físicos da sua área de influência. Considerando que a maior parte dos ecótipos florestais de grande significado adaptativo localiza-se fora das unidades de conservação, medidas complementares são  indispensáveis, preferencialmente, com a participação de produtores rurais, sobretudo os de pequena escala, por estarem presentes em todo o território nacional. A estratégia proposta tem como ponto fundamental evitar o plantio de sementes ou mudas em
    locais distantes de suas origens, visando preservar as características adaptativas próprias de cada ecossistema. Para isso, recomendam-se procedimentos para a amostragem de matrizes e instalação de povoamentos florestais para conservação mediante uso pelos produtores rurais.

  5. Avaliação de Risco em Investimentos Florestais Evaluation of Risk in Investments Forestry

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    Flávio José Simioni

    2011-03-01

    Full Text Available

    A avaliação econômica de projetos de investimentos é comumente utilizada como forma de buscar parâmetros indicativos de sua viabilidade. Entretanto, as condições de incertezas em relação ao ambiente econômico dificultam o processo de tomada de decisão. No caso dos plantios florestais, a complexidade é ainda maior em função do alto tempo de retorno do investimento. Uma das alternativas que pode ser utilizada pelos investidores é a transformação das incertezas em risco. Assim, o objetivo do artigo é verificar a adequação do emprego do Método de Monte Carlo (MMC na avaliação do risco em plantios florestais de Pinus spp. O procedimento consiste na simulação da Taxa Interna de Retorno (TIR e do Valor Presente Líquido (VPL do projeto, a partir da simulação de variáveis previamente selecionadas no fluxo de caixa. O método mostrou-se eficiente na análise de risco de plantios florestais
    Economic evaluation of investment projects of is usually used as a form to search for parameters that are indicative of its viability. However, a condition of uncertainty in relation to the economic environment makes it difficult in order to help the process of decision making. In the case of the forest activities, the complexity is still bigger in function of the long time required for the return of the investment. One of the alternatives that can be used by the investors is the transformation of uncertainty into risk. Thus, the objective of the article is to verify the adequacy of the Monte Carlo Method (MMC in the risk evaluation of in forest activities with Pinus spp. The procedure  consists of the simulation of the Internal Tax of Return (ITR and of Net Present Value (NPV of the project, from the simulation of variables previously selected in the cash flow. The method revealed efficient in the risk analysis of forest activities. 

  6. Transformação genética em espécies florestais.

    OpenAIRE

    Claudia Studart-Guimarães; Cristiano Lacorte; Ana Cristina Miranda Brasileiro

    2010-01-01

    A transformação genética, que compreende a introdução de genes exógenos de forma controlada no genoma de uma célula vegetal e posterior regeneração da planta transgênica, tem contribuído com os programas de melhoramento genético de plantas pela obtenção de genótipos com novas características de interesse. O melhoramento de espécies florestais é limitado por características intrínsecas a tais espécies, como a altura dos indivíduos e o ciclo longo de vida. A transformação genética constitui, po...

  7. Avaliação do impacte de fogos florestais nos recursos hídricos subterrâneos

    OpenAIRE

    Ferreira, J.P.L.; Quinta-Nova, L.C.; Leitão, T.

    2012-01-01

    Foram apresentados os estudos desenvolvidos no âmbito do projeto “Avaliação do impacte de fogos florestais nos recursos hídricos subterrâneos” (POCI/AGR/59180/2004), designadamente: (1) caracterização e análise do coberto vegetal lenhoso e o seu contributo para a produção de cinzas resultantes de incêndios florestais; (2) estudos relativos à caracterização dos solos, águas e cinzas da combustão de matéria vegetal das áreas estudadas, da biomassa e o potencial de transferência d...

  8. Estudo do momento ótimo de reforma para povoamentos de Eucalyptus spp - o caso da redução dos custos.

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    Álvaro Nogueira de Souza

    2010-08-01

    Full Text Available Os objetivos deste trabalho foram: a propor e verificar a eficiência de um modelo matemático que permita estudar os efeitos do progresso tecnológico (redução dos custos sobre a época ótima de substituir povoamentos de Eucalyptus spp; b determinar a rotação florestal de um povoamento de Eucalyptus spp; c verificar qual seria o momento de substituir se as receitas estivessem constantes desde o início dos incentivos fiscais, ou seja, na década de 60, e, d projetar o momento de substituir o povoamento no futuro, considerando os custos decrescentes e a produtividade constante a valores de hoje. Utilizou-se a Função Gompertz para o cálculo da produção de madeira. O critério utilizado para a avaliação econômica da viabilidade dos projetos foi o Valor Presente Líquido. O modelo proposto permitiu calcular o efeito do progresso tecnológico nos custos no período entre 1960 e 2000 e projetar os valores dos custos para o período entre 2000 e 2040. Concluiu-se que: a a rotação, com valores atuais, encontra-se, em 7 anos, mantidas as receitas da década de 60; b o momento ótimo de reforma estaria em seis cortes; c o modelo mostrou-se eficiente para estimativas em um horizonte de até 40 anos; o estudo da cadeia de substituição mostrou que as épocas ótimas de reforma caíram ao longo dos anos, de seis cortes na década de 60, três na década de 80 e dois atualmente; a tendência é permanecer nos dois cortes passando a três com um pequeno aumento na produtividade das talhadias.

  9. A regeneração natural sob plantações florestais: desertos verdes ou redutos de biodiversidade?

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    Ricardo Augusto Gorne Viani

    2010-09-01

    Full Text Available Se, por um lado, plantios florestais comerciais têm sido apontados como "desertos verdes", por outro, diversos estudos realizados nas últimas duas décadas demonstram o contrário, sugerindo que tais florestas podem catalisar a regeneração natural em seu sub-bosque e, assim, contribuir para a conservação da biodiversidade. Com a finalidade de obter uma visão ampla e multifacetada sobre as plantações florestais e seu potencial para a conservação e a restauração da diversidade biológica, efetuou-se a compilação dos principais resultados de estudos que tratam da regeneração natural sob plantios florestais, com destaque para os realizados no Brasil. Os resultados compilados são bastante heterogêneos, indicando que fatores históricos e ambientais, como densidade de copas e disponibilidade de luz no sub-bosque, idade do plantio, espécie florestal plantada, distância de remanescentes de vegetação nativa, manejo das florestas plantadas e histórico de utilização da área influenciam direta ou indiretamente a riqueza, a densidade e a estrutura da regeneração natural sob os plantios. No entanto, inevitavelmente, os estudos investigados reforçam a idéia de que plantios florestais comerciais podem funcionar como redutos da biodiversidade, ao menos para alguns grupos de seres vivos, e também como facilitadores da restauração ecológica de florestas nativas. Com relação ao Brasil, conclui-se que, embora abundantes, os estudos já feitos concentram-se em determinadas regiões e biomas e são, em sua maioria, descritivos. É desejável, portanto, a realização de estudos que investiguem experimentalmente os fatores específicos que influenciam a dinâmica da regeneração natural sob os plantios e sistemas de manejo que proporcionem uma combinação ótima de produção e conservação da biodiversidade. É desejável ainda que esses estudos abranjam também outras regiões fitogeográficas do País, onde planta

  10. Regeneração natural em remanescentes florestais e áreas reflorestadas da várzea do rio Mogi-Guaçu, Luiz Antônio - SP Natural regeneration in forest remainders and reforested areas of "Mogi-Guaçu" river floodplain in Luiz Antônio county, São Paulo, Brazil

    Directory of Open Access Journals (Sweden)

    Assíria Maria Ferreira da Nóbrega

    2008-10-01

    Full Text Available O trabalho objetivou descrever e avaliar a estrutura da regeneração de espécies arbóreas em dois remanescentes naturais e em três áreas reflorestadas com espécies nativas e em um povoamento de Eucalyptus robusta, situados em área de várzea do rio Mogi-Guaçu, Luiz Antônio, SP (21º31'S e 47º55'W. Foram amostradas 40 subparcelas de 2 m² em cada remanescente natural e sub-bosque de eucalipto e 60 subparcelas de 3,5 m² em cada área reflorestada. Foram amostrados todos os indivíduos arbóreos de regeneração com altura > a 10 cm e diâmetro do caule até a altura do peito (DAP 5 cm. Foram identificados 1.990 indivíduos, pertencentes a 24 famílias, 46 gêneros e 51 espécies. Cabralea canjerana, Psidium cattleyanum, Nectandra megapotamica, Acacia polyphylla e Syzygium cumini estavam entre as espécies mais representadas nas quatro categorias de tamanho. O reflorestamento com espécies nativas em áreas degradadas da várzea do rio Mogi-Guaçu promoveu a regeneração natural com biodiversidade superior aos remanescentes naturais de florestas ciliares sob efeito de borda e contribuiu para com o processo de restauração de ecossistemas florestais. O povoamento de Eucalyptus robusta com cerca de 20 anos de idade favoreceu a regeneração de espécies climácicas e secundárias.The phytosociology of the woody stratum of both young regenerating individuals and seed banks are quality indicators of heterogeneous reforestations. The objetive of this research was to evaluate the structure of regeneration of the arboreal species in two natural remainders, in three areas reforested with native species and in a Eucalyptus robusta settlement located in a floodplain of Mogi-Guaçu river in Luiz Antônio County (21°31´S and 47°55´W, São Paulo, Brazil. Sampling was collected in 40 subplots of 2 m²in of each natural remainder and each eucalyptus sub-forest, as well as 60 subplots of 3.5 m²in each area reforested. All individuals with height

  11. Crescimento de plântulas de alface (Lactuca sativa L. em solo oriundo de um povoamento de Luetzelburgia auriculata (Allemão Ducke

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    Érika do Nascimento Fernandes Pinto

    2016-04-01

    Full Text Available Esta pesquisa buscou conhecer características alelopáticas e de fertilidade de um solo oriundo de povoamento de Luetzelburgia auriculata (Allemão Ducke, através da avaliação do crescimento de plantas de alface. Inicialmente, realizou-se a coleta do solo sob o povoamento da L. auriculata (SPL e de uma área externa a esse povoamento (SAE, na Fazenda Cachoeira de São Porfírio, em Várzea-PB, e encaminhou-se para o Centro de Saúde e Tecnologia Rural da Universidade Federal de Campina Grande, Campus de Patos. Em delineamento inteiramente casualizado, aplicaram-se cinco tratamentos com cinco repetições, colocando-se três sementes de alface por vaso contendo os seguintes tratamentos: T1=100%SAE; T2=100%SPL; T3=75%SPL; T4=50%SPL e T5=25%SPL. Aos 63 dias da semeadura, realizou-se a colheita e mensuraram-se as variáveis: comprimento da parte aérea, da raiz, peso da massa fresca da parte aérea, área foliar e número de folhas de cada indivíduo e a análise química dos substratos. Aplicou-se a ANOVA e o teste de Tukey a 5% de probabilidade. O solo do povoamento da L. auriculata (SPL apresentou uma maior quantidade de nutrientes em relação ao solo da área externa ao povoamento (SAE e influenciou positivamente no crescimento das plantas de alface. No entanto, em apenas três dos cinco tratamentos aplicados (T1, T2 e T3, a alface se desenvolveu. Em T1, T2 e T3 as variáveis analisadas diferiram estatisticamente em função da origem dos solos utilizados e da proporção do esterco bovino. O solo oriundo do povoamento de L. auriculata não apresentou efeito alelopático sobre os parâmetros de crescimento da alface.Seedling growth lettuce (Lactuca sativa L. in soil arising out of a settlement Luetzelburgia auriculata (Allemão DuckeAbstract: This research aimed to know allelopathic characteristics and fertility of the soil arising out settlement Luetzelburgia auriculata (Allemão Ducke by assessing the growth of lettuce plants. Initially

  12. Análise de processo hierárquico para gerir as estradas florestais

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    Robson José de Oliveira

    Full Text Available Este trabalho teve como objetivo hierarquizar os defeitos mais importantes encontrados em duas empresas do setor de estradas florestais, localizadas nos estados de Minas Gerais e Bahia, onde foram aplicados questionários a engenheiros e professores que atuam nesta área. Por meio destes questionários, foram coletados dados sobre quantidade e severidade de sete defeitos - seção transversal inadequada, drenagem lateral imprópria, corrugação, excesso de poeira, buracos, trilha de roda e perda de agregados -, que foram analisados pelo método objetivo denominado Índice de Condição de Rodovias Não Pavimentadas (ICRNP. Com o intuito de garantir uma maior precisão para realizar inferência sobre os defeitos, utilizaram-se as Redes Neurais Artificiais (RNA's, listando, assim, por ordem de importância, os problemas mais graves que tornam a malha viária intrafegável. Os resultados mostram que 33% dos trechos analisados necessitam de maior urgência para a realização de manutenção, atingindo a classificação de muito pobre, o que pode causar empecilhos aos usuários desta estrada. Seção transversal inadequada e drenagem lateral imprópria foram os defeitos mais encontrados nas estradas.

  13. Estabelecimento de Espécies Florestais Nativas Via Semeadura Direta no Rio Piauitinga - Sergipe

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    Janisson Batista de Jesus

    2017-04-01

    Full Text Available RESUMO A técnica de semeadura direta vem se destacando nos projetos de recuperação florestal pela redução de custos na implantação e tem sido cada vez mais utilizada. Este trabalho foi realizado com o objetivo de avaliar a emergência, sobrevivência e estabelecimento de espécies florestais nativas, por meio de sementes em áreas de mata ciliar no Rio Piauitinga, município de Lagarto, SE. As espécies utilizadas foram Libidibia ferrea var. leiostachya (Benth. L. P. Queiroz, Cassia grandis L. f., Cecropia pachystachya Trec., Enterolobium contortisiliquum (Vell. Morong e Guazuma ulmifolia Lam. O experimento em campo foi implantado em Delineamento em Blocos Casualizados (DBC com quatro repetições, em esquema fatorial, testando-se as cinco espécies com e sem tratamento para superação de dormência. A semeadura direta mostrou-se uma técnica viável para a área de estudo apenas para as espécies L. ferrea var. leiostachya, E. contortisiliquum e Cassia grandis, utilizando-se sementes com e sem dormência.

  14. Representatividade ambiental e fragmentação florestal em áreas dominadas por plantios homogêneos: uma proposta para o arranjo espacial de fragmentos florestais

    OpenAIRE

    Sarcinelli, Tathiane Santi

    2006-01-01

    Este trabalho apresenta um estudo da paisagem de áreas florestais dominadas por plantios homogêneos de eucalipto e florestas nativas. Os objetivos foram avaliar a configuração espacial e a heterogeneidade fisiográfica e pedológica de fragmentos florestais nativos e estabelecer cenários de arranjo destes fragmentos de forma a maximizar a representatividade ambiental da paisagem e com isso as chances de preservação do mais vasto espectro possível da fauna e flora, tendo em vista a escassez de m...

  15. Diagnóstico da fauna silvestre em empresas florestais brasileiras Diagnosis of wild fauna in brazilian forest companies

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    Giovanna Debortoli Medeiros

    2009-02-01

    Full Text Available Com o objetivo de conhecer a situação atual da fauna silvestre em empresas florestais brasileiras, foram pesquisadas 42 razões sociais, entre Associadas e Co-Participantes da Sociedade de Investigações Florestais (SIF, as quais possuem plantios florestais próprios. As informações foram obtidas com base em questionário enviado às referidas empresas, via correio eletrônico, sendo as respostas obtidas também por esse mecanismo. Entre os vários resultados, destaca-se o fato de que 90,9% das empresas associadas já realizaram levantamentos qualitativos da fauna silvestre. No entanto, de modo geral há notória carência de infra-estrutura nas empresas pesquisadas para atender a trabalhos específicos de manejo e conservação da fauna silvestre.Forty-two companies, associates and co-participants of the Forest Investigation Society (SIF and owners of private forest plantations, were assessed to determine the current situation of wild fauna in Brazilian forest companies. Information was obtained through a questionnaire sent to and received from the companies by e-mail. One of the several results obtained was that 90.9% of the associate companies had already carried out qualitative surveys on wild fauna stands.. On the other hand, in general, there is a total lack of infrastructure in the surveyed companies, to specifically assist in the management and conservation of wild fauna.

  16. Produtos Florestais Não Madeireiros: Importância e Manejo Sustentável da Floresta

    OpenAIRE

    Fiedler, Nilton Cesar; Universidade Federal do Espírito Santo; Soares, Thelma Shirlen; UFVJM-Universidade Federal dos Vales do Jequitinhonha e Mucuri; Silva, Gilson Fernandes da; UFES

    2010-01-01

     A extração de produtos florestais não madeireiros no Brasil tem apresentado, a cada dia, grande importância social, econômica e ambiental, já que atua prioritariamente em pequenas propriedades e preserva parte importante da biodiversidade das florestas nativas. No entanto, as políticas públicas e o desenvolvimento científico devem estar voltados para disponibilizar, a estes projetos de extração, meios que permitam a manutenção de suas atividades sem que haja comprometimento de sua viabilidad...

  17. Caracterização da madeira de quatro espécies florestais

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    Javan Pereira Motta

    2014-12-01

    Full Text Available O conhecimento das relações existentes entre a estrutura anatômica da madeira com suas propriedades físicas ou mecânicas é importante para seu uso adequado. Este trabalho teve como objetivo caracterizar a anatomia microscópica e propriedades físicas da madeira de quatro diferentes espécies florestais. A madeira estudada foi proveniente das seguintes espécies: Cedrela fissilis (Cedro, Híbrido clonal Eucalyptus urophylla × Eucalyptus grandis (Eucalipto urograndis, Hovenia dulcis (Uva do Japão e Gallesia integrifolia (Pau d'alho. Para a determinação da retratibilidade, utilizou-se a norma MB26/40 da ABNT (1940; as dimensões lineares foram obtidas com palmer, precisão de 0,001mm. O estudo da anatomia da madeira seguiu as recomendações da norma de procedimento em estudos de anatomia de madeira, da COPANT (1974 e também da IAWA (1989. Os caracteres anatômicos avaliados foram: diâmetro tangencial (µm e frequência de vasos (nomm-2; comprimento de fibra (µm, diâmetro de lume (µm e espessura de parede de fibra (µm; altura (µm, largura (µm e frequência de raios (nomm-1. Os valores do coeficiente anisotrópico foram de 1,16; 1,77; 1,81 e 1,84 para a madeira de C. fissilis, H. dulcis, Híbrido clonal e G. integrifolia, respectivamente, demonstrando que a madeira de C. fissilis possui elevada estabilidade dimensional e as demais madeiras, valores aceitáveis para esse coeficiente.

  18. Efeito do alumínio sobre o crescimento de duas espécies florestais

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    A. N. Beutler

    2001-12-01

    Full Text Available Para estudar o efeito do Al no crescimento inicial de duas espécies florestais, foi instalado um experimento em novembro de 1998, em solução nutritiva, em casa de vegetação do Departamento de Ciência do Solo da Universidade Federal de Lavras. Após duas semanas em solução nutritiva diluída a 1/3 e sem Al, duas plantas de Moringa (Moringa oleifera e duas de Angico (Anandenantha peregrina foram transplantadas para vasos de 1,5 L e crescidas em solução nutritiva. Os teores de Al utilizados foram de 0,0; 2,5; 5,0; 7,5; e 10,0 mg L-1, com pH 4,0 ± 0,2, ajustado diariamente durante 70 dias. Após este período, foi determinada a altura das plantas, as quais, posteriormente, foram divididas em parte aérea e raiz, para determinação da matéria seca e dos teores de N e P. Os teores crescentes de Al reduziram progressivamente a altura das plantas e a produção de matéria seca das raízes nas duas espécies e da parte aérea no Angico. O teor de nitrogênio na Moringa diminuiu com o incremento nos teores de Al. O teor de fósforo na parte aérea da Moringa e do Angico diminui a partir de 5 mg L-1 de Al na solução nutritiva.

  19. De Novo Glutamine Synthesis

    Science.gov (United States)

    He, Qiao; Shi, Xinchong; Zhang, Linqi; Yi, Chang; Zhang, Xuezhen

    2016-01-01

    Purpose: The aim of this study was to investigate the role of de novo glutamine (Gln) synthesis in the proliferation of C6 glioma cells and its detection with 13N-ammonia. Methods: Chronic Gln-deprived C6 glioma (0.06C6) cells were established. The proliferation rates of C6 and 0.06C6 cells were measured under the conditions of Gln deprivation along with or without the addition of ammonia or glutamine synthetase (GS) inhibitor. 13N-ammonia uptake was assessed in C6 cells by gamma counting and in rats with C6 and 0.06C6 xenografts by micro–positron emission tomography (PET) scanning. The expression of GS in C6 cells and xenografts was assessed by Western blotting and immunohistochemistry, respectively. Results: The Gln-deprived C6 cells showed decreased proliferation ability but had a significant increase in GS expression. Furthermore, we found that low concentration of ammonia was sufficient to maintain the proliferation of Gln-deprived C6 cells, and 13N-ammonia uptake in C6 cells showed Gln-dependent decrease, whereas inhibition of GS markedly reduced the proliferation of C6 cells as well as the uptake of 13N-ammoina. Additionally, microPET/computed tomography exhibited that subcutaneous 0.06C6 xenografts had higher 13N-ammonia uptake and GS expression in contrast to C6 xenografts. Conclusion: De novo Gln synthesis through ammonia–glutamate reaction plays an important role in the proliferation of C6 cells. 13N-ammonia can be a potential metabolic PET tracer for Gln-dependent tumors. PMID:27118759

  20. Fungos micorrízicos arbusculares em diferentes coberturas florestais em Vitória da Conquista, Bahia

    Directory of Open Access Journals (Sweden)

    Renata Soares dos Santos

    Full Text Available Os fungos micorrízicos arbusculares (FMAs são organismos mutualistas obrigatórios, que facilitam a sobrevivência e o desenvolvimento de plantas. São influenciados pela cobertura florestal e por outros fatores bióticos e abióticos. O objetivo deste trabalho foi avaliar a composição e a diversidade dos FMAs em solo sob três diferentes coberturas florestais, em Vitória da Conquista-BA. O plantio de Madeira-nova apresentou maior abundância de esporos que o plantio de Eucalipto. O fragmento de Mata nativa apresentou um grande número de espécies quando comparado com os plantios, sendo seis exclusivas deste local e com potencial de apresentar uma maior diversidade. Os FMAs apresentaram diferenças marcantes de composição e diversidade nas coberturas florestais avaliadas. A grande abundância de esporos e a homogeneidade amostral das espécies no plantio de Madeira-nova são fatores facilitadores para um futuro isolamento de FMAs.

  1. ESTIMATIVA DA BIOMASSA E DO CONTEÚDO DE NUTRIENTES DE UM POVOAMENTO DE Eucalyptus globulus (Labillardière SUB-ESPÉCIE maidenii

    Directory of Open Access Journals (Sweden)

    Mauro Valdir Schumacher

    2000-12-01

    Full Text Available O presente trabalho teve por objetivo estimar a produção de biomassa acima do solo e determinar o conteúdo de nutrientes nos diferentes componentes das árvores de um povoamento de Eucalyptus globulus subespécie maidenii. Os dados foram coletados em um talhão de 4 anos de idade, plantado em solo argiloso, no município de Butiá, Rio Grande do Sul. Para determinar a quantidade de biomassa, foi utilizada uma equação de regressão (lnY = a + b * lnX cujos coeficientes foram calculados com base em nove árvores amostradas em diferentes classes diamétricas. A biomassa total acima do solo foi de 83,2 Mg ha-1, em que 13; 10; 9 e 68 % encontravam-se distribuídos nas folhas, ramos, casca e madeira, respectivamente. Do total dos elementos na árvore, na madeira do tronco foram encontrados 29; 29; 40; 12,5 e 34% de N, P, K, Ca e Mg respectivamente. Já na copa das árvores, esses mesmos elementos representaram 64; 56; 48,5; 32 e 39%. A casca foi o componente que acumulou as maiores quantidades de cálcio, (55,3% do total.

  2. Estimativa do crescimento de povoamentos de Eucalyptus baseada na teoria dos modelos não lineares em multinível de efeito misto.

    Directory of Open Access Journals (Sweden)

    Natalino Calegario

    2010-08-01

    Full Text Available O presente estudo foi baseado na utilização da teoria dos modelos não-lineares de efeito misto em multiníveis para a modelagem do crescimento em altura de povoamentos clonais de Eucalyptus. A base de dados utilizada representa medições de árvores individuais, tomadas em diferentes locais e no tempo, sendo a mesma classificada de longidudinal, irregularmente espaçada, não-balanceada, com autocorrelação e com a presença de heterogeneidade de variância. O modelo logístico de três parâmetros foi utilizado para a estimativa do crescimento em altura. Os parâmetros do modelo foram estimados como de efeitos fixos e aleatórios em dois níveis: unidade amostral (nível 1 e árvore individual dentro das unidades amostrais (nível 2. A inclusão de tais níveis reduziu sensivelmente o erro padrão da estimativa para o modelo. As estimativas também foram melhoradas com a modelagem da heterogeneidade da variância, utilizando estruturas diagonais, e da autocorrelação, com a estrutura ARMA(2,1.

  3. Análise ambiental de fragmentos florestais em assentamentos rurais

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    Stela Maris Alves ASCENÇO

    2003-12-01

    Full Text Available O processo de Reforma Agrária constitui-se em um agente transformador e ao mesmo tempo criador de espaços diferenciados, já que está associado às formas de apropriação e exploração da superfície terrestre. Dessa forma, os assentamentos rurais, produtos desse processo de transformação, tornam-se objetos de estudos da Geografia. Por causa das rápidas e inevitáveis transformações no uso da terra ocorridas nos assentamentos, que conduzem à fragmentação e até à supressão da vegetação natural, o objetivo da presente pesquisa consistiu em identificar e caracterizar ambientalmente os fragmentos florestais de ocorrência natural em áreas de assentamentos rurais, mais especificamente no Projeto de Assentamento Ireno Alves dos Santos, situado nos Municípios de Rio Bonito do Iguaçu e Nova Laranjeiras - PR, no período de 1996 a 2002; tais fragmentos são remanescentes da Floresta Ombrófila Mista e Floresta Estacional Semidecidual, cuja manutenção tornou-se bastante delicada, uma vez que deixaram de fazer parte de uma área florestada maior e passaram a ficar “ilhadas”, cercadas por áreas agrícolas, desencadeando diversas alterações ambientais (efeitos de borda. O objetivo proposto foi atendido mediante a aplicação de metodologia para a identificação e manejo de fragmentos de áreas naturais proposta por PIRES et al. (1998. As tarefas necessárias ao desenvolvimento da metodologia foram operacionalizadas a partir de técnicas de Geoprocessamento e Sensoriamento Remoto, que permitiram a elaboração de mapas temáticos digitais representando a evolução da fragmentação florestal; ao final, foi gerado o mapasíntese da espacialização dos fragmentos florestais. Algumas hipóteses procuraram explicar as causas para as alterações verificadas ao longo dos anos na área do assentamento, tais como: a instalação da empresa madeireira proprietária da área; a construção da Usina Hidrelétrica de Salto Santiago; a

  4. Influência da queima controlada no pH do solo em povoamentos de Pinus spp, na região de Sacramento, MG.

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    João Gomes Neto

    2009-09-01

    Full Text Available Normal 0 21 false false false MicrosoftInternetExplorer4 O objetivo do presente trabalho foi estudar a influência da queima na variação do pH em solo com povoamento de Pinus caribaea Morolet var. hondurensis e Pinus oocarpa Schiedler. A pesquisa desenvolveu-se na região de Sacramento, Minas Gerais, em latossolo vermelho-amarelo, fase argilosa. Foram selecionados 2 talhões (250 x 600 m para cada espécie, demarcados por aceiros e queimados em dois períodos, às 10 e 16 horas, segundo a técnica de queima contra o vento. As áreas experimentais foram divididas em 8 parcelas, por espécie, em um delineamento completamente ao acaso. A coleta dos dados foi feita antes, imediatamente após, 7 meses e 14 meses após a queima em perfis de solo de 0-50 cm, abertos na interseção entre linhas e filas das árvores. Foram coletadas amostras da serrapilheira e de solo a várias profundidades. Verificou-se que após a queima, o pH em cloreto de potássio teve uma ligeira elevação, estabilizando-se até o final do período, em ambas as espécies estudadas. Para o pH em água, houve também uma ligeira elevação após a queima no Pinus oocarpa e um aumento significativo no final do período, para ambas espécies estudadas.

  5. Pesquisa de novos elementos Pesquisa de novos elementos

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    Gil Mário de Macedo Grassi

    1978-11-01

    Full Text Available The present study deals with the discovery of new elements synthesized by man. The introduction discusses in general the theories about nuclear transmutation, which is the method employed in these syntheses. The study shows the importance of the Periodical Table since it is through this table that one can reach a prevision of new elements and its, properties. The discoveries of the transuranic elements, together wich the data of their first preparations are also tabulated The stability of these elements is also discussed, and future speculations are showedNeste trabalho estuda-se, teoricamente, a descoberta de novos elementos sintetizados pelo homem Na introdução apresentamos um apanhado geral sobre as teorias a respeito da transmutação nuclear, que é o método utilizado nestas sínteses. Em seguida, mostramos a importância da Tabela Periódica, pois é através dela que se chega à previsão dos novos elementos e de suas propriedades. As descobertas dos transurânicos, Já realizadas com êxito, juntamente com os dados de suas primeiras preparações são tabelados. A estabilidade destes novos elementos também é discutida, e apresentadas futuras especulações.

  6. Influência do tratamento térmico do resíduo sólido industrial (Grits na resistência mecânica de um latossolo para pavimentos de estradas florestais Influence of the thermal treatment of industrial solid residue (Grits on the mechanical resistance of a latosol for forest engineering roads

    Directory of Open Access Journals (Sweden)

    Carlos Cardoso Machado

    2003-08-01

    Full Text Available Em estudos que envolvem o tratamento de solos com aditivos químicos com fins rodoviários, merecem especial importância aquelas pesquisas orientadas no sentido de descobrir novos meios de torná-los mais econômicos e, ao mesmo tempo, mais resistentes. No presente trabalho, o resíduo sólido industrial Grits, oriundo do processo de fabricação de papel e celulose, foi aplicado a um latossolo denominado ETA, característico da microrregião de Viçosa, Minas Gerais, Brasil, com o intuito de melhorar suas características mecânicas para sua aplicação em pavimentos de estradas florestais. O Grits, após receber tratamento térmico a 200, 300, 400, 500 e 600 ºC, em mufla, foi misturado no teor de 10%, em peso, ao solo anteriormente citado. Parâmetros geotécnicos, característicos dos ensaios de compactação e resistência à compressão simples, foram utilizados para avaliar o efeito do tratamento térmico nas misturas solo+10% Grits. Os resultados indicaram que o Grits tem potencial para estabilização de solos de pavimentos de estradas florestais, sendo o melhor resultado alcançado para o Grits tratado a 600 ºC, pois houve ganhos de resistência mecânica.Road engineering studies involving chemical stabilization of soils deserve special recognition mainly those directed to lowering the costs of forest engineering roads. This work focuses on soil stabilization of a characteristic Latosol from Viçosa, Minas Gerais, Brazil, herein named ETA, using a residue from paper and cellulose industry production, herein called Grits. Grits content of 10% related to soil dry weight was used throughout the study after residue thermal treatment using a furnace at 200, 300, 400, 500 and 600 ºC. Geotechnical standard parameters from compaction and unconfined compression tests were used to evaluate the effect of thermal treatment on the mechanical response of soil-Grits mixtures. Unconfined compression testing data show that Grits is a promising soil

  7. Estimativa de Parâmetros Biofísicos de Povoamentos de Eucalyptus Através de Dados SAR / Estimation of Biophysical Parameters in the Eucalyptus Stands by SAR Data

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    Fábio Furlan Gama

    2006-10-01

    Full Text Available O objetivo deste trabalho foi estabelecer as relações entre os parâmetros dendométricos de florestas e a resposta da radiometria e da interferometria obtidas por sensores SAR (Synthetic Aperture Radar, utilizando técnicas de regressão multivariada. Uma área de povoamento de Eucalyptus grandis, com 6,1 anos de plantio, foi selecionada para estudo. Os resultados indicaram que o volume das parcelas foi altamente correlacionado com o logaritmo da altura interferométrica (LogHint obtida pela diferença entre os modelos interferométricos nas bandas X e P, enquanto que o DAP (Diâmetro à Altura do Peito apresentou melhor relação com a combinação da coerência interferométrica na banda PVV (CohPVV e o LogHint. A altura comercial da vegetação, similarmente ao DAP, foi melhor explicada com a combinação da CohPvv e o LogHint. Os resultados obtidos demonstraram que, devido ao povoamento ser constituído de indivíduos cuja estrutura era predominantemente cilíndrica de orientação vertical, houve uma maior interação com a polarização VV. Os resultados indicaram também que a resposta radiométrica na banda P, de maior comprimento de onda, não foi tão eficaz quanto a interferometria (CohPvv e o LogHint para estimativa dos parâmetros dendométricos estudados, obtendo índices de determinação de 84 a 88% em relação ao inventário florestal das áreas.

  8. Contribuição dos produtos florestais não madeireiros na geração de renda na Floresta Nacional do Tapajós - Pará

    OpenAIRE

    Guerra, Fabiola Gisela Pinto de Queiroz

    2013-01-01

    Esta pesquisa teve como objetivo analisar e contribuição dos Produtos Florestais Não Madeireiros na geração de renda para as comunidades na Floresta Nacional do Tapajós Nela são apresentados os principais produtos florestais não madeireiros comercializados na Flona Tapajós, suas cadeias produtivas, as quantidades extraídas, custos de produção, preços, receitas e margens de lucro. A metodologia utilizada para coleta dos dados junto aos extrativistas e suas associações comunitárias se deu atrav...

  9. A Public Trial De Novo

    DEFF Research Database (Denmark)

    Vedel, Jane Bjørn; Gad, Christopher

    2011-01-01

    This article addresses the concept of “industrial interests” and examines its role in a topical controversy about a large research grant from a private foundation, the Novo Nordisk Foundation, to the University of Copenhagen. The authors suggest that the debate took the form of a “public trial” w.......” The article ends with a discussion of some implications of the analysis, including that policy making, academic research, and public debates might benefit from more detailed accounts of interests and stakes.......This article addresses the concept of “industrial interests” and examines its role in a topical controversy about a large research grant from a private foundation, the Novo Nordisk Foundation, to the University of Copenhagen. The authors suggest that the debate took the form of a “public trial......” where the grant and close(r) intermingling between industry and public research was prosecuted and defended. First, the authors address how the grant was framed in the media. Second, they redescribe the case by introducing new “evidence” that, because of this framing, did not reach “the court...

  10. de novo computational enzyme design.

    Science.gov (United States)

    Zanghellini, Alexandre

    2014-10-01

    Recent advances in systems and synthetic biology as well as metabolic engineering are poised to transform industrial biotechnology by allowing us to design cell factories for the sustainable production of valuable fuels and chemicals. To deliver on their promises, such cell factories, as much as their brick-and-mortar counterparts, will require appropriate catalysts, especially for classes of reactions that are not known to be catalyzed by enzymes in natural organisms. A recently developed methodology, de novo computational enzyme design can be used to create enzymes catalyzing novel reactions. Here we review the different classes of chemical reactions for which active protein catalysts have been designed as well as the results of detailed biochemical and structural characterization studies. We also discuss how combining de novo computational enzyme design with more traditional protein engineering techniques can alleviate the shortcomings of state-of-the-art computational design techniques and create novel enzymes with catalytic proficiencies on par with natural enzymes. Copyright © 2014 Elsevier Ltd. All rights reserved.

  11. Análise da trafegabilidade em estradas florestais utilizando métodos computacionais Analysis of the traffic performance in forest roads using computational methods

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    Robson Jose de Oliveira

    2013-04-01

    Full Text Available As estradas florestais são o principal meio de integração entre as florestas e as empresas. A partir do exposto, percebe-se a necessidade não apenas da correta aplicação de atividades de manutenção, mas também de se determinar o tempo exato para tal intervenção. Partindo desse pressuposto, este trabalho apresenta os resultados da apreciação de dois métodos de classificação da qualidade de estradas não pavimentadas, com o intuito de se verificar a aplicabilidade dos mesmos na caracterização das estradas florestais brasileiras e servir como base para um sistema de gestão das operações de manutenção destas vias. Foram medidos os principais defeitos em estradas florestais seguindo um método denominado de Índice de Condição de Rodovia Não Pavimentada (ICRNP, que serviram de base para gerar um banco de dados para testar a eficiência do uso de redes neurais artificiais (RNA na administração das estradas florestais, minimizando custos e paralisações de tráfego. Concluiu-se que a utilização das redes neurais artificiais apresentou resultados superiores ao método do ICRNP.The forest roads are the main integration mode between forests and companies. Therefore, there is a need for defining not only the required maintenance activities, but also the exact time for such intervention. Starting from this premise this paper presents the results of the assessment of two methods of classification of the quality of unpaved roads in order to verify which one reflects the field reality and thus can serve as the basis for a unpaved road management system. In this paper main defects in forest roads were measured following a method named Unsurfaced Road Condition Index (URCI which served as a database for testing the efficiency of using artificial neural networks (ANN in the management of forest roads taking into account costs minimization and traffic stoppage. It was concluded that the use of artificial neural networks showed

  12. Espécies florestais de restingas como potenciais instrumentos para gestão costeira e tecnologia social em Caravelas, Bahia (Brasil)

    OpenAIRE

    Dias,Henrique Machado; Soares,Mario Luiz Gomes; Neffa,Elza

    2014-01-01

    http://dx.doi.org/10.5902/1980509815732Em Caravelas, município localizado no sul do estado da Bahia, as principais formações vegetais são as florestas de mangue e as restingas apresentando, estas últimas, alto grau de degradação. O objetivo deste artigo consiste em descrever as principais espécies florestais de restingas e seus usos diretos associados, com vistas à recuperação e ao manejo de áreas degradadas e à geração de trabalho e renda, compondo, dessa forma, importante ferramenta para a ...

  13. Espécies florestais de restingas como potenciais instrumentos para gestão costeira e tecnologia social em Caravelas, Bahia (Brasil)

    OpenAIRE

    Dias, Henrique Machado; Soares, Mario Luiz Gomes; Neffa, Elza

    2014-01-01

    Em Caravelas, município localizado no sul do estado da Bahia, as principais formações vegetais são as florestas de mangue e as restingas apresentando, estas últimas, alto grau de degradação. O objetivo deste artigo consiste em descrever as principais espécies florestais de restingas e seus usos diretos associados, com vistas à recuperação e ao manejo de áreas degradadas e à geração de trabalho e renda, compondo, dessa forma, importante ferramenta para a gestão integrada da zona costeira. Para...

  14. Estrutura e armazenamento de água em um Argissolo sob pastagem cultivada, floresta nativa e povoamento de eucalipto no Rio Grande do Sul

    Directory of Open Access Journals (Sweden)

    Luis Eduardo Akiyoshi Sanches Suzuki

    2014-02-01

    Full Text Available Práticas pouco adequadas de manejo têm ocasionado a compactação e a degradação da estrutura do solo. Identificar atributos que melhor representem essas alterações são relevantes na recuperação e na indicação de práticas para evitar danos na estrutura do solo. Objetivou-se avaliar o impacto de diferentes usos em atributos estruturais e hídricos de um Argissolo Vermelho. O estudo foi realizado no município de Butiá, na região fisiográfica da Serra do Sudeste do Estado do Rio Grande do Sul, em um Argissolo Vermelho distrófico. As áreas analisadas corresponderam a: floresta antropizada constituída por espécies arbóreas e arbustivas (Floresta; pastagem com cinco anos de idade, com braquiária brizanta (Brachiaria brizantha consorciada com pensacola (Paspalum lourai e trevo (Trifolium sp. (Pastagem; povoamento de Eucalyptus saligna com 20 anos de idade (Eucalipto 20; e plantio clonal de Eucalyptus saligna conduzido em segunda rotação, com 4,5 anos de idade (Eucalipto 4,5. Avaliaram-se nessas áreas a textura, a condutividade hidráulica, a porosidade, a densidade, o diâmetro médio ponderado de agregados (DMP, a curva de retenção de água, a distribuição do tamanho de poros e o parâmetro S, obtendo-se as seguintes conclusões: até a camada de 0,10 m na Pastagem, e 0,40 m no Eucalipto 4,5, os agregados foram formados pela ação da textura e matéria orgânica e pelo efeito compressivo, decorrente do pisoteio dos bovinos e da colheita do eucalipto. Conforme a profundidade aumentou, ocorreu redução do DMP de agregados, em razão da diminuição da matéria orgânica, e aumento do cascalho, especialmente para as áreas de Pastagem e Eucalipto 4,5, e ao menor efeito da compressão do solo. A textura e a matéria orgânica evidenciaram influência na agregação do solo e, mesmo em pequena proporção, o cascalho reduziu o DMP de agregados, pois sua baixa reatividade e seu maior diâmetro dificultaram a formação de

  15. Avaliação da continuidade espacial de características dendrométricas em diferentes idades de povoamentos clonais de Eucalyptus sp. Evaluation of spatial continuity of dendrometric characteristics of clonal stands of Eucalyptus sp. at different ages

    Directory of Open Access Journals (Sweden)

    Honório Kanegae Junior

    2007-10-01

    Full Text Available O conhecimento da estrutura de continuidade espacial das características dendrométricas pode propiciar um eficiente controle de variação sobre as variáveis que se deseja estimar nos inventários sucessivos. Esse controle pode ser efetivado pelo uso de estratificadores baseados em mapas resultantes da krigagem estatística. Entretanto, o uso da krigagem carece de informações sobre a questão da continuidade espacial das variáveis descritoras dos povoamentos de Eucalyptus sp., assim como o comportamento dessas características no tempo. Este estudo teve como objetivo avaliar a estrutura de continuidade espacial de três características dendrométricas de 23 povoamentos clonais de Eucalyptus sp. em três medições sucessivas, localizados em regiões distintas do Estado de São Paulo. Para cada povoamento, variável e medição, ajustaram-se semivariogramas experimentais pelo método dos Quadrados Mínimos Ponderados. Através do grau de dependência espacial obtido pelos semivariogramas experimentais, avaliou-se o comportamento da continuidade espacial das variáveis. Mais de 70% dos povoamentoss analisados apresentaram de média a forte dependência espacial para volume e 80% para as variáveis área basal e altura dominante. O alcance das variáveis apresentou variações de 300 a 3.000 m, dependendo do povoamento e da idade de medição. O porcentual de povoamentos com forte dependência espacial decresce com a idade, tendendo ao patamar de média dependência espacial, em todas as variáveis analisadas. O grau de dependência espacial ao longo de sucessivas medições variou de povoamento para povoamento e de medições para medições, podendo diminuir ou aumentar com o tempo, indicando que em cada povoamento e medição seja feita uma análise específica da continuidade espacial da variável de interesse.The knowledge on the structure of spatial continuity of dendrometric characteristics can provide an efficient control of

  16. CHUVA DE SEMENTES COMO INDICADORA DO ESTÁDIO DE CONSERVAÇÃO DE FRAGMENTOS FLORESTAIS EM SOROCABA - SP

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    Fatima Conceição Márquez Piña-Rodrigues

    2014-12-01

    Full Text Available O objetivo do estudo foi analisar o nível de degradação de fragmentos florestais a partir do uso da chuva de sementes como indicador ambiental. Fragmentos (n= 5 de Floresta Estacional Semidecidual na região de Sorocaba - SP foram estudados de agosto a outubro de 2007 e janeiro a dezembro de 2008, utilizando-se coletores instalados em 11 parcelas (10 x 10 m. Do material coletado foram separadas as frações de sementes e frutos para identificação e classificação por síndrome de dispersão e hábito. Os resultados demonstraram que, embora os fragmentos F4 e F5 apresentem os maiores índices de riqueza, diversidade e equitabilidade, há a dominância de espécies anemocóricas e herbáceas. Os fragmentos F1, F2 e F4 foram os com maior aporte de sementes, respectivamente com 36,8%, 26,8% e 17,8% e os fragmentos F3 e F5, apenas 12,6% e 5,9%. O aporte de propágulos foi sazonal sendo maior na transição da estação seca para a úmida, o que resulta em 63% do total de propágulos aportados. A síndrome com maior representatividade foi a anemocoria (86%, comum em áreas abertas e degradadas. Os resultados obtidos indicam a viabilidade da aplicação do estudo quantitativo da chuva de sementes para o monitoramento da restauração de fragmentos, tendo sido eficiente em detectar diferenças ambientais entre os fragmentos.  

  17. Unidades de colheita: estratégia para evitar a compactação dos solos florestais

    Directory of Open Access Journals (Sweden)

    Gilson A. Milde

    2010-12-01

    Full Text Available Solos com umidade ótima de compactação menor que a capacidade de campo e solos com má drenagem são mais propensos a serem compactados nas operações de exploração florestal. O conhecimento dessas variáveis permite classificar os solos quanto à sua suscetibilidade à compactação, no entanto essas determinações demandam tempo, recursos e equipamentos específicos. Utilizando 13 solos florestais com ampla variação textural, das fazendas Ariona e Santa Rosa pertencentes à Cia. Suzano de Papel e Celulose, situadas no Estado de São Paulo, desenvolveu-se um índice, denominado diâmetro médio ponderado de partículas, que permitiu estimar a umidade ótima de compactação, a capacidade de campo e o limite líquido baseado apenas na distribuição de tamanho de partículas. Com base nessas características físicas e no consumo médio diário de água de um plantio de eucalipto, foram estabelecidas unidades de colheita a partir do número de dias de repouso necessários para o teor de água de um solo ficar abaixo da umidade ótima de compactação. Tais unidades agrupam solos que precisam do mesmo número de dias após uma chuva (0 a 10 dias para poderem ser explorados, visando diminuir o impacto da colheita florestal e, em consequência, evitar a necessidade de preparo do solo para diminuir a compactação provocada por essas operações.

  18. UniNovo: a universal tool for de novo peptide sequencing.

    Science.gov (United States)

    Jeong, Kyowon; Kim, Sangtae; Pevzner, Pavel A

    2013-08-15

    Mass spectrometry (MS) instruments and experimental protocols are rapidly advancing, but de novo peptide sequencing algorithms to analyze tandem mass (MS/MS) spectra are lagging behind. Although existing de novo sequencing tools perform well on certain types of spectra [e.g. Collision Induced Dissociation (CID) spectra of tryptic peptides], their performance often deteriorates on other types of spectra, such as Electron Transfer Dissociation (ETD), Higher-energy Collisional Dissociation (HCD) spectra or spectra of non-tryptic digests. Thus, rather than developing a new algorithm for each type of spectra, we develop a universal de novo sequencing algorithm called UniNovo that works well for all types of spectra or even for spectral pairs (e.g. CID/ETD spectral pairs). UniNovo uses an improved scoring function that captures the dependences between different ion types, where such dependencies are learned automatically using a modified offset frequency function. The performance of UniNovo is compared with PepNovo+, PEAKS and pNovo using various types of spectra. The results show that the performance of UniNovo is superior to other tools for ETD spectra and superior or comparable with others for CID and HCD spectra. UniNovo also estimates the probability that each reported reconstruction is correct, using simple statistics that are readily obtained from a small training dataset. We demonstrate that the estimation is accurate for all tested types of spectra (including CID, HCD, ETD, CID/ETD and HCD/ETD spectra of trypsin, LysC or AspN digested peptides). UniNovo is implemented in JAVA and tested on Windows, Ubuntu and OS X machines. UniNovo is available at http://proteomics.ucsd.edu/Software/UniNovo.html along with the manual.

  19. Riqueza de formigas (Hymenoptera, Formicidae epigéicas em povoamentos de Eucalyptus spp. (Myrtaceae de diferentes idades no Rio Grande do Sul, Brasil Richness of epigaeic ants (Hymenoptera, Formicidae in Eucalyptus spp. plantations with different ages in Rio Grande do Sul, Brazil

    Directory of Open Access Journals (Sweden)

    Ricardo Carvalho Fonseca

    2004-03-01

    Full Text Available Este estudo descreve as comunidades de formigas de solo em povoamentos de eucalipto implantados em ecossistema de restinga no Rio Grande do Sul. As coletas de formigas foram feitas em seis povoamentos de Eucalyptus grandis Hill ex Maiden e de Eucalyptus saligna Smith com idades de 31, 19, sete e cinco anos. Para as coletas de formigas, foram selecionados ao acaso 24 talhões, quatro por povoamento. Em cada talhão, foram traçados três transectos com 100 m de comprimento, afastados entre si 12 m. Ao longo dos transectos, foram enterradas 30 armadilhas, tipo pitfall, com iscas de sardinha, afastadas entre si 10 m e mantidas por 24 horas. Foi coletado um total de 21.033 formigas pertencentes a cinco subfamílias, 12 tribos, 19 gêneros e 49 espécies. De acordo com o estimador de riqueza jackknife de primeira ordem, não houve diferenças significativas entre as riquezas das comunidades de formigas considerando as espécies de eucalipto (U = 81,500; g.l.=1; P=0,582 e as idades dos povoamentos (U=2,504; g.l.=3; P=0,547. Os resultados indicam que a riqueza de espécies de formigas não está relacionada à espécie de eucalipto e/ou à idade do povoamento implantado na restinga.The present study describes the epigaeic ant communities in eucalyptus plantations in sandbank in Rio Grande do Sul State. Ant collections were performed in six plantations of Eucalyptus grandis Hill ex Maiden and Eucalyptus saligna Smith with ages varying between five to 31 years old. A total of 24 areas (four/area were randomly selected for ant collections. In each one, three transects of 100 m were designed at intervals of 12 m. Along each transect, ten pitfall traps with sardine baits were placed, at intervals of 10 m for a 24-hour-period. A total of 21,033 ants were collected, belonging to five subfamilies, 12 tribes, 19 genera and 49 species. According to the jackknife estimator of first order, there was no significant difference between the ant communities richness

  20. Variabilidade genética de Eugenia uniflora L. em remanescentes florestais em diferentes estádios sucessionais

    Directory of Open Access Journals (Sweden)

    Roberto Valmorbida Aguiar

    2013-04-01

    Full Text Available A compreensão da diversidade genética fornece elementos básicos sobre a dinâmica e funcionamento de populações, auxiliando na conservação e uso sustentável das espécies. Supõe-se que populações sucessionais precoces poderiam ser geneticamente mais diferenciadas do que populações sucessionais mais tardias. Visando testar esta hipótese, o presente trabalho teve como objetivo analisar a variabilidade genética de populações de Eugenia uniflora L. em manchas florestais em diferentes estádios sucessionais. Foram selecionadas duas áreas em diferentes estádios de sucessão, sendo a primeira em estádio inicial e a segunda em estádio avançado. A área de estudo apresenta um remanescente florestal em transição de Floresta Ombrófila Mista e Floresta Estacional Semidecídua. Por meio da técnica de RAPD (Random Amplified Polymorphic DNA e análise multivariada, a diversidade gênica esperada e a porcentagem de loci polimórficos foram estimadas, além da similaridade genética entre as populações de cada mancha florestal e a diversidade de cada área por meio do índice de diversidade de Simpson. Os resultados indicaram 79% de loci polimórficos para a área em estádio avançado e 70% para a área em estádio inicial de sucessão. A similaridade genética entre pares de indivíduos variou entre 0,55 e 0,86 na área em estádio inicial de sucessão e entre 0,45 e 0,78 para a área em estádio avançado. Não houve diferenças significativas entre a diversidade das duas áreas (P = 89. Um escalonamento multidimensional não-métrico indicou menor distância genética entre os indivíduos da área em estádio inicial. Da mesma forma, uma análise de similaridade - ANOSIM indicou separação entre os indivíduos das duas áreas.

  1. Alterações edáficas sob plantios puros e misto de espécies florestais nativas do sudeste da Bahia, Brasil

    Directory of Open Access Journals (Sweden)

    A. C. Gama-Rodrigues

    1999-09-01

    Full Text Available O objetivo deste trabalho foi relacionar o acúmulo de serapilheira com sua composição química e desta com as características físicas e químicas do solo, em plantios puros e misto de espécies florestais nativas. O trabalho foi desenvolvido em solos de tabuleiro do sudeste da Bahia, Brasil, no período de agosto de 1994 a novembro de 1996, em plantios, com 22 anos de idade, de pau-roxo (Peltogyne angustiflora, putumuju (Centrolobium robustum, arapati (Arapatiella psilophylla, arapaçu (Sclerolobium chrysophyllum, claraíba (Cordia trichotoma e óleo-comumbá (Macrolobium latifolium . Foram utilizadas uma floresta secundária, praticamente em estado clímax, e uma capoeira, de 40 anos de idade. O solo na camada de 0-5 cm estava mais bem estruturado no plantio misto do que sob as outras coberturas vegetais. A estruturação dessa camada foi positivamente relacionada com o acúmulo de C orgânico no solo e de serapilheira sobre este. O nível de fertilidade do solo (0-10 cm sob as espécies implantadas nos sistemas puros e misto foi superior ao da capoeira e da floresta natural. A fitomassa e a qualidade nutricional da serapilheira revelaram a capacidade diferenciada das coberturas florestais para absorver e reciclar nutrientes; o plantio misto representou uma situação intermediária em relação ao sistema de plantios puros. A quantidade de serapilheira acumulada dependeu da sua composição química. Segundo resultados deste trabalho, a estruturação e o nível de fertilidade do solo distinguiram-se de acordo com as coberturas florestais, em razão da quantidade, da composição química e da taxa de decomposição da serapilheira. As espécies claraíba, arapaçu e pau-roxo revelaram-se promissoras em melhorar a fertilidade do solo. Contudo, o plantio misto mostrou ser o sistema florestal mais adequado, por proporcionar simultaneamente melhor estruturação, maior quantidade de C orgânico, maiores níveis de nutrientes do solo e

  2. Fitoseídeos (Acari: Phytoseiidae associados a cafezais e fragmentos florestais vizinhos Phytoseiids (Acari: Phytoseiidae associated to coffee plantations and adjacent forest fragments

    Directory of Open Access Journals (Sweden)

    Ester Azevedo Silva

    2010-10-01

    Full Text Available Existem poucas informações sobre a fauna de ácaros predadores (Phytoseiidae em ambientes naturais brasileiros adjacentes a agroecossistemas cafeeiros (Coffea spp. ou sobre a influência que essa vegetação exerce como reservatório de ácaros predadores. Neste estudo, objetivou-se avaliar a diversidade destes organismos em cafeeiros e fragmentos florestais adjacentes. Coletaram-se amostras das espécies Calyptranthes clusiifolia (Miq. O. Berg (Myrtaceae, Esenbeckia febrifuga (A. St.-Hil. A. Juss. ex Mart. (Rutaceae, Metrodorea stipularis Mart. (Rutaceae e Allophylus semidentatus (Miq. Radlk. (Sapindaceae, em oito fragmentos florestais, de 5 a 51 ha, e cafezais adjacentes, nos meses de junho (final período chuvoso e outubro (final período seco nos anos 2004 e 2005, na região Sul do Estado de Minas Gerais. Ácaros foram extraídos das folhas, utilizando o método de lavagem e, em seguida, montados em lâminas de microscopia em meio de Hoyer, para identificação específica. No total foram identificados 2.348 fitoseídeos, sendo 2.090 nos fragmentos florestais e 258 espécimes nos cafezais adjacentes, pertencentes a 38 espécies. Servindo-se de análise faunística, a espécie Iphiseiodes zuluagai Denmark & Muma, 1972 apresentou os melhores índices no agroecossistema cafeeiro, sendo muito frequente e constante nas épocas estudadas. Nos fragmentos florestais Amblyseius herbicolus Chant, 1959, Iphiseiodes affs. neonobilis Denmark & Muma, 1978, Leonseius regularis DeLeon, 1965 e Euseius alatus DeLeon, 1966 foram dominantes, muito abundantes, muito frequentes e constantes nas épocas estudadas. Podemos concluir que a vegetação nativa abriga ácaros predadores, inimigos naturais de ácaros-praga, que ocorrem na cultura cafeeira, possibilitando o desenvolvimento de programas de manejo ecológico com áreas de vegetação natural e agroecossistemas cafeeiros adjacentes.There is little information about the fauna of predatory mites

  3. de novo'' aneurysms following endovascular procedures

    International Nuclear Information System (INIS)

    Briganti, F.; Cirillo, S.; Caranci, F.; Esposito, F.; Maiuri, F.

    2002-01-01

    Two personal cases of ''de novo'' aneurysms of the anterior communicating artery (ACoA) occurring 9 and 4 years, respectively, after endovascular carotid occlusion are described. A review of the 30 reported cases (including our own two) of ''de novo'' aneurysms after occlusion of the major cerebral vessels has shown some features, including a rather long time interval after the endovascular procedure of up to 20-25 years (average 9.6 years), a preferential ACoA (36.3%) and internal carotid artery-posterior communicating artery (ICA-PCoA) (33.3%) location of the ''de novo'' aneurysms, and a 10% rate of multiple aneurysms. These data are compared with those of the group of reported spontaneous ''de novo'' aneurysms after SAH or previous aneurysm clipping. We agree that the frequency of ''de novo'' aneurysms after major-vessel occlusion (two among ten procedures in our series, or 20%) is higher than commonly reported (0 to 11%). For this reason, we suggest that patients who have been submitted to endovascular major-vessel occlusion be followed up for up to 20-25 years after the procedure, using non-invasive imaging studies such as MR angiography and high-resolution CT angiography. On the other hand, periodic digital angiography has a questionable risk-benefit ratio; it may be used when a ''de novo'' aneurysm is detected or suspected on non-invasive studies. The progressive enlargement of the ACoA after carotid occlusion, as described in our case 1, must be considered a radiological finding of risk for ''de novo'' aneurysm formation. (orig.)

  4. Viabilidade técnica dos taninos de quatro espécies florestais de ocorrência no semi-árido brasileiro no curtimento de peles.

    Directory of Open Access Journals (Sweden)

    Juarez Benigno Paes

    2010-08-01

    Full Text Available Os taninos vegetais são encontrados em várias espécies florestais. Atualmente, os curtidores da Região Nordeste têm no angico-vermelho (Anadenanthera colubrina var. cebil, sua única fonte de taninos. Este estudo teve como objetivos avaliar o potencial tanífero e a capacidade curtente dos taninos, por meios das características físico-mecânicas das peles curtidas, de quatro espécies florestais de ocorrência no Semi-Árido brasileiro, visando a possibilitar a diversificação de espécies a serem utilizadas nos curtumes da região. Os taninos foram obtidos de angico (Anadenanthera colubrina var. cebil, cajueiro (Anacardium occidentale, jurema-preta (Mimosa tenuiflora e de jurema-vermelha (Mimosa arenosa. Peles de caprinos foram curtidas com os taninos extraídos dessas espécies e comparadas a peles curtidas com tanino comercial de acácia negra ("Seta Natur". Amostras de peles curtidas foram submetidas a testes de resistência à tração, ao alongamento e ao rasgamento progressivo. Verificaram-se bons resultados das peles curtidas com os taninos obtidos de jurema-preta e jurema-vermelha. Pela abundância no Semi-Árido brasileiro, a jurema-preta e a jurema-vermelha apresentam potencial de exploração para obtenção de taninos, havendo a necessidade pesquisas que indiquem as melhores formas de aplicação dos taninos obtidos.

  5. VIABILIDADE TÉCNICA DOS TANINOS DE QUATRO ESPÉCIES FLORESTAIS DE OCORRÊNCIA NO SEMI-ÁRIDO BRASILEIRO NO CURTIMENTO DE PELES

    Directory of Open Access Journals (Sweden)

    Juarez Benigno Paes

    2006-08-01

    Full Text Available Os taninos vegetais são encontrados em várias espécies florestais. Atualmente, os curtidores da Região Nordeste têm no angico-vermelho (Anadenanthera colubrina var. cebil, sua única fonte de taninos. Este estudo teve como objetivos avaliar o potencial tanífero e a capacidade curtente dos taninos, por meios das características físico-mecânicas das peles curtidas, de quatro espécies florestais de ocorrência no Semi-Árido brasileiro, visando a possibilitar a diversificação de espécies a serem utilizadas nos curtumes da região. Os taninos foram obtidos de angico (Anadenanthera colubrina var. cebil, cajueiro (Anacardium occidentale, jurema-preta (Mimosa tenuiflora e de jurema-vermelha (Mimosa arenosa. Peles de caprinos foram curtidas com os taninos extraídos dessas espécies e comparadas a peles curtidas com tanino comercial de acácia negra (”Seta Natur”. Amostras de peles curtidas foram submetidas a testes de resistência à tração, ao alongamento e ao rasgamento progressivo. Verificaram-se bons resultados das peles curtidas com os taninos obtidos de jurema-preta e jurema-vermelha. Pela abundância no Semi-Árido brasileiro, a jurema-preta e a jurema-vermelha apresentam potencial de exploração para obtenção de taninos, havendo a necessidade pesquisas que indiquem as melhores formas de aplicação dos taninos obtidos.

  6. Soluções de redução de consumo energético para redes de sensores sem fio (RSSFs aplicadas à ambientes florestais

    Directory of Open Access Journals (Sweden)

    Paulo César Sedrez Moncks

    2016-07-01

    Full Text Available Redes de sensores sem fio (RSSFs têm sido utilizadas para aplicações de monitoramento nos mais diversos cenários, como controle industrial, gerenciamento de tráfego, segurança pública, automação residencial, saúde e também monitoramento ambiental. Estas redes são compostas de sensores com restrição de recursos onde a eficiência energética é parte essencial para sua real aplicabilidade. É apresentada neste artigo a sistematização feita das características de três técnicas para redução do consumo energético das redes de sensores sem fio, e como principal objetivo desta sistematização espera-se fornecer elementos para avaliar a aplicabilidade de RSSFs nas tarefas de predição de risco e monitoramento de incêndios florestais. Foi possível concluir que o uso de RSSFs aplicadas a ambientes florestais ainda é uma frente de pesquisa em aberto, sobretudo no que se refere à durabilidade da vida útil da rede. Ainda que as técnicas de redução de consumo energético propostas nos trabalhos avaliados apresentem ganhos, é necessário aprofundar as pesquisas para alcançar um tempo maior de duração das baterias e com isso tornar viável a instalação de nodos em florestas.

  7. Initial Development of Tree Species in Silvopastoral System in Southern Brazil Desenvolvimento Inicial de Espécies Florestais em Sistema Silvipastoril na Região Sudeste

    Directory of Open Access Journals (Sweden)

    Maria Luiza Franceschi Nicodemo

    2010-02-01

    Full Text Available The selection of adapted tree species is fundamental for the success of silvopastoral systems. The present study aimed to evaluate the initial development of native trees seedlings planted on pastureland chosen by their economic value and nitrogen retrieval. The seedlings were planted in strips containing three lines. Between each strip there was an area of 15 m with pasture. From the measurements of tree height, diameter at the base, damage by insects or by diseases, it was reported the best performances for canafístula (Peltophorum dubium, pau-jacaré (Piptadenia gonoacantha, mutambo (Guazuma ulmifolia and capixingui (Croton floribundus. Ipê-felpudo (Zeyheria tuberculosa showed the worst performance of all under the conditions evaluated. Survival rate in eleven months for pau-jacaré was under 50%.

    A seleção de espécies florestais adequadas é de fundamental importância para o sucesso dos sistemas silvipastoris. O objetivo deste trabalho foi avaliar o desenvolvimento inicial de espécies florestais nativas escolhidas pelo valor econômico e aporte de nitrogênio, plantadas em pastagem. Mudas foram plantadas em faixas com três linhas de árvores. As áreas de 15 m entre as faixas de árvores eram ocupadas por pastagem. A partir da avaliação de crescimento em altura, em diâmetro da base, danos por insetos ou por doenças, registrou-se melhor desempenho inicial de canafístula (Peltophorum dubium, pau-jacaré (Piptadenia gonoacantha, mutambo (Guazuma ulmifolia e capixingui (Croton floribundus. O ipê-felpudo (Zeyheria tuberculosa teve o pior desempenho nas condições estudadas. A taxa de sobrevivência em onze meses do pau-jacaré foi inferior a 50%.

     

    doi: 10.4336/2009.pfb.60.89

  8. CARACTERIZAÇÃO E SUSCEPTIBILIDADE ECOLÓGICA DOS FRAGMENTOS FLORESTAIS NAS BACIAS DO RIBEIRÃO DOURADINHO E RIBEIRÃO ESTIVA - MINAS GERAIS

    Directory of Open Access Journals (Sweden)

    Josimar dos Reis de Souza

    2014-09-01

    Full Text Available Os fragmentos florestais estão sujeitos ao fenômeno conhecido como Efeito de Borda, que afeta a função ecológica dessas áreas em relação ao tamanho, formato do fragmento, matriz ao entorno e manejo das áreas de borda. Desse modo, este trabalho teve como principal objetivo discutir o grau de susceptibilidade ecológica dos fragmentos florestais das bacias do Ribeirão Douradinho e Estiva em Minas Gerais. O uso das imagens RapidEye permitiram o mapeamento das unidades de fragmentos existentes nas bacias. Sob a perspectiva da Ecometria da Paisagem, foram analisados para cada fragmento os índices: área, densidade, tamanho, borda, forma, proximidade entre os fragmentos e área central. Como conclusão do trabalho, verificou-se que o nível de fragmentação florestal é elevado, com 273 unidades, somando 76,35 km², menos de 1% da área das bacias. Os fragmentos foram agrupados em: muito pequeno 5 e 10 e 100 ha, com 15 unidades (5,5%. No geral, os fragmentos inclusos nas categorias muito pequeno e pequeno não possuem área sem influência do efeito de borda, o que dificulta a preservação da biodiversidade destes ecossistemas, ou seja, áreas susceptíveis a perda ecológica. O Ribeirão Panga, afluente do Ribeirão Douradinho, é o que possui maior índice de densidade e proximidade da distribuição dos fragmentos analisados. É também onde está localizada a Reserva de Preservação Permanente (RPPN da Universidade Federal de Uberlândia, que apresentou o maior índice de circularidade.

  9. USO DAS CARACTERÍSTICAS TECNOLÓGICAS DA MADEIRA PARA O AGRUPAMENTO DE ESPÉCIES FLORESTAIS

    Directory of Open Access Journals (Sweden)

    Rafael Rodolfo Melo

    2013-11-01

    Full Text Available O trabalho teve como objetivos determinar as propriedades físicas e mecânicas da madeira de 30 espécies florestais oriundas do  Estado do  Rio Grande do Sul e avaliar as inter-relações destas propriedades  e a similaridade entre as espécies. Quanto  às  propriedades físicas  avaliaram-se  a massa específica, os coeficientes de retratibilidade linear  nos sentidos radial e tangencial  e, o coeficiente de retratibilidade volumétrico. Para as propriedades mecânicas foram realizados os ensaios de flexão estática (madeira  saturada  e  a 12% de umidade, compressão paralela às fibras (madeira  saturada e a 12% de umidade, tração perpendicular, cisalhamento, fendilhamento, dureza Janka e flexão dinâmica. Todos os ensaios foram conduzidos seguindo a norma brasileira de estruturas de madeira. A melhor estabilidade dimensional foi observada para  as espécies leiteiro (Sapium glandulosum e timbaúva (Enterolobiumn contortisiliquum. Já  a  maior resistência  mecânica  foi obtida pelo pessegueiro-bravo (Prunus subcoriacea e maria-preta (Diospyros inconstans. Na análise de inter-relações entre as propriedades, a massa específica foi a que teve o maior número de correlações significativas. A análise de Cluster foi uma ferramenta eficaz para o agrupamento das madeiras considerando suas similaridades.Palavra-chave: tecnologia da madeira, propriedades físico-mecânicas, qualidade da madeira.GROUPING OF FOREST SPECIES BY TECHNOLOGICAL CHARACTERISTICS OF WOODS ABSTRACTThis work aimed to evaluate the  physical and mechanical properties  of 30 Southern-Brazilian woods, interrelationships and similarity of these properties. For the physical properties were evaluated the basic density and shrinkages (radial, tangential and volumetric. For the mechanical properties were evaluated the static  bending, parallel compression, perpendicular traction, shear, splitting,  Janka hardness and dynamic bending. These tests were

  10. Estádio sucessional e fatores geográficos como determinantes da similaridade florística entre comunidades florestais no Planalto Atlântico, Estado de São Paulo, Brasil

    OpenAIRE

    Durigan,Giselda; Bernacci,Luís Carlos; Franco,Geraldo Antonio Daher Correa; Arbocz,Géza de Faria; Metzger,Jean Paul; Catharino,Eduardo Luís Martins

    2008-01-01

    A análise das relações de similaridade florística entre comunidades geralmente conduz ao estabelecimento de padrões, condicionados por fatores diversos que determinam a ocorrência ou não das espécies em diferentes locais. Em busca de tais padrões, foram analisadas as relações de similaridade florística entre comunidades florestais localizadas na região do Planalto de Ibiúna, estado de São Paulo, Brasil. Incluíram-se na análise 21 fragmentos florestais e seis sítios em uma Reserva Florestal co...

  11. DeNovoGUI: an open source graphical user interface for de novo sequencing of tandem mass spectra.

    Science.gov (United States)

    Muth, Thilo; Weilnböck, Lisa; Rapp, Erdmann; Huber, Christian G; Martens, Lennart; Vaudel, Marc; Barsnes, Harald

    2014-02-07

    De novo sequencing is a popular technique in proteomics for identifying peptides from tandem mass spectra without having to rely on a protein sequence database. Despite the strong potential of de novo sequencing algorithms, their adoption threshold remains quite high. We here present a user-friendly and lightweight graphical user interface called DeNovoGUI for running parallelized versions of the freely available de novo sequencing software PepNovo+, greatly simplifying the use of de novo sequencing in proteomics. Our platform-independent software is freely available under the permissible Apache2 open source license. Source code, binaries, and additional documentation are available at http://denovogui.googlecode.com .

  12. Modular Engineering Concept at Novo Nordisk Engineering

    DEFF Research Database (Denmark)

    Moelgaard, Gert; Miller, Thomas Dedenroth

    1997-01-01

    This report describes the concept of a new engineering method at Novo Nordisk Engineering: Modular Engineering (ME). Three tools are designed to support project phases with different levels of detailing and abstraction. ME supports a standard, cross-functional breakdown of projects that facilitates...

  13. Volumetric models for tropical pine in pure stand in Rondônia State, Brazil Modelos volumétricos para Pinus tropicais, em povoamento homogêneo, no Estado de Rondônia

    Directory of Open Access Journals (Sweden)

    Allan Libanio Pelissari

    2011-09-01

    Full Text Available

    This study aimed to adjust volumetric models to tropical pines, in pure stand, in the municipality of Vilhena, Rondonia State.  The data came from 20 felled trees of Pinus caribaea var.  hondurensis and 10 Pinus tecunumanii trees with discs collected at fixed positions of 0.20 m, 0.70 m, 1.30 m and in distances of one meter along the stem, for later counting and measurement of the growth rings at ages from 4 to 12 years. Eight volumetric models were adjusted. The selection criteria used were: standard error of estimate, adjusted coefficient of  determination, F test, significance of regression coefficients,  mean deviation, standard deviation of the differences, sum of square of the relative residual, percentage of the residuals and graphic analysis of residuals. The models from Näslund  modified and from Spurr presented, respectively, best fit to estimate the volume for Pinus caribaea var. hondurensis submitted to the first thinning and for Pinus tecunumanii, with  ages between 4 and 12 years, in Vilhena, Rondonia State, Brazil.

    doi: 10.4336/2011.pfb.31.67.173

    Este trabalho teve como objetivo ajustar modelos volumétricos para Pinus tropicais, em povoamento homogêneo, no Município  de Vilhena, RO. Para a coleta de dados, foram derrubadas 20  árvores de Pinus caribaea var. hondurensis e 10 de Pinus  tecunumanii, sendo coletados discos em posições fixas de 0,20  m; 0,70 m; 1,30 m e em distâncias de um metro ao longo do  fuste, para a posterior contagem e mensuração dos anéis de crescimento nas idades de 4 a 12 anos. Foram ajustados oito modelos volumétricos e o critério de seleção considerou os  resultados do erro padrão da estimativa, coeficiente de determinação ajustado, teste F, significância dos coeficientes de regressão, desvio médio, desvio-padrão das diferenças, soma de quadrados do resíduo relativo, resíduo percentual

  14. Ecologia da paisagem de remanescentes florestais na bacia hidrográfica do Ribeirão das Pedras - Campinas -SP

    Directory of Open Access Journals (Sweden)

    Thiago Luiz Etto

    2013-12-01

    Full Text Available A fragmentação dos extratos florestais e o uso de terras, muitas vezes sem os cuidados necessários para mitigação dos impactos decorrentes das atividades antrópicas, geram ecossistemas fragilizados por fenômenos como o efeito de borda, ou seja, alterações localizadas nas áreas de contato entre a matriz antropizada e o remanescente florestal. Nesse contexto, este trabalho teve por objetivo estudar a fragilidade dos fragmentos encontrados na Bacia Hidrográfica do Ribeirão das Pedras, no Município de Campinas, SP, Brasil, utilizando técnicas de geoprocessamento. Com a base cartográfica do município, avaliaram-se o tamanho do fragmento e a tendência de formato alongado ou circular. Com base em dados cartográficos de 1962, 1972 e 2006, observou-se o declínio quantitativo e qualitativo dos fragmentos. Devido ao processo de urbanização não planejada do município, os fragmentos de menor área foram desmatados. Estes, apesar de não terem capacidade ecológica para sustentar níveis tróficos mais elevados, servem como "trampolins ecológicos", contribuindo para o fluxo biológico. De maneira análoga, os remanescentes maiores também foram desmatados e sua área, reduzida. De maneira geral, o formato dos fragmentos passou a tender para o formato alongado, o que sugere maior contato entre os remanescentes e a matriz antrópica, aumentando, assim, a vulnerabilidade dos fragmentos. Destaca-se o caso do remanescente de Cerrado encontrado no extremo nordeste da bacia que possui tendência de formato alongado (IC = 0,62 e área reduzida (0,38 ha, mostrando-se, assim, muito vulnerável às pressões antrópicas. Assim, conclui-se que os fragmentos florestais da bacia hidrográfica estudada estão altamente vulneráveis.

  15. ESPÉCIES FLORESTAIS DE RESTINGAS COMO POTENCIAIS INSTRUMENTOS PARA GESTÃO COSTEIRA E TECNOLOGIA SOCIAL EM CARAVELAS, BAHIA (BRASIL

    Directory of Open Access Journals (Sweden)

    Henrique Machado Dias

    2014-09-01

    Full Text Available http://dx.doi.org/10.5902/1980509815732Em Caravelas, município localizado no sul do estado da Bahia, as principais formações vegetais são as florestas de mangue e as restingas apresentando, estas últimas, alto grau de degradação. O objetivo deste artigo consiste em descrever as principais espécies florestais de restingas e seus usos diretos associados, com vistas à recuperação e ao manejo de áreas degradadas e à geração de trabalho e renda, compondo, dessa forma, importante ferramenta para a gestão integrada da zona costeira. Para isso, a elaboração de listagens florísticas e visitas ao campo foram necessárias para reconhecimento do ambiente. Na seleção das espécies, uma literatura referente ao uso, manejo e valor agregado de cada uma das espécies identificadas foi utilizada e, a partir daí, foram reconhecidas quatro espécies com potencialidade para geração de trabalho e renda nos moldes dessa proposta: mangaba (Hancornia speciosa, pitanga (Eugenia uniflora, caju (Anacardium occidentale e aroeira (Schinus terebinthifolius. As três primeiras apresentam associação de seus frutos ao uso alimentar, servindo a aroeira como condimentação, com alta valorização no mercado mundial, e o caju, a partir da sua estrutura fértil (castanha e polpa. A identificação dos subprodutos vegetais fornecidos assegura a utilização sustentada das espécies e do ambiente e os Produtos Florestais Não Madeiráveis podem ser estratégicos no gerenciamento costeiro, tornando-se instrumento para se alcançar inclusão social através da geração de trabalho e renda, sob o movimento da Tecnologia Social, contribuindo, portanto, para a redução da vulnerabilidade social de comunidades costeiras tradicionais.

  16. Extreme-Scale De Novo Genome Assembly

    Energy Technology Data Exchange (ETDEWEB)

    Georganas, Evangelos [Intel Corporation, Santa Clara, CA (United States); Hofmeyr, Steven [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Joint Genome Inst.; Egan, Rob [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Computational Research Division; Buluc, Aydin [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Joint Genome Inst.; Oliker, Leonid [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Joint Genome Inst.; Rokhsar, Daniel [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Computational Research Division; Yelick, Katherine [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Joint Genome Inst.

    2017-09-26

    De novo whole genome assembly reconstructs genomic sequence from short, overlapping, and potentially erroneous DNA segments and is one of the most important computations in modern genomics. This work presents HipMER, a high-quality end-to-end de novo assembler designed for extreme scale analysis, via efficient parallelization of the Meraculous code. Genome assembly software has many components, each of which stresses different components of a computer system. This chapter explains the computational challenges involved in each step of the HipMer pipeline, the key distributed data structures, and communication costs in detail. We present performance results of assembling the human genome and the large hexaploid wheat genome on large supercomputers up to tens of thousands of cores.

  17. Wegener's granulomatosis occurring de novo during pregnancy.

    Science.gov (United States)

    Alfhaily, F; Watts, R; Leather, A

    2009-01-01

    Wegener's granulomatosis (WG) is rarely diagnosed during the reproductive years and uncommonly manifests for the first time during pregnancy. We report a case of de novo WG presenting at 30 weeks gestation with classical symptoms of WG (ENT, pulmonary). The diagnosis was confirmed by radiological, laboratory, and histological investigations. With a multidisciplinary approach, she had a successful vaginal delivery of a healthy baby. She was treated successfully by a combination of steroids, azathioprine and intravenous immunoglobulin in the active phase of disease for induction of remission and by azathioprine and steroids for maintenance of remission. The significant improvement in her symptoms allowed us to continue her pregnancy to 37 weeks when delivery was electively induced. Transplacental transmission of PR3-ANCA occurred but the neonate remained well. This case of de novo WG during pregnancy highlights the seriousness of this disease and the challenge in management of such patients.

  18. Quantificação e Avaliação das Principais Espécies Florestais Licenciadas no Estado do Acre de 2005 a 2012

    Directory of Open Access Journals (Sweden)

    Flávia Alessandra Pinheiro da Rocha Cordeiro e Silva

    Full Text Available O presente trabalho teve como objetivo avaliar, identificar e quantificar os 15 principais gêneros e espécies florestais exploradas legalmente no estado do Acre, na Amazônia brasileira, bem como analisar o número de autorizações emitidas para exploração de florestas manejadas, o volume de madeira e a área de manejo licenciada pelo Instituto de Meio Ambiente do Acre de janeiro de 2005 a agosto de 2012. Os dados coletados demonstraram que a área e o volume de madeira licenciados apresentaram um crescimento no período analisado, atingindo o ápice em 2010 e 2011, respectivamente. Os 15 principais gêneros e espécies licenciados foram: cumaru-ferro (Dipteryx spp., garapeira (Apuleia spp., sumaúma (Ceiba spp., açacu (Hura crepitans L., matamatá (Eschweilera spp., jatobá (Hymenaea spp., tauari (Couratari spp., manitê (Brosimun spp., caucho (Castilla ulei Warb., cedro (Cedrela spp., guariúba (Clarisia racemosa Ruiz e Pav., faveira (Parkia spp., copaíba (Copaifera spp., guaribeiro (Phyllocarpus riedelii Tul. e abiurana (Pouteria spp..

  19. Tombamento de mudas de espécies florestais causado por Sclerotium rolfsii Sacc Damping-off of forest species caused by Sclerotium rolfsii Sacc

    Directory of Open Access Journals (Sweden)

    Reginaldo Gonçalves Mafia

    2007-08-01

    Full Text Available O estudo objetivou avaliar a gama de hospedeiros de Sclerotium rolfsii por inoculação controlada das seguintes espécies florestais nativas e exóticas: Anadenanthera peregrina (angico-vermelho, Chorisia speciosa (paineira-rosa, Clitoria fairchildiana (sombreiro, Copaifera langsdorffii (copaíba, Delonix regia (flamboyant-vermelho, Enterolobium contortisiliquum (orelha-de-negro, Leucaena leucocephala (leucena, Mabea fistulifera (canudo-de-pito, Platymiscium pubescens (tamboril-da-mata, Senna macranthera (fedegoso, Spathodea campanulata (espatódea e Tabebuia avellanedae (ipê-roxo, bem como comprovar o tombamento de mudas em pré e pós-emergência. Todas as espécies foram suscetíveis ao tombamento de mudas causado por S. rolfsii, em pré e em pós-emergência.The host range of Sclerotium rolfsii was evaluated by controlled inoculation of the following native and exotic forest species: Anadenanthera peregrina (angico vermelho, Chorisia speciosa (paineira rosa, Clitoria fairchildiana (sombreiro, Copaifera langsdorffii (copaíba, Delonix regia (flamboyant vermelho, Enterolobium contortisiliquum (orelha de negro, Leucaena leucocephala (leucena, Mabea fistulifera (canudo-de-pito, Platymiscium pubescens (tamboril da mata, Senna macranthera (fedegoso, Spathodea campanulata (espatódea e Tabebuia avellanedae (ipê roxo. The fungus caused damping-off in pre and post emergence in all tested species.

  20. MRUniNovo: an efficient tool for de novo peptide sequencing utilizing the hadoop distributed computing framework.

    Science.gov (United States)

    Li, Chuang; Chen, Tao; He, Qiang; Zhu, Yunping; Li, Kenli

    2017-03-15

    Tandem mass spectrometry-based de novo peptide sequencing is a complex and time-consuming process. The current algorithms for de novo peptide sequencing cannot rapidly and thoroughly process large mass spectrometry datasets. In this paper, we propose MRUniNovo, a novel tool for parallel de novo peptide sequencing. MRUniNovo parallelizes UniNovo based on the Hadoop compute platform. Our experimental results demonstrate that MRUniNovo significantly reduces the computation time of de novo peptide sequencing without sacrificing the correctness and accuracy of the results, and thus can process very large datasets that UniNovo cannot. MRUniNovo is an open source software tool implemented in java. The source code and the parameter settings are available at http://bioinfo.hupo.org.cn/MRUniNovo/index.php. s131020002@hnu.edu.cn ; taochen1019@163.com. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  1. Análise da distribuição de focos de calor no município de Novo Progresso, Pará

    Directory of Open Access Journals (Sweden)

    Andréia Caroline Lima Lopes

    2017-06-01

    Full Text Available Os incêndios são um dos principais causadores de danos aos ecossistemas florestais. Existem diversas formas de detecção dos focos de calor. Entretanto, para países com grande extensão territorial como o Brasil, é mais eficiente e barato o monitoramento por imagens de satélite. A partir disso, objetivou-se analisar a distribuição de focos de calor no município de Novo Progresso, Pará no período de 2010 a 2015, por meio de dados do monitoramento realizado por satélites de referência pertencentes ao Instituto Nacional de Pesquisas Espaciais. Após a organização das informações obtidas através do Banco de Dados de Queimadas, foram feitas análises dos fatores socioeconômicos e ambientais que intensificam o surgimento de focos de incêndios com o auxílio da literatura científica. Observou-se que os focos se concentraram na região nordeste do munícipio, ao longo da BR-163, apresentando maior ocorrência nos meses de agosto e setembro, o que pode estar relacionado com o período de estiagem do município. Analysis of the Distribution of hotspots in the Novo Progresso Town, Pará, BrazilAbstract: Fires are a major cause of damage to forest ecosystems. There are several ways of detecting hotspots. However, for countries with a vast territory as Brazil, the monitoring by satellite images is more efficient and cheaper. The aim of this study was to analyze the distribution of hotspots in the county of Novo Progresso, Pará, from 2010 to 2015 through data monitoring performed by reference satellites of the National Institute for Space Research. After organizing the information obtained through the Hotspots Database, analyses of socioeconomic and environmental factors that enhance the appearance of fire outbreaks were made with the assistance of scientific literature. It was observed that the outbreaks are concentrated in the northeastern area of the county along the BR-163, presenting higher occurrence in August and September, which

  2. Uso de diferentes alternativas para viabilizar a relação hipsométrica no povoamento florestal Use of different alternatives to allow the use of the hypsometric relation in forest stands

    Directory of Open Access Journals (Sweden)

    Thelma Shirlen Soares

    2004-12-01

    Full Text Available Este estudo teve como objetivo testar diversos modelos hipsométricos tradicionais e genéricos selecionados na literatura florestal, observando-se seus ajustes e comportamentos em diferentes agrupamentos de variáveis independentes que caracterizam um povoamento florestal. Esses modelos hipsométricos foram ajustados, sendo o critério de seleção da equação mais precisa através do coeficiente de determinação ajustado e erro-padrão residual. Para identificar se equações selecionadas para cada situação são estatisticamente diferentes, adotou-se o delineamento inteiramente casualizado no esquema de parcelas subdivididas. Nos casos em que foi detectado diferença significativa na análise de variância, aplicou-se o teste de médias de Scott e Knott, constando que o ajuste por parcela utilizando modelos tradicionais é o procedimento ideal para estimar a altura das árvores. Porém, o ajuste do modelo genérico propiciou boas estimativas, indicando a possibilidade de seu uso em substituição aos modelos tradicionais.This study aimed to test several traditional and generic hypsometric models, analyzing the adjustments and behavior in different groupings of independent variables that characterize a forest stand. Traditional and generic hypsometric models were determined, the most exact equation was selected through the determination coefficient and residual standard error. To verify whether equations selected for each situation are different, a complete randomized experimental design in split plot arrangement was adopted. The Scott & Knott mean test was applied for the cases where it was detected significant difference in the variance analysis were detected. It was verified that the adjustment per plot using traditional models is the ideal procedure to estimate tree height. However, the adjustment of the generic model gave good estimates, indicating the possibility of its use in substitution to the traditional models.

  3. O projeto PREFER : informação de apoio à prevenção de incêndios florestais e à recuperação de áreas ardidas, com recurso à deteção remota

    OpenAIRE

    Lourenço, Luciano; Oliveira, Sandra; Félix, Fernando; Gonçalves, António Bento; Nunes, Adélia; Vieira, António

    2014-01-01

    [Introdução] O PREFER (Space-based Information Support for Prevention and Recovery of Forest Fires Emergency in the MediteRranean Area) é um projeto de investigação europeu, iniciado em Dezembro de 2012 e enquadrado no Programa-Quadro 7, tendo-se iniciado em dezembro de 2012 e pretende contribuir para a gestão de incêndios florestais na Europa Mediterrânea, uma vez que os incêndios florestais são um dos principais riscos ambientais que afetam esta região. Entre 2000 e ...

  4. Distribuição espacial e sazonal de anfíbios em quatro poças na região serrana do Espírito Santo, sudeste do Brasil: influência de corredores florestais

    Directory of Open Access Journals (Sweden)

    Rodrigo Barbosa Ferreira

    2012-06-01

    Full Text Available Este estudo avaliou a composição da anurofauna, bem como a distribuição espacial e temporal das espécies em quatro poças permanentes em uma região montanhosa do Espírito Santo, sudeste do Brasil. Duas dessas poças são conectadas a fragmentos florestais por corredores florestais e as outras duas poças são circundadas por plantação de eucalipto e habitação humana. Foram registradas 22 espécies, incluídas em cinco famílias, entre dezembro de 2003 a novembro de 2004. Hylidae foi a mais rica e abundante, apresentando elevada sobreposição espacial. Nove espécies foram coletadas em vegetação abaixo de 0,60 m, sendo o sítio de vocalização mais utilizado. Riqueza de espécies e abundância foram maiores em meses chuvosos. Poças com corredores abrigaram maior riqueza de espécies. Adicionalmente quatorze espécies foram exclusivamente encontradas nessas poças. A estrutura da comunidade de anuros em poças permanentes nessa paisagem fragmentada é aparentemente determinada pela presença ou ausência de corredores florestais conectando fragmentos em topos de morro às poças d'água ocorrentes ao longo dos vales.

  5. De novo malignancy after pancreas transplantation in Japan.

    Science.gov (United States)

    Tomimaru, Y; Ito, T; Marubashi, S; Kawamoto, K; Tomokuni, A; Asaoka, T; Wada, H; Eguchi, H; Mori, M; Doki, Y; Nagano, H

    2015-04-01

    Long-term immunosuppression is associated with an increased risk of cancer. Especially, the immunosuppression in pancreas transplantation is more intensive than that in other organ transplantation because of its strong immunogenicity. Therefore, it suggests that the risk of post-transplant de novo malignancy might increase in pancreas transplantation. However, there have been few studies of de novo malignancy after pancreas transplantation. The aim of this study was to analyze the incidence of de novo malignancy after pancreas transplantation in Japan. Post-transplant patients with de novo malignancy were surveyed and characterized in Japan. Among 107 cases receiving pancreas transplantation in Japan between 2001 and 2010, de novo malignancy developed in 9 cases (8.4%): post-transplant lymphoproliferative disorders in 6 cases, colon cancer in 1 case, renal cancer in 1 case, and brain tumor in 1 case. We clarified the incidence of de novo malignancy after pancreas transplantation in Japan. Copyright © 2015 Elsevier Inc. All rights reserved.

  6. Novos paradigmas literários

    Directory of Open Access Journals (Sweden)

    Denise Azevedo Duarte Guimarães

    2005-12-01

    Full Text Available O artigo estuda a emergência de novos paradigmas literários, procurando refletir acerca das textualidades contemporâneas. Focaliza os hipertextos informatizados e a poesia multimídia, com o intuito de desvendar como estão sendo criados novos procedimentos expressivos e em que medida eles podem ser identificados com reflexões teóricas anteriores acerca do texto literário impresso. Remete a questões ligadas à leitura dos diferentes tipos de signos e aos modos como eles se integram para a constituição dessas novíssimas linguagens híbridas em novos suportes.El artículo estudia la emergencia de nuevos paradigmas literarios, procurando reflejar acerca de las textualidades contemporáneas. Enfoca los hipertextos informatizados y la poesía multimedia, intentando desvendar cómo están siendo creados nuevos procedimientos expresivos y en qué medida ellos pueden ser identificados a reflexiones teóricas anteriores acerca del texto literario impreso. Remite a cuestiones ligadas a la lectura de los diferentes tipos de signos y a los modos cómo ellos se interaccionan para la constitución de los novísimos lenguajes híbridos en nuevos supuestos.This article investigates the emergence of new literary paradigms as it tries to understand new contemporary textualities. It analyses some hypertexts and multimedia poetry trying to trace how new expressive procedures are being created. How can these new languages be identified and what are their relations to previous theories which dealt with the literary printed text? This study approaches questions linked to the reading of different types of signs and the modes they function towards the fabrication of these new hybrid languages.

  7. Caracterização e análise do coberto vegetal lenhoso e o seu contributo para a produção de cinzas resultantes de incêndios florestais

    OpenAIRE

    Quinta-Nova, L.C.; Fernandez, P.

    2008-01-01

    No Projecto POCI/AGR/59180/2004, concluído em 2009 (cf. Lobo-Ferreira et al., 2009), apresenta-se uma metodologia para avaliação quantitativa dos impactos dos fogos florestais na quantidade e qualidade das águas superficiais e subterrâneas. Nesta metodologia procura-se avaliar as alterações que possam ter ocorrido após o fogo: (A) em volumes de recarga, (B) volumes de escoamento superficial, (C) qualidade das águas superficiais e subterrâneas. Esta metodologia considera: (1) tipo e densid...

  8. Os incêndios florestais no inverno de 2011-2012 no distrito de Braga – resultado da evolução natural ou de mudanças climáticas?

    OpenAIRE

    Gonçalves, António Bento; Vieira, António; Leite, Flora Ferreira

    2012-01-01

    O Inverno de 2011-2012 foi marcado por uma seca prolongada a que se associou uma vaga de incêndios. Usando o distrito de Braga como caso de estudo, analisamos o período de 1 de janeiro a 15 de março de 2012 em termos de incêndios florestais, relacionando-os com eventuais mudanças climáticas em curso. Forest fires in 2011-2012 winter in the district of Braga – natural evolution or climate change? The winter of 2011-2012 was marked by a prolonged drought and a wave of forest fires. ...

  9. O uso de recursos florestais e as políticas econômicas brasileiras: uma visão histórica e parcial de um processo de desenvolvimento

    Directory of Open Access Journals (Sweden)

    Carlos José Caetano Bacha

    2004-06-01

    Full Text Available Este artigo analisa o uso de recursos florestais no Brasil, evidenciando que a destruição de nossas florestas e o uso insustentável dos remanescentes florestais sempre se associaram com as políticas desenvolvimentistas adotadas no País. Estas políticas, por sua vez, se fundamentaram nos principais modelos econômicos em voga a cada período. O trabalho apresenta uma discussão acerca da importância das florestas para uma nação e ressalta que o Brasil as está destruindo em grande escala, enquanto diversos outros países as ampliam. Este processo de desmatamento no Brasil já não se justifica pela necessidade de terra para a produção agropecuária. Por meio de um instrumental analítico, o trabalho verifica as políticas florestais e seus resultados desde o Brasil colônia e as associam com os principais modelos existentes a cada período. O trabalho também analisa o processo de reflorestamento no Brasil, demonstrando que o mesmo não compensa a perda de florestas nativas. Ao seu final, o artigo discute algumas políticas que permitem o uso racional dos recursos florestais no Brasil sem impedir a expansão de outras atividades econômicas.This paper analyzes the use of forests in Brazil, pointing out the destruction of native forests and its unsustainable uses are due to development policies. The latter is connected with the main economic models that prevailed during each time period. The paper discusses about the importance of forests for a nation and it points out Brazil is world’s number one in losing forests, while other countries are increasing their forests. That deforestation is not necessary in order to keep Brazil’s agriculture growing. The paper makes an analysis of forest policies and their results along Brazil’s history. The paper also analyzed the reforestation in Brazil and shows it is not compensating the deforestation process. At the end, the paper suggests some policies that are able to keep the expansion of

  10. Preferência de saúva limão, Atta sexdens rubropilosa Forel, 1908 (Hymenoptera, formicidae a diferentes espécies florestais, em condições de laboratório.

    Directory of Open Access Journals (Sweden)

    Otávio Peres Filho

    2010-08-01

    Full Text Available Avaliou-se a preferência de saúva limão, Atta sexdens rubropilosa Forel, 1908, para 41 espécies florestais nativas e exóticas, em condições de laboratório. As espécies mais transportadas foram gmelina (Gmelina arborea, leucena (Leucaena leucocephala, pau-ferro (Caesalpinia ferrea, albizia (Albizia lebbeck e orelha-de-negro (Enterolobium contortisiliquum e as menos transportadas foram eucalipto (Eucalyptus grandis, jequitibá (Cariniana strellensis e mutamba (Guazuma tomentosa.

  11. PREFERÊNCIA DE SAÚVA LIMÃO, Atta sexdens rubropilosa Forel, 1908 (HYMENOPTERA, FORMICIDAE A DIFERENTES ESPÉCIES FLORESTAIS, EM CONDIÇÕES DE LABORATÓRIO

    Directory of Open Access Journals (Sweden)

    Otávio Peres Filho

    2002-08-01

    Full Text Available Avaliou-se a preferência de saúva limão, Atta sexdens rubropilosa Forel, 1908, para 41 espécies florestais nativas e exóticas, em condições de laboratório. As espécies mais transportadas foram gmelina (Gmelina arborea, leucena (Leucaena leucocephala, pau-ferro (Caesalpinia ferrea, albizia (Albizia lebbeck e orelha-de-negro (Enterolobium contortisiliquum e as menos transportadas foram eucalipto (Eucalyptus grandis, jequitibá (Cariniana strellensis e mutamba (Guazuma tomentosa .

  12. Avaliação do potencial de espécies florestais alternativas, de rápido crescimento, para produção de painéis de madeira aglomerada

    OpenAIRE

    Trianoski, Rosilani

    2012-01-01

    A indústria de base florestal tem evoluído notadamente nos últimos anos, e continua em acentuada expansão tecnológica, tanto em termos de processos como de produtos. Entre os diversos tipos de produtos florestais, os painéis de madeira aglomerada tem se destacado, apresentando as maiores taxas de crescimento devido à ampla diversidade de produtos e a flexibilidade de aplicação para os mais variados fins, suprindo tanto em quantidade quanto em qualidade as demandas do setor madeireiro. Para at...

  13. De novo autoimmune hepatitis after liver transplantation.

    Science.gov (United States)

    Lohse, Ansgar W; Weiler-Norman, Christina; Burdelski, Martin

    2007-10-01

    The Kings College group was the first to describe a clinical syndrome similar to autoimmune hepatitis in children and young adults transplanted for non-immune mediated liver diseases. They coined the term "de novo autoimmune hepatitis". Several other liver transplant centres confirmed this observation. Even though the condition is uncommon, patients with de novo AIH are now seen in most of the major transplant centres. The disease is usually characterized by features of acute hepatitis in otherwise stable transplant recipients. The most characteristic laboratory hallmark is a marked hypergammaglobulinaemia. Autoantibodies are common, mostly ANA. We described also a case of LKM1-positivity in a patients transplanted for Wilson's disease, however this patients did not develop clinical or histological features of AIH. Development of SLA/LP-autoantibodies is also not described. Therefore, serologically de novo AIH appears to correspond to type 1 AIH. Like classical AIH patients respond promptly to treatment with increased doses of prednisolone and azathioprine, while the calcineurin inhibitors cyclosporine or tacrolimus areof very limited value - which is not surprising, as almost all patients develop de novo AIH while receiving these drugs. Despite the good response to treatment, most patients remain a clinical challenge as complete stable remissions are uncommon and flares, relapses and chronic disease activity can often occur. Pathogenetically this syndrome is intriguing. It is not clear, if the immune response is directed against allo-antigens, neo-antigens in the liver, or self-antigens, possibly shared by donor and host cells. It is very likely that the inflammatory milieu due to alloreactive cells in the transplanted organ contribute to the disease process. Either leading to aberrant antigen presentation, or providing co-stimulatory signals leading to the breaking of self-tolerance. The development of this disease in the presence of treatment with calcineurin

  14. GENÉTICA DA CONSERVAÇÃO DE Cabralea canjerana (Vell. Mart. (Meliaceae EM FRAGMENTOS FLORESTAIS DE MATA ATLÂNTICA NA APA FERNÃO DIAS

    Directory of Open Access Journals (Sweden)

    Arthur Tavares de Oliveira Melo

    2015-04-01

    Full Text Available A Mata Atlântica é o bioma brasileiro mais severamente afetado pela fragmentação ambiental. A análise da estruturação da diversidade genética, assim como de características demográficas e quantitativas, permite inferir parâmetros populacionais importantes para os programas de conservação de espécies ameaçadas. Cabralea canjerana ssp. canjerana (Meliaceae é uma espécie arbórea dioica considerada modelo para estudos de conservação da Mata Atlântica. Cento e oitenta e três indivíduos de oito subpopulações de C. canjerana foram coletados em fragmentos florestais na Área de Proteção Ambiental (APA Fernão Dias, no Sul do Estado de Minas Gerais, Brasil. Utilizando marcadores microssatélites, a diversidade genética foi estimada e contrastada com medidas quantitativas e medidas geográficas dessas oito subpopulações. Elevados níveis de diversidade genética foram encontrados. Uma porção pequena, porém significativa, da variância genética total está estruturada entre as populações (θ = 0,053, que foram estruturadas em dois grupos distintos. As estimativas dos níveis de diversidade genética nas populações localizadas acima de 1.800 m de altitude foram maiores, corroborando a importância dessas populações na manutenção da diversidade genética. A densidade populacional observada também foi maior nos fragmentos de maior altitude (r = 0,849; p-valor = 0,007. Não houve correlação significativa entre as variáveis fenotípicas (altura dos indivíduos e diâmetro a 1,50 m acima do solo e as medidas de diversidade genética. Esforços conservacionistas para que aumentem o fluxo gênico entre esses fragmentos florestais devem ser estimulados, principalmente entre os fragmentos de baixa altitude e os fragmentos de elevada altitude. É comprovado que populações situadas em elevadas altitudes possuem maior número de indivíduos por hectare e, portanto, maiores índices de diversidade genética. Essas

  15. Répteis squamata de remanescentes florestais do Campus da Universidade Federal do Rio Grande do Norte, Natal-RN, Brasil

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    De Sales, Raul Fernandes Dantas

    2009-09-01

    Full Text Available Inventários faunísticos são fundamentais para o conhecimento da biodiversidade e, conseqüentemente, para o planejamento e tomada de decisões sobre estratégias de conservação. Para conhecer a diversidade e composição dos répteis Squamata, assim como a distribuição das espécies por microhábitat em três fragmentos florestais na área do Campus da Universidade Federal do Rio Grande do Norte (UFRN, efetuaram-se excursões quinzenais diurnas, de março a junho de 2008. As buscas ativas foram realizadas ao longo de transecções percorridas aleatoriamente, efetuando-se os registros das espécies, dos microhábitats e do horário de observação. Um total de 92 espécimes, correspondentes a 10 espécies, foi coletados nas três áreas estudadas. A consulta da Coleção Herpetológica da UFRN possibilitou adicionar outras oito espécies, totalizando 18 espécies para o Campus da UFRN. As espécies mais abundantes foram Mabuya heathi, Hemidactylus mabouia e Tropidurus hispidus. O coeficiente de similaridade faunística binário de Sorensen mostrou 59 % de similaridade com os Squamata do Parque Estadual das Dunas do Natal (PEDN, área de conservação contígua com a área estudada. Apesar do grande adensamento urbano, os fragmentos florestais do Campus Central da UFRN abrigam espécies de formações abertas e de áreas florestadas, com destaque para os primeiros registros de Coleodactylus natalensis e de Amphisbaena heathi nessa vegetação relictual, fatos que justificam a preservação desses fragmentos em prol da manutenção destas espécies endêmicas do Rio Grande do Norte. Fauna inventories are crucial for increasing knowledge of biodiversity as well as for planning and conservation strategies. To assess the taxonomic composition and microhabitat distribution of squamate reptiles in three forest fragments on the campus of the Universidade Federal do Rio Grande do Norte (UFRN, field collections were carried out quarterly from March

  16. FATORES EDÁFICOS E AS VARIAÇÕES FLORÍSTICAS DA REGENERAÇÃO NATURAL EM DUAS FORMAÇÕES FLORESTAIS

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    Daniel Gonçalves Jardim

    2016-06-01

    Full Text Available Os ecossistemas litorâneos são influenciados pelas características do solo que junto com a disponibilidade de nutrientes atuam como fator determinante da composição florística e da estrutura de uma comunidade vegetal. Com o objetivo de verificar a correlação entre os fatores edáficos e a composição de espécies em duas formações florestais da Área de Proteção Ambiental Algodoal-Maiandeua, Maracanã, Pará, foram delimitadas três parcelas de 50 x 50 m (0,75 ha na floresta de restinga seca e duas (0,50 ha na floresta inundável. Cada parcela foi dividida em 50 subparcelas de 2 x 2 m distribuídas aleatoriamente e foram identificados e quantificados todos os indivíduos com altura ≥ 5 cm e ≤ 80 cm, calculada a densidade relativa e coletadas 5 amostras simples de solo por parcela. Para relacionar os gradientes ao componente edáfico foi realizada a análise de correspondência canônica (CCA. Na floresta de restinga seca a CCA mostrou maior correlação entre Myrcia fallax, Pradosia pedicellata, Protium heptaphyllum e Parkia pendula com Fe, P, Cu, Ca, K e MO e na floresta inundável Symphonia globulifera e Virola surinamensis tiveram alta relação com CaCl2, KCl, H2O, Zn e N. Foi constatada a separação das espécies mais bem representadas nas duas florestas e respectivos nutrientes do solo. Palavras-chave: Floresta de restinga seca, floresta inundável, nutrientes no solo.

  17. Gestão de custos florestais: um estudo de caso utilizando o Activity-Based Costing Forest management costs: a case study utilizing Activity-Based Costing

    Directory of Open Access Journals (Sweden)

    Alcir Ribeiro Carneiro de Almeida

    1999-08-01

    Full Text Available No atual cenário de industrialização globalizada, tornou-se fundamental a eficácia no gerenciamento dos custos considerados inevitavelmente necessários. Programas convencionais de redução dos custos não consideram o grau de agregação de valor das atividades de rotina pela distorção dos sistemas contábeis atuais. No presente estudo, apresentam-se os principais motivos da falta de relevância das informações de custo, comenta-se sobre o problema da redução de desperdícios florestais e suas conseqüências. A partir de um estudo de caso em uma empresa do setor florestal, demonstra-se uma simulação do Activity Based Costing (ABC em uma determinada área da empresa, concluindo-se que a adoção de sistemas de custeio mais aprimorados, tal como o ABC, devem fazer parte de programas que busquem o aumento da competitividade do setor florestal.In the current view of globalized industrialization, it has become fundamental to manage essential costs effectively. Conventional programs for reducing costs, do no consider the value agregation grade of routine activities because of the distortion of current accounting systems. This study, presents the main reasons for the lack of relevance of the cost information, commenting on the problem of the reduction of forest waste and its consequences. Using a case study in a company from the forest sector, a simulation of Activity Based Costing (ABC is demonstrated in a determined area of the company it is concluded that the adoption of a more refined cost system, such as the ABC, should be included in programs, that seek to increase the competitiveness of the forest sector.

  18. De Novo Construction of Redox Active Proteins.

    Science.gov (United States)

    Moser, C C; Sheehan, M M; Ennist, N M; Kodali, G; Bialas, C; Englander, M T; Discher, B M; Dutton, P L

    2016-01-01

    Relatively simple principles can be used to plan and construct de novo proteins that bind redox cofactors and participate in a range of electron-transfer reactions analogous to those seen in natural oxidoreductase proteins. These designed redox proteins are called maquettes. Hydrophobic/hydrophilic binary patterning of heptad repeats of amino acids linked together in a single-chain self-assemble into 4-alpha-helix bundles. These bundles form a robust and adaptable frame for uncovering the default properties of protein embedded cofactors independent of the complexities introduced by generations of natural selection and allow us to better understand what factors can be exploited by man or nature to manipulate the physical chemical properties of these cofactors. Anchoring of redox cofactors such as hemes, light active tetrapyrroles, FeS clusters, and flavins by His and Cys residues allow cofactors to be placed at positions in which electron-tunneling rates between cofactors within or between proteins can be predicted in advance. The modularity of heptad repeat designs facilitates the construction of electron-transfer chains and novel combinations of redox cofactors and new redox cofactor assisted functions. Developing de novo designs that can support cofactor incorporation upon expression in a cell is needed to support a synthetic biology advance that integrates with natural bioenergetic pathways. © 2016 Elsevier Inc. All rights reserved.

  19. Padrões para germinação, pureza, umidade e peso de mil sementes em análises de sementes de espécies florestais nativas do Rio Grande do Sul

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    Fernanda de Oliveira Brüning

    2011-06-01

    Full Text Available O presente trabalho teve como objetivo propor padrões de confiabilidade, em relação à germinação, pureza, peso de mil sementes e grau de umidade das sementes, visando ao controle de qualidade das análises de sementes de espécies florestais. Para tanto, foram utilizados resultados de análises de sementes de espécies florestais em laboratório, a partir do ano de 1997 até 2007, obtidos dos arquivos do Laboratório de Análise de Sementes da Fundação Estadual de Pesquisa Agropecuária do Estado do Rio Grande do Sul. Os padrões de confiabilidade foram construídos com base em uma análise de normalidade dos dados e da utilização do critério do pseudossigma. Os limites se mostraram eficientes no estabelecimento do valor mínimo aceitável para que um lote de sementes seja comercializado, propondo que valores de germinação dentro dos limites de confiabilidade baixos devem ser descartados, pois não apresentam índices germinativos aceitáveis. 

  20. Antimicrobial peptide capsids of de novo design.

    Science.gov (United States)

    De Santis, Emiliana; Alkassem, Hasan; Lamarre, Baptiste; Faruqui, Nilofar; Bella, Angelo; Noble, James E; Micale, Nicola; Ray, Santanu; Burns, Jonathan R; Yon, Alexander R; Hoogenboom, Bart W; Ryadnov, Maxim G

    2017-12-22

    The spread of bacterial resistance to antibiotics poses the need for antimicrobial discovery. With traditional search paradigms being exhausted, approaches that are altogether different from antibiotics may offer promising and creative solutions. Here, we introduce a de novo peptide topology that-by emulating the virus architecture-assembles into discrete antimicrobial capsids. Using the combination of high-resolution and real-time imaging, we demonstrate that these artificial capsids assemble as 20-nm hollow shells that attack bacterial membranes and upon landing on phospholipid bilayers instantaneously (seconds) convert into rapidly expanding pores causing membrane lysis (minutes). The designed capsids show broad antimicrobial activities, thus executing one primary function-they destroy bacteria on contact.

  1. De novo pathway-based biomarker identification

    DEFF Research Database (Denmark)

    Alcaraz, Nicolas; List, Markus; Batra, Richa

    2017-01-01

    in a large cohort of breast cancer samples from The Cancer Genome Atlas (TCGA) revealed that MGs are considerably more stable than SG models, while also providing valuable insight into the cancer hallmarks that drive them. In addition, when tested on an independent benchmark non-TCGA dataset, MG features......Gene expression profiles have been extensively discussed as an aid to guide the therapy by predicting disease outcome for the patients suffering from complex diseases, such as cancer. However, prediction models built upon single-gene (SG) features show poor stability and performance on independent...... on their molecular subtypes can provide a detailed view of the disease and lead to more personalized therapies. We propose and discuss a novel MG approach based on de novo pathways, which for the first time have been used as features in a multi-class setting to predict cancer subtypes. Comprehensive evaluation...

  2. Uso de biossólidos em povoamento de eucalipto: efeito em atributos químicos do solo, no crescimento e na absorção de nutrientes

    Directory of Open Access Journals (Sweden)

    L. M. S. Vaz

    2002-09-01

    Full Text Available Com o objetivo de avaliar o efeito da aplicação de doses crescentes de biossólido (0, 5, 10, 15, 20 e 40 t ha-1, base seca em atributos químicos do solo, crescimento e absorção de macro e micronutrientes em um povoamento de Eucalyptus grandis, foi instalado um experimento na Estação Experimental de Itatinga da ESALQ/USP, Itatinga (SP. Alguns tratamentos tiveram suplementação de K e P e, como referência, em um dos tratamentos foi aplicada adubação mineral como praticado em empresas florestadoras com alta tecnologia na região.O solo da área foi caracterizado como Latossolo Vermelho-Amarelo distrófico textura média. Seis meses após a aplicação do biossólido, não foram constatadas alterações do pH e dos teores de P, Mg, Zn, Cu e B no solo. Foi observada elevação dos teores de K, Ca e S no solo, bem como redução das concentrações de Al, Fe e Mn, dependendo da dose de biossólido aplicada. Diferentemente, 13 meses após a aplicação do biossólido, percebeu-se a elevação do pH e dos teores de P, Ca, K e S somente na camada de 0-5 cm. Nas duas épocas de amostragem do solo, a elevação das doses de biossólido ocasionou redução dos teores de MO somente na camada de 0-5 cm. Em compasso com a mineralização da MO no solo, os teores de N e S no tecido foliar elevaram-se com o aumento das doses de biossólido em ambas as épocas de amostragem. A disponibilidade de P assimilável (P-resina elevou-se, consideravelmente, com o tempo de contato do biossólido com o solo, resultando em maior absorção de P e crescimento das plantas. A aplicação de fertilizante fosfatado no sulco ou cova de plantio, conjuntamente com o biossólido, mostrou-se necessária para elevar o crescimento inicial das plantas, assegurando atendimento das elevadas demandas iniciais deste nutriente. A suplementação de K em plantações jovens de eucalipto poderá não ser necessária para doses de biossólido maiores que 10 t ha-1, quando as

  3. Modelagem do volume do povoamento para Mimosa scabrella Benth. na regição metropolitana de Curitiba Stand volume modelling of Mimosa scabrella benth. from Curitiba metropolitan region

    Directory of Open Access Journals (Sweden)

    Sebastião do Amaral Machado

    2008-06-01

    Full Text Available O objetivo desta pesquisa foi modelar o volume total com casca do povoamento da bracatinga (Mimosa scabrella Benth.. Coletaram-se dados em bracatingais com regeneração induzida pelo fogo, em 14 municípios da Região Metropolitana de Curitiba (RMC, Estado do Paraná - Brasil. Utilizou-se uma base de dados constituída por 229 unidades amostrais de 100 a 400 m². Em cada parcela, mensurou-se o diâmetro à altura do peito, bem como a altura total de todas as árvores, em bracatingais de 3 a 18 anos de idade. Para a estimativa do volume total com casca, testaram-se vários modelos de regressão selecionados da literatura, o que gerou uma matriz com 58 variáveis independentes, visando construir modelos por meio do método Stepwise. As equações de melhor ajuste foram validadas utilizando-se o teste Qui-quadrado, a análise gráfica de resíduos e o erro-padrão da estimativa. Várias equações tiveram bom desempenho, apresentaram valores de coeficiente de determinação ajustados superiores a 0,995, erro-padrão da estimativa inferior a 3% e adequada distribuição de resíduos. As duas equações de melhor desempenho foram validadas, apresentando erro-padrão da estimativa de 2,37% e 2,13%, valor não-significativo para o teste do Qui-quadrado e equilibrada distribuição dos resíduos.The objective of this research was to model the stand volume outside bark of Mimosa scabrella Benth. stands, from the Curitiba Metropolitan Region (CMR, Parana State - Brazil. To reach this aim, a database of 229 permanent and temporary sample plots measuring from 100 to 400 m² each, from 14 municipalities in the CMR, was used. In each sample plot, the diameter at breast height and the total height of all 3- to 18-year-old bracatinga trees were measured. To estimate the total volume, regression models selected from the literature were tested. A set of 58 independent variables was generated also to construct models by the Stepwise method. The equations of best

  4. Redistribuição das chuvas pelas copas de um povoamento de seringueira, José Bonifácio, SP. Rainwater redistribution under a rubber tree stand in the José Bonifacio county, SP.

    Directory of Open Access Journals (Sweden)

    Valdemir Antonio RODRIGUES

    2009-06-01

    Full Text Available A presente pesquisa foi desenvolvida emum povoamento de seringueira, clone RRIM 600,com 15 anos de idade, município de JoséBonifácio, SP. A pesquisa avaliou a redistribuiçãodas chuvas no período de agosto de 1996 a julhode 1997 (ano hídrico 1996/97, por meio dequantificação das precipitações pluvial total,interna e efetiva; do escoamento pelo tronco; eestimativa da interceptação das chuvas pelas copasdo seringal. Foram instalados pluviômetros a céuaberto e sob o dossel das árvores e, nos troncos dasárvores, coletores de água. A precipitação médiaanual foi de 1.514,5 mm, a precipitação interna foide 1.065,7 mm e o escoamento pelo tronco, de107,7 mm. A interceptação das chuvas pelas copase a precipitação efetiva resultaram em 341,1 e1.173,4 mm, respectivamente; correspondendo a22,5% e 77,5% do total da precipitação no seringal.A proporção de água que chega ao solo através doescoamento pelo tronco na seringueira foi superioraos obtidos em estudos similares realizados naregião Sudeste do Brasil. Os menores e maioresvalores percentuais de interceptação ocorreram noperíodo de estiagem, enquanto no período chuvosoos valores foram intermediários. Os valores mínimosocorreram durante os meses do período deestiagem, durante os quais as árvores estãodesfolhadas, enquanto os maiores valores ocorreramlogo a seguir, quando as chuvas que ainda têmcaracterísticas do período de estiagem ocorreramsobre as árvores com a folhagem recomposta.This research was developed in a 15years old rubber-tree plantation (RRIM 600,located in the municipality of José Bonifácio,São Paulo State. The reasearch evaluate the rainredistribution between August 1996 and July 1997(water year 1996/1997. It was estimated the grossand net precipitation, the throughfall, the stemflowand the crown interception loss. Non-recordingrain gauges were installed at an open area andunder the rubber tree canopy. Stemflow collectorswere installed at the

  5. Revisão sobre alguns grupos de inseticidas utilizados no manejo integrado de pragas florestais / A review of some insecticide groups used in forest pest integrated management

    Directory of Open Access Journals (Sweden)

    Álvaro Boson de Castro Faria

    2009-08-01

    Full Text Available ResumoMuito embora os princípios, critérios e indicadores da certificação florestal exijam das empresas a valorização do controle biológico e a diminuição do uso de pesticidas, atualmente podemos nos valer de estratégias químicas que permitem minimizar os impactos sobre organismos não alvo, em que, respeitadas as devidas autorizações e disposições legais, são utilizadas como estratégias dos programas de controle e manejo integrados. Este trabalho tem como objetivo apresentar uma revisão bibliográfica a qual se estabeleceu um grau de evolução entre os inseticidas no controle de pragas florestais. O desenvolvimento classifica os grupos químicos de defensivos em quatro gerações: na primeira, os produtos inorgânicos; na segunda, os organoclorados, os organofosforados, os carbamatos e os piretróides; na terceira geração, os reguladores de crescimento e os fagos-inibidores; e na quarta, a biotecnologia e os produtos neonicotinóides, seu modo de ação e seus métodos de aplicação. As técnicas precisam ter como meta o aumento das produtividades ao ponto em que, simultaneamente, preservem o meio ambiente no seu sentido mais amplo, inclusive, considerando o ser humano como parte deste sistema.AbstractThe principles, criteria and forest certification indicators demand from companies more use of biological control and instead of esticides use. However, nowadays it’s common to see the use chemical strategies that allow minimizing impacts on non-target organisms. Respecting the due authorizations and legal dispositions, these strategies is used in the integrated pest management (IPM programs. This paper presents a revision of literature, establishing a degree of evolution amongst the insecticides used in forest pest control. The chemical groups are classified in four generations: in the first, the non-organics; in the second, the organochlorides, organophosphate, carbamates and piretroids; in the third, the insect growth

  6. Sistemas de manejo em plantios florestais de eucalipto e perdas de solo e água na região do Vale do Rio Doce, MG

    Directory of Open Access Journals (Sweden)

    Mayesse Aparecida da Silva

    2011-12-01

    Full Text Available A erosão hídrica é a principal responsável pela perda da capacidade produtiva dos solos sob florestas plantadas e alteração da quantidade e qualidade da água em sub-bacias. Assim, este trabalho objetivou avaliar a influência dos sistemas de manejo adotados nos plantios florestais com eucalipto (eucalipto em nível - EN, eucalipto em desnível - ED e eucalipto em desnível com queima - EDQ sobre as perdas de solo e água por erosão hídrica em relação às perdas em floresta nativa (FN, pastagem (PP e solo descoberto (SD, num Latossolo Vermelho (LV e Latossolo Vermelho-Amarelo (LVA, e indicar qual o período mais crítico no manejo do solo, em relação à erosão hídrica, durante o ciclo de cultivo do eucalipto. O estudo foi conduzido em dois municípios: Belo Oriente (LVA e Guanhães (LV, situados no Vale do Rio Doce, região Centro-Leste do estado de Minas Gerais. Com exceção do sistema SD no LVA, as perdas de solo foram abaixo do limite de tolerância admissível para essas classes de solos, nestas regiões, que são de 11,22 Mg ha-1 ano-1 no LV e de 7,17 Mg ha-1 ano-1 para o LVA. As perdas de água nos sistemas com eucalipto foram menores no plantio em nível, no LVA. Nos sistemas com eucalipto, os períodos iniciais após o plantio apresentam as maiores perdas de solo e água com redução ao final do ciclo. Por outro lado, no LVA os sistemas com solo descoberto e floresta nativa apresentaram aumento das perdas de água com o decorrer do tempo avaliado, indicando adequação dos sistemas com eucalipto.

  7. Los "intelectuales" y el Estado Novo

    Directory of Open Access Journals (Sweden)

    Luís REIS TORGAL

    2010-02-01

    Full Text Available RESUMEN: El concepto de “intelectual” es difícil de definir y sin duda se debate constantemente. Sin embargo, es importante reflexionar sobre él a fin de comprender su significado y los problemas que implica. Sea como fuere, a un Estado autoritario “moderno” se le supone una única ideología que tiene que difundirse por medio de una propaganda bien organizada, proceso en el que los intelectuales desempeñan un papel significativo. El “Nuevo Estado” de Salazar encaja en esta categoría y sin duda el conocimiento acerca de sus “intelectuales” es fundamental. En este artículo, el objetivo es proporcionar algunos ejemplos interesantes de “intelectuales” o de simples “funcionarios políticos” con inclinación intelectual a fin de indicar el sentido y complejidad de un estudio con una dimensión distinta sobre este asunto. A este fin han sido seleccionadas tres personalidades responsables de la actividad ideológica y cultural de gran relieve en el Estado de Salazar: António Ferro, João Ameal y Costa Brochado. Palabras clave: Estado Novo; Authotitarianism; Salazar, António de Oliveira; Intellectuals; Ferro, António; Brochado, Idalino da Costa; Ameal, João. ABSTRACT: The concept of the “intellectual” is difficult to define and undoubtedly constantly debated. It is nevertheless important to reflect on it in order to understand its meaning and the problems involved with it. Be that as it may, a “modern” authoritarian State presumes a single ideology which has to be diffused by means of well-organised propaganda, in which process “intellectuals” play a significant role. Salazar’s “New State” fits this category and, undoubtedly, knowledge about its “intellectuals” is fundamental. The objective in this article is to provide some interesting examples of “intellectuals” or simple “political functionar- ies” with an intellectual bent so as to indicate the sense and complexity of a study of a

  8. Icarus: visualizer for de novo assembly evaluation.

    Science.gov (United States)

    Mikheenko, Alla; Valin, Gleb; Prjibelski, Andrey; Saveliev, Vladislav; Gurevich, Alexey

    2016-11-01

    : Data visualization plays an increasingly important role in NGS data analysis. With advances in both sequencing and computational technologies, it has become a new bottleneck in genomics studies. Indeed, evaluation of de novo genome assemblies is one of the areas that can benefit from the visualization. However, even though multiple quality assessment methods are now available, existing visualization tools are hardly suitable for this purpose. Here, we present Icarus-a novel genome visualizer for accurate assessment and analysis of genomic draft assemblies, which is based on the tool QUAST. Icarus can be used in studies where a related reference genome is available, as well as for non-model organisms. The tool is available online and as a standalone application. http://cab.spbu.ru/software/icarus CONTACT: aleksey.gurevich@spbu.ruSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  9. [Diagnosis and management of de novo epilepsy].

    Science.gov (United States)

    Louise, Tyvaert

    2018-03-01

    The diagnosis of de novo epilepsy is complex. An accurate diagnostic approach has to be followed based on specific key steps. Epileptic seizure or non-epileptic malaise: risk of diagnosis error around 20%. Facing a first unprovoked seizure, the practitioner has to know the risk factors specifically linked to an increase risk of seizure recurrence. In presence of these factors, an antiepileptic drug would be indicated. The first antiepileptic drug has to be highly selected according to the epilepsy type and causes but also to the patient characteristics (sex, age, comorbidities, associated drugs, profession, and way of life…) An exhaustive patient Education needs to support the first antiepileptic drug prescription: (sleep and nutritional advices, benefit of observance, antiepileptic drugs features and side effects, follow-up, prognosis…) A regular follow-up is essential to control the observance, tolerability and efficacy of the antiepileptic drug, and to control also the good acceptance of the disease. A systematic research of common comorbidities may be also performed. Electroencephalogram and antiepileptic drugs levels are unnecessary in the classical follow up of known epileptic patients (except specific cases). Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  10. De novo origin of human protein-coding genes.

    Directory of Open Access Journals (Sweden)

    Dong-Dong Wu

    2011-11-01

    Full Text Available The de novo origin of a new protein-coding gene from non-coding DNA is considered to be a very rare occurrence in genomes. Here we identify 60 new protein-coding genes that originated de novo on the human lineage since divergence from the chimpanzee. The functionality of these genes is supported by both transcriptional and proteomic evidence. RNA-seq data indicate that these genes have their highest expression levels in the cerebral cortex and testes, which might suggest that these genes contribute to phenotypic traits that are unique to humans, such as improved cognitive ability. Our results are inconsistent with the traditional view that the de novo origin of new genes is very rare, thus there should be greater appreciation of the importance of the de novo origination of genes.

  11. De Novo Origin of Human Protein-Coding Genes

    Science.gov (United States)

    Wu, Dong-Dong; Irwin, David M.; Zhang, Ya-Ping

    2011-01-01

    The de novo origin of a new protein-coding gene from non-coding DNA is considered to be a very rare occurrence in genomes. Here we identify 60 new protein-coding genes that originated de novo on the human lineage since divergence from the chimpanzee. The functionality of these genes is supported by both transcriptional and proteomic evidence. RNA–seq data indicate that these genes have their highest expression levels in the cerebral cortex and testes, which might suggest that these genes contribute to phenotypic traits that are unique to humans, such as improved cognitive ability. Our results are inconsistent with the traditional view that the de novo origin of new genes is very rare, thus there should be greater appreciation of the importance of the de novo origination of genes. PMID:22102831

  12. Identifying wrong assemblies in de novo short read primary ...

    Indian Academy of Sciences (India)

    2016-08-05

    Aug 5, 2016 ... Most of these assemblies are done using some de novo short read assemblers and other related approaches. .... benchmarking projects like Assemblathon 1, Assemblathon ... from a large insert library (at least 1000 bases).

  13. Arginine de novo and nitric oxide production in disease states

    OpenAIRE

    Luiking, Yvette C.; Ten Have, Gabriella A. M.; Wolfe, Robert R.; Deutz, Nicolaas E. P.

    2012-01-01

    Arginine is derived from dietary protein intake, body protein breakdown, or endogenous de novo arginine production. The latter may be linked to the availability of citrulline, which is the immediate precursor of arginine and limiting factor for de novo arginine production. Arginine metabolism is highly compartmentalized due to the expression of the enzymes involved in arginine metabolism in various organs. A small fraction of arginine enters the NO synthase (NOS) pathway. Tetrahydrobiopterin ...

  14. De Novo Collapsing Glomerulopathy in a Renal Allograft Recipient

    Directory of Open Access Journals (Sweden)

    Kanodia K

    2008-01-01

    Full Text Available Collapsing glomerulopathy (CG, characterized histologically by segmental/global glomerular capillary collapse, podocyte hypertrophy and hypercellularity and tubulo-interstitial injury; is characterized clinically by massive proteinuria and rapid progressive renal failure. CG is known to recur in renal allograft and rarely de novo. We report de novo CG 3 years post-transplant in a patient who received renal allograft from haplo-identical type donor.

  15. Language and national identity in Novo Cinema Galego

    Directory of Open Access Journals (Sweden)

    Brais ROMERO SUÁREZ

    2015-12-01

    Full Text Available The talk of town since its inception in 2010, the Cinema Novo Galego has been successful in all competitions and festivals that has been present. From the FIPRESCI prize in Cannes to the Best Emerging Director at Locarno, this new wave of cinema places Galicia in the world film stage. But does Novo Cinema Galego an accurate representation of Galicia? What's the role of Galicia in this movement?

  16. Avifauna da Zona da Mata de Minas Gerais: municípios de Goianá e Rio Novo, com alguns registros para Coronel Pacheco e Juiz de Fora Avifaunal inventory of the "Zona da Mata" of Minas Gerais: Goianá and Rio Novo, with some records for Coronel Pacheco and Juiz de Fora municipalities

    Directory of Open Access Journals (Sweden)

    Rômulo Ribon

    2004-04-01

    Full Text Available A partir da oportunidade criada pelos Estudos de Impacto Ambiental para implantação do Aeroporto Regional da Zona da Mata, fez-se a caracterização qualitativa preliminar da avifauna dos municípios de Goianá e Rio Novo, na Zona da Mata, sudeste de Minas Gerais. Alguns registros para áreas limítrofes dos municípios de Juiz de Fora e Coronel Pacheco são também fornecidos. A região, originalmente coberta por Mata Atlântica, é hoje composta por um mosaico de pastagens, fragmentos florestais, pomares domésticos e ambientes limícolas. Foram registradas 185 espécies de aves, sendo os ambientes de mata os mais ricos em espécies. Neste artigo serão dadas informações sobre o habitat, o método de registro das espécies e, para algumas delas, sobre a atividade reprodutiva. A presença da planície de inundação do rio Novo proporciona ambiente para espécies normalmente pouco abundantes no restante da Zona da Mata. Destacam-se a extinção local de pelo menos duas espécies registradas no século XIX, a presença de algumas aves ameaçadas de extinção e a importância de estudos de impacto ambiental como oportunidade, muitas vezes perdida, para obtenção de informações biológicas.The support provided by the Environmental Impact Assessment for the construction of the Zona da Mata Regional Airport allowed the conduction of a qualitative sampling of the bird community at Goianá and Rio Novo municipalities, in the "Zona da Mata" region, southeastern Minas Gerais, Brazil. Some records for neighboring areas at Juiz de Fora and Coronel Pacheco municipalities are also given. The region is located in the Semidecidual Lowland Atlantic Forest domain but the current landscape is a mosaic of artificial pasturelands, secondary forest fragments, small orchards around farms' headquarters, small ponds for fish farming, and marshes at the Rio Novo floodplain. We recorded 185 bird species with the forest fragments being the richest habitat

  17. Transformação da paisagem e o uso dos recursos florestais na agricultura familiar: um estudo de caso em área de Mata Atlântica

    Directory of Open Access Journals (Sweden)

    Gisele Garcia Alarcon

    2011-06-01

    Full Text Available São Bonifácio está localizado na região das serras do leste catarinense, no bioma Mata Atlântica. A agricultura e a pecuária leiteira, praticadas na pequena propriedade, compõem o setor responsável por garantir ocupação da maior parte da população. Este estudo tem como objetivo analisar a relação entre agricultores familiares e os recursos florestais da paisagem. O estímulo a práticas produtivas que não valorizam a floresta associado à ausência de políticas de incentivo para o manejo florestal de espécies nativas, foram determinantes para a redução das áreas florestadas em São Bonifácio nas últimas cinco décadas.

  18. Caracterização mineralógica, potencial de reserva e sustentabilidade agrícola de alguns sítios florestais de eucalipto da região do Vale do Rio Doce (MG

    Directory of Open Access Journals (Sweden)

    A. Reatto

    1998-06-01

    Full Text Available Foram estudados alguns solos da região do Vale do Rio Doce (MG em 1991, nos municípios de Ipatinga, Nova Era e Guanhães, provenientes de áreas de reflorestamento de Eucalyptus grandis. Selecionaram-se oito sítios florestais com solos de diferentes classes taxonômicas, e uma detalhada caracterização mineralógica e avaliação do potencial de reserva de nutrientes foram desenvolvidas. Os solos estudados foram mineralogicamente classificados como: caulinítico não-sesquioxídicos (2 e 5; caulinítico-sesquioxídico (1; gibbsítico-sesquioxídicos (4, 6 e 7; hematítico (3 e gibbsítico (8. Os principais argilominerais e óxidos de ferro e alumínio presentes nesses solos são caulinita, gibbsita, hematita, goethita e maghemita. A reserva mineral de médio a longo prazo para potássio é praticamente inexistente, estando presente, embora com baixa magnitude, nos solos 2 e 5, na forma de micas e feldspatos. As relações Ca-trocável/Ca-total e Mg-trocável/Mg-total exprimem baixa capacidade de reposição desses nutrientes nos solos estudados. Sugere-se a adição de nutrientes de acordo com os níveis críticos exigidos na implantação e manutenção do ciclo do eucalipto, em virtude da ausência de sustentabilidade desses sítios florestais em termos de reserva de nutrientes a curto, médio e longo prazos.

  19. Durabilidade de solos estabilizados quimicamente com vistas á aplicação em estradas florestais Durability of chemically stabilized soils for forest road applications

    Directory of Open Access Journals (Sweden)

    Carlos Cardoso Machado

    2006-12-01

    Full Text Available Este artigo é direcionado à caracterização do parâmetro durabilidade de dois solos típicos da microrregião de Viçosa, Minas Gerais, para fins de aplicação em estradas florestais, considerando-se, para tanto, as seguintes condições: (a solos estabilizados com o resíduo industrial "grits"; (b solos melhorados com cal ou cimento; e (c solos estabilizados com grits e melhorados com cal ou cimento, a partir de resultados de ensaios de durabilidade por molhagem e secagem. Trabalhou-se com um solo residual maduro (solo 1 e um solo residual jovem de gnaisse (solo 2 da Zona da Mata Norte de Minas Gerais, Brasil. O programa de ensaios de laboratório envolveu: (a teor de grits: 24% calculado em relação ao peso de solo seco; (b teor de cal ou cimento: 10 e 20%, calculados em relação ao peso de grits seco; (c energias de compactação: referentes aos ensaios Proctor normal e modificado; e (d período de cura: sete dias em câmara úmida. Os resultados do programa de ensaios indicaram que: (a as misturas solo-cal, solo-cimento, solo-grits-cal e solo-grits-cimento, em ambas as energias empregadas, resistiram a todos os ciclos do ensaio de durabilidade por molhagem e secagem; (b a mistura solo 1 + grits + cal apresentou o melhor resultado, quando compactada na energia modificada, com perdas da ordem de 7%; com relação ao solo 2, o melhor resultado foi obtido quando se trabalhou com grits mais cimento, na energia modificada, com perdas da ordem de 9%; e (c sob o aspecto durabilidade, as misturas solo-grits só apresentam potencial para emprego como material de construção rodoviária quando melhoradas com cal ou cimento.This paper addresses the assessment of the durability properties of mixtures of two soils using laboratory wetting and drying durability tests for forest road applications, as follows: (a soils stabilization with the industrial waste grits; (b soil improvement using lime or cement; (c soil stabilization using grits, and soil

  20. Composição florística de trechos florestais na borda sul-amazônica Floristic composition of forest patches in Southern Amazonia

    Directory of Open Access Journals (Sweden)

    Natália Macedo Ivanauskas

    2004-09-01

    Full Text Available Este estudo apresenta a composição florística de trechos de uma faixa de vegetação de transição existente na região centro-leste do Estado de Mato Grosso, mais precisamente no município de Gaúcha do Norte (13° 10'S e 53° 15' O, onde dá-se o contato entre a Floresta Ombrófila e a Floresta Estacional. O levantamento florístico foi realizado em março de 1999 e bimestralmente a partir de agosto de 1999 até março de 2001, em excursões com duração média de 5 dias, por meio de caminhadas na borda e no interior de florestas, sendo coletadas fanerógamas em fase reprodutiva. Também foram incluídas amostras vegetativas de espécies arbustivo-arbóreas, que não floresceram ou frutificaram durante o período de amostragem, amostradas em 3ha destinados ao levantamento fitossociológico. O levantamento florístico resultou em 72 famílias, 168 gêneros e 268 espécies. Do total de espécies, 66% apresentaram hábito arbóreo e 18% foram lianas. As ervas e arbustos praticamente restringiram-se às áreas de borda ou clareiras, somando 13%. Já a flora epifítica mostrou-se pouco expressiva (1%, quando comparada ao restante da Amazônia, em conseqüência do clima regional mais seco. Hemiepífitas, parasitas e palmeiras constituíram o percentual restante. Constatou-se que 39 espécies amostradas em Gaúcha do Norte ainda não haviam sido depositadas em herbários que mantém coleções representativas da flora matogrossense, enfatizando a carência de coletas nas áreas florestais do Estado.This paper shows the floristic composition of forest patches in a zone of transition vegetation which exists in the central-east region of Mato Grosso state, more specifically in the municipality of Gaúcha do Norte (13° 10'S and 53° 15' W where it connects the tropical rain-forest and the seasonal forest. The floristic survey was performed in March 1999 and bisemesterly from August 1999 to March 2001 (during excursions of an average of five days

  1. Clinicopathologic factors associated with de novo metastatic breast cancer.

    Science.gov (United States)

    Shen, Tiansheng; Siegal, Gene P; Wei, Shi

    2016-12-01

    While breast cancers with distant metastasis at presentation (de novo metastasis) harbor significantly inferior clinical outcomes, there have been limited studies analyzing the clinicopathologic characteristics in this subset of patients. In this study, we analyzed 6126 breast cancers diagnosed between 1998 and 2013 to identify factors associated with de novo metastatic breast cancer. When compared to patients without metastasis at presentation, race, histologic grade, estrogen/progesterone receptor (ER/PR) and HER2 statuses were significantly associated with de novo metastasis in the entire cohort, whereas age, histologic grade, PR and HER2 status were the significant parameters in the subset of patients with locally advanced breast cancer (Stage IIB/III). The patients with de novo metastatic breast cancer had a significant older mean age and a lower proportion of HER2-positive tumors when compared to those with metastatic recurrence. Further, the HER2-rich subtype demonstrated a drastically higher incidence of de novo metastasis when compared to the luminal and triple-negative breast cancers in the entire cohort [odds ratio (OR)=5.68 and 2.27, respectively] and in the patients with locally advanced disease (OR=4.02 and 2.12, respectively), whereas no significant difference was seen between de novo metastatic cancers and those with metastatic recurrence. Moreover, the luminal and HER2-rich subtypes showed bone-seeking (OR=1.92) and liver-homing (OR=2.99) characteristics, respectively, for the sites of de novo metastasis, while the latter was not observed in those with metastatic recurrence. Our data suggest that an algorithm incorporating clinicopathologic factors, especially histologic grade and receptor profile, remains of significant benefit during decision making in newly diagnosed breast cancer in the pursuit of precision medicine. Copyright © 2016 Elsevier GmbH. All rights reserved.

  2. NovoPen Echo® insulin delivery device

    Directory of Open Access Journals (Sweden)

    Hyllested-Winge J

    2016-01-01

    Full Text Available Jacob Hyllested-Winge,1 Thomas Sparre,2 Line Kynemund Pedersen2 1Novo Nordisk Pharma Ltd, Tokyo, Japan; 2Novo Nordisk A/S, Søborg, Denmark Abstract: The introduction of insulin pen devices has provided easier, well-tolerated, and more convenient treatment regimens for patients with diabetes mellitus. When compared with vial and syringe regimens, insulin pens offer a greater clinical efficacy, improved quality of life, and increased dosing accuracy, particularly at low doses. The portable and discreet nature of pen devices reduces the burden on the patient, facilitates adherence, and subsequently contributes to the improvement in glycemic control. NovoPen Echo® is one of the latest members of the NovoPen® family that has been specifically designed for the pediatric population and is the first to combine half-unit increment (=0.5 U of insulin dosing with a simple memory function. The half-unit increment dosing amendments and accurate injection of 0.5 U of insulin are particularly beneficial for children (and insulin-sensitive adults/elders, who often require small insulin doses. The memory function can be used to record the time and amount of the last dose, reducing the fear of double dosing or missing a dose. The memory function also provides parents with extra confidence and security that their child is taking insulin at the correct doses and times. NovoPen Echo is a lightweight, durable insulin delivery pen; it is available in two different colors, which may help to distinguish between different types of insulin, providing more confidence for both users and caregivers. Studies have demonstrated a high level of patient satisfaction, with 80% of users preferring NovoPen Echo to other pediatric insulin pens. Keywords: NovoPen Echo®, memory function, half-unit increment dosing, adherence, children, adolescents 

  3. De novo status epilepticus with isolated aphasia.

    Science.gov (United States)

    Flügel, Dominique; Kim, Olaf Chan-Hi; Felbecker, Ansgar; Tettenborn, Barbara

    2015-08-01

    Sudden onset of aphasia is usually due to stroke. Rapid diagnostic workup is necessary if reperfusion therapy is considered. Ictal aphasia is a rare condition but has to be excluded. Perfusion imaging may differentiate acute ischemia from other causes. In dubious cases, EEG is required but is time-consuming and laborious. We report a case where we considered de novo status epilepticus as a cause of aphasia without any lesion even at follow-up. A 62-year-old right-handed woman presented to the emergency department after nurses found her aphasic. She had undergone operative treatment of varicosis 3 days earlier. Apart from hypertension and obesity, no cardiovascular risk factors and no intake of medication other than paracetamol were reported. Neurological examination revealed global aphasia and right pronation in the upper extremity position test. Computed tomography with angiography and perfusion showed no abnormalities. Electroencephalogram performed after the CT scan showed left-sided slowing with high-voltage rhythmic 2/s delta waves but no clear ictal pattern. Intravenous lorazepam did improve EEG slightly, while aphasia did not change. Lumbar puncture was performed which likely excluded encephalitis. Magnetic resonance imaging showed cortical pathological diffusion imaging (restriction) and cortical hyperperfusion in the left parietal region. Intravenous anticonvulsant therapy under continuous EEG resolved neurological symptoms. The patient was kept on anticonvulsant therapy. Magnetic resonance imaging after 6 months showed no abnormalities along with no clinical abnormalities. Magnetic resonance imaging findings were only subtle, and EEG was without clear ictal pattern, so the diagnosis of aphasic status remains with some uncertainty. However, status epilepticus can mimic stroke symptoms and has to be considered in patients with aphasia even when no previous stroke or structural lesions are detectable and EEG shows no epileptic discharges. Epileptic origin is

  4. Biophysical characterization of a de novo elastin

    Science.gov (United States)

    Greenland, Kelly Nicole

    Natural human elastin is found in tissue such as the lungs, arteries, and skin. This protein is formed at birth with no mechanism present to repair or supplement the initial quantity formed. As a result, the functionality and durability of elastin's elasticity is critically important. To date, the mechanics of this ability to stretch and recoil is not fully understood. This study utilizes de novo protein design to create a small library of simplistic versions of elastin-like proteins, demonstrate the elastin-like proteins, maintain elastin's functionality, and inquire into its structure using solution nuclear magnetic resonance (NMR). Elastin is formed from cross-linked tropoelastin. Therefore, the first generation of designed proteins consisted of one protein that utilized homogony of interspecies tropoelastin by using three common domains, two hydrophobic and one cross-linking domains. Basic modifications were made to open the hydrophobic region and also to make the protein easier to purify and characterize. The designed protein maintained its functionality, self-aggregating as the temperature increased. Uniquely, the protein remained self-aggregated as the temperature returned below the critical transition temperature. Self-aggregation was additionally induced by increasing salt concentrations and by modifying the pH. The protein appeared to have little secondary structure when studied with solution NMR. These results fueled a second generation of designed elastin-like proteins. This generation contained variations designed to study the cross-linking domain, one specific hydrophobic domain, and the effect of the length of the elastin-like protein. The cross-linking domain in one variation has been significantly modified while the flanking hydrophobic domains have remained unchanged. This characterization of this protein will answer questions regarding the specificity of the homologous nature of the cross-linking domain of tropoelastin across species. A second

  5. Purine biosynthesis de novo by lymphocytes in gout

    International Nuclear Information System (INIS)

    Kamoun, P.; Chanard, J.; Brami, M.; Funck-Brentano, J.L.

    1978-01-01

    A method of measurement in vitro of purine biosynthesis de novo in human circulating blood lymphocytes is proposed. The rate of early reactions of purine biosynthesis de novo was determined by the incorporation of [ 14 C]formate into N-formyl glycinamide ribonucleotide when the subsequent reactions of the metabolic pathway were completely inhibited by the antibiotic azaserine. Synthesis of 14 C-labelled N-formyl glycinamide ribonucleotide by lymphocytes was measured in healthy control subjects and patients with primary gout or hyperuricaemia secondary to renal failure, with or without allopurinol therapy. The average synthesis was higher in gouty patients without therapy than in control subjects, but the values contained overlap the normal range. In secondary hyperuricaemia the synthesis was at same value as in control subjects. These results are in agreement with the inconstant acceleration of purine biosynthesis de novo in gouty patients as seen by others with measurement of [ 14 C]glycine incorporation into urinary uric acid. (author)

  6. Airline Maintenance Manpower Optimization from the De Novo Perspective

    Science.gov (United States)

    Liou, James J. H.; Tzeng, Gwo-Hshiung

    Human resource management (HRM) is an important issue for today’s competitive airline marketing. In this paper, we discuss a multi-objective model designed from the De Novo perspective to help airlines optimize their maintenance manpower portfolio. The effectiveness of the model and solution algorithm is demonstrated in an empirical study of the optimization of the human resources needed for airline line maintenance. Both De Novo and traditional multiple objective programming (MOP) methods are analyzed. A comparison of the results with those of traditional MOP indicates that the proposed model and solution algorithm does provide better performance and an improved human resource portfolio.

  7. Persistent hyperthyroidism and de novo Graves' ophthalmopathy after total thyroidectomy.

    Science.gov (United States)

    Tay, Wei Lin; Loh, Wann Jia; Lee, Lianne Ai Ling; Chng, Chiaw Ling

    2017-01-01

    We report a patient with Graves' disease who remained persistently hyperthyroid after a total thyroidectomy and also developed de novo Graves' ophthalmopathy 5 months after surgery. She was subsequently found to have a mature cystic teratoma containing struma ovarii after undergoing a total hysterectomy and salpingo-oophorectomy for an incidental ovarian lesion. It is important to investigate for other causes of primary hyperthyroidism when thyrotoxicosis persists after total thyroidectomy.TSH receptor antibody may persist after total thyroidectomy and may potentially contribute to the development of de novo Graves' ophthalmopathy.

  8. Demanda dos principais metais e novos materiais : analise de tendencias

    OpenAIRE

    Wilson Trigueiro de Sousa

    1990-01-01

    Resumo: Neste trabalho são analisadas algumas tendências na área de novos materiais na tentativa de obter um melhor entendimento das repercussões das atuais inovações tecnológicas para o setor mineral. Inicialmente são revisados os principais estudos sobre as mudanças ocorridas por volta de 1972/74 no comportamento da demanda dos metais mais importantes. Entre as possíveis causas, está o progresso técnico, que tornou possível o surgimento de novos materiais e o aperfeiçoamento de outros em us...

  9. Decomposição e liberação de nutrientes do folhedo de espécies florestais nativas em plantios puros e mistos no sudeste da Bahia

    Directory of Open Access Journals (Sweden)

    Gama-Rodrigues A. C.

    2003-01-01

    Full Text Available As taxas de decomposição e os fluxos de nutrientes do folhedo de espécies florestais são distintos em plantios puros e mistos, porque são regulados não apenas pela qualidade do substrato, mas também pela qualidade do microambiente de acordo com o tipo de sistema de produção florestal. O objetivo deste trabalho foi estimar as taxas de decomposição e a liberação de N e P do folhedo de espécies florestais em dois sistemas de plantio. Este trabalho foi desenvolvido em solos de tabuleiro do sudeste da Bahia, em plantios puros e mistos, com 22 anos de idade, de pau-roxo, Peltogyne angustiflora; putumuju, Centrolobium robustum; arapati, Arapatiella psilophylla; arapaçu, Sclerolobium chrysophyllum; claraíba, Cordia trichotoma, e óleo-comumbá, Macrolobium latifolium. Também foram utilizadas uma floresta secundária, praticamente em estado clímax, e uma capoeira, de 40 anos de idade. A decomposição de folhedo, colocado em sacos de malha de 1 mm, foi seguida durante um ano. O modelo que proporcionou melhor ajuste foi exponencial de 1ª ordem. No plantio misto, as taxas de decomposição do folhedo do pau-roxo e óleo-comumbá foram significativamente superiores àquelas dessas espécies em seus plantios puros, ao contrário do observado para o arapati. No entanto, as taxas de decomposição do folhedo do putumuju, arapaçu e claraíba não foram alteradas significativamente. O P, e não o N, seria o nutriente mais limitante para a decomposição do folhedo dessas espécies. A liberação de N e P do folhedo de cada espécie variou de acordo com o microambiente. Dentre os ecossistemas heterogêneos, a taxa de decomposição do folhedo do plantio misto diferiu significativamente apenas da floresta natural. A maior liberação do N ocorreu no plantio misto; já para o P, a capoeira foi o ecossistema que apresentou significativamente a menor liberação. Conclui-se que o plantio misto proporciona maior capacidade em reciclar matéria org

  10. Model-Based GUI Testing Using Uppaal at Novo Nordisk

    DEFF Research Database (Denmark)

    H. Hjort, Ulrik; Rasmussen, Jacob Illum; Larsen, Kim Guldstrand

    2009-01-01

    This paper details a collaboration between Aalborg University and Novo Nordiskin developing an automatic model-based test generation tool for system testing of the graphical user interface of a medical device on an embedded platform. The tool takes as input an UML Statemachine model and generates...

  11. Engineering and introduction of de novo disulphide bridges in ...

    Indian Academy of Sciences (India)

    The engineeringof de novo disulphide bridges has been explored as a means to increase the thermal stability of enzymes in the rationalmethod of protein engineering. In this study, Disulphide by Design software, homology modelling and moleculardynamics simulations were used to select appropriate amino acid pairs for ...

  12. De novo synthesis of milk triglycerides in humans

    Science.gov (United States)

    Mammary gland (MG) de novo lipogenesis contributes significantly to milk fat in animals but little is known in humans. Objective: To test the hypothesis that the incorporation of 13C carbons from [U-13C]glucose into fatty acids (FA) and glycerol in triglycerides (TG) will be greater: 1) in milk tha...

  13. Response monitoring in de novo patients with Parkinson's disease.

    Directory of Open Access Journals (Sweden)

    Rita Willemssen

    Full Text Available BACKGROUND: Parkinson's disease (PD is accompanied by dysfunctions in a variety of cognitive processes. One of these is error processing, which depends upon phasic decreases of medial prefrontal dopaminergic activity. Until now, there is no study evaluating these processes in newly diagnosed, untreated patients with PD ("de novo PD". METHODOLOGY/PRINCIPAL FINDINGS: Here we report large changes in performance monitoring processes using event-related potentials (ERPs in de novo PD-patients. The results suggest that increases in medial frontal dopaminergic activity after an error (Ne are decreased, relative to age-matched controls. In contrast, neurophysiological processes reflecting general motor response monitoring (Nc are enhanced in de novo patients. CONCLUSIONS/SIGNIFICANCE: It may be hypothesized that the Nc-increase is at costs of dopaminergic activity after an error; on a functional level errors may not always be detected and correct responses sometimes be misinterpreted as errors. This pattern differs from studies examining patients with a longer history of PD and may reflect compensatory processes, frequently occurring in pre-manifest stages of PD. From a clinical point of view the clearly attenuated Ne in the de novo PD patients may prove a useful additional tool for the early diagnosis of basal ganglia dysfunction in PD.

  14. Foldability of a Natural De Novo Evolved Protein.

    Science.gov (United States)

    Bungard, Dixie; Copple, Jacob S; Yan, Jing; Chhun, Jimmy J; Kumirov, Vlad K; Foy, Scott G; Masel, Joanna; Wysocki, Vicki H; Cordes, Matthew H J

    2017-11-07

    The de novo evolution of protein-coding genes from noncoding DNA is emerging as a source of molecular innovation in biology. Studies of random sequence libraries, however, suggest that young de novo proteins will not fold into compact, specific structures typical of native globular proteins. Here we show that Bsc4, a functional, natural de novo protein encoded by a gene that evolved recently from noncoding DNA in the yeast S. cerevisiae, folds to a partially specific three-dimensional structure. Bsc4 forms soluble, compact oligomers with high β sheet content and a hydrophobic core, and undergoes cooperative, reversible denaturation. Bsc4 lacks a specific quaternary state, however, existing instead as a continuous distribution of oligomer sizes, and binds dyes indicative of amyloid oligomers or molten globules. The combination of native-like and non-native-like properties suggests a rudimentary fold that could potentially act as a functional intermediate in the emergence of new folded proteins de novo. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. Towards accurate de novo assembly for genomes with repeats

    NARCIS (Netherlands)

    Bucur, Doina

    2017-01-01

    De novo genome assemblers designed for short k-mer length or using short raw reads are unlikely to recover complex features of the underlying genome, such as repeats hundreds of bases long. We implement a stochastic machine-learning method which obtains accurate assemblies with repeats and

  16. On the performance of de novo pathway enrichment

    DEFF Research Database (Denmark)

    Batra, Richa; Alcaraz, Nicolas; Gitzhofer, Kevin

    2017-01-01

    De novo pathway enrichment is a powerful approach to discover previously uncharacterized molecular mechanisms in addition to already known pathways. To achieve this, condition-specific functional modules are extracted from large interaction networks. Here, we give an overview of the state...

  17. De Novo Coding Variants Are Strongly Associated with Tourette Disorder

    DEFF Research Database (Denmark)

    Willsey, A Jeremy; Fernandez, Thomas V; Yu, Dongmei

    2017-01-01

    Whole-exome sequencing (WES) and de novo variant detection have proven a powerful approach to gene discovery in complex neurodevelopmental disorders. We have completed WES of 325 Tourette disorder trios from the Tourette International Collaborative Genetics cohort and a replication sample of 186 ...

  18. Illumina-based de novo transcriptome sequencing and analysis

    Indian Academy of Sciences (India)

    In the present study, we used Illumina HiSeq technology to perform de novo assembly of heart and musk gland transcriptomes from the Chinese forest musk deer. A total of 239,383 transcripts and 176,450 unigenes were obtained, of which 37,329 unigenes were matched to known sequences in the NCBI nonredundant ...

  19. De novo structural modeling and computational sequence analysis ...

    African Journals Online (AJOL)

    Different bioinformatics tools and machine learning techniques were used for protein structural classification. De novo protein modeling was performed by using I-TASSER server. The final model obtained was accessed by PROCHECK and DFIRE2, which confirmed that the final model is reliable. Until complete biochemical ...

  20. Direct Visualization of De novo Lipogenesis in Single Living Cells

    Science.gov (United States)

    Li, Junjie; Cheng, Ji-Xin

    2014-10-01

    Increased de novo lipogenesis is being increasingly recognized as a hallmark of cancer. Despite recent advances in fluorescence microscopy, autoradiography and mass spectrometry, direct observation of de novo lipogenesis in living systems remains to be challenging. Here, by coupling stimulated Raman scattering (SRS) microscopy with isotope labeled glucose, we were able to trace the dynamic metabolism of glucose in single living cells with high spatial-temporal resolution. As the first direct visualization, we observed that glucose was largely utilized for lipid synthesis in pancreatic cancer cells, which occurs at a much lower rate in immortalized normal pancreatic epithelial cells. By inhibition of glycolysis and fatty acid synthase (FAS), the key enzyme for fatty acid synthesis, we confirmed the deuterium labeled lipids in cancer cells were from de novo lipid synthesis. Interestingly, we also found that prostate cancer cells exhibit relatively lower level of de novo lipogenesis, but higher fatty acid uptake compared to pancreatic cancer cells. Together, our results demonstrate a valuable tool to study dynamic lipid metabolism in cancer and other disorders.

  1. Particulated articular cartilage: CAIS and DeNovo NT.

    Science.gov (United States)

    Farr, Jack; Cole, Brian J; Sherman, Seth; Karas, Vasili

    2012-03-01

    Cartilage Autograft Implantation System (CAIS; DePuy/Mitek, Raynham, MA) and DeNovo Natural Tissue (NT; ISTO, St. Louis, MO) are novel treatment options for focal articular cartilage defects in the knee. These methods involve the implantation of particulated articular cartilage from either autograft or juvenile allograft donor, respectively. In the laboratory and in animal models, both CAIS and DeNovo NT have demonstrated the ability of the transplanted cartilage cells to "escape" from the extracellular matrix, migrate, multiply, and form a new hyaline-like cartilage tissue matrix that integrates with the surrounding host tissue. In clinical practice, the technique for both CAIS and DeNovo NT is straightforward, requiring only a single surgery to affect cartilage repair. Clinical experience is limited, with short-term studies demonstrating both procedures to be safe, feasible, and effective, with improvements in subjective patient scores, and with magnetic resonance imaging evidence of good defect fill. While these treatment options appear promising, prospective randomized controlled studies are necessary to refine the indications and contraindications for both CAIS and DeNovo NT.

  2. Influência dos créditos de carbono na viabilidade financeira de três projetos florestais Influence of carbon credits on the financial viability of three forest projects

    Directory of Open Access Journals (Sweden)

    Marcos Hiroshi Nishi

    2005-04-01

    Full Text Available O presente trabalho teve como objetivo estudar a influência dos créditos de carbono na viabilidade financeira de três projetos florestais. Os projetos analisados foram: heveicultura, eucalipto e pinus para produção de borracha, celulose e resina, respectivamente. O Valor Presente Líquido (VPL, a Taxa Interna de Retorno (TIR, o Valor Esperado da Terra (VET e o Valor Anual Equivalente (VAE foram os indicadores utilizados na avaliação financeira, a uma taxa de desconto de 10% ao ano. Os resultados deste trabalho indicaram que, com esta taxa, os projetos de eucalipto e pinus foram viáveis sem os recursos adicionais dos CERs (Certificados de Emissões Reduzidas, ressaltando-se que a inclusão dos créditos de carbono propiciou aumento da viabilidade financeira destes. Já o projeto da heveicultura mostrou-se viável apenas com os Certificados de Carbono. A receita advinda da venda dos CERs aumentou consideravelmente a viabilidade financeira dos três projetos, mesmo considerando a tonelada de CO2 a US$3,00. Caso o Protocolo de Kyoto seja ratificado, haverá um incremento no preço pago pela tonelada de CO2, que ocasionará o aumento da contribuição dos CERs em projetos florestais.The objective of the present work was to study the influence of carbon credits on the financial viability of three forest projects. The analyzed projects were: heveiculture, eucalyptus and pinus for production of natural rubber, cellulose and resin, respectively. The Net Present Value (NPV, the Internal Return Rate (IRR, the Soil Expected Value (SEV and the Equivalent Annual Value (EAV were the indicators used in the financial evaluation, using a discount rate of 10% a year. The results of this work demonstrated that with this rate, the projects of eucalyptus and pinus were viable without additional resources from the CERs (Certificates of Emissions Reduced, and the inclusion of the carbon credits induced an increase in their financial viability. The heveiculture

  3. Crescimento inicial de espécies florestais na recomposição da mata ciliar em taludes submetidos à técnica da bioengenharia de solos.

    Directory of Open Access Journals (Sweden)

    Francisco Sandro Rodrigues Holanda

    2010-08-01

    Full Text Available A Bacia Hidrográfica do rio São Francisco, vem sendo submetida a fortes impactos ambientais por meio de alterações do regime hidrológico e sedimentológico, além de avançada destruição da sua mata ciliar. A vegetação ciliar possui importante função na proteção das margens dos rios promovida pela cobertura vegetal e seu sistema radicular, melhorando a agregação de um solo pouco coeso, diminuindo o arraste de partículas e, consequentemente resultando em menor taxa de erosão e assoreamento do curso d'água. Este trabalho teve como objetivo avaliar o crescimento inicial de espécies florestais em talude marginal submetido à técnica de bioengenharia de solos no rio São Francisco. A bioengenharia de solos foi composta pela cobertura longitudinal do talude com o biotêxtil (Tela Fibrax® 400BF, e em razão das variações diárias de cota do rio foram também utilizados retentores de sedimentos (Bemalonga® D40 para redução ao impacto da água na base do talude, evitando o solapamento promovido pelo fluxo e refluxo das ondas. Antes da fixação do biotêxtil, foram semeadas a lanço sementes da espécie Brachiaria decumbens para promoção de uma rápida cobertura vegetal. Em seguida foram plantadas mudas de seis espécies florestais nativas da região: aroeira vermelha (Schinus terebinthifolius Raddi., pau-pombo (Tapirira guianensis Aubl., mulungu (Erythrina velutina Willd., tamboril (Enterolobium contortisiliquum (Vellozo Morong, canafístula (Cassia grandis L.f. e pau-ferro (Caesalpinia leiostachya (Bentham Ducke. O desenvolvimento das mudas foi analisado por meio da Taxa de Crescimento Relativo de Altura da parte aérea e Diâmetro do colo. Após 360 dias, ao final das avaliações, observou-se que o maior número de indivíduos vivos foi identificado no tratamento com bioengenharia de solos. A grande densidade e agressivo crescimento da espécie Brachiaria decumbens na área com biotêxtil, trouxe danos para o

  4. Genome-wide patterns and properties of de novo mutations in humans

    NARCIS (Netherlands)

    Francioli, Laurent C.; Polak, Paz P.; Koren, Amnon; Menelaou, Androniki; Chun, Sung; Renkens, Ivo; van Duijn, Cornelia M.; Swertz, Morris; Wijmenga, Cisca; van Ommen, Gertjan; Slagboom, P. Eline; Boomsma, Dorret I.; Ye, Kai; Guryev, Victor; Arndt, Peter F.; Kloosterman, Wigard P.; de Bakker, Paul I. W.; Sunyaev, Shamil R.

    Mutations create variation in the population, fuel evolution and cause genetic diseases. Current knowledge about de novo mutations is incomplete and mostly indirect(1-10). Here we analyze 11,020 de novo mutations from the whole genomes of 250 families. We show that de novo mutations in the offspring

  5. Genome-wide patterns and properties of de novo mutations in humans

    NARCIS (Netherlands)

    Francioli, L.C.; Polak, P.P.; Koren, A.; Menelaou, A.; Chun, S.; Renkens, I.; van Duijn, C.M.; Swertz, M.A.; Wijmenga, C.; van Ommen, G.J.; Slagboom, P.E.; Boomsma, D.I.; Ye, K.; Guryev, V.; Arndt, P.F.; Kloosterman, W.P.; Bakker, P.I.W.; Sunyaev, S.R.; Dijk, F.; Neerincx, P.B.T.; Pulit, S.L.; Deelen, P.; Elbers, C.C.; Palamara, P.F.; Pe'er, I.; Abdellaoui, A.; van Oven, M.; Vermaat, M.; Li, M.; Laros, J.F.J.; Stoneking, M.; de Knijff, P.; Kayser, M.; Veldink, J.H.; Van den Berg, L.H.; Byelas, H.; den Dunnen, J.T.; Dijkstra, M.; Amin, N.; van der Velde, K.J.; Hottenga, J.J.; van Setten, J.; van Leeuwen, E.M.; Kanterakis, A.; Kattenberg, V.M.; Karssen, L.C.; van Schaik, B.D.C.; Bot, J.; Nijman, I.J.; van Enckevort, D.; Mei, H.; Koval, V.; Estrada, K.; Medina-Gomez, C.; Lameijer, E.W.; Moed, M.H.; Hehir-Kwa, J.Y.; Handsaker, R.E.; McCarroll, S.A.; Vuzman, D.; Sohail, M.; Hormozdiari, F.; Marschall, T.; Schönhuth, A.; Beekman, M.; de Craen, A.J.; Suchiman, H.E.D.; Hofman, A.; Oostra, B.; Isaacs, A.; Rivadeneira, F.; Uitterlinden, A.G.; Willemsen, G.; Platteel, M.; Pitts, S.J.; Potluri, S.; Sundar, P.; Cox, D.R.; Li, Q.; Li, Y.; Du, Y.; Chen, R.; Cao, H.; Li, N.; Cao, S.; Wang, J.; Bovenberg, J.A.; Brandsma, M.

    2015-01-01

    Mutations create variation in the population, fuel evolution and cause genetic diseases. Current knowledge about de novo mutations is incomplete and mostly indirect. Here we analyze 11,020 de novo mutations from the whole genomes of 250 families. We show that de novo mutations in the offspring of

  6. Características físico-química, energética e dimensões das fibras de três espécies florestais do semiárido brasileiro

    Directory of Open Access Journals (Sweden)

    Juarez Benigno Paes

    Full Text Available Esta pesquisa teve como objetivo avaliar as características físico-química, energética e dimensões das fibras das madeiras de angico-vermelho (Anadenanthera colubrina var. cebil, jurema-preta (Mimosa tenuiflora e jurema-vermelha (Mimosa arenosa, espécies de ocorrência no Semiárido Brasileiro e empregadas para energia. Para tanto, foram colhidas cinco árvores de cada espécie estudada. A caracterização física foi realizada no Laboratório de Tecnologia de Produtos Florestais (LTPF da Universidade Federal de Campina Grande e a caracterização química e a análise das dimensões das fibras no Laboratório de Papel e Celulose da Universidade Federal de Viçosa. De modo geral, as madeiras ensaiadas tiveram características físicas e dimensões das fibras semelhantes. Quanto às características químicas, a jurema-preta teve maior solubilidade em álcool:tolueno, maior teor de lignina total e menores teores de holocelulose e cinzas do que as demais espécies, tendo três vezes menos cinzas do que a madeira de angico-vermelho e a metade do apresentado pela jurema-vermelha.

  7. Avaliação dos bancos de sementes do solo de fragmentos florestais de mata estacional semidecidual clímax e secundária e seu potencial em recuperar áreas degradadas

    Directory of Open Access Journals (Sweden)

    Marissol Aparecida Peres

    2009-08-01

    Full Text Available O banco de sementes do solo é constituído por serrapilheira e sementes não germinadas capazes de substituir plantas que possam ter desaparecido da floresta. O objetivo deste estudo foi avaliar o banco de sementes do solo de fragmentos de floresta estacional semidecidual em diferentes estágios de sucessão e o seu potencial em recuperar áreas degradadas. A partir da coleta do banco de sementes do solo em dois fragmentos florestais de Mata Clímax e Secundária foi instalado o experimento com 4 tratamentos (Mata Clímax a pleno sol; Mata Clímax sombreada; Mata Secundária a pleno solo; Mata Secundária sombreada utilizando 4 repetições no delineamento de blocos casualizados. A avaliação consistiu em identificar e quantificar as plântulas emergidas. Observouse que a Mata Secundária apresentou maior diversidade florística e densidade de indivíduos que a Mata Clímax, que o sombreamento mostrou efeito positivo no potencial de germinação do banco de sementes do solo das Matas Clímax e Secundária e que o banco de sementes do solo apresenta potencial em recuperar áreas degradadas.

  8. Adequação dos índices da análise econômico-financeira às empresas florestais Adequateness of the economic and financial analysis in forestry companies

    Directory of Open Access Journals (Sweden)

    Anselmo Chaves Neto

    2007-10-01

    Full Text Available Existem diversos métodos para a análise econômico-financeira das empresas. Dentre eles, por diversas razões, o mais utilizado é o da análise pelo emprego de índices (MATARAZZO, 1998. Contudo, uma pesquisa na bibliografia brasileira especializada possibilitou identificar mais de duas centenas de índices diferentes. A sua seleção, mediante o critério de emprego pelo maior número de autores, reduziu-os para vinte e seis índices. Em face das características operacionais específicas das empresas florestais - seu longo ciclo operacional - pressupôs-se que o emprego daqueles índices, de uso generalizado na análise econômico-financeira de empresas quaisquer - de ciclo operacional relativamente curto - não fosse adequado para a análise das empresas florestais. Atualmente, não existe nenhuma referência sobre índices específicos para análise econômico-financeira de empresas florestais. Pressupôs-se que esta diferença entre os ciclos operacionais resultaria em desempenhos econômico-financeiros, bem como em condições patrimoniais, totalmente diversos. Também não existe nenhuma referência sobre este pressuposto. Dentre outros, um dos algoritmos de grande utilidade para a pesquisa é fornecido pela análise fatorial, segundo JOHNSON & WICHERN (1998. Conforme os mesmos autores, essa técnica extrai as informações sobre a estrutura de covariância, resumidas na matriz de correlação, e possibilita classificar as variáveis originais segundo a sua participação na variância total dos dados. Isso posto, esta pesquisa teve como objetivo principal investigar, com o uso da análise fatorial, em que medida os índices usualmente empregados para a análise econômico-financeira de empresas quaisquer podem ser empregados na análise das empresas florestais. Os vinte e seis índices selecionados foram aplicados sobre os balanços de duzentas e trinta e sete empresas, constituídas sob a modalidade jurídica de sociedades an

  9. IMPORTÂNCIA DE REMANESCENTES FLORESTAIS PARA CONSERVAÇÃO DA BIODIVERSIDADE: ESTUDO DE CASO NA MATA ATLÂNTICA EM SERGIPE ATRAVÉS DE SENSORIAMENTO REMOTO

    Directory of Open Access Journals (Sweden)

    André Luiz Conceição Santos, Celso Morato de Carvalho, Thiago Morato de Carvalho

    2014-07-01

    Full Text Available São discutidos aspectos relevantes sobre fragmentos florestados para a conservação da biodiversidade e especificamente são analisados 403 remanescentes florestais (31.000 ha na mata atlântica de Sergipe através de sensoriamento remoto com base em imagens Spot 5 e fotografias aéreas. Os remanescentes foram categorizados em cinco grupamentos: i Santa Luzia do Itanhy-Estância, ii Aracaju-São Cristóvão-Itabaiana, iii Rosário do Catete, iv Japaratuba, v Pacatuba-Japoatã. A maioria dos fragmentos variou entre 17 – 70 ha; os grupamentos entre Aracaju e Santa Luzia do Itanhy estão entre os maiores. A conectividade entre os fragmentos variou entre 2-19 km; as distâncias médias entre fragmentos variaram em torno de 1 km. Os índices de circularidade variaram entre 0,006-0,31, mostrando prevalência de fragmentos com bordas irregulares.

  10. Melhoramento do cafeeiro: IV - Café Mundo Novo

    Directory of Open Access Journals (Sweden)

    A. Carvalho

    1952-06-01

    Full Text Available Em um conjunto de cafeeiros existentes em Mundo Novo, hoje Urupês, na região Araraquarense do Estado de São Paulo, foram feitas seleções de vários cafeeiros baseando-se no seu aspecto vegetativo, na produção existente na época da seleção e na provável produção do ano seguinte. Estudou-se a origem da plantação inicial desse café, tanto em Urupês como em Jaú, chegando-se à conclusão de que é provavelmente originário desta última localidade. Progênies do café "Mundo Novo", anteriormente conhecido por "Sumatra" e derivado de plantas selecionadas em Urupês e Jaú, acham-se em estudo em seis localidades do Estado : Campinas, Ribeirão Prêto, Pindorama, Mococa, Jaú e Monte Alegre do Sul. No presente trabalho são apenas aproveitados dados referentes à variabilidade morfológica e característicos da produção das progênies dos primeiros cafeeiros selecionados em Urupês e estudados em Campinas, Jaú, Pindorama e Mococa. Em tôdas as localidades, observou-se variação nos caracteres morfológicos das progênies, verificando-se a ocorrência de plantas quase improdutivas. A maioria das progênies, no entanto, se caracteriza por acentuado vigor vegetativo. Foram estudadas as produções totais das progénies e das plantas, no período 1946-1951, notando-se que algumas progénies se salientaram pela elevada produção em tôdas as localidades. Os tipos de sementes "moca", "concha" e "chato" foram determinados em amostras de tôdas as plantas, por um período de três anos, notando-se que a variação ocorrida é da mesma ordem que a encontrada em outros cafeeiros em seleção. Procurou-se eliminar, pela seleção, cafeeiros com elevada produção de frutos sem sementes em uma ou duas lojas, característico êsse que parece ser hereditário. Os resultados obtidos de cruzamento entre os melhores cafeeiros "Mundo Novo" de Campinas e plantas da variedade murta, indicaram que esses cafeeiros são do tipo bourbon. Provavelmente

  11. Recurrence risk in de novo structural chromosomal rearrangements.

    Science.gov (United States)

    Röthlisberger, Benno; Kotzot, Dieter

    2007-08-01

    According to the textbook of Gardner and Sutherland [2004], the standard on genetic counseling for chromosome abnormalities, the recurrence risk of de novo structural or combined structural and numeric chromosome rearrangements is less than 0.5-2% and takes into account recurrence by chance, gonadal mosaicism, and somatic-gonadal mosaicism. However, these figures are roughly estimated and neither any systematic study nor exact or evidence-based risk calculations are available. To address this question, an extensive literature search was performed and surprisingly only 29 case reports of recurrence of de novo structural or combined structural and numeric chromosomal rearrangements were found. Thirteen of them were with a trisomy 21 due to an i(21q) replacing one normal chromosome 21. In eight of them low-level mosaicism in one of the parents was found either in fibroblasts or in blood or in both. As a consequence of the low number of cases and theoretical considerations (clinical consequences, mechanisms of formation, etc.), the recurrence risk should be reduced to less than 1% for a de novo i(21q) and to even less than 0.3% for all other de novo structural or combined structural and numeric chromosomal rearrangements. As the latter is lower than the commonly accepted risk of approximately 0.3% for indicating an invasive prenatal diagnosis and as the risk of abortion of a healthy fetus after chorionic villous sampling or amniocentesis is higher than approximately 0.5%, invasive prenatal investigation in most cases is not indicated and should only be performed if explicitly asked by the parents subsequent to appropriate genetic counseling. (c) 2007 Wiley-Liss, Inc.

  12. Novos encontros de anofelíneos em recipientes artificiais

    Directory of Open Access Journals (Sweden)

    Oswaldo Paulo Forattini

    1998-12-01

    Full Text Available Assinalam-se novos encontros de anofelíneos em recipientes artificiais. Um deles diz respeito a formas imaturas de Anopheles bellator em criadouros experimentais e outro é concernente ao achado de An. albitarsis l.s., em recipiente abandonado. Tecem-se considerações sobre a pressão seletiva representada pela produção, cada vez maior, de objetos descartáveis.

  13. Infant Mortality in Novo Hamburgo: Associated Factors and Cardiovascular Causes

    Energy Technology Data Exchange (ETDEWEB)

    Brum, Camila de Andrade [Instituto de Cardiologia/Fundação Universitária de Cardiologia (IC/FUC), Porto Alegre, RS (Brazil); Stein, Airton Tetelbom [Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS (Brazil); Grupo Hospitalar Conceição (GHC), Porto Alegre, RS (Brazil); Universidade Luterana do Brasil (ULBRA), Porto Alegre, RS (Brazil); Pellanda, Lucia Campos, E-mail: luciapell.pesquisa@cardiologia.org.br [Instituto de Cardiologia/Fundação Universitária de Cardiologia (IC/FUC), Porto Alegre, RS (Brazil); Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS (Brazil)

    2015-04-15

    Infant mortality has decreased in Brazil, but remains high as compared to that of other developing countries. In 2010, the Rio Grande do Sul state had the lowest infant mortality rate in Brazil. However, the municipality of Novo Hamburgo had the highest infant mortality rate in the Porto Alegre metropolitan region. To describe the causes of infant mortality in the municipality of Novo Hamburgo from 2007 to 2010, identifying which causes were related to heart diseases and if they were diagnosed in the prenatal period, and to assess the access to healthcare services. This study assessed infants of the municipality of Novo Hamburgo, who died, and whose data were collected from the infant death investigation records. Of the 157 deaths in that period, 35.3% were reducible through diagnosis and early treatment, 25% were reducible through partnership with other sectors, 19.2% were non-preventable, 11.5% were reducible by means of appropriate pregnancy monitoring, 5.1% were reducible through appropriate delivery care, and 3.8% were ill defined. The major cause of death related to heart disease (13.4%), which was significantly associated with the variables ‘age at death’, ‘gestational age’ and ‘birth weight’. Regarding access to healthcare services, 60.9% of the pregnant women had a maximum of six prenatal visits. It is mandatory to enhance prenatal care and newborn care at hospitals and basic healthcare units to prevent infant mortality.

  14. Infant Mortality in Novo Hamburgo: Associated Factors and Cardiovascular Causes

    Directory of Open Access Journals (Sweden)

    Camila de Andrade Brum

    2015-04-01

    Full Text Available Background: Infant mortality has decreased in Brazil, but remains high as compared to that of other developing countries. In 2010, the Rio Grande do Sul state had the lowest infant mortality rate in Brazil. However, the municipality of Novo Hamburgo had the highest infant mortality rate in the Porto Alegre metropolitan region. Objective: To describe the causes of infant mortality in the municipality of Novo Hamburgo from 2007 to 2010, identifying which causes were related to heart diseases and if they were diagnosed in the prenatal period, and to assess the access to healthcare services. Methods: This study assessed infants of the municipality of Novo Hamburgo, who died, and whose data were collected from the infant death investigation records. Results: Of the 157 deaths in that period, 35.3% were reducible through diagnosis and early treatment, 25% were reducible through partnership with other sectors, 19.2% were non-preventable, 11.5% were reducible by means of appropriate pregnancy monitoring, 5.1% were reducible through appropriate delivery care, and 3.8% were ill defined. The major cause of death related to heart disease (13.4%, which was significantly associated with the variables ‘age at death’, ‘gestational age’ and ‘birth weight’. Regarding access to healthcare services, 60.9% of the pregnant women had a maximum of six prenatal visits. Conclusion: It is mandatory to enhance prenatal care and newborn care at hospitals and basic healthcare units to prevent infant mortality.

  15. Generative Recurrent Networks for De Novo Drug Design.

    Science.gov (United States)

    Gupta, Anvita; Müller, Alex T; Huisman, Berend J H; Fuchs, Jens A; Schneider, Petra; Schneider, Gisbert

    2018-01-01

    Generative artificial intelligence models present a fresh approach to chemogenomics and de novo drug design, as they provide researchers with the ability to narrow down their search of the chemical space and focus on regions of interest. We present a method for molecular de novo design that utilizes generative recurrent neural networks (RNN) containing long short-term memory (LSTM) cells. This computational model captured the syntax of molecular representation in terms of SMILES strings with close to perfect accuracy. The learned pattern probabilities can be used for de novo SMILES generation. This molecular design concept eliminates the need for virtual compound library enumeration. By employing transfer learning, we fine-tuned the RNN's predictions for specific molecular targets. This approach enables virtual compound design without requiring secondary or external activity prediction, which could introduce error or unwanted bias. The results obtained advocate this generative RNN-LSTM system for high-impact use cases, such as low-data drug discovery, fragment based molecular design, and hit-to-lead optimization for diverse drug targets. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

  16. Infant Mortality in Novo Hamburgo: Associated Factors and Cardiovascular Causes

    International Nuclear Information System (INIS)

    Brum, Camila de Andrade; Stein, Airton Tetelbom; Pellanda, Lucia Campos

    2015-01-01

    Infant mortality has decreased in Brazil, but remains high as compared to that of other developing countries. In 2010, the Rio Grande do Sul state had the lowest infant mortality rate in Brazil. However, the municipality of Novo Hamburgo had the highest infant mortality rate in the Porto Alegre metropolitan region. To describe the causes of infant mortality in the municipality of Novo Hamburgo from 2007 to 2010, identifying which causes were related to heart diseases and if they were diagnosed in the prenatal period, and to assess the access to healthcare services. This study assessed infants of the municipality of Novo Hamburgo, who died, and whose data were collected from the infant death investigation records. Of the 157 deaths in that period, 35.3% were reducible through diagnosis and early treatment, 25% were reducible through partnership with other sectors, 19.2% were non-preventable, 11.5% were reducible by means of appropriate pregnancy monitoring, 5.1% were reducible through appropriate delivery care, and 3.8% were ill defined. The major cause of death related to heart disease (13.4%), which was significantly associated with the variables ‘age at death’, ‘gestational age’ and ‘birth weight’. Regarding access to healthcare services, 60.9% of the pregnant women had a maximum of six prenatal visits. It is mandatory to enhance prenatal care and newborn care at hospitals and basic healthcare units to prevent infant mortality

  17. Web Access to Digitised Content of the Exhibition Novo Mesto 1848-1918 at the Dolenjska Museum, Novo Mesto

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    Majda Pungerčar

    2013-09-01

    Full Text Available EXTENDED ABSTRACTFor the first time, the Dolenjska museum Novo mesto provided access to digitised museum resources when they took the decision to enrich the exhibition Novo mesto 1848-1918 by adding digital content. The following goals were identified: the digital content was created at the time of exhibition planning and design, it met the needs of different age groups of visitors, and during the exhibition the content was accessible via touch screen. As such, it also served for educational purposes (content-oriented lectures or problem solving team work. In the course of exhibition digital content was accessible on the museum website http://www.novomesto1848-1918.si. The digital content was divided into the following sections: the web photo gallery, the quiz and the game. The photo gallery was designed in the same way as the exhibition and the print catalogue and extended by the photos of contemporary Novo mesto and accompanied by the music from the orchestron machine. The following themes were outlined: the Austrian Empire, the Krka and Novo mesto, the town and its symbols, images of the town and people, administration and economy, social life and Novo mesto today followed by digitised archive materials and sources from that period such as the Commemorative book of the Uniformed Town Guard, the National Reading Room Guest Book, the Kazina guest book, the album of postcards and the Diploma of Honoured Citizen Josip Gerdešič. The Web application was also a tool for a simple and on line selection of digitised material and the creation of new digital content which proved to be much more convenient for lecturing than Power Point presentations. The quiz consisted of 40 questions relating to the exhibition theme and the catalogue. Each question offered a set of three answers only one of them being correct and illustrated by photography. The application auto selected ten questions and valued the answers immediately. The quiz could be accessed

  18. Agrupamento em amostras de sementes de espécies florestais nativas do Estado do Rio Grande do Sul - Brasil Cluster in seeds samples of native forest species from the State of Rio Grande do Sul - Brazil

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    Fabiano de Oliveira Fortes

    2008-09-01

    Full Text Available Este trabalho teve como objetivos agrupar por espécie as matrizes de porta-sementes mais similares, utilizando as variáveis observadas em análises de sementes de espécies florestais nativas no Centro de Pesquisas Florestais e Conservação do Solo, Santa Maria, Rio Grande do Sul, analisadas a partir de 1997 até março de 2001. Para a análise de agrupamento, foram utilizadas todas as espécies que possuíam quatro ou mais análises de amostras de sementes por lote coletado, pelo método de agrupamento aglomerativo hierárquico tendo a distância euclidiana média padronizada como medida de similaridade. O dendograma foi construído utilizando o método da ligação completa. Utilizou-se também a técnica de componentes principais para a redução do número de variáveis. O gênero Schinus sp. e as espécies nativas Cassia leptophylla Vogel, Peltophorum dubium (Spreng. Taub., Cedrela fissilis Vell., Allophylus edulis (A. St.-Hil., Cambess. & A. Juss. Radlk., Lafoensia pacari A. St.-Hil., Enterolobium contortisiliquum (Vell. Morong. e Apuleia leiocarpa (Vogel J. F. Macbr. foram as espécies em que, no terceiro e quarto componentes principais, conseguiram explicar aproximadamente 80% da variação existente no conjunto de dados com a umidade e a percentagem de germinação de plântulas anormais, sendo eliminadas na maioria das espécies e as percentagem de germinação de plântulas normais e de sementes mortas presentes em todos os grupos. A análise de agrupamento mostrou-se eficiente na separação dos grupos de todas as espécies testadas sendo que a procedência pouco influenciou na formação dos grupos.This research had the objectives of clustering, the most similar seeds matrixes by species, using the observed variables in analysis of seed samples of native forest species in the Center of Forest Researches and Conservation of the Soil, Santa Maria, Rio Grande do Sul, since 1997 up to March 2001. For the cluster analysis, all the

  19. Morphometric of four species in agroforestry systems in the municipality of Porto Velho, Rondônia. = Morfometria de quatro espécies florestais em sistemas agroflorestais no munícipio de Porto Velho, Rondônia

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    Tiago Monteiro Condé

    2013-04-01

    produtiva (16,5 anos do Projeto RECA (Reflorestamento Econômico Consorciado e Adensado no município de Porto Velho, Rondônia. A implantação dos SAF´s ocorreu mediante a supressão da vegetação por meio do processo de derrubada e queima da floresta nativa. Foram coletados aleatoriamente dados morfométricos de indivíduos com DAP > 10 cm das quatro espécies florestais em 1 ha de cada propriedade rural , totalizando uma área amostral de 20 ha (20 propriedades. A amostragem foi composta por 25 indivíduos de Andiroba, 40 de Castanheira-do-Brasil, 23 de Copaíba e 46 de Mogno. A Andiroba foi bastante semelhante ao Mogno em relação à Porcentagem de Copa(PC, Índice de Abrangência (IA e Forma de Copa (FC e ambas demonstraram potencialidade para plantios adensados com fins madeireiros. A Castanheira-do-Brasil e a Copaíba obtiveram os maiores valores de FC (1,66; 1,79 e Área de Copa (92,60;57,51, respectivamente, indicando copas frondosas, características silviculturais interessantes para o extrativismo de sementes. Foi simulado o espaço vital para que às quatro espécies desenvolvessem sem competição entre copas. Concluiu-se que, ambas as espécies apresentaram potencial para plantio visando à extração de produtos madeireiros e não madeireiros em áreas florestais submetidas ao desmatamento e degradação na Amazônia.

  20. Species composition and similarities among anuran assemblages of forest sites in southeastern Brazil Composição de espécies e similaridades entre taxocenoses de anuros de áreas florestais do sudeste do Brasil

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    Jaime Bertoluci

    2007-08-01

    Full Text Available Neotropical forests show high anuran species richness, but some Brazilian forest formations, like cerradão, semideciduous forests and restingas, remain poorly known. The composition of anuran species were determined for four forest sites belonging to different biomes in southeastern Brazil, based on two complementary techniques (visual encounter survey and survey on breeding sites, both applied simultaneously. A total of 60 anuran species belonging to eight families was recorded. Species richness and levels of endemism were higher in the Atlantic rainforest site. Sites located in the Cerrado domain were more alike than those located in the Atlantic Forest Domain. Similarity in anuran species composition was negatively correlated to the geographical distance among sites, which explains part of similarities in species composition. Factors affecting these occurrence patterns are discussed. One species (if its identity is confirmed is considered Data Deficient by IUCN (The World Conservation Union, though it is not included in the Brazilian list of threatened amphibians. The presence of certain species with special habitats and microclimate requirements (bioindicators suggests well-preserved ecosystems.As florestas neotropicais apresentam altas riquezas de espécies de anuros, mas algumas formações florestais brasileiras, como o cerradão, as florestas semidecíduas e as restingas, permanecem pouco conhecidas. A composição de espécies de anuros de quatro áreas florestais pertencentes a diferentes biomas do sudeste do Brasil foi determinada com base em duas técnicas complementares (procura visual e investigação nos sítios reprodutivos, aplicadas de forma simultânea. Registramos um total de 60 espécies de anuros, incluídas em oito famílias. A riqueza de espécies e o nível de endemismo foram maiores na área coberta por floresta pluvial atlântica. As áreas localizadas no domínio do Cerrado foram mais similares entre si do que as

  1. Uso de resíduos em pavimentos de estradas florestais: caracterização de solos e misturas solo-grits Application of waste in forest road pavements: characterization of soils and soil-grits mixtures

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    Reginaldo Sérgio Pereira

    2006-08-01

    Full Text Available Este artigo aborda uma etapa preliminar de um estudo direcionado às propriedades de engenharia de misturas de solos e aditivos químicos, para fins de aplicação em estradas florestais. Trabalhou-se com amostras de dois solos da Zona da Mata Norte de Minas Gerais, Brasil, de texturas arenosa e argilosa, estabilizadas com o resíduo industrial denominado "grits" proveniente de indústria de celulose. Foram realizados ensaios geotécnicos nos solos e nas misturas solo-aditivo químico, como se segue: análise granulométrica, peso específico dos sólidos, limites de Atterberg e compactação. Os resultados encontrados dos ensaios de laboratório revelaram que o resíduo apresentou bom desempenho como agente estabilizante, alterando significativamente a plasticidade e os parâmetros de compactação dos solos analisados.This paper addresses data from a research program in development on engineering properties of soil-chemical stabilizer mixtures for forest road application. Soil samples from sandy and clayey soils from the Zona da Mata Norte of Minas Gerais, Brazil, stabilized with grits (waste from cellulose industries were used throughout the study. The laboratory-testing program comprised the following geotechnical tests: sieve analysis, density of solid particles, Atterberg limits and compaction. Data supported the good behavior of waste as stabilizer agent changing significantly soil plasticity and compaction parameters.

  2. Produtos agrícolas e florestais como alimento suplementar de tambaqui em policultivo com jaraqui Agricultural and forest products as supplementary feeding for tambaqui in polyculture with jaraqui

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    Sérgio Fonseca Guimarães

    2004-03-01

    Full Text Available O objetivo deste trabalho foi avaliar o desempenho de tambaqui (Colossoma macropomum, em policultivo com jaraqui (Semaprochilodus insignis, alimentado com produtos agrícolas e florestais como suplemento. Dois viveiros, medindo 644 m² (Viveiro A, consorciado com suínos e 1.075 m² (Viveiro B, não-consorciado, foram utilizados com 0,5 tambaqui/m² e 0,1 jaraqui/m². Após 371 dias, os tambaquis apresentaram crescimento de 18,6±4,5 g para 997,1±195,08 g no Viveiro A e de 81,4±18,8 g para 519,9±191,7 g no Viveiro B. O manejo alimentar do Viveiro A pode ser uma alternativa sustentável de produção de tambaqui em substituição às rações comerciais.The objective of this paper was to evaluate the performance of tambaqui (Colossoma macropomum in a polyculture trial with jaraqui (Semaprochilodus insignis, using agricultural and forest products as supplementary feeding for tambaqui. Two ponds, measuring 644 m² (Pond A, associated with pigs and 1,075 m² (Pond B, non associated, were stocked with 0.5 tambaqui/m² and 0.1 jaraqui/m². After 371 days, tambaqui showed a mean growth from 18.6±4.5 g to 997.1±195.08 g in Pond A, and from 81.4±18.8 g to 519.9±191.7 g in Pond B. Feeding management of Pond A may be a sustainable alternative of tambaqui production in substitution to commercial rations.

  3. De novo assembly of highly diverse viral populations

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    Yang Xiao

    2012-09-01

    Full Text Available Abstract Background Extensive genetic diversity in viral populations within infected hosts and the divergence of variants from existing reference genomes impede the analysis of deep viral sequencing data. A de novo population consensus assembly is valuable both as a single linear representation of the population and as a backbone on which intra-host variants can be accurately mapped. The availability of consensus assemblies and robustly mapped variants are crucial to the genetic study of viral disease progression, transmission dynamics, and viral evolution. Existing de novo assembly techniques fail to robustly assemble ultra-deep sequence data from genetically heterogeneous populations such as viruses into full-length genomes due to the presence of extensive genetic variability, contaminants, and variable sequence coverage. Results We present VICUNA, a de novo assembly algorithm suitable for generating consensus assemblies from genetically heterogeneous populations. We demonstrate its effectiveness on Dengue, Human Immunodeficiency and West Nile viral populations, representing a range of intra-host diversity. Compared to state-of-the-art assemblers designed for haploid or diploid systems, VICUNA recovers full-length consensus and captures insertion/deletion polymorphisms in diverse samples. Final assemblies maintain a high base calling accuracy. VICUNA program is publicly available at: http://www.broadinstitute.org/scientific-community/science/projects/viral-genomics/ viral-genomics-analysis-software. Conclusions We developed VICUNA, a publicly available software tool, that enables consensus assembly of ultra-deep sequence derived from diverse viral populations. While VICUNA was developed for the analysis of viral populations, its application to other heterogeneous sequence data sets such as metagenomic or tumor cell population samples may prove beneficial in these fields of research.

  4. Uncovering Clinical Features of De Novo Philadelphia Positive Myelodysplasia.

    Science.gov (United States)

    Armas, Aristides; Chen, Chen; Mims, Martha; Rivero, Gustavo

    2017-01-01

    Myelodysplastic syndrome (MDS) is cytogenetically heterogeneous and retains variable risk for acute myeloid leukemia transformation. Though not yet fully understood, there is an association between genetic abnormalities and defects in gene expression. The functional role for infrequent cytogenetic alteration remains unclear. An uncommon chromosomic abnormality is the presence of the Philadelphia (Ph) chromosome. Here, we report a patient with Ph+ MDS treated with low dose Dasatinib who achieved hematologic response for 7 months. In addition, we also examined the English literature on all de novo Ph + MDS cases between 1996 and 2015 to gain insight into clinical features and outcome.

  5. Perspective on Biotransformation and De Novo Biosynthesis of Licorice Constituents.

    Science.gov (United States)

    Zhao, Yujia; Lv, Bo; Feng, Xudong; Li, Chun

    2017-12-27

    Licorice, an important herbal medicine, is derived from the dried roots and rhizomes of Glycyrrhiza genus plants. It has been widely used in food, pharmaceutical, tobacco, and cosmetics industries with high economic value. However, overexploitation of licorice resources has severely destroyed the local ecology. Therefore, producing bioactive compounds of licorice through the biotransformation and bioengineering methods is a hot spot in recent years. In this perspective, we comprehensively summarize the biotransformation of licorice constituents into high-value-added derivatives by biocatalysts. Furthermore, successful cases and the strategies for de novo biosynthesizing compounds of licorice in microbes have been summarized. This paper will provide new insights for the further research of licorice.

  6. De Novo and Recurrence of Nonalcoholic Steatohepatitis After Liver Transplantation.

    Science.gov (United States)

    Kappus, Matthew; Abdelmalek, Manal

    2017-05-01

    Nonalcoholic fatty liver disease (NAFLD) is the most common cause of chronic liver disease in developing countries. Approximately 25% of patients with NAFLD develop nonalcoholic steatohepatitis (NASH). NASH-related cirrhosis is now a leading listing indication for liver transplantation in the United States. Although posttransplant survival for NASH-related cirrhosis is comparable with that of other liver diseases, many patients have features of metabolic syndrome, which can contribute to a recurrence of NAFLD or NASH. This article reviews the epidemiology, pathophysiology, and treatment of de novo and recurrence of NASH after liver transplantation. Copyright © 2017 Elsevier Inc. All rights reserved.

  7. The historical town core and traffic in Novo mesto

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    Lilijana Jankovič

    2001-01-01

    Full Text Available The historical town core of Novo mesto is subject to intolerable traffic conditions. Individual car use is suffocating the town core, but simultaneously good access is essential for shopkeepers and other inhabitants since buses don’t go there. The project proposes changes to the traffic regime, its basic goals are to redesign the town square into a pedestrian place and to eliminate transitory traffic by rerouting vehicles to less burdened side roads. It introduces short-term parking, smaller parking garages in the core and larger parking spaces on the edge and routes the buses through the town core.

  8. Model-Based GUI Testing Using Uppaal at Novo Nordisk

    Science.gov (United States)

    Hjort, Ulrik H.; Illum, Jacob; Larsen, Kim G.; Petersen, Michael A.; Skou, Arne

    This paper details a collaboration between Aalborg University and Novo Nordiskin developing an automatic model-based test generation tool for system testing of the graphical user interface of a medical device on an embedded platform. The tool takes as input an UML Statemachine model and generates a test suite satisfying some testing criterion, such as edge or state coverage, and converts the individual test case into a scripting language that can be automatically executed against the target. The tool has significantly reduced the time required for test construction and generation, and reduced the number of test scripts while increasing the coverage.

  9. Novo-desenvolvimento, capital social e desigualdade social

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    Ana Cristina de Oliveira Oliveira

    2012-03-01

    Full Text Available Este artigo aborda a tendência de enfrentamento da desigualdade social a partir, no campo econômico, da versão do novo-desenvolvimentismo e, no campo político e ideológico, a partir da noção de capital social, na tentativa de realizar um "capitalismo com face mais humana". Discutiremos duas ordens de questões, considerando a especificidade da formação social brasileira de capitalismo dependente: 1 a “construção de Estados fortes” para

    assegurar as condições de acumulação do capital, ampliando as margens do mercado de consumo, aliviando a pobreza e controlando possíveis tensões políticas e 2 a difusão da necessidade de construir uma sociedade em harmonia, que se traduz na incorporação da ética empreendedora dos empresários em todas as esferas sociais. Entendemos que este escopo político-econômico revela uma nova pedagogia da hegemonia, sustentada numa suposta alternativa
    de gerenciamento das novas expressões da “questão social”, voltada para educar o conformismo e ocultar o conflito de classes.
    Palavras-chave:  questão social; novo-desenvolvimentismo; capital social; inclusão forçada

  10. De novo biosynthesis of anthocyanins in Saccharomyces cerevisiae.

    Science.gov (United States)

    Eichenberger, Michael; Hansson, Anders; Fischer, David; Dürr, Lara; Naesby, Michael

    2018-06-01

    Anthocyanins (ACNs) are plant secondary metabolites responsible for most of the red, purple and blue colors of flowers, fruits and vegetables. They are increasingly used in the food and beverage industry as natural alternative to artificial colorants. Production of these compounds by fermentation of microorganisms would provide an attractive alternative. In this study, Saccharomyces cerevisiae was engineered for de novo production of the three basic anthocyanins, as well as the three main trans-flavan-3-ols. Enzymes from different plant sources were screened and efficient variants found for most steps of the biosynthetic pathway. However, the anthocyanidin synthase was identified as a major obstacle to efficient production. In yeast, this enzyme converts the majority of its natural substrates leucoanthocyanidins into the off-pathway flavonols. Nonetheless, de novo biosynthesis of ACNs was shown for the first time in yeast and for the first time in a single microorganism. It provides a framework for optimizing the activity of anthocyanidin synthase and represents an important step towards sustainable industrial production of these highly relevant molecules in yeast.

  11. Origins of De Novo Genes in Human and Chimpanzee.

    Science.gov (United States)

    Ruiz-Orera, Jorge; Hernandez-Rodriguez, Jessica; Chiva, Cristina; Sabidó, Eduard; Kondova, Ivanela; Bontrop, Ronald; Marqués-Bonet, Tomàs; Albà, M Mar

    2015-12-01

    The birth of new genes is an important motor of evolutionary innovation. Whereas many new genes arise by gene duplication, others originate at genomic regions that did not contain any genes or gene copies. Some of these newly expressed genes may acquire coding or non-coding functions and be preserved by natural selection. However, it is yet unclear which is the prevalence and underlying mechanisms of de novo gene emergence. In order to obtain a comprehensive view of this process, we have performed in-depth sequencing of the transcriptomes of four mammalian species--human, chimpanzee, macaque, and mouse--and subsequently compared the assembled transcripts and the corresponding syntenic genomic regions. This has resulted in the identification of over five thousand new multiexonic transcriptional events in human and/or chimpanzee that are not observed in the rest of species. Using comparative genomics, we show that the expression of these transcripts is associated with the gain of regulatory motifs upstream of the transcription start site (TSS) and of U1 snRNP sites downstream of the TSS. In general, these transcripts show little evidence of purifying selection, suggesting that many of them are not functional. However, we find signatures of selection in a subset of de novo genes which have evidence of protein translation. Taken together, the data support a model in which frequently-occurring new transcriptional events in the genome provide the raw material for the evolution of new proteins.

  12. A simple method suitable to study de novo root organogenesis

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    Xiaodong eChen

    2014-05-01

    Full Text Available De novo root organogenesis is the process in which adventitious roots regenerate from detached or wounded plant tissues or organs. In tissue culture, appropriate types and concentrations of plant hormones in the medium are critical for inducing adventitious roots. However, in natural conditions, regeneration from detached organs is likely to rely on endogenous hormones. To investigate the actions of endogenous hormones and the molecular mechanisms guiding de novo root organogenesis, we developed a simple method to imitate natural conditions for adventitious root formation by culturing Arabidopsis thaliana leaf explants on B5 medium without additive hormones. Here we show that the ability of the leaf explants to regenerate roots depends on the age of the leaf and on certain nutrients in the medium. Based on these observations, we provide examples of how this method can be used in different situations, and how it can be optimized. This simple method could be used to investigate the effects of various physiological and molecular changes on the regeneration of adventitious roots. It is also useful for tracing cell lineage during the regeneration process by differential interference contrast observation of -glucuronidase staining, and by live imaging of proteins labeled with fluorescent tags.

  13. De novo transcriptome assembly of Setatria italica variety Taejin

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    Yeonhwa Jo

    2016-06-01

    Full Text Available Foxtail millet (Setaria italica belonging to the family Poaceae is an important millet that is widely cultivated in East Asia. Of the cultivated millets, the foxtail millet has the longest history and is one of the main food crops in South India and China. Moreover, foxtail millet is a model plant system for biofuel generation utilizing the C4 photosynthetic pathway. In this study, we carried out de novo transcriptome assembly for the foxtail millet variety Taejin collected from Korea using next-generation sequencing. We obtained a total of 8.676 GB raw data by paired-end sequencing. The raw data in this study can be available in NCBI SRA database with accession number of SRR3406552. The Trinity program was used to de novo assemble 145,332 transcripts. Using the TransDecoder program, we predicted 82,925 putative proteins. BLASTP was performed against the Swiss-Prot protein sequence database to annotate the functions of identified proteins, resulting in 20,555 potentially novel proteins. Taken together, this study provides transcriptome data for the foxtail millet variety Taejin by RNA-Seq.

  14. De novo transcriptome assembly of the mycoheterotrophic plant Monotropa hypopitys

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    Alexey V. Beletsky

    2017-03-01

    Full Text Available Monotropa hypopitys (pinesap is a non-photosynthetic obligately mycoheterotrophic plant of the family Ericaceae. It obtains the carbon and other nutrients from the roots of surrounding autotrophic trees through the associated mycorrhizal fungi. In order to understand the evolutionary changes in the plant genome associated with transition to a heterotrophic lifestyle, we performed de novo transcriptomic analysis of M. hypopitys using next-generation sequencing. We obtained the RNA-Seq data from flowers, flower bracts and roots with haustoria using Illumina HiSeq2500 platform. The raw data obtained in this study can be available in NCBI SRA database with accession number of SRP069226. A total of 10.3 GB raw sequence data were obtained, corresponding to 103,357,809 raw reads. A total of 103,025,683 reads were filtered after removing low-quality reads and trimming the adapter sequences. The Trinity program was used to de novo assemble 98,349 unigens with an N50 of 1342 bp. Using the TransDecoder program, we predicted 43,505 putative proteins. 38,416 unigenes were annotated in the Swiss-Prot protein sequence database using BLASTX. The obtained transcriptomic data will be useful for further studies of the evolution of plant genomes upon transition to a non-photosynthetic lifestyle and the loss of photosynthesis-related functions.

  15. Análise espacial da distribuição de cigarras (Quesada gigas Oliver em povoamentos de paricá (Schizolobium amazonicum Huber ex Ducke na região de Dom Eliseu, PA Analysis of the spatial distribution of buzzers (Quesada gigas Oliver in parica stands(Schizolobium amazonicum Huber ex Ducke in Dom Eliseu-PA

    Directory of Open Access Journals (Sweden)

    Vicente Paulo Soares

    2008-04-01

    Full Text Available O objetivo deste estudo foi avaliar, através da análise espacial de dados geográficos, a precisão de procedimentos de mapeamento das populações de cigarras (Quesada gigas Oliver em povoamentos de paricá (Schizolobium amazonicum Huber ex Ducke, localizados no Município de Dom Eliseu, PA, mediante a aplicação de dois interpoladores (krigagem e inverso do quadrado da distância. Para tal, foram registradas amostras na intensidade de um ponto a cada 30 ha, onde se realizou a contagem do número de cigarras por planta (cigarras/árvore, obedecendo à estratégia de amostragem convencionalmente usada pela empresa proprietária do reflorestamento em estudo. As análises indicaram que a intensidade amostral empregada neste trabalho não foi suficiente para permitir a detecção de forte dependência espacial do número de cigarras/árvore nas áreas estudadas. Devido a essa baixa dependência espacial, os resultados dos dois métodos de interpolação (krigagem ordinária e inverso do quadrado da distância apresentaram-se semelhantes. Já os deste trabalho indicaram que as estratégias de amostragem utilizadas devem ser melhoradas para gerar mapas de predição mais precisos da quantidade de cigarras/árvore nos reflorestamentos de paricá.The objective of this study was to evaluate the occurrence of buzzers (Quesada gigas Oliver in Parica (Schizlobium amazonicum Huber ex Ducke stands using spatial geographic data analysis, in Dom Eliseu, Para, Brazil, based on the application of two interpolators (kriging and distance square inverse.Thus, points were set up in a density of one point for every 30 hectares, with one tree sampled per point, obeying the sample strategy conventionally used by the company which owns the reforestation stand under study. The analysis indicated that the sampling intensity utilized in this work was not sufficient to allow a strong spatial dependence of the number of buzzers/tree in the study area. Due to this low

  16. Combined "de novo" and "ex novo" lipid fermentation in a mix-medium of corncob acid hydrolysate and soybean oil by Trichosporon dermatis.

    Science.gov (United States)

    Huang, Chao; Luo, Mu-Tan; Chen, Xue-Fang; Qi, Gao-Xiang; Xiong, Lian; Lin, Xiao-Qing; Wang, Can; Li, Hai-Long; Chen, Xin-De

    2017-01-01

    Microbial oil is one important bio-product for its important function in energy, chemical, and food industry. Finding suitable substrates is one key issue for its industrial application. Both hydrophilic and hydrophobic substrates can be utilized by oleaginous microorganisms with two different bio-pathways (" de novo " lipid fermentation and " ex novo " lipid fermentation). To date, most of the research on lipid fermentation has focused mainly on only one fermentation pathway and little work was carried out on both " de novo " and " ex novo " lipid fermentation simultaneously; thus, the advantages of both lipid fermentation cannot be fulfilled comprehensively. In this study, corncob acid hydrolysate with soybean oil was used as a mix-medium for combined " de novo " and " ex novo " lipid fermentation by oleaginous yeast Trichosporon dermatis . Both hydrophilic and hydrophobic substrates (sugars and soybean oil) in the medium can be utilized simultaneously and efficiently by T. dermatis . Different fermentation modes were compared and the batch mode was the most suitable for the combined fermentation. The influence of soybean oil concentration, inoculum size, and initial pH on the lipid fermentation was evaluated and 20 g/L soybean oil, 5% inoculum size, and initial pH 6.0 were suitable for this bioprocess. By this technology, the lipid composition of extracellular hydrophobic substrate (soybean oil) can be modified. Although adding emulsifier showed little beneficial effect on lipid production, it can modify the intracellular lipid composition of T. dermatis . The present study proves the potential and possibility of combined " de novo " and " ex novo " lipid fermentation. This technology can use hydrophilic and hydrophobic sustainable bio-resources to generate lipid feedstock for the production of biodiesel or other lipid-based chemical compounds and to treat some special wastes such as oil-containing wastewater.

  17. Interplay between De Novo Biosynthesis and Sequestration of Cyanogenic Glucosides in Arthropods

    DEFF Research Database (Denmark)

    Fürstenberg-Hägg, Joel

    (Zygaenidae, Lepidoptera) both sequester (take up and accumulate) the CNglcs linamarin and lotaustralin from their food plants (Fabacea) and biosynthesize them de novo from valine and isoleucine. The presented research demonstrates that de novo biosynthesis of CNglcs in Z. filipendulae is dependent...

  18. 76 FR 68767 - Draft Guidance for Industry and Food and Drug Administration Staff; De Novo Classification...

    Science.gov (United States)

    2011-11-07

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES Food and Drug Administration [Docket No. FDA-2011-D-0689] Draft Guidance for Industry and Food and Drug Administration Staff; De Novo Classification Process... for Industry and Food and Drug Administration Staff; De Novo Classification Process (Evaluation of...

  19. De novo mutation in the dopamine transporter gene associates dopamine dysfunction with autism spectrum disorder

    DEFF Research Database (Denmark)

    Hamilton, P J; Campbell, N G; Sharma, S

    2013-01-01

    De novo genetic variation is an important class of risk factors for autism spectrum disorder (ASD). Recently, whole-exome sequencing of ASD families has identified a novel de novo missense mutation in the human dopamine (DA) transporter (hDAT) gene, which results in a Thr to Met substitution...

  20. De novo mutations in synaptic transmission genes including DNM1 cause epileptic encephalopathies

    DEFF Research Database (Denmark)

    2014-01-01

    in five individuals and de novo mutations in GABBR2, FASN, and RYR3 in two individuals each. Unlike previous studies, this cohort is sufficiently large to show a significant excess of de novo mutations in epileptic encephalopathy probands compared to the general population using a likelihood analysis (p...... = 8.2 × 10(-4)), supporting a prominent role for de novo mutations in epileptic encephalopathies. We bring statistical evidence that mutations in DNM1 cause epileptic encephalopathy, find suggestive evidence for a role of three additional genes, and show that at least 12% of analyzed individuals have...... analyzed exome-sequencing data of 356 trios with the "classical" epileptic encephalopathies, infantile spasms and Lennox Gastaut syndrome, including 264 trios previously analyzed by the Epi4K/EPGP consortium. In this expanded cohort, we find 429 de novo mutations, including de novo mutations in DNM1...

  1. Genes from scratch--the evolutionary fate of de novo genes.

    Science.gov (United States)

    Schlötterer, Christian

    2015-04-01

    Although considered an extremely unlikely event, many genes emerge from previously noncoding genomic regions. This review covers the entire life cycle of such de novo genes. Two competing hypotheses about the process of de novo gene birth are discussed as well as the high death rate of de novo genes. Despite the high death rate, some de novo genes are retained and remain functional, even in distantly related species, through their integration into gene networks. Further studies combining gene expression with ribosome profiling in multiple populations across different species will be instrumental for an improved understanding of the evolutionary processes operating on de novo genes. Copyright © 2015 The Author. Published by Elsevier Ltd.. All rights reserved.

  2. CRESCIMENTO INICIAL DE ESPÉCIES FLORESTAIS DE DIFERENTES GRUPOS SUCESSIONAIS EM RESPOSTA A DOSES DE FÓSFORO INITIAL GROWTH OF FOREST SPECIES OF DIFFERENT SUCCESSIONAL GROUPS IN RESPONSE TO PHOSPHORUS DOSES

    Directory of Open Access Journals (Sweden)

    ÁLVARO VILELA DE RESENDE

    1999-11-01

    Full Text Available Objetivando avaliar a resposta de espécies florestais ao fornecimento de P, conduziu-se um ensaio sob condições de casa de vegetação, cultivando-se mudas das espécies arbóreas pioneiras (aroeira - Lithraea molleoides; aroeirinha - Schinus terebinthifolius; jacaré - Piptadenia gonoacantha; sabiá - Mimosa caesalpiniaefolia; sesbânia - Sesbania virgata, clímax exigente em luz (jatobá - Hymenaea courbaril, e clímax tolerantes a sombra (guanandi - Calophyllum brasiliensis; ipê-amarelo - Tabebuia serratifolia; óleo-bálsamo - Myroxylon peruiferum. Utilizaram-se cinco doses de P, correspondentes a 0, 100, 250, 500 e 800 mg dm-3 de P. Foram avaliados o diâmetro do caule, a altura e a matéria seca de raízes, parte aérea e total das plantas. As espécies pioneiras foram mais responsivas ao fornecimento de P, indicando a necessidade do suprimento deste nutriente para o adequado desenvolvimento destas espécies. As espécies clímax mostraram-se pouco sensíveis ao suprimento de P, refletindo um baixo requerimento na fase de mudas. Diferenças em relação à taxa de crescimento e ao tamanho das sementes podem estar ligadas ao comportamento contrastante observado para espécies pioneiras e clímax.With the aim of evaluating the responses of forest species to phosphorus supply, an assay under greenhouse conditions was carried out, where seedlings of pioneer tree species (Lithraea molleoides, Schinus terebinthifolius, Piptadenia gonoacantha, Mimosa caesalpiniaefolia, Sesbania virgata, a light-demander climax species (Hymenaea courbaril, and the shade-tolerant climaxes species (Calophyllum brasiliensis, Tabebuia serratifolia, Myroxylon peruiferum were cultivated. Five phosphorus doses were used, corresponding to 0, 100, 250, 500 and 800 mg dm-3 of P. Stem diameter, height, and root, shoot and total dry matter yield of the plants were evaluated. The pioneers species were more responsive to phosphorus furnishing, indicating the need of

  3. Desempenho de Espécies Florestais e Pastagens em Sistemas Silvipastoris no Estado do Pará Performance of Tree Species and Pastures in Silvopastoral Systems in the State of Pará, Brazil

    Directory of Open Access Journals (Sweden)

    Célia Maria Braga Calandrini de Azevedo

    2010-02-01

    Full Text Available

    Propor modelos alternativos de uso-da-terra que sejam econômicos e ecologicamente sustentáveis tem sido um grande desafio da pesquisa agrícola na Amazônia. Os sistemas silvipastoris (SSPs têm sido considerados promissores para integrar o cultivo arbóreo nos sistemas pecuários e recuperar pastagens degradadas da Amazônia. Em Paragominas, Estado do Pará, foram estudados nove sistemas silvipastoris constituídos da combinação binária das espécies florestais paricá (Schizolobium amazonicum, tatajuba (Bagassa guianensis e eucalipto (Eucalyptus tereticornis, plantadas em faixas de 6 m de largura, afastadas de 12 m, com as pastagens capim braquiarão (Brachiaria brizantha, capim quicuio da amazônia (B. humidicola, e capim colonião (Panicum maximum e em capim dictioneura (B. dictyoneura, plantadas nas entre-faixas. O sistema de manejo se caracterizava por ser rotacionado com 14 dias de permanência e 42 dias de descanso, e foi avaliado no período de agosto de 1990 a novembro de 1991. As melhores interações foram paricá e capim braquiarão e eucalipto e capim braquiarão.

     

    doi: 10.4336/2009.pfb.60.57

    Proposing economic and ecological land-use alternatives has been a great challenge for agricultural research in the Brazilian Amazon. The silvopastoral systems (SPS are promising to integrate trees in the livestock production system and reclaim degraded pastures in the Amazon region. In Municipality of Paragominas, State of Pará, nine SPS composed by combination of three tree species (Schizolobium amazonicum, Bagassa guianensis and Eucalyptus tereticornis, planted in 6 m-lane, spaced by 12 m – and three pastures (Brachiaria brizantha, B. humidicola and Panicum maximum / dictioneura B. dictyoneura, planted in the inter-lane space. Steers grazed the one-hectare experimental parcels simulating a rotational grazing system with 14 days - grazing period and 42 days – rest period, and was evaluated during August 1990 to

  4. DISTRIBUIÇÃO ESPAÇO-TEMPORAL DA RÃ INVASORA, Lithobates catesbeianus (ANURA, RANIDAE (SHAW, 1802 EM DOIS REMANESCENTES FLORESTAIS DA MATA ATLÂNTICA NO SUL DO BRASIL

    Directory of Open Access Journals (Sweden)

    Jackson Fábio Preuss

    2017-06-01

    Full Text Available A rã-touro (Lithobates catesbeianus é a mais notória espécie de anuro invasora. Foi introduzida no Brasil visando à criação comercial. Escapes acidentais e solturas têm favorecido a ocorrência desta espécie em ambientes naturais. O objetivo deste trabalho foi a avaliar a distribuição temporal e espacial da rã-touro, Lithobates catesbeianus em ambientes naturais. Entre novembro de 2014 e outubro de 2015 realizamos coletas noturnas em seis ambientes aquáticos de dois remanescentes florestais de Mata Atlântica, localizados no oeste do estado de Santa Catarina, Brasil. Durante esse período registramos o número de indivíduos em atividade, para a descrição física do habitat foi registrado o tipo de ambiente aquático, e para descrição do habitat registrou-se os parâmetros físicos da água/ambiente (temperatura da água, pH, temperatura do ar, pluviosidade e umidade relativa do ar. Foram registrados um total de 126 indivíduos, sendo 105 adultos e 21 juvenis. A rã touro foi registrada em atividade durante todo o período de estudo, utilizando corpos d’água lênticos e permanentes (lagoas, charcos e riachos. A espécie foi encontrada em todos os meses amostrados, sendo mais frequente no período de maiores temperaturas (dezembro; N= 31. A abundância foi relacionada significativamente à temperatura média da água (R2 = 0,62; p = 0,0013; N = 98. Entretanto, independente dos parâmetros físicos/ambientais investigados, esta espécie pode ser encontrada em todos os habitats investigados. No presente estudo, Lithobates catesbeianus apresentou alto grau de tolerância em ambientes naturais o qual evidencia-se como um fator negativo a biodiversidade local. Palavras-chave: rã-touro, ambientes naturais, fator negativo.

  5. Fisiologia de espécies florestais da Amazônia: fotossíntese, respiração e relações hídricas

    Directory of Open Access Journals (Sweden)

    Ricardo Antonio Marenco

    2014-12-01

    Full Text Available A bacia amazônica tem mais de seis milhões de quilômetros quadrados e abriga a maior floresta tropical do mundo, sendo particularmente importante pela sua biodiversidade e pelo seu papel na ciclagem de água e carbono. Fotossíntese, condutância estomática e fluxo de seiva de espécies florestais da Amazônia apresentam variação ao longo do dia seguindo a variação diurna observada na irradiância, temperatura e o déficit de pressão de vapor. Em decorrência da fotorrespiração, cerca de 25% do carbono fixado é retornado para a atmosfera. Os aumentos na concentração de CO2 na atmosfera previstos para as próximas décadas poderão apresentar efeito positivo na assimilação de carbono deste ecossistema florestal. Em comparação à época chuvosa, redução da umidade do solo e aumento no déficit de pressão de vapor (associado à baixa umidade do ar e alta temperatura favorecem o fechamento dos estômatos em detrimento da fotossíntese. Desse modo, em comparação com a estação chuvosa, a fotossíntese líquida é menor no período seco. No geral, na Amazônia as árvores que atingem o dossel da floresta crescem a taxas maiores na época chuvosa. Exceto em anos de menor precipitação, o ecossistema florestal atua como sumidouro de carbono na época chuvosa. Mais estudos são necessários para determinar como e de que forma fatores específicos do ambiente físico influenciam a assimilação de carbono e o crescimento de árvores nos diversos grupos funcionais na Amazônia.

  6. Avaliação da influência da certificação florestal no cumprimento da legislação ambiental em plantações florestais

    Directory of Open Access Journals (Sweden)

    Vanessa Maria Basso

    2011-08-01

    Full Text Available Nas últimas décadas tem surgido uma maior preocupação ambiental advinda das mudanças climáticas e dos desmatamentos contínuos das florestas tropicais. Com isso, exigiu-se uma forma de garantir e atestar que os produtos florestais não fossem ilegais (extraídos indevidamente de mata nativa e, um dos instrumentos desenvolvidos para este fim, foi a certificação florestal. No Brasil, ela está presente há mais de uma década, através do FSC (Forest Stewardship Council, uma ONG (Organização Não Governamental que estabeleceu um padrão para a certificação do manejo florestal. Neste tipo de certificação existem princípios, critérios e indicadores a cumprir na unidade de manejo florestal. Assim, este trabalho teve por objetivo verificar a contribuição da certificação florestal no cumprimento da legislação ambiental e florestal nas unidades de manejo florestal de plantações. Buscaram - se os dados nos relatórios públicos das unidades de manejo certificadas de 1996 a 2007. Foram analisados os relatórios da avaliação principal e monitoramento para a identificação e análise das principais não-conformidades do Princípio 1 (Obediência às leis a aos princípios e critérios do FSC. Pelos resultados obtidos, verificou-se que as principais não conformidades estavam relacionadas às legislações ambiental e trabalhista. Estas, em sua maioria, foram referentes à problemas com as Áreas de Preservação Permanente (APP e Reserva Legal (RL. Entretanto, ressalta-se que no processo de certificação é necessário que as não conformidades sejam corrigidas em um prazo estabelecido. Assim, conclui-se que a certificação contribui para o atendimento da legislação nas unidades de manejo florestal de plantações.

  7. Peptide de novo sequencing of mixture tandem mass spectra

    DEFF Research Database (Denmark)

    Gorshkov, Vladimir; Hotta, Stéphanie Yuki Kolbeck; Braga, Thiago Verano

    2016-01-01

    they decrease the identification performance using database search engines. De novo sequencing approaches are expected to be even more sensitive to the reduction in mass spectrum quality resulting from peptide precursor co-isolation and thus prone to false identifications. The deconvolution approach matched...... complementary b-, y-ions to each precursor peptide mass, which allowed the creation of virtual spectra containing sequence specific fragment ions of each co-isolated peptide. Deconvolution processing resulted in equally efficient identification rates but increased the absolute number of correctly sequenced...... peptides. The improvement was in the range of 20–35% additional peptide identifications for a HeLa lysate sample. Some correct sequences were identified only using unprocessed spectra; however, the number of these was lower than those where improvement was obtained by mass spectral deconvolution. Tight...

  8. Herpes simplex virus 1 induces de novo phospholipid synthesis

    Energy Technology Data Exchange (ETDEWEB)

    Sutter, Esther [Electron Microscopy, Institute of Veterinary Anatomy, University of Zuerich (Switzerland); Oliveira, Anna Paula de; Tobler, Kurt [Electron microscopy, Institute of Virology, University of Zuerich (Switzerland); Schraner, Elisabeth M. [Electron Microscopy, Institute of Veterinary Anatomy, University of Zuerich (Switzerland); Sonda, Sabrina [Institute of Parasitology, University of Zuerich (Switzerland); Kaech, Andres [Center for Microscopy and Image Analysis, University of Zuerich (Switzerland); Lucas, Miriam S. [Electron Microscopy ETH Zuerich (EMEZ), Swiss Federal Institute of Technology, Zuerich (Switzerland); Ackermann, Mathias [Electron microscopy, Institute of Virology, University of Zuerich (Switzerland); Wild, Peter, E-mail: pewild@access.uzh.ch [Electron Microscopy, Institute of Veterinary Anatomy, University of Zuerich (Switzerland)

    2012-08-01

    Herpes simplex virus type 1 capsids bud at nuclear membranes and Golgi membranes acquiring an envelope composed of phospholipids. Hence, we measured incorporation of phospholipid precursors into these membranes, and quantified changes in size of cellular compartments by morphometric analysis. Incorporation of [{sup 3}H]-choline into both nuclear and cytoplasmic membranes was significantly enhanced upon infection. [{sup 3}H]-choline was also part of isolated virions even grown in the presence of brefeldin A. Nuclei expanded early in infection. The Golgi complex and vacuoles increased substantially whereas the endoplasmic reticulum enlarged only temporarily. The data suggest that HSV-1 stimulates phospholipid synthesis, and that de novo synthesized phospholipids are inserted into nuclear and cytoplasmic membranes to i) maintain membrane integrity in the course of nuclear and cellular expansion, ii) to supply membrane constituents for envelopment of capsids by budding at nuclear membranes and Golgi membranes, and iii) to provide membranes for formation of transport vacuoles.

  9. De-novo design of antimicrobial peptides for plant protection.

    Directory of Open Access Journals (Sweden)

    Benjamin Zeitler

    Full Text Available This work describes the de-novo design of peptides that inhibit a broad range of plant pathogens. Four structurally different groups of peptides were developed that differ in size and position of their charged and hydrophobic clusters and were assayed for their ability to inhibit bacterial growth and fungal spore germination. Several peptides are highly active at concentrations between 0,1 and 1 µg/ml against plant pathogenic bacteria, such as Pseudomonas syringae, Pectobacterium carotovorum, and Xanthomonas vesicatoria. Importantly, no hemolytic activity could be detected for these peptides at concentrations up to 200 µg/ml. Moreover, the peptides are also active after spraying on the plant surface demonstrating a possible way of application. In sum, our designed peptides represent new antimicrobial agents and with the increasing demand for antimicrobial compounds for production of "healthy" food, these peptides might serve as templates for novel antibacterial and antifungal agents.

  10. De novo SOX11 mutations cause Coffin-Siris syndrome.

    Science.gov (United States)

    Tsurusaki, Yoshinori; Koshimizu, Eriko; Ohashi, Hirofumi; Phadke, Shubha; Kou, Ikuyo; Shiina, Masaaki; Suzuki, Toshifumi; Okamoto, Nobuhiko; Imamura, Shintaro; Yamashita, Michiaki; Watanabe, Satoshi; Yoshiura, Koh-ichiro; Kodera, Hirofumi; Miyatake, Satoko; Nakashima, Mitsuko; Saitsu, Hirotomo; Ogata, Kazuhiro; Ikegawa, Shiro; Miyake, Noriko; Matsumoto, Naomichi

    2014-06-02

    Coffin-Siris syndrome (CSS) is a congenital disorder characterized by growth deficiency, intellectual disability, microcephaly, characteristic facial features and hypoplastic nails of the fifth fingers and/or toes. We previously identified mutations in five genes encoding subunits of the BAF complex, in 55% of CSS patients. Here we perform whole-exome sequencing in additional CSS patients, identifying de novo SOX11 mutations in two patients with a mild CSS phenotype. sox11a/b knockdown in zebrafish causes brain abnormalities, potentially explaining the brain phenotype of CSS. SOX11 is the downstream transcriptional factor of the PAX6-BAF complex, highlighting the importance of the BAF complex and SOX11 transcriptional network in brain development.

  11. De novo transcriptome assembly of shrimp Palaemon serratus

    Directory of Open Access Journals (Sweden)

    Alejandra Perina

    2017-03-01

    Full Text Available The shrimp Palaemon serratus is a coastal decapod crustacean with a high commercial value. It is harvested for human consumption. In this study, we used Illumina sequencing technology (HiSeq 2000 to sequence, assemble and annotate the transcriptome of P. serratus. RNA was isolated from muscle of adults individuals and, from a pool of larvae. A total number of 4 cDNA libraries were constructed, using the TruSeq RNA Sample Preparation Kit v2. The raw data in this study was deposited in NCBI SRA database with study accession number of SRP090769. The obtained data were subjected to de novo transcriptome assembly using Trinity software, and coding regions were predicted by TransDecoder. We used Blastp and Sma3s to annotate the identified proteins. The transcriptome data could provide some insight into the understanding of genes involved in the larval development and metamorphosis.

  12. De novo assembly of a haplotype-resolved human genome.

    Science.gov (United States)

    Cao, Hongzhi; Wu, Honglong; Luo, Ruibang; Huang, Shujia; Sun, Yuhui; Tong, Xin; Xie, Yinlong; Liu, Binghang; Yang, Hailong; Zheng, Hancheng; Li, Jian; Li, Bo; Wang, Yu; Yang, Fang; Sun, Peng; Liu, Siyang; Gao, Peng; Huang, Haodong; Sun, Jing; Chen, Dan; He, Guangzhu; Huang, Weihua; Huang, Zheng; Li, Yue; Tellier, Laurent C A M; Liu, Xiao; Feng, Qiang; Xu, Xun; Zhang, Xiuqing; Bolund, Lars; Krogh, Anders; Kristiansen, Karsten; Drmanac, Radoje; Drmanac, Snezana; Nielsen, Rasmus; Li, Songgang; Wang, Jian; Yang, Huanming; Li, Yingrui; Wong, Gane Ka-Shu; Wang, Jun

    2015-06-01

    The human genome is diploid, and knowledge of the variants on each chromosome is important for the interpretation of genomic information. Here we report the assembly of a haplotype-resolved diploid genome without using a reference genome. Our pipeline relies on fosmid pooling together with whole-genome shotgun strategies, based solely on next-generation sequencing and hierarchical assembly methods. We applied our sequencing method to the genome of an Asian individual and generated a 5.15-Gb assembled genome with a haplotype N50 of 484 kb. Our analysis identified previously undetected indels and 7.49 Mb of novel coding sequences that could not be aligned to the human reference genome, which include at least six predicted genes. This haplotype-resolved genome represents the most complete de novo human genome assembly to date. Application of our approach to identify individual haplotype differences should aid in translating genotypes to phenotypes for the development of personalized medicine.

  13. Application of Generative Autoencoder in De Novo Molecular Design.

    Science.gov (United States)

    Blaschke, Thomas; Olivecrona, Marcus; Engkvist, Ola; Bajorath, Jürgen; Chen, Hongming

    2018-01-01

    A major challenge in computational chemistry is the generation of novel molecular structures with desirable pharmacological and physiochemical properties. In this work, we investigate the potential use of autoencoder, a deep learning methodology, for de novo molecular design. Various generative autoencoders were used to map molecule structures into a continuous latent space and vice versa and their performance as structure generator was assessed. Our results show that the latent space preserves chemical similarity principle and thus can be used for the generation of analogue structures. Furthermore, the latent space created by autoencoders were searched systematically to generate novel compounds with predicted activity against dopamine receptor type 2 and compounds similar to known active compounds not included in the trainings set were identified. © 2018 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

  14. De novo development of artistic creativity in Alzheimer's disease.

    Science.gov (United States)

    Chakravarty, Ambar

    2011-10-01

    The case of an 82-year-old female with probable Alzheimer's disease (AD), who developed unusual artistic creativity after development of her disease, is described. The possible pathogenetic mechanism is discussed. The patient showed no inclination toward visual arts during her premorbid years. However, 4 years after development of AD suggestive symptoms she started painting beautiful pictures rather impulsively. Some such paintings have been appreciated even by a qualified art expert. Such de novo development of artistic creativity had been described earlier in subjects with the semantic form of fronto-temporal dementia (FTD), but not in AD. The prevailing concept of lateralized compromise and paradoxical functional facilitation, proposed in connection with FTD subjects, may not be applicable in AD subjects where the affection is more diffuse and more posterior in the brain. Hence, the likely pathogenetic mechanism involved in the case described may remain uncertain. Possibilities are discussed.

  15. Novo teste para diagnóstico das afasias

    Directory of Open Access Journals (Sweden)

    José G. Albernaz

    1953-06-01

    Full Text Available Um novo teste para diagnóstico e contrôle do tratamento das diferentes formas de afasia, especialmente adaptado para a língua portuguêsa, é apresentado e descrito em detalhe. O teste, que será de valor para clínicos e psicólogos interessados no tratamento e reabilitação de pacientes afásicos, se executa em cêrca de 30 minutos, interpreta-se fàcilmente e fornece os elementos necessários para o planejamento da reeducação da linguagem. Além disso, a repetição do teste de tempos em tempos indicará os progressos do paciente e sugerirá modificações do plano de tratamento no momento oportuno.

  16. De novo identification of viral pathogens from cell culture hologenomes

    Directory of Open Access Journals (Sweden)

    Patowary Ashok

    2012-01-01

    Full Text Available Abstract Background Fast, specific identification and surveillance of pathogens is the cornerstone of any outbreak response system, especially in the case of emerging infectious diseases and viral epidemics. This process is generally tedious and time-consuming thus making it ineffective in traditional settings. The added complexity in these situations is the non-availability of pure isolates of pathogens as they are present as mixed genomes or hologenomes. Next-generation sequencing approaches offer an attractive solution in this scenario as it provides adequate depth of sequencing at fast and affordable costs, apart from making it possible to decipher complex interactions between genomes at a scale that was not possible before. The widespread application of next-generation sequencing in this field has been limited by the non-availability of an efficient computational pipeline to systematically analyze data to delineate pathogen genomes from mixed population of genomes or hologenomes. Findings We applied next-generation sequencing on a sample containing mixed population of genomes from an epidemic with appropriate processing and enrichment. The data was analyzed using an extensive computational pipeline involving mapping to reference genome sets and de-novo assembly. In depth analysis of the data generated revealed the presence of sequences corresponding to Japanese encephalitis virus. The genome of the virus was also independently de-novo assembled. The presence of the virus was in addition, verified using standard molecular biology techniques. Conclusions Our approach can accurately identify causative pathogens from cell culture hologenome samples containing mixed population of genomes and in principle can be applied to patient hologenome samples without any background information. This methodology could be widely applied to identify and isolate pathogen genomes and understand their genomic variability during outbreaks.

  17. The limits of de novo DNA motif discovery.

    Directory of Open Access Journals (Sweden)

    David Simcha

    Full Text Available A major challenge in molecular biology is reverse-engineering the cis-regulatory logic that plays a major role in the control of gene expression. This program includes searching through DNA sequences to identify "motifs" that serve as the binding sites for transcription factors or, more generally, are predictive of gene expression across cellular conditions. Several approaches have been proposed for de novo motif discovery-searching sequences without prior knowledge of binding sites or nucleotide patterns. However, unbiased validation is not straightforward. We consider two approaches to unbiased validation of discovered motifs: testing the statistical significance of a motif using a DNA "background" sequence model to represent the null hypothesis and measuring performance in predicting membership in gene clusters. We demonstrate that the background models typically used are "too null," resulting in overly optimistic assessments of significance, and argue that performance in predicting TF binding or expression patterns from DNA motifs should be assessed by held-out data, as in predictive learning. Applying this criterion to common motif discovery methods resulted in universally poor performance, although there is a marked improvement when motifs are statistically significant against real background sequences. Moreover, on synthetic data where "ground truth" is known, discriminative performance of all algorithms is far below the theoretical upper bound, with pronounced "over-fitting" in training. A key conclusion from this work is that the failure of de novo discovery approaches to accurately identify motifs is basically due to statistical intractability resulting from the fixed size of co-regulated gene clusters, and thus such failures do not necessarily provide evidence that unfound motifs are not active biologically. Consequently, the use of prior knowledge to enhance motif discovery is not just advantageous but necessary. An implementation of

  18. Cinema utópico: a construção de um novo homem e um novo mundo

    OpenAIRE

    Erika Savernini Lopes

    2011-01-01

    O cinema, desde seus primórdios, prefigurou o espaço cibernético como um novo espaço imaterial construído coletivamente. A concepção desse outro lugar não físico para o qual o homem poderia migrar estabelece para o cinema e para o ciberespaço uma relação direta com as utopias. Na acepção do romance filosófico de Thomas More, a Utopia define-se como um outro espaço não-existente, irrealizável e ideal que diagnostica o atual. O cinema carregaria caracteres fundamentais da Utopia tanto no que se...

  19. On the Origin of De Novo Genes in Arabidopsis thaliana Populations.

    Science.gov (United States)

    Li, Zi-Wen; Chen, Xi; Wu, Qiong; Hagmann, Jörg; Han, Ting-Shen; Zou, Yu-Pan; Ge, Song; Guo, Ya-Long

    2016-08-03

    De novo genes, which originate from ancestral nongenic sequences, are one of the most important sources of protein-coding genes. This origination process is crucial for the adaptation of organisms. However, how de novo genes arise and become fixed in a population or species remains largely unknown. Here, we identified 782 de novo genes from the model plant Arabidopsis thaliana and divided them into three types based on the availability of translational evidence, transcriptional evidence, and neither transcriptional nor translational evidence for their origin. Importantly, by integrating multiple types of omics data, including data from genomes, epigenomes, transcriptomes, and translatomes, we found that epigenetic modifications (DNA methylation and histone modification) play an important role in the origination process of de novo genes. Intriguingly, using the transcriptomes and methylomes from the same population of 84 accessions, we found that de novo genes that are transcribed in approximately half of the total accessions within the population are highly methylated, with lower levels of transcription than those transcribed at other frequencies within the population. We hypothesized that, during the origin of de novo gene alleles, those neutralized to low expression states via DNA methylation have relatively high probabilities of spreading and becoming fixed in a population. Our results highlight the process underlying the origin of de novo genes at the population level, as well as the importance of DNA methylation in this process. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  20. Glucagon infusion increases rate of purine synthesis de novo in rat liver

    International Nuclear Information System (INIS)

    Itakura, Mitsuo; Maeda, Noriaki; Tsuchiya, Masami; Yamashita, Kamejiro

    1987-01-01

    Based on the parallel increases of glucagon, the second peak of hepatic cAMP, and the rate of purine synthesis de novo in the prereplicative period in regenerating rate liver after a 70% hepatectomy, it was hypothesized that glucagon is responsible for the increased rate of purine synthesis de novo. To test this hypothesis, the effect of glucagon or dibutyryl cAMP infusion on the rate of purine synthesis de novo in rat liver was studied. Glucagon infusion but not insulin or glucose infusion increased the rate of purine synthesis de novo, which was assayed by [ 14 C]glycine or [ 14 C]formate incorporation, by 2.7- to 4.3-fold. Glucagon infusion increased cAMP concentrations by 4.9-fold and 5-phosphoribosyl-1-pyrophosphate concentrations by 1.5-fold in liver but did not change the specific activity of amidophosphoribosyltransferase or purine ribonucleotide concentrations. Dibutyryl cAMP infusion also increased the rate of purine synthesis de novo by 2.2- to 4.0-fold. Because glucagon infusion increased the rate of purine synthesis de novo in the presence of unchanged purine ribonucleotide concentrations, it is concluded that glucagon after infusion or in animals after a 70% hepatectomy is playing an anabolic role to increase the rate of purine synthesis de novo by increasing cAMP and 5-phosphoribosyl-1-pyrophosphate concentrations

  1. Role of de novo biosynthesis in ecosystem scale monoterpene emissions from a boreal Scots pine forest

    Directory of Open Access Journals (Sweden)

    R. Taipale

    2011-08-01

    Full Text Available Monoterpene emissions from Scots pine have traditionally been assumed to originate as evaporation from specialized storage pools. More recently, the significance of de novo emissions, originating directly from monoterpene biosynthesis, has been recognized. To study the role of biosynthesis at the ecosystem scale, we measured monoterpene emissions from a Scots pine dominated forest in southern Finland using the disjunct eddy covariance method combined with proton transfer reaction mass spectrometry. The interpretation of the measurements was based on a correlation analysis and a hybrid emission algorithm describing both de novo and pool emissions. During the measurement period May–August 2007, the monthly medians of daytime emissions were 200, 290, 180, and 200 μg m−2 h−1. The emissions were partly light dependent, probably due to de novo biosynthesis. The emission potential for both de novo and pool emissions exhibited a decreasing summertime trend. The ratio of the de novo emission potential to the total emission potential varied between 30 % and 46 %. Although the monthly changes were not significant, the ratio always differed statistically from zero, suggesting that the role of de novo biosynthesis was observable. Given the uncertainties in this study, we conclude that more accurate estimates of the contribution of de novo emissions are required for improving monoterpene emission algorithms for Scots pine dominated forests.

  2. Sequencing and de novo assembly of 150 genomes from Denmark as a population reference

    DEFF Research Database (Denmark)

    Maretty, Lasse; Jensen, Jacob Malte; Petersen, Bent

    2017-01-01

    or by performing local assembly. However, these approaches are biased against discovery of structural variants and variation in the more complex parts of the genome. Hence, large-scale de novo assembly is needed. Here we show that it is possible to construct excellent de novo assemblies from high......-coverage sequencing with mate-pair libraries extending up to 20 kilobases. We report de novo assemblies of 150 individuals (50 trios) from the GenomeDenmark project. The quality of these assemblies is similar to those obtained using the more expensive long-read technology. We use the assemblies to identify a rich set...

  3. Eculizumab for drug-induced de novo posttransplantation thrombotic microangiopathy: A case report.

    Science.gov (United States)

    Safa, Kassem; Logan, Merranda S; Batal, Ibrahim; Gabardi, Steven; Rennke, Helmut G; Abdi, Reza

    2015-02-01

    De novo thrombotic microangiopathy (TMA) following renal transplantation is a severe complication associated with high rates of allograft failure. Several immunosuppressive agents are associated with TMA. Conventional approaches to managing this entity, such as withdrawal of the offending agent and/or plasmapheresis, often offer limited help, with high rates of treatment failure and graft loss. We herein report a case of drug induced de novo TMA successfully treated using the C5a inhibitor eculizumab in a renal transplant patient. This report highlights a potentially important role for eculizumab in settings where drug-induced de novo TMA is refractory to conventional therapies.

  4. De novo assembly and phasing of a Korean human genome.

    Science.gov (United States)

    Seo, Jeong-Sun; Rhie, Arang; Kim, Junsoo; Lee, Sangjin; Sohn, Min-Hwan; Kim, Chang-Uk; Hastie, Alex; Cao, Han; Yun, Ji-Young; Kim, Jihye; Kuk, Junho; Park, Gun Hwa; Kim, Juhyeok; Ryu, Hanna; Kim, Jongbum; Roh, Mira; Baek, Jeonghun; Hunkapiller, Michael W; Korlach, Jonas; Shin, Jong-Yeon; Kim, Changhoon

    2016-10-13

    Advances in genome assembly and phasing provide an opportunity to investigate the diploid architecture of the human genome and reveal the full range of structural variation across population groups. Here we report the de novo assembly and haplotype phasing of the Korean individual AK1 (ref. 1) using single-molecule real-time sequencing, next-generation mapping, microfluidics-based linked reads, and bacterial artificial chromosome (BAC) sequencing approaches. Single-molecule sequencing coupled with next-generation mapping generated a highly contiguous assembly, with a contig N50 size of 17.9 Mb and a scaffold N50 size of 44.8 Mb, resolving 8 chromosomal arms into single scaffolds. The de novo assembly, along with local assemblies and spanning long reads, closes 105 and extends into 72 out of 190 euchromatic gaps in the reference genome, adding 1.03 Mb of previously intractable sequence. High concordance between the assembly and paired-end sequences from 62,758 BAC clones provides strong support for the robustness of the assembly. We identify 18,210 structural variants by direct comparison of the assembly with the human reference, identifying thousands of breakpoints that, to our knowledge, have not been reported before. Many of the insertions are reflected in the transcriptome and are shared across the Asian population. We performed haplotype phasing of the assembly with short reads, long reads and linked reads from whole-genome sequencing and with short reads from 31,719 BAC clones, thereby achieving phased blocks with an N50 size of 11.6 Mb. Haplotigs assembled from single-molecule real-time reads assigned to haplotypes on phased blocks covered 89% of genes. The haplotigs accurately characterized the hypervariable major histocompatability complex region as well as demonstrating allele configuration in clinically relevant genes such as CYP2D6. This work presents the most contiguous diploid human genome assembly so far, with extensive investigation of

  5. Efeito da densidade de povoamento na produtividade final em carpas (Cyprinus carpio var specularis em fase de engorda, durante o verão Effect of population density on the productivity of carp (Cyprinus carpio var specularis, in the fattening stage, during the summer

    Directory of Open Access Journals (Sweden)

    Álvaro Graeff

    2000-06-01

    Full Text Available O objetivo desta pesquisa foi estudar o efeito da densidade de povoamento na produtividade final, em carpas na fase de engorda, no período de verão. O delineamento foi inteiramente casualizado com três tratamentos (1; 0,5; e 0,33 peixes/m² e três repetições. Os peixes foram estocados com peso e comprimento médios de 2,40 g e 5,35; 5,40 e 5,39 cm, respectivamente, nos tratamentos 1, 2 e 3, com 45 dias de idade. As dietas foram formuladas com 27% PB e 2925 kcal/kg de ração, sendo fornecidas diariamente, na quantidade de 3% do peso vivo. O comportamento dos tratamentos foi estudado por intermédio da análise de regressão. Os resultados para o comprimento e peso dos peixes foram 25,68; 28,66; e 31,21 cm e 255,00; 424,00; e 519,66 g, respectivamente. Os tratamentos 1 e 3 apresentaram modelo de regressão linear diferente do tratamento 2, que apresentou modelo quadrático. Na biomassa total, os resultados foram 1881; 1512; e 1302 kg/ha/período e os modelos de regressão significativos para os tratamentos 1e 3 foram lineares e para o tratamento 2 quadrático. A conversão alimentar apresentou modelo de regressão linear para todos tratamentos. Em condições similares, podem-se recomendar todas densidades sugeridas, com base na produção final e sobrevivência.This study aimed to evaluate impact of stocking density on final productivity in the production of mirror common carp in fattening stage, during the summer. A completely randomized design with three treatments (1, .5, .33 fishes/m² and three replicates was used. The fish were stocked with an average weight of 2.40 g and average length of 5.35, 5.40 and 5.39 cm, respectively, in the treatments 1, 2 and 3, with 45 days of age. The diets were formulated with 27% CP and 2925 kcal/kg of diet and supplied daily at a rate of 3% of body weight. Regression analysis was used to evaluate the behavior of each treatment. For the fish lengths, the results were 25.68, 28.66 and 31.21 cm

  6. Avaliação multicriterial no mapeamento de risco de incêndios florestais, em ambiente sig, na bacia do Rio Corumbataí, SP Multi-criteria evaluation of a GIS environment in a forest fire hazard mapping for the Corumbataí River basin, SP, Brazil

    Directory of Open Access Journals (Sweden)

    Hilton Luis Ferraz da Silveira

    2008-04-01

    Full Text Available Um dos agentes mais empregados na supressão de áreas florestais no Estado de São Paulo é o fogo, por meio de queimadas que, quando fora de controle, podem converter-se em incêndios responsáveis pela destruição de extensos ecossistemas. Na Bacia do Rio Corumbataí, SP, os incêndios são um dos causadores de fragmentação e degradação da cobertura florestal. Nesse contexto, este trabalho objetivou a realização do mapeamento de risco de incêndios florestais na Bacia do Rio Corumbataí, utilizando-se a avaliação multicriterial (Método da Média Ponderada Ordenada em um Sistema de Informações Geográficas. Os fatores importantes do estudo foram: declividade do terreno, face de exposição ao sol, pluviosidade, proximidade da malha viária, proximidade dos centros urbanos, proximidade da rede hidrográfica, vizinhança dos fragmentos e face de exposição aos ventos. A combinação dos mapas de fatores resultou no mapa de risco regional da bacia. Para a confecção do mapa de risco em nível de fragmento, determinou-se o risco associado a cada fragmento, a partir da análise de uma faixa de 30 m em seu entorno. O risco foi reclassificado em três classes: baixo, médio e alto. Com base no mapa final, verificou-se que: aproximadamente 20% dos fragmentos de mata nativa pertencem à classe de risco alto, 55% à classe de risco médio e 25% à classe de risco baixo. Nas condições atuais de uso e cobertura do solo, bem como de manejo das áreas agrícolas e pastagens, os remanescentes florestais da Bacia do Rio Corumbataí estão sob séria ameaça de degradação por incêndios florestais.Fire is one of the agents most used in the suppression of forest areas in the State of São Paulo, Brazil, and, when out of control, it can be responsible for the destruction of extensive ecosystems. In the case of the Corumbataí river basin, SP, fire is one of the main causes of forest fragmentation and degradation. The purpose of this study was

  7. Visitantes florais do maracujá-amarelo (Passiflora edulis f. flavicarpa Deg. Passifloraceae em áreas de cultivo com diferentes proximidades a fragmentos florestais na região Norte Fluminense, RJ Yellow passion fruit (Passiflora edulis f. flavicarpa Deg. Passifloraceae floral visitors in cultivated areas within different distances from forest remnants in north Rio de Janeiro state

    Directory of Open Access Journals (Sweden)

    Cristine Rodrigues Benevides

    2009-01-01

    Full Text Available Este trabalho teve como objetivos estudar a biologia floral e identificar os principais polinizadores do maracujá-amarelo em áreas de cultivo com diferentes proximidades a fragmentos florestais no norte do estado do Rio de Janeiro. A floração do maracujá-amarelo teve duração de nove meses, no período de setembro a maio. As flores iniciavam a antese às 12:00 h e abriam-se ao longo do dia até às 16:30 h. O processo de curvatura dos estiletes ocorreu ao longo da antese e 72,4% das flores curvaram seus estiletes. A produção de néctar deu-se continuamente, atingindo 18μl/flor/hora e a concentração de solutos totais variou entre 38 e 42%. Xylocopa frontalis e Xylocopa ordinaria foram os principais polinizadores do maracujá-amarelo pela freqüência de visitas, comportamento intrafloral e porte corporal. Estas espécies de abelhas, além de Apis mellifera, estiveram presentes em todas as áreas de cultivo. A maior riqueza de visitantes polinizadores do maracujá-amarelo foi observada em áreas de cultivo próximas a fragmentos florestais, fato relacionado à presença de certos grupos de abelhas nativas, como Centridini e Euglossina (Apidae que dependem de áreas florestais para nidificação e alimentação. A proximidade a fragmentos florestais também é importante para o fornecimento de recursos alimentares e de nidificação ao longo do ano para a manutenção de populações de Xylocopa.This work aimed to identify the main pollinators and study the floral biology of the yellow passion fruit cultivated in areas within different distances from forest remnants in north Rio de Janeiro state. The yellow passion fruit flowering lasted nine months, from September to March. Anthesis started at 12:00 h and the opening process lasted until 16:30 h. The styles bent down during the anthesis and 72.4% of the flowers had its styles curved. Nectar was produced continuously, reaching 18μl/flower/hour, and the total solute concentration varied

  8. De novo transcriptome assembly of mangosteen (Garcinia mangostana L. fruit

    Directory of Open Access Journals (Sweden)

    Deden Derajat Matra

    2016-12-01

    Full Text Available Garcinia mangostana L. (Mangosteen, of the family Clusiaceae, is one of the economically important tropical fruits in Indonesia. In the present study, we performed de novo transcriptomic analysis of Garcinia mangostana L. through RNA-Seq technology. We obtained the raw data from 12 libraries through Ion Proton System. Clean reads of 191,735,809 were obtained from 307,634,890 raw reads. The raw data obtained in this study can be accessible in DDBJ database with accession number of DRA005014 with bioproject accession number of PRJDB5091. We obtained 268,851 transcripts as well as 155,850 unigenes, having N50 value of 555 and 433 bp, respectively. Transcript/unigene length ranged from 201 to 5916 bp. The unigenes were annotated with two main databases from NCBI and UniProtKB, respectively having annotated-sequences of 73,287 and 73,107, respectively. These transcriptomic data will be beneficial for studying transcriptome of Garcinia mangostana L.

  9. Massively parallel de novo protein design for targeted therapeutics

    KAUST Repository

    Chevalier, Aaron; Silva, Daniel-Adriano; Rocklin, Gabriel J.; Hicks, Derrick R.; Vergara, Renan; Murapa, Patience; Bernard, Steffen M.; Zhang, Lu; Lam, Kwok-Ho; Yao, Guorui; Bahl, Christopher D.; Miyashita, Shin-Ichiro; Goreshnik, Inna; Fuller, James T.; Koday, Merika T.; Jenkins, Cody M.; Colvin, Tom; Carter, Lauren; Bohn, Alan; Bryan, Cassie M.; Ferná ndez-Velasco, D. Alejandro; Stewart, Lance; Dong, Min; Huang, Xuhui; Jin, Rongsheng; Wilson, Ian A.; Fuller, Deborah H.; Baker, David

    2017-01-01

    De novo protein design holds promise for creating small stable proteins with shapes customized to bind therapeutic targets. We describe a massively parallel approach for designing, manufacturing and screening mini-protein binders, integrating large-scale computational design, oligonucleotide synthesis, yeast display screening and next-generation sequencing. We designed and tested 22,660 mini-proteins of 37-43 residues that target influenza haemagglutinin and botulinum neurotoxin B, along with 6,286 control sequences to probe contributions to folding and binding, and identified 2,618 high-affinity binders. Comparison of the binding and non-binding design sets, which are two orders of magnitude larger than any previously investigated, enabled the evaluation and improvement of the computational model. Biophysical characterization of a subset of the binder designs showed that they are extremely stable and, unlike antibodies, do not lose activity after exposure to high temperatures. The designs elicit little or no immune response and provide potent prophylactic and therapeutic protection against influenza, even after extensive repeated dosing.

  10. Sequencing and De Novo Transcriptome Assembly of Brachypodium sylvaticum (Poaceae

    Directory of Open Access Journals (Sweden)

    Samuel E. Fox

    2013-03-01

    Full Text Available Premise of the study: We report the de novo assembly and characterization of the transcriptomes of Brachypodium sylvaticum (slender false-brome accessions from native populations of Spain and Greece, and an invasive population west of Corvallis, Oregon, USA. Methods and Results: More than 350 million sequence reads from the mRNA libraries prepared from three B. sylvaticum genotypes were assembled into 120,091 (Corvallis, 104,950 (Spain, and 177,682 (Greece transcript contigs. In comparison with the B. distachyon Bd21 reference genome and GenBank protein sequences, we estimate >90% exome coverage for B. sylvaticum. The transcripts were assigned Gene Ontology and InterPro annotations. Brachypodium sylvaticum sequence reads aligned against the Bd21 genome revealed 394,654 single-nucleotide polymorphisms (SNPs and >20,000 simple sequence repeat (SSR DNA sites. Conclusions: To our knowledge, this is the first report of transcriptome sequencing of invasive plant species with a closely related sequenced reference genome. The sequences and identified SNP variant and SSR sites will provide tools for developing novel genetic markers for use in genotyping and characterization of invasive behavior of B. sylvaticum.

  11. LESSONS IN DE NOVO PEPTIDE SEQUENCING BY TANDEM MASS SPECTROMETRY

    Science.gov (United States)

    Medzihradszky, Katalin F.; Chalkley, Robert J.

    2015-01-01

    Mass spectrometry has become the method of choice for the qualitative and quantitative characterization of protein mixtures isolated from all kinds of living organisms. The raw data in these studies are MS/MS spectra, usually of peptides produced by proteolytic digestion of a protein. These spectra are “translated” into peptide sequences, normally with the help of various search engines. Data acquisition and interpretation have both been automated, and most researchers look only at the summary of the identifications without ever viewing the underlying raw data used for assignments. Automated analysis of data is essential due to the volume produced. However, being familiar with the finer intricacies of peptide fragmentation processes, and experiencing the difficulties of manual data interpretation allow a researcher to be able to more critically evaluate key results, particularly because there are many known rules of peptide fragmentation that are not incorporated into search engine scoring. Since the most commonly used MS/MS activation method is collision-induced dissociation (CID), in this article we present a brief review of the history of peptide CID analysis. Next, we provide a detailed tutorial on how to determine peptide sequences from CID data. Although the focus of the tutorial is de novo sequencing, the lessons learned and resources supplied are useful for data interpretation in general. PMID:25667941

  12. De novo transcriptome assembly of a sour cherry cultivar, Schattenmorelle

    Directory of Open Access Journals (Sweden)

    Yeonhwa Jo

    2015-12-01

    Full Text Available Sour cherry (Prunus cerasus in the genus Prunus in the family Rosaceae is one of the most popular stone fruit trees worldwide. Of known sour cherry cultivars, the Schattenmorelle is a famous old sour cherry with a high amount of fruit production. The Schattenmorelle was selected before 1650 and described in the 1800s. This cultivar was named after gardens of the Chateau de Moreille in which the cultivar was initially found. In order to identify new genes and to develop genetic markers for sour cherry, we performed a transcriptome analysis of a sour cherry. We selected the cultivar Schattenmorelle, which is among commercially important cultivars in Europe and North America. We obtained 2.05 GB raw data from the Schattenmorelle (NCBI accession number: SRX1187170. De novo transcriptome assembly using Trinity identified 61,053 transcripts in which N50 was 611 bp. Next, we identified 25,585 protein coding sequences using TransDecoder. The identified proteins were blasted against NCBI's non-redundant database for annotation. Based on blast search, we taxonomically classified the obtained sequences. As a result, we provide the transcriptome of sour cherry cultivar Schattenmorelle using next generation sequencing.

  13. Spaced Seed Data Structures for De Novo Assembly

    Directory of Open Access Journals (Sweden)

    Inanç Birol

    2015-01-01

    Full Text Available De novo assembly of the genome of a species is essential in the absence of a reference genome sequence. Many scalable assembly algorithms use the de Bruijn graph (DBG paradigm to reconstruct genomes, where a table of subsequences of a certain length is derived from the reads, and their overlaps are analyzed to assemble sequences. Despite longer subsequences unlocking longer genomic features for assembly, associated increase in compute resources limits the practicability of DBG over other assembly archetypes already designed for longer reads. Here, we revisit the DBG paradigm to adapt it to the changing sequencing technology landscape and introduce three data structure designs for spaced seeds in the form of paired subsequences. These data structures address memory and run time constraints imposed by longer reads. We observe that when a fixed distance separates seed pairs, it provides increased sequence specificity with increased gap length. Further, we note that Bloom filters would be suitable to implicitly store spaced seeds and be tolerant to sequencing errors. Building on this concept, we describe a data structure for tracking the frequencies of observed spaced seeds. These data structure designs will have applications in genome, transcriptome and metagenome assemblies, and read error correction.

  14. De novo protein structure generation from incomplete chemical shift assignments

    Energy Technology Data Exchange (ETDEWEB)

    Shen Yang [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Vernon, Robert; Baker, David [University of Washington, Department of Biochemistry and Howard Hughes Medical Institute (United States); Bax, Ad [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)], E-mail: bax@nih.gov

    2009-02-15

    NMR chemical shifts provide important local structural information for proteins. Consistent structure generation from NMR chemical shift data has recently become feasible for proteins with sizes of up to 130 residues, and such structures are of a quality comparable to those obtained with the standard NMR protocol. This study investigates the influence of the completeness of chemical shift assignments on structures generated from chemical shifts. The Chemical-Shift-Rosetta (CS-Rosetta) protocol was used for de novo protein structure generation with various degrees of completeness of the chemical shift assignment, simulated by omission of entries in the experimental chemical shift data previously used for the initial demonstration of the CS-Rosetta approach. In addition, a new CS-Rosetta protocol is described that improves robustness of the method for proteins with missing or erroneous NMR chemical shift input data. This strategy, which uses traditional Rosetta for pre-filtering of the fragment selection process, is demonstrated for two paramagnetic proteins and also for two proteins with solid-state NMR chemical shift assignments.

  15. Massively parallel de novo protein design for targeted therapeutics

    KAUST Repository

    Chevalier, Aaron

    2017-09-26

    De novo protein design holds promise for creating small stable proteins with shapes customized to bind therapeutic targets. We describe a massively parallel approach for designing, manufacturing and screening mini-protein binders, integrating large-scale computational design, oligonucleotide synthesis, yeast display screening and next-generation sequencing. We designed and tested 22,660 mini-proteins of 37-43 residues that target influenza haemagglutinin and botulinum neurotoxin B, along with 6,286 control sequences to probe contributions to folding and binding, and identified 2,618 high-affinity binders. Comparison of the binding and non-binding design sets, which are two orders of magnitude larger than any previously investigated, enabled the evaluation and improvement of the computational model. Biophysical characterization of a subset of the binder designs showed that they are extremely stable and, unlike antibodies, do not lose activity after exposure to high temperatures. The designs elicit little or no immune response and provide potent prophylactic and therapeutic protection against influenza, even after extensive repeated dosing.

  16. De novo transcriptome assembly of Sorghum bicolor variety Taejin

    Directory of Open Access Journals (Sweden)

    Yeonhwa Jo

    2016-06-01

    Full Text Available Sorghum (Sorghum bicolor, also known as great millet, is one of the most popular cultivated grass species in the world. Sorghum is frequently consumed as food for humans and animals as well as used for ethanol production. In this study, we conducted de novo transcriptome assembly for sorghum variety Taejin by next-generation sequencing, obtaining 8.748 GB of raw data. The raw data in this study can be available in NCBI SRA database with accession number of SRX1715644. Using the Trinity program, we identified 222,161 transcripts from sorghum variety Taejin. We further predicted coding regions within the assembled transcripts by the TransDecoder program, resulting in a total of 148,531 proteins. We carried out BLASTP against the Swiss-Prot protein sequence database to annotate the functions of the identified proteins. To our knowledge, this is the first transcriptome data for a sorghum variety derived from Korea, and it can be usefully applied to the generation of genetic markers.

  17. Massively parallel de novo protein design for targeted therapeutics

    Science.gov (United States)

    Chevalier, Aaron; Silva, Daniel-Adriano; Rocklin, Gabriel J.; Hicks, Derrick R.; Vergara, Renan; Murapa, Patience; Bernard, Steffen M.; Zhang, Lu; Lam, Kwok-Ho; Yao, Guorui; Bahl, Christopher D.; Miyashita, Shin-Ichiro; Goreshnik, Inna; Fuller, James T.; Koday, Merika T.; Jenkins, Cody M.; Colvin, Tom; Carter, Lauren; Bohn, Alan; Bryan, Cassie M.; Fernández-Velasco, D. Alejandro; Stewart, Lance; Dong, Min; Huang, Xuhui; Jin, Rongsheng; Wilson, Ian A.; Fuller, Deborah H.; Baker, David

    2018-01-01

    De novo protein design holds promise for creating small stable proteins with shapes customized to bind therapeutic targets. We describe a massively parallel approach for designing, manufacturing and screening mini-protein binders, integrating large-scale computational design, oligonucleotide synthesis, yeast display screening and next-generation sequencing. We designed and tested 22,660 mini-proteins of 37–43 residues that target influenza haemagglutinin and botulinum neurotoxin B, along with 6,286 control sequences to probe contributions to folding and binding, and identified 2,618 high-affinity binders. Comparison of the binding and non-binding design sets, which are two orders of magnitude larger than any previously investigated, enabled the evaluation and improvement of the computational model. Biophysical characterization of a subset of the binder designs showed that they are extremely stable and, unlike antibodies, do not lose activity after exposure to high temperatures. The designs elicit little or no immune response and provide potent prophylactic and therapeutic protection against influenza, even after extensive repeated dosing. PMID:28953867

  18. De novo malignancy is associated with renal transplant tourism.

    Science.gov (United States)

    Tsai, Meng-Kun; Yang, Ching-Yao; Lee, Chih-Yuan; Yeh, Chi-Chuan; Hu, Rey-Heng; Lee, Po-Huang

    2011-04-01

    Despite the objections to transplant tourism raised by the transplant community, many patients continue travel to other countries to receive commercial transplants. To evaluate some long-term complications, we reviewed medical records of 215 Taiwanese patients (touring group) who received commercial cadaveric renal transplants in China and compared them with those of 321 transplant recipients receiving domestic cadaveric renal transplants (domestic group) over the same 20-year period. Ten years after transplant, the graft and patient survival rates of the touring group were 55 and 81.5%, respectively, compared with 60 and 89.3%, respectively, of the domestic group. The difference between the two groups was not statistically significant. The 10-year cumulative cancer incidence of the touring group (21.5%) was significantly higher than that of the domestic group (6.8%). Univariate and multivariate stepwise regression analyses (excluding time on immunosuppression, an uncontrollable factor) indicated that transplant tourism was associated with significantly higher cancer incidence. Older age at transplantation was associated with a significantly increased cancer risk; however, the risk of de novo malignancy significantly decreased with longer graft survival. Thus, renal transplant tourism may be associated with a higher risk of post-transplant malignancy, especially in patients of older age at transplantation. © 2011 International Society of Nephrology

  19. Programming peptidomimetic syntheses by translating genetic codes designed de novo.

    Science.gov (United States)

    Forster, Anthony C; Tan, Zhongping; Nalam, Madhavi N L; Lin, Hening; Qu, Hui; Cornish, Virginia W; Blacklow, Stephen C

    2003-05-27

    Although the universal genetic code exhibits only minor variations in nature, Francis Crick proposed in 1955 that "the adaptor hypothesis allows one to construct, in theory, codes of bewildering variety." The existing code has been expanded to enable incorporation of a variety of unnatural amino acids at one or two nonadjacent sites within a protein by using nonsense or frameshift suppressor aminoacyl-tRNAs (aa-tRNAs) as adaptors. However, the suppressor strategy is inherently limited by compatibility with only a small subset of codons, by the ways such codons can be combined, and by variation in the efficiency of incorporation. Here, by preventing competing reactions with aa-tRNA synthetases, aa-tRNAs, and release factors during translation and by using nonsuppressor aa-tRNA substrates, we realize a potentially generalizable approach for template-encoded polymer synthesis that unmasks the substantially broader versatility of the core translation apparatus as a catalyst. We show that several adjacent, arbitrarily chosen sense codons can be completely reassigned to various unnatural amino acids according to de novo genetic codes by translating mRNAs into specific peptide analog polymers (peptidomimetics). Unnatural aa-tRNA substrates do not uniformly function as well as natural substrates, revealing important recognition elements for the translation apparatus. Genetic programming of peptidomimetic synthesis should facilitate mechanistic studies of translation and may ultimately enable the directed evolution of small molecules with desirable catalytic or pharmacological properties.

  20. Dominant de novo DSP mutations cause erythrokeratodermia-cardiomyopathy syndrome.

    Science.gov (United States)

    Boyden, Lynn M; Kam, Chen Y; Hernández-Martín, Angela; Zhou, Jing; Craiglow, Brittany G; Sidbury, Robert; Mathes, Erin F; Maguiness, Sheilagh M; Crumrine, Debra A; Williams, Mary L; Hu, Ronghua; Lifton, Richard P; Elias, Peter M; Green, Kathleen J; Choate, Keith A

    2016-01-15

    Disorders of keratinization (DOK) show marked genotypic and phenotypic heterogeneity. In most cases, disease is primarily cutaneous, and further clinical evaluation is therefore rarely pursued. We have identified subjects with a novel DOK featuring erythrokeratodermia and initially-asymptomatic, progressive, potentially fatal cardiomyopathy, a finding not previously associated with erythrokeratodermia. We show that de novo missense mutations clustered tightly within a single spectrin repeat of DSP cause this novel cardio-cutaneous disorder, which we term erythrokeratodermia-cardiomyopathy (EKC) syndrome. We demonstrate that DSP mutations in our EKC syndrome subjects affect localization of desmosomal proteins and connexin 43 in the skin, and result in desmosome aggregation, widening of intercellular spaces, and lipid secretory defects. DSP encodes desmoplakin, a primary component of desmosomes, intercellular adhesion junctions most abundant in the epidermis and heart. Though mutations in DSP are known to cause other disorders, our cohort features the unique clinical finding of severe whole-body erythrokeratodermia, with distinct effects on localization of desmosomal proteins and connexin 43. These findings add a severe, previously undescribed syndrome featuring erythrokeratodermia and cardiomyopathy to the spectrum of disease caused by mutation in DSP, and identify a specific region of the protein critical to the pathobiology of EKC syndrome and to DSP function in the heart and skin. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  1. De Novo Design of Bioactive Small Molecules by Artificial Intelligence.

    Science.gov (United States)

    Merk, Daniel; Friedrich, Lukas; Grisoni, Francesca; Schneider, Gisbert

    2018-01-01

    Generative artificial intelligence offers a fresh view on molecular design. We present the first-time prospective application of a deep learning model for designing new druglike compounds with desired activities. For this purpose, we trained a recurrent neural network to capture the constitution of a large set of known bioactive compounds represented as SMILES strings. By transfer learning, this general model was fine-tuned on recognizing retinoid X and peroxisome proliferator-activated receptor agonists. We synthesized five top-ranking compounds designed by the generative model. Four of the compounds revealed nanomolar to low-micromolar receptor modulatory activity in cell-based assays. Apparently, the computational model intrinsically captured relevant chemical and biological knowledge without the need for explicit rules. The results of this study advocate generative artificial intelligence for prospective de novo molecular design, and demonstrate the potential of these methods for future medicinal chemistry. © 2018 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

  2. De novo Biosynthesis of "Non-Natural" Thaxtomin Phytotoxins.

    Science.gov (United States)

    Winn, Michael; Francis, Daniel; Micklefield, Jason

    2018-03-30

    Thaxtomins are diketopiperazine phytotoxins produced by Streptomyces scabies and other actinobacterial plant pathogens that inhibit cellulose biosynthesis in plants. Due to their potent bioactivity and novel mode of action there has been considerable interest in developing thaxtomins as herbicides for crop protection. To address the need for more stable derivatives, we have developed a new approach for structural diversification of thaxtomins. Genes encoding the thaxtomin NRPS from S. scabies, along with genes encoding a promiscuous tryptophan synthase (TrpS) from Salmonella typhimurium, were assembled in a heterologous host Streptomyces albus. Upon feeding indole derivatives to the engineered S. albus strain, tryptophan intermediates with alternative substituents are biosynthesized and incorporated by the NRPS to deliver a series of thaxtomins with different functionalities in place of the nitro group. The approach described herein, demonstrates how genes from different pathways and different bacterial origins can be combined in a heterologous host to create a de novo biosynthetic pathway to "non-natural" product target compounds. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. De novo DNA methylation during monkey pre-implantation embryogenesis.

    Science.gov (United States)

    Gao, Fei; Niu, Yuyu; Sun, Yi Eve; Lu, Hanlin; Chen, Yongchang; Li, Siguang; Kang, Yu; Luo, Yuping; Si, Chenyang; Yu, Juehua; Li, Chang; Sun, Nianqin; Si, Wei; Wang, Hong; Ji, Weizhi; Tan, Tao

    2017-04-01

    Critical epigenetic regulation of primate embryogenesis entails DNA methylome changes. Here we report genome-wide composition, patterning, and stage-specific dynamics of DNA methylation in pre-implantation rhesus monkey embryos as well as male and female gametes studied using an optimized tagmentation-based whole-genome bisulfite sequencing method. We show that upon fertilization, both paternal and maternal genomes undergo active DNA demethylation, and genome-wide de novo DNA methylation is also initiated in the same period. By the 8-cell stage, remethylation becomes more pronounced than demethylation, resulting in an increase in global DNA methylation. Promoters of genes associated with oxidative phosphorylation are preferentially remethylated at the 8-cell stage, suggesting that this mode of energy metabolism may not be favored. Unlike in rodents, X chromosome inactivation is not observed during monkey pre-implantation development. Our study provides the first comprehensive illustration of the 'wax and wane' phases of DNA methylation dynamics. Most importantly, our DNA methyltransferase loss-of-function analysis indicates that DNA methylation influences early monkey embryogenesis.

  4. A crise financeira global e depois: um novo capitalismo?

    Directory of Open Access Journals (Sweden)

    Luiz Carlos Bresser-Pereira

    2010-03-01

    Full Text Available A crise financeira global de 2008 foi conseqüência do processo de financeirização, a criação maciça de riqueza financeira fictícia iniciada da década de 1980, e da hegemonia de uma ideologia reacionária, o neoliberalismo, baseada em mercados auto-regulados e eficientes. Dessa crise emergirá um novo capitalismo, embora sua natureza seja de difícil previsão. Não será financeirizado, mas serão retomadas as tendências presentes nos trinta anos dourados em direção ao capitalismo global e baseado no conhecimento, além da tendência de expansão da democracia, tornando-a mais social e participativa.The 2008 global financial crisis was a consequence of the processes of financialization, the massive creation of fictitious financial wealth which began in the 1980's, and of the hegemony of a reactionary ideology, neoliberalism, based on the belief of the self-regulating capacity and efficiency of markets. From this crisis a new capitalism will emerge, althought its chacarteristics are hard to foresee. It will not be financial, but the tendencies of the 30 "golden years" toward global and knowledge-based capitalism, and the tendency of expansion of democracy will be among them.

  5. Enzyme-like replication de novo in a microcontroller environment.

    Science.gov (United States)

    Tangen, Uwe

    2010-01-01

    The desire to start evolution from scratch inside a computer memory is as old as computing. Here we demonstrate how viable computer programs can be established de novo in a Precambrian environment without supplying any specific instantiation, just starting with random bit sequences. These programs are not self-replicators, but act much more like catalysts. The microcontrollers used in the end are the result of a long series of simplifications. The objective of this simplification process was to produce universal machines with a human-readable interface, allowing software and/or hardware evolution to be studied. The power of the instruction set can be modified by introducing a secondary structure-folding mechanism, which is a state machine, allowing nontrivial replication to emerge with an instruction width of only a few bits. This state-machine approach not only attenuates the problems of brittleness and encoding functionality (too few bits available for coding, and too many instructions needed); it also enables the study of hardware evolution as such. Furthermore, the instruction set is sufficiently powerful to permit external signals to be processed. This information-theoretic approach forms one vertex of a triangle alongside artificial cell research and experimental research on the creation of life. Hopefully this work helps develop an understanding of how information—in a similar sense to the account of functional information described by Hazen et al.—is created by evolution and how this information interacts with or is embedded in its physico-chemical environment.

  6. Rapid centriole assembly in Naegleria reveals conserved roles for both de novo and mentored assembly.

    Science.gov (United States)

    Fritz-Laylin, Lillian K; Levy, Yaron Y; Levitan, Edward; Chen, Sean; Cande, W Zacheus; Lai, Elaine Y; Fulton, Chandler

    2016-03-01

    Centrioles are eukaryotic organelles whose number and position are critical for cilia formation and mitosis. Many cell types assemble new centrioles next to existing ones ("templated" or mentored assembly). Under certain conditions, centrioles also form without pre-existing centrioles (de novo). The synchronous differentiation of Naegleria amoebae to flagellates represents a unique opportunity to study centriole assembly, as nearly 100% of the population transitions from having no centrioles to having two within minutes. Here, we find that Naegleria forms its first centriole de novo, immediately followed by mentored assembly of the second. We also find both de novo and mentored assembly distributed among all major eukaryote lineages. We therefore propose that both modes are ancestral and have been conserved because they serve complementary roles, with de novo assembly as the default when no pre-existing centriole is available, and mentored assembly allowing precise regulation of number, timing, and location of centriole assembly. © 2016 Wiley Periodicals, Inc.

  7. De Novo Human Cardiac Myocytes for Medical Research: Promises and Challenges

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    Veronique Hamel

    2017-01-01

    Full Text Available The advent of cellular reprogramming technology has revolutionized biomedical research. De novo human cardiac myocytes can now be obtained from direct reprogramming of somatic cells (such as fibroblasts, from induced pluripotent stem cells (iPSCs, which are reprogrammed from somatic cells, and from human embryonic stem cells (hESCs. Such de novo human cardiac myocytes hold great promise for in vitro disease modeling and drug screening and in vivo cell therapy of heart disease. Here, we review the technique advancements for generating de novo human cardiac myocytes. We also discuss several challenges for the use of such cells in research and regenerative medicine, such as the immature phenotype and heterogeneity of de novo cardiac myocytes obtained with existing protocols. We focus on the recent advancements in addressing such challenges.

  8. Novel de novo BRCA2 mutation in a patient with a family history of breast cancer

    DEFF Research Database (Denmark)

    Hansen, Thomas V O; Bisgaard, Marie Luise; Jønson, Lars

    2008-01-01

    whole blood. The paternity was determined by single nucleotide polymorphism (SNP) microarray analysis. Parental origin of the de novo mutation was determined by establishing mutation-SNP haplotypes by variant specific PCR, while de novo and mosaic status was investigated by sequencing of DNA from......BACKGROUND: BRCA2 germ-line mutations predispose to breast and ovarian cancer. Mutations are widespread and unclassified splice variants are frequently encountered. We describe the parental origin and functional characterization of a novel de novo BRCA2 splice site mutation found in a patient...... and synthesis of a truncated BRCA2 protein. The aberrant splicing was verified by RT-PCR analysis on RNA isolated from whole blood of the affected patient. The mutation was not found in any of the patient's parents or in the mother's carcinoma, showing it is a de novo mutation. Variant specific PCR indicates...

  9. Spontaneous de novo vaginal adenosis resembling Bartholin’s ...

    African Journals Online (AJOL)

    Adebayo Alade Adewole

    Spontaneous de novo vaginal adenosis resembling Bartholin's cyst: A case report ... 6 by 5 cm. The cervix, uterus, adnexa and Pouch of Douglas (POD) were normal. .... of vaginal cancer.2–4 Although, DES exposed daughters have an.

  10. Avaliação técnica do trator florestal arrastador "skidder" com diferentes tipos de rodados na extração de madeira em povoamentos de pinus Technical evalution of a skidder with different wheeled types in log extraction activies of pine plantation

    Directory of Open Access Journals (Sweden)

    Eduardo da Silva Lopes

    2007-12-01

    Full Text Available Este trabalho teve como principal objetivo a avaliação técnica das atividades de extração de madeira usando tratores florestais arrastadores skidders equipados com rodado de pneus e com rodado de pneus recoberto com semi-esteiras. A avaliação técnica consistiu em determinar os índices de produtividade da operação de extração da madeira por meio de um estudo de tempos e movimentos, em que a operação foi dividida em fases do ciclo de trabalho. Foram determinadas as produtividades das máquinas em diferentes situações de distâncias de extração e declividades de terreno. Os resultados indicaram que o tempo médio do ciclo operacional do skidder com rodado de pneus foi 7,1% menor em relação ao skidder de pneus recobertos por esteiras, o que explicado se pela maior eficiência dos pneus sobre a superfície do terreno. O skidder de pneus apresentou melhor eficiência na situação de declividade entre 10 e 20%, devido à maior agilidade do rodado de pneus e capacidade em desenvolver maior velocidade, enquanto o skidder com rodado de pneus recoberto por esteiras apresentou velocidade operacional constante. Em declividade acima de 20%, o skidder de pneus recoberto com esteiras realizou normalmente o arraste da madeira, enquanto o skidder de pneus não entrou em operação devido à elevada patinagem dos pneus e diminuição da capacidade de tração.The objective of this study was to evaluate technical log extraction activities using a skidder with tires and a skidder with tracks over the tires. Technical evaluation consisted in determining log extraction productivity indexes based on motion and time study, in which the extraction activities were grouped into work cycle phases. Machine productivity was determined in different extraction distances and slope degree situations. The results showed that the operational cycle average time of the tire skidder was 7.1% smaller that the skidder with tracks over the tires, explained by the

  11. Avaliação de populações de possíveis rizobactérias em solos sob espécies florestais Evaluation of possible rhizobacteria populations in soils under forest species

    Directory of Open Access Journals (Sweden)

    Rodrigo Matheus Pereira

    2008-10-01

    Full Text Available Embora estudos recentes relatem a utilização de RCPC (Rizobactérias Promotoras de Crescimento de Plantas no Brasil, raríssimos trabalhos avaliam a presença natural dessas espécies bacterianas no solo. O objetivo deste trabalho foi avaliar a ocorrência de RPCP em duas amostras de solo sob diferentes tipos de manejo, através da construção e do seqüenciamento de bibliotecas de DNA metagenômico. Utilizaram-se oligonucleotídeos específicos para amplificação da região hipervariável do espaço intergênico dos genes ribossomais 16S-23S de DNA extraído de diferentes solos, sob Eucalyptus sp. e sob mata. Os fragmentos obtidos foram inseridos em vetor e clonados. As bibliotecas geraram 495 clones, que foram seqüenciados e identificados através de comparações realizadas pelo software Blast. O solo sob Eucalyptus sp. apresentou maior número de RPCP do que sob mata. Os filos Actinobacteria e Proteobacteria eram maiores no solo sob Eucalyptus sp., estando o filo Firmicutes ausente no solo sob mata. Somente oito espécies diferentes de RPCP foram detectadas: Bacillus subtilis, Bacillus megaterium, Bradyrhizobium japonicum, Bradyrhizobium elkanii, Bradyrhizobium sp., Frankia sp., Pseudomonas fluorescens e Pseudomonas gladioli. O trabalho forneceu valiosos dados sobre a presença de RPCP em solos com espécies florestais e sua possível utilização em reflorestamentos, assim como para o melhor conhecimento desses microrganismos nos solos do Brasil.Although new studies describe the use of PGPR (Plant Growth-Promoting Rhizobacteria in Brazil, they rarely evaluate the natural existence of these bacterial species in the soil. The objective of this study was to evaluate PGPR in two samples under different use types, one with native forest and the other with eucalyptus, through construction and sequencing of a metagenomic DNA library. Using specific probes from the internally transcribed region of 16S-23S rRNA genes, fragments of PCR products

  12. Gradiente fitofisionômico-edáfico em formações florestais de Restinga no sudeste do Brasil Phytophysiognomic-edaphic gradient of forest formations in restinga areas of southeastern Brazil

    Directory of Open Access Journals (Sweden)

    Luiz Fernando Silva Magnago

    2010-09-01

    Full Text Available A presente pesquisa teve como objetivo analisar as variações fitofisionômicas em quatro formações florestais, em relação aos gradientes de inundação e características pedológicas. O estudo foi no Parque Natural Municipal de Jacarenema, Vila Velha, Espírito Santo. Quatro perfis de solo com profundidades variadas foram abertos, onde uma amostra foi coletada em cada horizonte existente por perfil. Para acompanhamento da flutuação do lençol freático, foram instalados piezômetros, em profundidade de 2 m em cada fitofisionomia. O reconhecimento e delimitação das unidades vegetacionais seguiu os critérios fisionômicos, ecológicos e aspectos florísticos apresentados pelas diferentes formações, sendo as características vegetacionais de cada fitocenose expressas por perfis ilustrativos. Nas fisionomias estudadas, foram identificadas quatro classes de solos distintas, sendo Organossolos Tiomórficos Sápricos solódicos muito mal drenados sob a Floresta Inundada, Gleissolos Tiomórficos Húmicos solódicos mal drenados sob a Floresta Inundável, Espodossolos Humilúvicos Hidromórficos dúricos moderadamente a imperfeitamente drenado sob a Floresta Não Inundável de Transição e Neossolos Quartzarênicos Órticos espódicos excessivamente drenados sob Floresta Não Inundável. Os resultados mostram a existência de respostas vegetacionais das florestas em virtude das variáveis edáficas.This research aimed to evaluate the phytophysiognomic variations in four forest formations related to flood gradient and edaphic characteristics. The study was carried out at the Jacarenema Nautral Municipal Park, Vila Velha, Espírito Santo state, Brazil. We made four soil profiles varying in depth, and collected one sample from each horizon per profile. Piezometers were set up at 2m depth in each phytophysiognomy to record groundwater variance. Recognition and delimitation of the vegetation units followed the phytophysiognomic, ecological and

  13. Atrazine and picloram adsorption in organic horizon forest samples under laboratory conditions Adsorção de atrazina e picloram em amostras florestais de horizonte orgânico

    Directory of Open Access Journals (Sweden)

    A.P. Pinho

    2007-03-01

    Full Text Available Adsorption of two herbicides, atrazine and picloram, displaying different sorption characteristics, were evaluated for O (organic horizon samples collected from SMZs (streamside management zones in Piedmont (Ultisol of Georgia, USA. Samples were randomly collected from within 5 SMZs selected for a study of surface flow in field trials. The five SMZs represented five different slope classes, 2, 5, 10, 15 and 20%. Results indicate that 0 horizons have the potential for sorbing atrazine from surface water moving through forested SMZs. Atrazine adsorption was nearly linear over a 24-hour period. Equilibrium adsorption, determined through 24-hour laboratory tests, resulted in a Freundlich coefficient of 67.5 for atrazine. For picloram, negative adsorption was observed in laboratory experiments. This seemed to be due to interference with ELISA analyses; however, this was not confirmed. The adsorption coefficient (Kd obtained for atrazine in 0 horizons was greater than it would have been expected for mineral soil (from 1 to 4. Picloram was not sorbed in 0 horizons at any significant degree. Although there is a significant potential for the direct adsorption of soluble forms of herbicides in SMZs, the actual value of this adsorption for protecting water is likely to be limited even for relatively strongly sorbed chemicals, such as atrazine, due to relatively slow uptake kinetics.Este trabalho avaliou a adsorção de dois herbicidas - atrazina e picloram - com diferentes características de sorção, em amostras florestais de horizonte orgânico (HO coletadas em matas ciliares de manejo (MCM localizadas em uma região de Piedmond (Ultisol, no estado da Geórgia, EUA. As amostras foram coletadas aleatoriamente dentro de cinco áreas de mata ciliar distintas, em classes de declividade de 2, 5, 10, 15 e 20%, as quais foram selecionadas para desenvolver experimentos de campo sobre o transporte de herbicidas por escoamento superficial. Os resultados indicam

  14. Crescimento inicial, níveis críticos de fósforo e frações fosfatadas em espécies florestais Initial growing, phosphorus critical levels and phosphate fractions in forest species

    Directory of Open Access Journals (Sweden)

    LUIZ ARNALDO FERNANDES

    2000-06-01

    Full Text Available Foi conduzido um experimento em casa de vegetação, com o objetivo de avaliar o crescimento de plântulas, os níveis críticos de P e algumas frações fosfatadas, em três espécies florestais submetidas a quatro doses de P. Mudas de aroeirinha (Schinus terenbinthifolius Raddi, paineira (Chorisia speciosa St. Hill. e jambolão (Syzygium jambolanum Lam. foram cultivadas em um Latossolo Variação Una, onde foram aplicados 0, 150, 300 e 600 mg dm-3 de P. Aos 180 dias após a germinação, as plantas foram colhidas e submetidas às análises químicas. Sob todas as doses de P, a paineira produziu maior biomassa da parte aérea e das raízes em comparação à aroeirinha e jambolão, além de apresentar maiores teores de P orgânico (Po e maior participação relativa do P orgânico (Po em relação ao P total solúvel em ácido em todos os níveis de fertilização fosfatada. O melhor crescimento da paineira foi atribuído a uma maior eficiência nos ajustes metabólicos desta espécie em relação à nutrição fosfatada, o que indica que esta espécie pode ser plantada em solos com diferentes níveis de P.An experiment under greenhouse conditions was carried out at Universidade Federal de Lavras, Minas Gerais State, Brazil, to evaluate the growth of seedlings, phosphorus critical levels and phosphate fractions, in forest species growing under four phosphorus levels. Seedlings of Schinus terenbinthifolius Raddi (aroeirinha, Chorisia speciosa St. Hill. (paineira and Syzygium jambolanum Lam. (jambolão were cultivated on an Oxisol fertilized with 0, 150, 300 and 600 mg dm-3 of P. The seedlings were harvested 180 days after germination and analysed for P forms. In all levels of phosphorus addition, the paineira produced higher aerial and root biomass than aroeirinha and jambolão, and presented higher contents of organic phosphorus and higher relative participation of organic phosphorus in the total acid soluble phosphorus under all phosphorus

  15. Flora pteridofítica de fragmentos florestais do Parque Estadual de Vassununga – Santa Rita do Passa Quatro, SP. Pteridophyte flora of forest fragments in Vassununga State Park – Santa Rita do Passa Quatro, São Paulo, Brazil.

    Directory of Open Access Journals (Sweden)

    Áurea Maria Therezinha COLLI

    2014-06-01

    Full Text Available Este trabalho apresenta o levantamento da flora pteridofítica de dois fragmentos florestais do Parque Estadual de Vassununga, unidade de conservação localizada no município de Santa Rita do Passa Quatro, SP. Para tanto, foram realizadas onze excursões por caminhos e trilhas de fiscalização e de pesquisa. Na Gleba Maravilha, que apresenta vegetação de Floresta Estacional Semidecidual Montana e Floresta Estacional Semidecidual Aluvial com inundação temporária, foram encontradas 10 famílias, 18 gêneros e 35 espécies, sendo Pteridaceae, Thelypteridaceae, Aspleniaceae, e Polypodiaceae as famílias mais ricas com nove, sete, seis e cinco espécies, respectivamente. Na Gleba Capão da Várzea, onde ocorre a Floresta Paludosa e o Campo Antrópico, ocorreram nove famílias, 14 gêneros e 24 espécies, onde Thelypteridaceae e Polypodiaceae se apresentaram como as mais ricas, com oito e seis espécies, respectivamente. As Glebas do Parque Estadual de Vassununga com as suas diferentes fisionomias vegetais são áreas importantes para a conservação de pteridófitas na região nordeste do Estado de São Paulo, principalmente as típicas de Floresta Estacional Semidecidual Montana e de Floresta Paludosa como Blechnum brasiliense, Campyloneurum angustifolium, Cyclodium meniscioides, Osmunda regalis, Pityrogramma calomelanos e Thelypteris opposita. This work presents a survey on pteridophyte flora of two forest fragments in Vassununga State Park, a conservation unit located in the city of Santa Rita do Passa Quatro, São Paulo, Brazil. In order to carry out the survey, a series of eleven tours on old inspection and research trails were made. In the Maravilha Tract, which consists of Seasonal Semi-Deciduous Montane Forest and Seasonal Semideciduous Alluvial Forest with temporary flooding, 10 families, 18 genera, and 35 species were found, the richest families were Pteridaceae, Thelypteridaceae, Aspleniaceae, and Polypodiaceae, with nine, seven

  16. Aplicações de misturas solo-"grits" em estradas florestais: resistência mecânica via CBR Application of soil-grits mixtures in forest roads: mechanical strength via CBR test

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    Reginaldo Sérgio Pereira

    2006-08-01

    Full Text Available Analisaram-se as potencialidades de emprego do resíduo sólido industrial "grits", oriundo da indústria de celulose, como agente estabilizante de dois solos da Zona da Mata Norte de Minas Gerais, Brasil, para fins de emprego em estradas florestais. Os solos estudados englobaram um residual maduro, de textura argilo-areno-siltosa, e um residual jovem, de textura areno-silto-argilosa. Para tanto, prepararam-se misturas envolvendo solos e o resíduo nos quantitativos de 4, 8, 12, 16, 20, 24 e 28% em relação às massas de solo seco. Fez-se uso do ensaio CBR para avaliar as características de resistência e expansão das misturas. A avaliação dos resultados do estudo permite concluir que o resíduo "grits" apresentou potencial significativo como estabilizante dos solos, observando-se que: (i a adição de "grits" aos solos foi responsável por ganhos nas suas resistências mecânicas, obtendo-se melhores resultados com o solo de textura areno-silto-argilosa; (ii com relação à expansão medida no ensaio CBR, observaram-se pequenos acréscimos para o solo de textura argilo-areno-siltosa e decréscimos para o solo de textura areno-silto-argilosa, com aumentos no teor de "grits"; e (iii as misturas solo-"grits" não responderam bem ao aumento da energia de compactação, quanto aos parâmetros CBR e expansãoCBR.This paper is directed to forest road engineering applications, and address the potentialities of using an industrial solid waste from the cellulose industry, named grits, in the stabilization process of two soils from Zona da Mata Norte of Minas Gerais States, Brazil. Soil types tested comprised a mature residual silty-sandy-clay and a young residual clayey-silty-sand. Soil-grits mixtures were prepared at 4, 8, 12, 16, 20, 24 and 28 % stabilizer contents referred to soil dry masses. Mechanical strength and swelling parameters were determined by CBR (California Bearing Ratio tests. The laboratory testing program data supported that

  17. Aves de fragmentos florestais em área de cultivo de cana-de-açúcar no sudeste do Brasil Birds of forest fragments in area of sugar-cane crops in southeastern Brazil

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    Augusto Piratelli

    Full Text Available Foi estudada a avifauna de quatro fragmentos florestais em uma área de cultivo de cana-de-açúcar na região de Campos dos Goytacazes, norte do estado do Rio de Janeiro. A dieta básica e a estrutura das guildas tróficas foi determinada. O estudo foi realizado de outubro de 2000 a julho de 2001, utilizando-se capturas com redes ornitológicas, registros visuais e auditivos e análise de fezes. Quarenta e quatro espécies foram registradas e agrupadas em oito guildas tróficas (insetívoros, granívoros, carnívoros, frugívoros, piscívoros, nectarívoros, onívoros e detritívoros. Estas espécies foram também subdivididas em guildas mais específicas, associadas a seus hábitats. Algumas espécies apenas sobrevoaram os fragmentos, como Egretta thula (Molina, 1782, enquanto outras foram consideradas residentes, como Manacus manacus (Linnaeus, 1766. Algumas, como Amazona amazonica (Linnaeus, 1766, somente utilizaram os fragmentos para repouso noturno. Espécies pequenas de sub-bosque provavelmente não se deslocaram entre fragmentos, dada a relativa grande distância entre eles. Predadores como Rupornis magnirostris (Gmelin, 1789 utilizaram tanto os fragmentos quando as áreas abertas e canaviais em seu entorno. Estes fragmentos estão em situação crítica, abrigando principalmente espécies generalistas e/ou especialistas de bordas; porém ainda são utilizados de alguma forma por espécies de interesse ecológico, como Rhynchocyclus olivaceus (Temminck, 1820 e A. amazonica.Birds of four forest fragments in areas of extensive sugar-cane plantation were studied in Campos dos Goytacazes, northern Rio de Janeiro State, Brazil, from October 2000 to July 2001. The basic diet of sampled species and their trophic guild allocation were determined. The study was carried out by means of capture with mist nets, visual and auditive records and analysis of faeces. Forty-four species were recorded and grouped in eight trophic guilds (insectivores

  18. The NOVO Network: the original scientific basis for its establishment and our R&D vision

    OpenAIRE

    Winkel, Jørgen; Edwards, Kasper; Dellve, L.; Schiller, B.; Westgaard, Rolf H.

    2017-01-01

    The NOVO network is a Nordic non-governmental professional association whose aims are to foster the scientific progress, knowledge and development of the working environment within Healthcare as an integrated part of production system development. The vision is a “Nordic Model for Sustainable Systems” in the healthcare sector. It was founded in 2006 in Copenhagen and was financially supported by the Nordic Council of Ministers from 2007 to 2015. The motivation to establish the NOVO Network ar...

  19. De novo nonsense mutations in ASXL1 cause Bohring-Opitz syndrome

    DEFF Research Database (Denmark)

    Hoischen, Alexander; van Bon, Bregje W M; Rodríguez-Santiago, Benjamín

    2011-01-01

    Bohring-Opitz syndrome is characterized by severe intellectual disability, distinctive facial features and multiple congenital malformations. We sequenced the exomes of three individuals with Bohring-Opitz syndrome and in each identified heterozygous de novo nonsense mutations in ASXL1, which...... is required for maintenance of both activation and silencing of Hox genes. In total, 7 out of 13 subjects with a Bohring-Opitz phenotype had de novo ASXL1 mutations, suggesting that the syndrome is genetically heterogeneous....

  20. Selecting Superior De Novo Transcriptome Assemblies: Lessons Learned by Leveraging the Best Plant Genome.

    Directory of Open Access Journals (Sweden)

    Loren A Honaas

    Full Text Available Whereas de novo assemblies of RNA-Seq data are being published for a growing number of species across the tree of life, there are currently no broadly accepted methods for evaluating such assemblies. Here we present a detailed comparison of 99 transcriptome assemblies, generated with 6 de novo assemblers including CLC, Trinity, SOAP, Oases, ABySS and NextGENe. Controlled analyses of de novo assemblies for Arabidopsis thaliana and Oryza sativa transcriptomes provide new insights into the strengths and limitations of transcriptome assembly strategies. We find that the leading assemblers generate reassuringly accurate assemblies for the majority of transcripts. At the same time, we find a propensity for assemblers to fail to fully assemble highly expressed genes. Surprisingly, the instance of true chimeric assemblies is very low for all assemblers. Normalized libraries are reduced in highly abundant transcripts, but they also lack 1000s of low abundance transcripts. We conclude that the quality of de novo transcriptome assemblies is best assessed through consideration of a combination of metrics: 1 proportion of reads mapping to an assembly 2 recovery of conserved, widely expressed genes, 3 N50 length statistics, and 4 the total number of unigenes. We provide benchmark Illumina transcriptome data and introduce SCERNA, a broadly applicable modular protocol for de novo assembly improvement. Finally, our de novo assembly of the Arabidopsis leaf transcriptome revealed ~20 putative Arabidopsis genes lacking in the current annotation.

  1. De novo FBXO11 mutations are associated with intellectual disability and behavioural anomalies.

    Science.gov (United States)

    Fritzen, Daniel; Kuechler, Alma; Grimmel, Mona; Becker, Jessica; Peters, Sophia; Sturm, Marc; Hundertmark, Hela; Schmidt, Axel; Kreiß, Martina; Strom, Tim M; Wieczorek, Dagmar; Haack, Tobias B; Beck-Wödl, Stefanie; Cremer, Kirsten; Engels, Hartmut

    2018-05-01

    Intellectual disability (ID) has an estimated prevalence of 1.5-2%. In most affected individuals, its genetic basis remains unclear. Whole exome sequencing (WES) studies have identified a multitude of novel causative gene defects and have shown that a large proportion of sporadic ID cases results from de novo mutations. Here, we present two unrelated individuals with similar clinical features and deleterious de novo variants in FBXO11 detected by WES. Individual 1, a 14-year-old boy, has mild ID as well as mild microcephaly, corrected cleft lip and alveolus, hyperkinetic disorder, mild brain atrophy and minor facial dysmorphism. WES detected a heterozygous de novo 1 bp insertion in the splice donor site of exon 3. Individual 2, a 3-year-old boy, showed ID and pre- and postnatal growth retardation, postnatal mild microcephaly, hyperkinetic and restless behaviour, as well as mild dysmorphism. WES detected a heterozygous de novo frameshift mutation. While ten individuals with ID and de novo variants in FBXO11 have been reported as part of larger studies, only one of the reports has some additional clinical data. Interestingly, the latter individual carries the identical mutation as our individual 2 and also displays ID, intrauterine growth retardation, microcephaly, behavioural anomalies, and dysmorphisms. Thus, we confirm deleterious de novo mutations in FBXO11 as a cause of ID and start the delineation of the associated clinical picture which may also comprise postnatal microcephaly or borderline small head size and behavioural anomalies.

  2. De novo giant A2 aneurysm following anterior communicating artery occlusion.

    Science.gov (United States)

    Ibrahim, Tarik F; Hafez, Ahmad; Andrade-Barazarte, Hugo; Raj, Rahul; Niemela, Mika; Lehto, Hanna; Numminen, Jussi; Jarvelainen, Juha; Hernesniemi, Juha

    2015-01-01

    De novo intracranial aneurysms are reported to occur with varying incidence after intracranial aneurysm treatment. They are purported to be observed, however, with increased incidence after Hunterian ligation; particularly in cases of carotid artery occlusion for giant or complex aneurysms deemed unclippable. We report a case of right-sided de novo giant A2 aneurysm 6 years after an anterior communicating artery (ACoA) aneurysm clipping. We believe this de novo aneurysm developed in part due to patient-specific risk factors but also a significant change in cerebral hemodynamics. The ACoA became occluded after surgery that likely altered the cerebral hemodynamics and contributed to the de novo aneurysm. We believe this to be the first reported case of a giant de novo aneurysm in this location. Following parent vessel occlusion (mostly of the carotid artery), there are no reports of any de novo aneurysms in the pericallosal arteries let alone a giant one. The patient had a dominant right A1 and the sudden increase in A2 blood flow likely resulted in increased wall shear stress, particularly in the medial wall of the A2 where the aneurysm occurred 2 mm distal to the A1-2 junction. ACoA preservation is a key element of aneurysm surgery in this location. Suspected occlusion of this vessel may warrant closer radiographic follow-up in patients with other risk factors for aneurysm development.

  3. Novas perspectivas para a gestão sustentável da Floresta Amazônica: explorando novos caminhos New perspectives for the sustainable management of the Amazon forest: exploring new avenues

    Directory of Open Access Journals (Sweden)

    Mirjam Ros-Tonen

    2007-06-01

    Full Text Available Com foco na indústria madeireira na região Amazônica do Brasil e com base numa comparação de resultados de uma pesquisa sobre o setor florestal realizada no início dos anos 90 e estudos realizados dez anos depois, este artigo explora várias tendências atuais com potência de mudar a gestão de florestas tropicais na região amazônica. Essas mudanças são relacionadas à a mudanças no suprimento de matéria prima, b globalização e abertura de mercados externos para madeira e outros produtos como a soja, c crescente escassez da madeira, d novos mercados e incentivos para o manejo florestal sustentável e manejo florestal comunitário, e e mudanças nos padrões de posse da terra, incluindo a descentralização da governança florestal e devolução de terras florestais. Concluímos que as mudanças apontam em direções diferentes. Enquanto a expansão dos mercados externos provoca o aumento do desmatamento, a descentralização e democratização da governança florestal e a preocupação global com a perda de serviços ambientais da floresta e de meios de vida para as populações locais criam novos incentivos para a gestão florestal sustentável. O maior desafio é encontrar meios para que a exploração florestal de base familiar e comunitária e as operações das serrarias nas áreas de assentamento sejam mais sustentáveis, por exemplo através de parcerias inovadoras do tipo empresa-comunidade.With a focus on the timber industry in the Brazilian Amazon region and based on a comparison of results of a study of the forestry sector carried out in the early 1990s and studies carried out about ten years later, this article explores various recent tendencies which have the potential to change tropical forest management in the Amazon region. These changes are related to a changes in the supply of roundwood, b globalisation and the opening of external markets for timber and other products like soy, c increasing scarcity of timber, d

  4. Determinantes dos novos contratos de fomento florestal na mesorregião do Vale do Rio Doce, Minas Gerais Determining factors for new private woodlot contracts in the Vale do Rio Doce meso regionin Minas Gerais

    Directory of Open Access Journals (Sweden)

    Uemerson Rodrigues de Souza

    2009-04-01

    Full Text Available O setor florestal tem exercido importante papel no desenvolvimento socioeconômico das regiões produtoras de madeira. Os benefícios são atribuídos à geração de renda (alternativa para pequenos e médios produtores rurais, impostos, divisas e incremento no PIB. As novas exigências do mercado, em termos de competitividade, levaram as empresas a criarem os programas de fomento florestal como forma de expandir a oferta de madeira e garantir sua base produtiva. Nesse contexto, surge a necessidade de se identificarem os fatores que determinam a realização de novos contratos de fomento florestal. A amostra estudada foi composta pelos produtores rurais da mesorregião do Vale do Rio Doce, Minas Gerais, que realizaram pelo menos um contrato de fomento entre os anos de 1995 e 2006. Os dados foram coletados por meio de questionários semiestruturados no ano de 2006. Para identificar os fatores, utilizou-se a Análise Estatística Multivariada, especificamente a técnica de análise de discriminante. Os resultados apontaram que o sistema de medição da madeira (SISMED, a área contratada (ACONTRAT e o tamanho da propriedade (TAMPROP foram, nessa ordem, os principais determinantes para a realização de novos contratos. Desse modo, sugere-se que as empresas florestais desenvolvam programas de acompanhamento técnico e formação dos produtores fomentados, no intuito de reduzir as desconfianças no SISMED e aumentar o volume de áreas plantadas por meio do fomento.The forestry sector has played an important role in the socio-economic development of wood-producing regions. Benefits include private income (an alternative for small and medium-sized rural producers, government tax income, balance of payment advantages, and increasing GNP. New market demands in terms of competitiveness have led cellulose companies to create private woodlot programs as a way to expand timber supplies and guarantee a productive basis. Within this context, arises the need

  5. De novo ORFs in Drosophila are important to organismal fitness and evolved rapidly from previously non-coding sequences.

    Directory of Open Access Journals (Sweden)

    Josephine A Reinhardt

    Full Text Available How non-coding DNA gives rise to new protein-coding genes (de novo genes is not well understood. Recent work has revealed the origins and functions of a few de novo genes, but common principles governing the evolution or biological roles of these genes are unknown. To better define these principles, we performed a parallel analysis of the evolution and function of six putatively protein-coding de novo genes described in Drosophila melanogaster. Reconstruction of the transcriptional history of de novo genes shows that two de novo genes emerged from novel long non-coding RNAs that arose at least 5 MY prior to evolution of an open reading frame. In contrast, four other de novo genes evolved a translated open reading frame and transcription within the same evolutionary interval suggesting that nascent open reading frames (proto-ORFs, while not required, can contribute to the emergence of a new de novo gene. However, none of the genes arose from proto-ORFs that existed long before expression evolved. Sequence and structural evolution of de novo genes was rapid compared to nearby genes and the structural complexity of de novo genes steadily increases over evolutionary time. Despite the fact that these genes are transcribed at a higher level in males than females, and are most strongly expressed in testes, RNAi experiments show that most of these genes are essential in both sexes during metamorphosis. This lethality suggests that protein coding de novo genes in Drosophila quickly become functionally important.

  6. Radioisotope devices at Novo-Krivorozhskij-ore-enrichment plant

    International Nuclear Information System (INIS)

    Levitskij, V.Ya.; Kucher, V.G.; Ministerstvo Chernoj Metallurgii Ukrainskoj SSR, Dnepropetrovsk, Bazovaya Opytno-Konstruktorskaya Izotopnaya lab.)

    1975-01-01

    Use of the ''Ferrite'' analyzers, AZhR and PAZh-1 and the GR-7 gamma relay in different engineering areas of the Novo-Krivorozh ore-enrichment plant is evaluated. The ''Ferrite'' radioisotopic analyzer was designed for rapid roentgeno-radiometric determination of the total iron and iron group element contents in powdered samples of ores and products of their treatment. From the density of the flux of the characteristic radiation it is possible to determine quantitatively the content of the element of interest in the analyzed material. The radioisotpic analyzer AZhR-1 is distinguished by its high efficiency in the analysis for total iron on products of processing of iron ore raw materials. The use of this apparatus allows complete replacement of the chemical method for rapid analysis of concentrates by the roentgeno-radiometric method, which decreases the total analytical work on determination of total iron and speeds up output of information on concentrate quality. The radioisotopic gamma analyzer PAZh-1 is designed for automatic and either continuous or discrete measurement of the total iron content in iron ore materials ground to 50 mm, carried on a conveyor, without selection or preparation of the samples for analysis. The analyzer operates on the principle of measuring the average frequency of impingement on a detector of gamma quanta back-scattered by the analyzed material. This frequency is determined by the percentage content of total iron in the material. The apparatus operates continuously. The mean square deviation of the apparatus values from chemical data is 0.93% Fesub(total). Use of the apparatus greatly increases the operativeness of the control and decreases the laboriousness of raw material sampling in an engineering stream. The radioisotopic data units GR-7 are designed for control of the level of materials in hoppers for recovery and burning of agglomerates. Use of this apparatus showed its great advantage over data units of other types

  7. Internet e Cultura: um novo olhar, veloz e voraz

    Directory of Open Access Journals (Sweden)

    Wilson de Oliveira Souza

    1999-01-01

    Full Text Available Em cada piscadela que damos, um novo mundo enxergamos. Com a globalização, o modo de ver o mundo muda radicalmente, principalmente devido ao complexo ritmo ditado pelas relações entre o meio ambiente e seus usuários. De forma sintetizada, podemos explicar que a globalização é resultado da terceira revolução tecnológica (tecnologias ligadas à busca, processamento, difusão e transmissão de informações; inteligência artificial; engenharia genética, da formação de áreas de livre comércio e blocos econômicos interligados (como o Mercosul, a União Européia e o Nafta e da crescente interligação e interdependência dos mercados físicos e financeiros em escala planetária. Essa trinca é responsável pela alteração, principalmente, da nova forma de enxergarmos a cultura, aceitando que a mundialização da cultura é um processo em curso, não concluído ainda, na qual as formas culturais nacionais ou locais entram em contato rapidamente. Com isso, quedam as barreiras territoriais, forçam as mediações e criam, no dizer de Featherstone, a "terceira cultura", entendendo como "um conjunto de práticas, conhecimentos, convenções e estilos de vida que se desenvolvem de modo a se tornar cada vez mais independente dos Estados-Nação".

  8. Phenolic Amides Are Potent Inhibitors of De Novo Nucleotide Biosynthesis.

    Science.gov (United States)

    Pisithkul, Tippapha; Jacobson, Tyler B; O'Brien, Thomas J; Stevenson, David M; Amador-Noguez, Daniel

    2015-09-01

    An outstanding challenge toward efficient production of biofuels and value-added chemicals from plant biomass is the impact that lignocellulose-derived inhibitors have on microbial fermentations. Elucidating the mechanisms that underlie their toxicity is critical for developing strategies to overcome them. Here, using Escherichia coli as a model system, we investigated the metabolic effects and toxicity mechanisms of feruloyl amide and coumaroyl amide, the predominant phenolic compounds in ammonia-pretreated biomass hydrolysates. Using metabolomics, isotope tracers, and biochemical assays, we showed that these two phenolic amides act as potent and fast-acting inhibitors of purine and pyrimidine biosynthetic pathways. Feruloyl or coumaroyl amide exposure leads to (i) a rapid buildup of 5-phosphoribosyl-1-pyrophosphate (PRPP), a key precursor in nucleotide biosynthesis, (ii) a rapid decrease in the levels of pyrimidine biosynthetic intermediates, and (iii) a long-term generalized decrease in nucleotide and deoxynucleotide levels. Tracer experiments using (13)C-labeled sugars and [(15)N]ammonia demonstrated that carbon and nitrogen fluxes into nucleotides and deoxynucleotides are inhibited by these phenolic amides. We found that these effects are mediated via direct inhibition of glutamine amidotransferases that participate in nucleotide biosynthetic pathways. In particular, feruloyl amide is a competitive inhibitor of glutamine PRPP amidotransferase (PurF), which catalyzes the first committed step in de novo purine biosynthesis. Finally, external nucleoside supplementation prevents phenolic amide-mediated growth inhibition by allowing nucleotide biosynthesis via salvage pathways. The results presented here will help in the development of strategies to overcome toxicity of phenolic compounds and facilitate engineering of more efficient microbial producers of biofuels and chemicals. Copyright © 2015, Pisithkul et al.

  9. Potencial forrageiro de novos clones de capim-elefante

    Directory of Open Access Journals (Sweden)

    Botrel Milton de Andrade

    2000-01-01

    Full Text Available O objetivo deste trabalho foi avaliar o comportamento de novos clones selecionados de capim-elefante. O experimento foi realizado na Embrapa Gado de Leite, em Coronel Pacheco -- MG, por um período de dois anos. Foi avaliado o potencial forrageiro de 20 clones de capim-elefante, obtidos pelo programa de melhoramento, e mais duas cultivares tradicionais (Cameroon e Taiwan A-146 usadas como testemunhas. O delineamento experimental foi o de blocos ao acaso com quatro repetições. As adubações para estabelecimento e manutenção foram realizadas de acordo com a análise do solo, visando suprir as exigências nutricionais do capim-elefante. Observaram-se diferenças significativas entre os clones, quanto ao potencial para produção de forragem, à relação folha/colmo e ao perfilhamento aéreo e basal. A maioria dos clones avaliados apresentou maior produção de matéria seca que as cultivares tradicionais, Cameroon e Taiwan A-146, durante o período seco e chuvoso. Não houve diferença significativa no teor de proteína bruta da matéria seca das cultivares controles (Cameroon e Taiwan A-146 e dos clones avaliados, em ambas as estações (águas e seca. O clone F 27-01, lançado pela Embrapa Gado de Leite com o nome de cultivar Pioneiro, destacou-se para quase todas as características agronômicas estudadas.

  10. Phenolic Amides Are Potent Inhibitors of De Novo Nucleotide Biosynthesis

    Science.gov (United States)

    Pisithkul, Tippapha; Jacobson, Tyler B.; O'Brien, Thomas J.; Stevenson, David M.

    2015-01-01

    An outstanding challenge toward efficient production of biofuels and value-added chemicals from plant biomass is the impact that lignocellulose-derived inhibitors have on microbial fermentations. Elucidating the mechanisms that underlie their toxicity is critical for developing strategies to overcome them. Here, using Escherichia coli as a model system, we investigated the metabolic effects and toxicity mechanisms of feruloyl amide and coumaroyl amide, the predominant phenolic compounds in ammonia-pretreated biomass hydrolysates. Using metabolomics, isotope tracers, and biochemical assays, we showed that these two phenolic amides act as potent and fast-acting inhibitors of purine and pyrimidine biosynthetic pathways. Feruloyl or coumaroyl amide exposure leads to (i) a rapid buildup of 5-phosphoribosyl-1-pyrophosphate (PRPP), a key precursor in nucleotide biosynthesis, (ii) a rapid decrease in the levels of pyrimidine biosynthetic intermediates, and (iii) a long-term generalized decrease in nucleotide and deoxynucleotide levels. Tracer experiments using 13C-labeled sugars and [15N]ammonia demonstrated that carbon and nitrogen fluxes into nucleotides and deoxynucleotides are inhibited by these phenolic amides. We found that these effects are mediated via direct inhibition of glutamine amidotransferases that participate in nucleotide biosynthetic pathways. In particular, feruloyl amide is a competitive inhibitor of glutamine PRPP amidotransferase (PurF), which catalyzes the first committed step in de novo purine biosynthesis. Finally, external nucleoside supplementation prevents phenolic amide-mediated growth inhibition by allowing nucleotide biosynthesis via salvage pathways. The results presented here will help in the development of strategies to overcome toxicity of phenolic compounds and facilitate engineering of more efficient microbial producers of biofuels and chemicals. PMID:26070680

  11. Parametrização do modelo 3-PG para eucalipto na região do cerrado de Minas Gerais

    Directory of Open Access Journals (Sweden)

    Jarbas Silva Borges

    2012-09-01

    Full Text Available http://dx.doi.org/10.5902/198050986623O modelo 3-PG é uma ferramenta eficaz para determinação do potencial produtivo de florestas de eucalipto. No entanto, as parametrizações deste modelo, hoje disponíveis, produzem resultados subestimados quando aplicadas à região do Cerrado de Minas Gerais. Dessa forma, o objetivo deste trabalho foi parametrizar o modelo 3-PG para plantios de eucalipto localizados na região do Cerrado de Minas Gerais. Para isso, foram utilizados dados de povoamentos de híbridos clonais de Eucalyptus grandis x Eucalyptus urophylla, com idades entre 3 e 84 meses, localizados nas regiões de Curvelo e Itacambira  – MG. As estimativas de crescimento obtidas pelo modelo 3-PG foram comparadas com dados de crescimento de povoamentos florestais medidos nas duas regiões, até a idade de 84 meses. O conjunto de valores de parâmetros e variáveis obtidos neste trabalho permitiu simular com acurácia, em termos das variáveis produzidas pelo modelo, os padrões de crescimento de povoamentos florestais presentes na região do Cerrado mineiro. Dessa forma, conclui-se que a parametrização promoveu melhorias no desempenho do modelo que resultaram em estimativas acuradas de crescimento.

  12. ''de novo'' aneurysms following endovascular procedures

    Energy Technology Data Exchange (ETDEWEB)

    Briganti, F.; Cirillo, S.; Caranci, F. [Department of Neurological Sciences, Services of Neuroradiology, ' ' Federico II' ' University, Naples (Italy); Esposito, F.; Maiuri, F. [Department of Neurological Sciences, Services of Neurosurgery, ' ' Federico II' ' University, Naples (Italy)

    2002-07-01

    Two personal cases of ''de novo'' aneurysms of the anterior communicating artery (ACoA) occurring 9 and 4 years, respectively, after endovascular carotid occlusion are described. A review of the 30 reported cases (including our own two) of ''de novo'' aneurysms after occlusion of the major cerebral vessels has shown some features, including a rather long time interval after the endovascular procedure of up to 20-25 years (average 9.6 years), a preferential ACoA (36.3%) and internal carotid artery-posterior communicating artery (ICA-PCoA) (33.3%) location of the ''de novo'' aneurysms, and a 10% rate of multiple aneurysms. These data are compared with those of the group of reported spontaneous ''de novo'' aneurysms after SAH or previous aneurysm clipping. We agree that the frequency of ''de novo'' aneurysms after major-vessel occlusion (two among ten procedures in our series, or 20%) is higher than commonly reported (0 to 11%). For this reason, we suggest that patients who have been submitted to endovascular major-vessel occlusion be followed up for up to 20-25 years after the procedure, using non-invasive imaging studies such as MR angiography and high-resolution CT angiography. On the other hand, periodic digital angiography has a questionable risk-benefit ratio; it may be used when a ''de novo'' aneurysm is detected or suspected on non-invasive studies. The progressive enlargement of the ACoA after carotid occlusion, as described in our case 1, must be considered a radiological finding of risk for ''de novo'' aneurysm formation. (orig.)

  13. Coccidioidomicose: novo caso brasileiro Coccidiodomycosis: a new Brazilian case

    Directory of Open Access Journals (Sweden)

    Mário A.P. Moraes

    1998-12-01

    Full Text Available É descrito um caso de coccidioidomicose pulmonar oriundo da zona rural de Bertolínia, PI. A manifestação clínica principal consistiu em dor torácica e o diagnóstico teve por base o achado do agente3/4Coccidioides immitis3/4em cortes histológicos. Formas teciduais do microrganismo3/4esférulas imaturas e maduras3/4estavam presentes nas lesões observadas em fragmento pulmonar removido do paciente por biópsia a céu aberto. Este novo caso autóctone da doença, como os outros anteriormente descritos no Brasil, procedia do interior semi-árido da Região Nordeste. O ambiente quente e seco do sertão nordestino oferece, sem dúvida, condições propícias ao desenvolvimento de C. immitis, um habitante do solo. As pessoas e animais do local devem adquirir a infecção ao revolver a terra, ato que os expõe à poeira contendo os propágulos do fungo.A case of pulmonary coccidioidomycosis from the rural zone of Bertolinia, PI, is reported. The patient, a farm worker, attributed his illness to the dust inhaled while digging a water well during the dry season of the year, some weeks before the onset of the clinical manifestations. The main symptoms of the disease were severe chest pain and moderate fever. The diagnosis was made histopathologically: tissue phase fungal organisms3/4immature spherules and spherules with endospores3/4were observed in histological sections of a lung fragment obtained by open chest biopsy. This is the twelfth autochthonous case of coccidioidomycosis found so far in Brazil. All of them involved native inhabitants of the semi-arid part of Northeastern Brazil. The hot and dry environment of the region seems to favor the development of C. immitis in the soil. Humans and animals probably acquire the infection by digging the soil, when they become exposed to the conidium-bearing dust raised by this activity.

  14. High frequencies of de novo CNVs in bipolar disorder and schizophrenia.

    LENUS (Irish Health Repository)

    Malhotra, Dheeraj

    2011-12-22

    While it is known that rare copy-number variants (CNVs) contribute to risk for some neuropsychiatric disorders, the role of CNVs in bipolar disorder is unclear. Here, we reasoned that a contribution of CNVs to mood disorders might be most evident for de novo mutations. We performed a genome-wide analysis of de novo CNVs in a cohort of 788 trios. Diagnoses of offspring included bipolar disorder (n = 185), schizophrenia (n = 177), and healthy controls (n = 426). Frequencies of de novo CNVs were significantly higher in bipolar disorder as compared with controls (OR = 4.8 [1.4,16.0], p = 0.009). De novo CNVs were particularly enriched among cases with an age at onset younger than 18 (OR = 6.3 [1.7,22.6], p = 0.006). We also confirmed a significant enrichment of de novo CNVs in schizophrenia (OR = 5.0 [1.5,16.8], p = 0.007). Our results suggest that rare spontaneous mutations are an important contributor to risk for bipolar disorder and other major neuropsychiatric diseases.

  15. Determinação de fósforo microbiano: comparação entre métodos e coberturas florestais Evaluation of microbial phosphorus: comparison of determination methods in forest soils

    Directory of Open Access Journals (Sweden)

    Ecila Mercês de Albuquerque Villani

    2009-08-01

    Full Text Available Muitos trabalhos mostram a importância da biomassa microbiana do solo (BMS, principalmente como fonte/dreno de C e de N em plantações florestais; contudo, são escassos os trabalhos relacionados ao fósforo microbiano (PBM, sobretudo aqueles relativos aos métodos de determinação do PBM nesses ecossistemas. O presente trabalho foi realizado com o objetivo de avaliar métodos de determinação do PBM em solo com diferentes coberturas vegetais. O trabalho consistiu da análise de amostras de Latossolo Vermelho-Amarelo distrófico muito argiloso (LVAd localizado no município de Viçosa (MG, coletadas nas profundidades de 0 a 5 e 5 a 10 cm, em áreas com as seguintes coberturas vegetais: pínus (Pinus taeda, eucalipto (Eucalyptus grandis e floresta nativa. Para determinação do P microbiano, foram empregados os métodos fumigação-extração (FE, irradiação com micro-ondas-extração (IE e irradiação com micro-ondas-extração com membrana de troca aniônica (EMTA. Em termos gerais, menores teores de PBM foram obtidos com o método irradiação-extração. Considerando a cobertura vegetal, foi detectada diferença significativa entre os três métodos sob floresta de eucalipto e floresta nativa, principalmente na camada superficial. Sob pínus, apenas o método IE diferiu dos demais, na camada subsuperficial. Menores coeficientes de variação (CV foram obtidos com o FE, retratando maior precisão do método. Entretanto, o método IE mostrou-se, em termos operacionais, o mais adequado à determinação do PBM quando se tem maior número de amostras. Com relação às coberturas vegetais, a grande variabilidade observada nos CVs obtidos para cada cobertura, nos três métodos testados, inviabiliza a escolha de um único método que apresente maior precisão na avaliação do PBM.Many studies have shown the importance of the soil microbial biomass, mainly as source/sink of carbon (C and nitrogen (N in forest stands. However, there are few

  16. De Novo Discovery of Structured ncRNA Motifs in Genomic Sequences

    DEFF Research Database (Denmark)

    Ruzzo, Walter L; Gorodkin, Jan

    2014-01-01

    De novo discovery of "motifs" capturing the commonalities among related noncoding ncRNA structured RNAs is among the most difficult problems in computational biology. This chapter outlines the challenges presented by this problem, together with some approaches towards solving them, with an emphas...... on an approach based on the CMfinder CMfinder program as a case study. Applications to genomic screens for novel de novo structured ncRNA ncRNA s, including structured RNA elements in untranslated portions of protein-coding genes, are presented.......De novo discovery of "motifs" capturing the commonalities among related noncoding ncRNA structured RNAs is among the most difficult problems in computational biology. This chapter outlines the challenges presented by this problem, together with some approaches towards solving them, with an emphasis...

  17. Defining the maize transcriptome de novo using deep RNA-Seq

    Energy Technology Data Exchange (ETDEWEB)

    Martin, Jeffrey; Gross, Stephen; Choi, Cindy; Zhang, Tao; Lindquist, Erika; Wei, Chia-Lin; Wang, Zhong

    2011-06-01

    De novo assembly of the transcriptome is crucial for functional genomics studies in bioenergy research, since many of the organisms lack high quality reference genomes. In a previous study we successfully de novo assembled simple eukaryote transcriptomes exclusively from short Illumina RNA-Seq reads [1]. However, extensive alternative splicing, present in most of the higher eukaryotes, poses a significant challenge for current short read assembly processes. Furthermore, the size of next-generation datasets, often large for plant genomes, presents an informatics challenge. To tackle these challenges we present a combined experimental and informatics strategy for de novo assembly in higher eukaryotes. Using maize as a test case, preliminary results suggest our approach can resolve transcript variants and improve gene annotations.

  18. Defining the maize transcriptome de novo using deep RNA-Seq

    Energy Technology Data Exchange (ETDEWEB)

    Martin, Jeffrey; Gross, Stephen; Choi, Cindy; Zhang, Tao; Lindquist, Erika; Wei, Chia-Lin; Wang, Zhong

    2011-06-02

    De novo assembly of the transcriptome is crucial for functional genomics studies in bioenergy research, since many of the organisms lack high quality reference genomes. In a previous study we successfully de novo assembled simple eukaryote transcriptomes exclusively from short Illumina RNA-Seq reads [1]. However, extensive alternative splicing, present in most of the higher eukaryotes, poses a significant challenge for current short read assembly processes. Furthermore, the size of next-generation datasets, often large for plant genomes, presents an informatics challenge. To tackle these challenges we present a combined experimental and informatics strategy for de novo assembly in higher eukaryotes. Using maize as a test case, preliminary results suggest our approach can resolve transcript variants and improve gene annotations.

  19. Sequencing and de novo assembly of 150 genomes from Denmark as a population reference

    DEFF Research Database (Denmark)

    Maretty, Lasse; Jensen, Jacob Malte; Petersen, Bent

    2017-01-01

    Hundreds of thousands of human genomes are now being sequenced to characterize genetic variation and use this information to augment association mapping studies of complex disorders and other phenotypic traits. Genetic variation is identified mainly by mapping short reads to the reference genome......-coverage sequencing with mate-pair libraries extending up to 20 kilobases. We report de novo assemblies of 150 individuals (50 trios) from the GenomeDenmark project. The quality of these assemblies is similar to those obtained using the more expensive long-read technology. We use the assemblies to identify a rich set...... or by performing local assembly. However, these approaches are biased against discovery of structural variants and variation in the more complex parts of the genome. Hence, large-scale de novo assembly is needed. Here we show that it is possible to construct excellent de novo assemblies from high...

  20. Sequencing and de novo assembly of 150 genomes from Denmark as a population reference

    DEFF Research Database (Denmark)

    Maretty, Lasse; Jensen, Jacob Malte; Petersen, Bent

    2017-01-01

    Hundreds of thousands of human genomes are now being sequenced to characterize genetic variation and use this information to augment association mapping studies of complex disorders and other phenotypic traits. Genetic variation is identified mainly by mapping short reads to the reference genome...... or by performing local assembly. However, these approaches are biased against discovery of structural variants and variation in the more complex parts of the genome. Hence, large-scale de novo assembly is needed. Here we show that it is possible to construct excellent de novo assemblies from high......-coverage sequencing with mate-pair libraries extending up to 20 kilobases. We report de novo assemblies of 150 individuals (50 trios) from the GenomeDenmark project. The quality of these assemblies is similar to those obtained using the more expensive long-read technology. We use the assemblies to identify a rich set...

  1. De novo synthesis of purine nucleotides in different fiber types of rat skeletal muscle

    International Nuclear Information System (INIS)

    Tullson, P.C.; John-Alder, H.; Hood, D.A.; Terjung, R.L.

    1986-01-01

    The contribution of de novo purine nucleotide synthesis to nucleotide metabolism in skeletal muscles is not known. The authors have determined rates of de novo synthesis in soleus (slow-twitch red), red gastrocnemius (fast-twitch red), and white gastrocnemius (fast-twitch white) using the perfused rat hindquarter. 14 C glycine incorporation into ATP was linear after 1 and 2 hours of perfusion with 0.2 mM added glycine. The intracellular (I) and extracellular (E) specific activity of 14 C glycine was determined by HPLC of phenylisothiocyanate derivatives of neutralized PCA extracts. The rates of de novo synthesis when expressed relative to muscle ATP content show slow and fast-twitch red muscles to be similar and about twice as great as fast-twitch white muscles. This could represent a greater turnover of the adenine nucleotide pool in more oxidative red muscle types

  2. A Pareto Algorithm for Efficient De Novo Design of Multi-functional Molecules.

    Science.gov (United States)

    Daeyaert, Frits; Deem, Micheal W

    2017-01-01

    We have introduced a Pareto sorting algorithm into Synopsis, a de novo design program that generates synthesizable molecules with desirable properties. We give a detailed description of the algorithm and illustrate its working in 2 different de novo design settings: the design of putative dual and selective FGFR and VEGFR inhibitors, and the successful design of organic structure determining agents (OSDAs) for the synthesis of zeolites. We show that the introduction of Pareto sorting not only enables the simultaneous optimization of multiple properties but also greatly improves the performance of the algorithm to generate molecules with hard-to-meet constraints. This in turn allows us to suggest approaches to address the problem of false positive hits in de novo structure based drug design by introducing structural and physicochemical constraints in the designed molecules, and by forcing essential interactions between these molecules and their target receptor. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Roça-de-toco: uso de recursos florestais e dinâmica da paisagem rural no litoral de Santa Catarina Slash-and-burn agriculture: use of forest resources and dynamics of rural landscape in Santa Catarina State, Brazil

    Directory of Open Access Journals (Sweden)

    Alexandre Siminski

    2007-06-01

    Full Text Available Os fragmentos florestais nas pequenas propriedades agrícolas de Santa Catarina fazem parte de um ciclo de cultivo de espécies anuais, através da agricultura de pousio (roça-de-toco. Neste estudo, procurou-se analisar o sistema de cultivo praticado pelos agricultores do município de São Pedro de Alcântara, litoral de Santa Catarina, utilizando a abordagem qualitativa. Como resultados, observou-se que em 65% das propriedades houve redução da área de cultivo nos últimos 10 anos, o tempo de repouso foi reduzido e as roças passaram a ser menos itinerantes. As restrições ao uso dos recursos florestais têm promovido alterações na composição da paisagem das propriedades agrícolas da região de estudo, onde se constata uma diminuição das áreas destinadas à agricultura de pousio e um aumento crescente das áreas com formações florestais secundárias, além do aumento da proporção de formações mais avançadas no processo de sucessão natural. Entretanto, uma simulação do uso da terra revelou que é possível, do ponto de vista da disponibilidade de áreas ao longo do tempo, a continuidade do sistema de pousio, principalmente quando este destina-se à subsistência.The secondary forests in the small farms of Santa Catarina State are traditionally used as a component of the slash-and-burn agriculture. The purpose of this study was to analyze the agricultural system in the municipality of São Pedro de Alcântara, on the coast zone of the State, using the qualitative research approach. The results showed that there was a reduction of the cultivated area in 65% of the farms in the last 10 years, the fallow period was reduced, and the rotation time of each field plot was shortened. The restrictions imposed by regulations on forest resources use have contributed to a change in the composition of the landscape of the study area, where a shrinkage of the area used for traditional agriculture in favor of a larger area of with

  4. A Terra em Transe: o cosmopolitismo às avessas do cinema novo

    Directory of Open Access Journals (Sweden)

    Angela Prysthon

    2008-11-01

    Full Text Available Usando como referencial teórico os estudos culturais, este artigo analisa o cinema novo brasileiro como parte de uma estratégia terceiro mundista de conceber a cultura. A partir da emergência do conceito de terceiro mundo e das lutas de descolonização nos anos 1950 e 1960, a ideologia cosmopolita foi sendo vista pelos intelectuais de esquerda como a versão cultural da aliança com as forças hegemônicas da Europa e dos Estados Unidos. O projeto do cinema novo chama a atenção por suas afinidades ideológicas com o terceiro mundismo, mas, paradoxalmente, trazendo à tona uma polí­tica cosmopolita da periferia. Palavras-chave cinema novo, identidade, cultura brasileira, terceiro mundismo, estudos culturais. Abstract Using the cultural studies theoretical framework, this paper analyzes the cinema novo movement in Brazil as a part of the Third World conception of culture. Following the creation of the term "Third World" and the international politics of colonial independence of the 1950s and 1960s, a cosmopolitan attitude was seen by the intellectuals of the left as a cultural version of the alliance with the hegemonic forces of Europe and North America. Even though the cinema novo project can be associated with the ideology of an united Third World ,it brings about, paradoxically, a very cosmopolitan politics of the periphery. Key words cinema novo, identity, Brazilian culture, third world, cultural studies.

  5. Precise detection of de novo single nucleotide variants in human genomes.

    Science.gov (United States)

    Gómez-Romero, Laura; Palacios-Flores, Kim; Reyes, José; García, Delfino; Boege, Margareta; Dávila, Guillermo; Flores, Margarita; Schatz, Michael C; Palacios, Rafael

    2018-05-07

    The precise determination of de novo genetic variants has enormous implications across different fields of biology and medicine, particularly personalized medicine. Currently, de novo variations are identified by mapping sample reads from a parent-offspring trio to a reference genome, allowing for a certain degree of differences. While widely used, this approach often introduces false-positive (FP) results due to misaligned reads and mischaracterized sequencing errors. In a previous study, we developed an alternative approach to accurately identify single nucleotide variants (SNVs) using only perfect matches. However, this approach could be applied only to haploid regions of the genome and was computationally intensive. In this study, we present a unique approach, coverage-based single nucleotide variant identification (COBASI), which allows the exploration of the entire genome using second-generation short sequence reads without extensive computing requirements. COBASI identifies SNVs using changes in coverage of exactly matching unique substrings, and is particularly suited for pinpointing de novo SNVs. Unlike other approaches that require population frequencies across hundreds of samples to filter out any methodological biases, COBASI can be applied to detect de novo SNVs within isolated families. We demonstrate this capability through extensive simulation studies and by studying a parent-offspring trio we sequenced using short reads. Experimental validation of all 58 candidate de novo SNVs and a selection of non-de novo SNVs found in the trio confirmed zero FP calls. COBASI is available as open source at https://github.com/Laura-Gomez/COBASI for any researcher to use. Copyright © 2018 the Author(s). Published by PNAS.

  6. De novo mutations in ATP1A3 cause alternating hemiplegia of childhood

    DEFF Research Database (Denmark)

    Heinzen, Erin L; Swoboda, Kathryn J; Hitomi, Yuki

    2012-01-01

    and their unaffected parents to identify de novo nonsynonymous mutations in ATP1A3 in all seven individuals. In a subsequent sequence analysis of ATP1A3 in 98 other patients with AHC, we found that ATP1A3 mutations were likely to be responsible for at least 74% of the cases; we also identified one inherited mutation...... affecting the level of protein expression. This work identifies de novo ATP1A3 mutations as the primary cause of AHC and offers insight into disease pathophysiology by expanding the spectrum of phenotypes associated with mutations in ATP1A3....

  7. NovoTTF™-100A System (Tumor Treating Fields) transducer array layout planning for glioblastoma: a NovoTAL™ system user study.

    Science.gov (United States)

    Chaudhry, Aafia; Benson, Laura; Varshaver, Michael; Farber, Ori; Weinberg, Uri; Kirson, Eilon; Palti, Yoram

    2015-11-11

    Optune™, previously known as the NovoTTF-100A System™, generates Tumor Treating Fields (TTFields), an effective anti-mitotic therapy for glioblastoma. The system delivers intermediate frequency, alternating electric fields to the supratentorial brain. Patient therapy is personalized by configuring transducer array layout placement on the scalp to the tumor site using MRI measurements and the NovoTAL System. Transducer array layout mapping optimizes therapy by maximizing electric field intensity to the tumor site. This study evaluated physician performance in conducting transducer array layout mapping using the NovoTAL System compared with mapping performed by the Novocure in-house clinical team. Fourteen physicians (7 neuro-oncologists, 4 medical oncologists, and 3 neurosurgeons) evaluated five blinded cases of recurrent glioblastoma and performed head size and tumor location measurements using a standard Digital Imaging and Communications in Medicine reader. Concordance with Novocure measurement and intra- and inter-rater reliability were assessed using relevant correlation coefficients. The study criterion for success was a concordance correlation coefficient (CCC) >0.80. CCC for each physician versus Novocure on 20 MRI measurements was 0.96 (standard deviation, SD ± 0.03, range 0.90-1.00), indicating very high agreement between the two groups. Intra- and inter-rater reliability correlation coefficients were similarly high: 0.83 (SD ±0.15, range 0.54-1.00) and 0.80 (SD ±0.18, range 0.48-1.00), respectively. This user study demonstrated an excellent level of concordance between prescribing physicians and Novocure in-house clinical teams in performing transducer array layout planning. Intra-rater reliability was very high, indicating reproducible performance. Physicians prescribing TTFields, when trained on the NovoTAL System, can independently perform transducer array layout mapping required for the initiation and maintenance of patients on TTFields

  8. Caracterização da saúde de trabalhadores florestais envolvidos na extração de madeira em regiões montanhosas Characterization of the health of workers involved in the extraction of wood in mountainous regions

    Directory of Open Access Journals (Sweden)

    Emilia Pio da Silva

    2009-12-01

    Full Text Available Este estudo teve como objetivo caracterizar a saúde dos trabalhadores florestais envolvidos na atividade de extração de madeira em regiões montanhosas. A pesquisa foi realizada em uma empresa florestal localizada no Distrito Florestal do Vale do Rio Doce, sendo estudados 100% dos trabalhadores. Para caracterização da saúde destes, foi utilizado um questionário estruturado em forma de entrevista, baseado na Pesquisa Nacional por Amostra de Domicílio (PNAD. Os resultados evidenciaram que as atividades de extração florestal têm causado impactos negativos sobre a saúde dos trabalhadores, visto que 66% deles disseram sentir dor em alguma parte do corpo, 79% afirmaram ter algum problema dentário, 86% relataram ficar expostos a fatores que prejudicavam sua saúde, 20% apresentaram algum distúrbio do sono, 9% não tinham acesso a saneamento básico e 29% já havia sofrido acidentes de trabalho. Ao término deste estudo, conclui-se que os trabalhadores florestais da extração de madeira estão expostos a situações de vida e trabalho que não contribuem para a promoção e manutenção da saúde desse pessoal.This study aimed to characterize the health of workers involved in the forest for the extraction of wood in the mountainous regions. The study was conducted in a forestry company, located in the Forestry District of Vale do Rio Doce, where 100% of the workers participated in the analysis. To characterize the health of the workers, a structured questionnaire in the form of interview was used, based on the PNAD (National Survey by Household Sample. The results showed that the activities of forest extraction have caused negative impacts on the health of workers, since 66% of workers declared to feel pain in some part of the body, 79% reported to have some dental problem, 86% said that they are exposed to factors that damage their health, 20% reported to present some disturbances of sleep, 9% did not have access to sanitation and 29

  9. Analysis of 60 706 Exomes Questions the Role of De Novo Variants Previously Implicated in Cardiac Disease

    DEFF Research Database (Denmark)

    Paludan-Müller, Christian; Ahlberg, Gustav; Ghouse, Jonas

    2017-01-01

    BACKGROUND: De novo variants in the exome occur at a rate of 1 per individual per generation, and because of the low reproductive fitness for de novo variants causing severe disease, the likelihood of finding these as standing variations in the general population is low. Therefore, this study...... sought to evaluate the pathogenicity of de novo variants previously associated with cardiac disease based on a large population-representative exome database. METHODS AND RESULTS: We performed a literature search for previous publications on de novo variants associated with severe arrhythmias...... trio studies (>1000 subjects). Of the monogenic variants, 11% (23/211) were present in ExAC, whereas 26% (802/3050) variants believed to increase susceptibility of disease were identified in ExAC. Monogenic de novo variants in ExAC had a total allele count of 109 and with ≈844 expected cases in Ex...

  10. Long-read sequencing and de novo assembly of a Chinese genome

    Science.gov (United States)

    Short-read sequencing has enabled the de novo assembly of several individual human genomes, but with inherent limitations in characterizing repeat elements. Here we sequence a Chinese individual HX1 by single-molecule real-time (SMRT) long-read sequencing, construct a physical map by NanoChannel arr...

  11. A De novo Mutation in Dystrophin Causing Muscular Dystrophy in a Female Patient

    Directory of Open Access Journals (Sweden)

    Hao Yu

    2017-01-01

    Conclusions: We identified two novel de novo mutations of DMD gene in two Chinese pedigrees, one of which caused a female patient with muscular dystrophy. The mutational analysis is important for DMD patients and carriers in the absence of a family history. The NGS can help detect the mutations in MLPA-negative patients.

  12. Effect of haemodilution, acidosis, and hypothermia on the activity of recombinant factor VIIa (NovoSeven)

    DEFF Research Database (Denmark)

    Viuff, D.; Lauritzen, B.; Pusateri, A.E.

    2008-01-01

    BACKGROUND: A range of plasma volume expanders is used clinically, often in settings where haemostasis may already be impaired. The haemostatic agent, recombinant activated factor VII (rFVIIa, NovoSeven), may be used to improve haemostasis but potential interactions with different volume expanders...

  13. Optimization of treatment protocols to prevent de novo development of antibiotic resistance in Pseudomonas aeruginosa

    NARCIS (Netherlands)

    Feng, Yanfang

    2016-01-01

    The ever-increasing rate of drug resistant bacteria has been one of the most challenging problem worldwide. This thesis studied the following subjects with mostly the clinically leading pathogen, P. aeruginosa, as the model strain: de novo development of antibiotic resistance in patient during the

  14. Norgal: Extraction and de novo assembly of mitochondrial DNA from whole-genome sequencing data

    DEFF Research Database (Denmark)

    Al-Nakeeb, Kosai Ali Ahmed; Petersen, Thomas Nordahl; Sicheritz-Pontén, Thomas

    2017-01-01

    and performing a de novo assembly on a subset of reads that contains these k-mers. The method was applied to WGS data from a panda, brown algae seaweed, butterfly and filamentous fungus. We were able to extract full circular mitochondrial genomes and obtained sequence identities to the reference sequences...

  15. 76 FR 61103 - Draft Guidance for Industry and Food and Drug Administration Staff; De Novo Classification...

    Science.gov (United States)

    2011-10-03

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES Food and Drug Administration [Docket No. FDA-2011-D-0689] Draft Guidance for Industry and Food and Drug Administration Staff; De Novo Classification Process... appropriate, and other forms of information technology. Draft Guidance for Industry and Food and Drug...

  16. De novo post-pollen mitosis II tobacco pollen tube transcriptome

    Czech Academy of Sciences Publication Activity Database

    Hafidh, Said; Breznenová, Katarína; Honys, David

    2012-01-01

    Roč. 7, č. 8 (2012), s. 918-921 ISSN 1559-2316 R&D Projects: GA ČR GPP501/11/P321; GA ČR GA522/09/0858 Institutional research plan: CEZ:AV0Z50380511 Keywords : de novo pollen tube transcriptome * male gametophyte development * pollen tube growth Subject RIV: ED - Physiology

  17. De novo mutations of KIAA2022 in females cause intellectual disability and intractable epilepsy

    NARCIS (Netherlands)

    de Lange, Iris M; Helbig, Katherine L; Weckhuysen, Sarah; Møller, Rikke S; Velinov, Milen; Dolzhanskaya, Natalia; Marsh, Eric; Helbig, Ingo; Devinsky, Orrin; Tang, Sha; Mefford, Heather C; Myers, Candace T; van Paesschen, Wim; Striano, Pasquale; van Gassen, Koen; van Kempen, Marjan; de Kovel, Carolien G F; Piard, Juliette; Minassian, Berge A; Nezarati, Marjan M; Pessoa, André; Jacquette, Aurelia; Maher, Bridget; Balestrini, Simona; Sisodiya, Sanjay; Warde, Marie Therese Abi; De St Martin, Anne; Chelly, Jamel; van 't Slot, Ruben; Van Maldergem, Lionel; Brilstra, Eva H; Koeleman, Bobby P C

    2016-01-01

    BACKGROUND: Mutations in the KIAA2022 gene have been reported in male patients with X-linked intellectual disability, and related female carriers were unaffected. Here, we report 14 female patients who carry a heterozygous de novo KIAA2022 mutation and share a phenotype characterised by intellectual

  18. Inflammatory bowel disease after liver transplantation : Risk factors for recurrence and De novo disease

    NARCIS (Netherlands)

    Verdonka, RC; Dijkstra, G; Haagsma, EB; Shostrom, VK; Van den Berg, AP; Kleibeuker, JH

    Inflammatory bowel disease (IBD) is associated with primary sclerosing cholangitis (PSC) and autoimmune hepatitis (AIH) and can recur or develop de novo after orthotopic liver transplantation (OLT). The aim of this study was to investigate the incidence and severity of IBD after liver

  19. Drug-Eluting Balloons in the Treatment of Coronary De Novo Lesions

    DEFF Research Database (Denmark)

    Richelsen, Rasmus Kapalu Broge; Overvad, Thure Filskov; Jensen, Svend Eggert

    2016-01-01

    Drug-eluting balloons (DEBs) have emerged as a new application in percutaneous coronary intervention. DEBs have proven successful in the treatment of in-stent restenosis, but their role in de novo lesions is less clear. This paper provides a review of the current studies where DEBs have been used...

  20. Whole-genome sequencing in autism identifies hot spots for de novo germline mutation

    DEFF Research Database (Denmark)

    Michaelson, Jacob J.; Shi, Yujian; Gujral, Madhusudan

    2012-01-01

    De novo mutation plays an important role in autism spectrum disorders (ASDs). Notably, pathogenic copy number variants (CNVs) are characterized by high mutation rates. We hypothesize that hypermutability is a property of ASD genes and may also include nucleotide-substitution hot spots. We...

  1. The Key Drivers behind Novo Nordisk’s Growth in the Diabetes Market in China

    Directory of Open Access Journals (Sweden)

    Hind Louiza CHITOUR

    2013-12-01

    Full Text Available To enter the Chinese Pharmaceutical market, “Big Pharma” has adopted different strategies to tackle the challenges specific to the country in terms of size, demographics, specific sales channels and logistics adjustments. While the majority of Global Pharmaceutical players have opted for an aggressive M&A approach to penetrate the Chinese market and gain local insight; the Danish Novo Nordisk has instead chosen a strategy focusing on innovation and developing its R&D structure to capitalize on the local talent pool. To illustrate Novo Nordisk’s growth strategy in the Mainland, we analyzed its competitiveness in the diabetes market by demonstrating the key drivers behind this success. We applied a various set of tools for this research: Novo Nordisk, Dong Bao Pharmaceutical executives’ interviews and personal observations accounting for the primary data, we also reviewed secondary data to perform a PEST analysis in addition to Porter’s competitive advantage model in order to extract the reasons behind Novo Nordisk’s marching success in the Mainland.

  2. A glance at quality score: implication for de novo transcriptome reconstruction of Illumina reads

    Directory of Open Access Journals (Sweden)

    Stanley Kimbung Mbandi

    2014-02-01

    Full Text Available Downstream analyses of short-reads from next-generation sequencing platforms are often preceded by a pre-processing step that removes uncalled and wrongly called bases. Standard approaches rely on their associated base quality scores to retain the read or a portion of it when the score is above a predefined threshold. It is difficult to differentiate sequencing error from biological variation without a reference using quality scores. The effects of quality score based trimming have not been systematically studied in de novo transcriptome assembly. Using RNA-Seq data produced from Illumina, we teased out the effects of quality score base filtering or trimming on de novo transcriptome reconstruction. We showed that assemblies produced from reads subjected to different quality score thresholds contain truncated and missing transfrags when compared to those from untrimmed reads. Our data supports the fact that de novo assembling of untrimmed data is challenging for de Bruijn graph assemblers. However, our results indicates that comparing the assemblies from untrimmed and trimmed read subsets can suggest appropriate filtering parameters and enable selection of the optimum de novo transcriptome assembly in non-model organisms.

  3. Evaluation of effect of Ophiostoma novo-ulmi on four major wood ...

    African Journals Online (AJOL)

    Evaluation of effect of Ophiostoma novo-ulmi on four major wood species of the elm family in Rasht (North West of Iran) ... the diameter size of vessels and the number of xylary rays in four species: Ulmus carpinifolia, Ulmus glabra, Zelkova carpinifolia and Celtis australis as important factors in host resistance to elm disease.

  4. De novo formation of centrosomes in vertebrate cells arrested during S phase

    NARCIS (Netherlands)

    Khodjakov, A; Rieder, CL; Sluder, G; Cassels, G; Sibon, O; Wang, CL

    2002-01-01

    The centrosome usually replicates in a semiconservative fashion, i.e., new centrioles form in association with preexisting "maternal" centrioles. De novo formation of centrioles has been reported for a few highly specialized cell types but it has not been seen in vertebrate somatic cells. We find

  5. Robust de novo pathway enrichment with KeyPathwayMiner 5

    DEFF Research Database (Denmark)

    Alcaraz, Nicolas; List, Markus; Dissing-Hansen, Martin

    2016-01-01

    Identifying functional modules or novel active pathways, recently termed de novo pathway enrichment, is a computational systems biology challenge that has gained much attention during the last decade. Given a large biological interaction network, KeyPathwayMiner extracts connected subnetworks tha...

  6. De novo insertions and deletions of predominantly paternal origin are associated with autism spectrum disorder

    Science.gov (United States)

    Dong, Shan; Walker, Michael F.; Carriero, Nicholas J.; DiCola, Michael; Willsey, A. Jeremy; Ye, Adam Y.; Waqar, Zainulabedin; Gonzalez, Luis E.; Overton, John D.; Frahm, Stephanie; Keaney, John F.; Teran, Nicole A.; Dea, Jeanselle; Mandell, Jeffrey D.; Bal, Vanessa Hus; Sullivan, Catherine A.; DiLullo, Nicholas M.; Khalil, Rehab O.; Gockley, Jake; Yuksel, Zafer; Sertel, Sinem M.; Ercan-Sencicek, A. Gulhan; Gupta, Abha R.; Mane, Shrikant M.; Sheldon, Michael; Brooks, Andrew I.; Roeder, Kathryn; Devlin, Bernie; State, Matthew W.; Wei, Liping; Sanders, Stephan J.

    2014-01-01

    SUMMARY Whole-exome sequencing (WES) studies have demonstrated the contribution of de novo loss-of-function single nucleotide variants to autism spectrum disorders (ASD). However, challenges in the reliable detection of de novo insertions and deletions (indels) have limited inclusion of these variants in prior analyses. Through the application of a robust indel detection method to WES data from 787 ASD families (2,963 individuals), we demonstrate that de novo frameshift indels contribute to ASD risk (OR=1.6; 95%CI=1.0-2.7; p=0.03), are more common in female probands (p=0.02), are enriched among genes encoding FMRP targets (p=6×10−9), and arise predominantly on the paternal chromosome (p<0.001). Based on mutation rates in probands versus unaffected siblings, de novo frameshift indels contribute to risk in approximately 3.0% of individuals with ASD. Finally, through observing clustering of mutations in unrelated probands, we report two novel ASD-associated genes: KMT2E (MLL5), a chromatin regulator, and RIMS1, a regulator of synaptic vesicle release. PMID:25284784

  7. Novo Jornalismo: fronteiras litero-factuais em A sangue Frio e em Radical Chique

    Directory of Open Access Journals (Sweden)

    Francisco Aquinei Timóteo Queirós

    2012-12-01

    Full Text Available A pesquisa busca analisar de que forma fato e ficção se entrecruzam no “movimento” do Novo Jornalismo, a partir das obras A sangue Frio e Radical Chique e o Novo Jornalismo, de Truman Capote e Tom Wolfe, respectivamente. Pretende-se, a partir da investigação do corpus em estudo, revelar os aspectos que aproximam o fato jornalístico, a notícia e a reportagem às técnicas literárias do romance, do conto e da crônica. O estudo investiga o Novo Jornalismo sob o viés de textos centrais das áreas de teoria literária e estudos jornalísticos utilizando autores como Mikhail Bakhtin, Hayden White, Paul Ricoeur, Muniz Sodré; além de referenciar outros escritores que, como Tom Wolfe e Truman Capote, fizeram parte de um grande movimento renovador do jornalismo literário nos anos 1950, 1960 e 1970 chamado, genericamente, de Novo Jornalismo.

  8. CycloBranch: De Novo Sequencing of Nonribosomal Peptides from Accurate Product Ion Mass Spectra

    Czech Academy of Sciences Publication Activity Database

    Novák, Jiří; Lemr, Karel; Schug, K. A.; Havlíček, Vladimír

    2015-01-01

    Roč. 26, č. 10 (2015), s. 1780-1786 ISSN 1044-0305 R&D Projects: GA ČR(CZ) GAP206/12/1150 Grant - others:OPPC(XE) CZ.2.16/3.1.00/24023 Institutional support: RVO:61388971 Keywords : De novo sequencing * Nonribosomal peptides * Linear Subject RIV: CE - Biochemistry Impact factor: 3.031, year: 2015

  9. Novo Jornalismo: fronteiras litero-factuais em A sangue Frio e em Radical Chique

    Directory of Open Access Journals (Sweden)

    Francisco Aquinei Timóteo Queirós

    2012-03-01

    Full Text Available http://dx.doi.org/10.5007/1984-784X.2012v12n18p130 A pesquisa busca analisar de que forma fato e ficção se entrecruzam no “movimento” do Novo Jornalismo, a partir das obras A sangue Frio e Radical Chique e o Novo Jornalismo, de Truman Capote e Tom Wolfe, respectivamente. Pretende-se, a partir da investigação do corpus em estudo, revelar os aspectos que aproximam o fato jornalístico, a notícia e a reportagem às técnicas literárias do romance, do conto e da crônica. O estudo investiga o Novo Jornalismo sob o viés de textos centrais das áreas de teoria literária e estudos jornalísticos utilizando autores como Mikhail Bakhtin, Hayden White, Paul Ricoeur, Muniz Sodré; além de referenciar outros escritores que, como Tom Wolfe e Truman Capote, fizeram parte de um grande movimento renovador do jornalismo literário nos anos 1950, 1960 e 1970 chamado, genericamente, de Novo Jornalismo.

  10. Predicting survival of de novo metastatic breast cancer in Asian women: systematic review and validation study.

    Science.gov (United States)

    Miao, Hui; Hartman, Mikael; Bhoo-Pathy, Nirmala; Lee, Soo-Chin; Taib, Nur Aishah; Tan, Ern-Yu; Chan, Patrick; Moons, Karel G M; Wong, Hoong-Seam; Goh, Jeremy; Rahim, Siti Mastura; Yip, Cheng-Har; Verkooijen, Helena M

    2014-01-01

    In Asia, up to 25% of breast cancer patients present with distant metastases at diagnosis. Given the heterogeneous survival probabilities of de novo metastatic breast cancer, individual outcome prediction is challenging. The aim of the study is to identify existing prognostic models for patients with de novo metastatic breast cancer and validate them in Asia. We performed a systematic review to identify prediction models for metastatic breast cancer. Models were validated in 642 women with de novo metastatic breast cancer registered between 2000 and 2010 in the Singapore Malaysia Hospital Based Breast Cancer Registry. Survival curves for low, intermediate and high-risk groups according to each prognostic score were compared by log-rank test and discrimination of the models was assessed by concordance statistic (C-statistic). We identified 16 prediction models, seven of which were for patients with brain metastases only. Performance status, estrogen receptor status, metastatic site(s) and disease-free interval were the most common predictors. We were able to validate nine prediction models. The capacity of the models to discriminate between poor and good survivors varied from poor to fair with C-statistics ranging from 0.50 (95% CI, 0.48-0.53) to 0.63 (95% CI, 0.60-0.66). The discriminatory performance of existing prediction models for de novo metastatic breast cancer in Asia is modest. Development of an Asian-specific prediction model is needed to improve prognostication and guide decision making.

  11. De novo nonsense mutations in ASXL1 cause Bohring-Opitz syndrome

    NARCIS (Netherlands)

    Hoischen, Alexander; van Bon, Bregje W. M.; Rodríguez-Santiago, Benjamín; Gilissen, Christian; Vissers, Lisenka E. L. M.; de Vries, Petra; Janssen, Irene; van Lier, Bart; Hastings, Rob; Smithson, Sarah F.; Newbury-Ecob, Ruth; Kjaergaard, Susanne; Goodship, Judith; McGowan, Ruth; Bartholdi, Deborah; Rauch, Anita; Peippo, Maarit; Cobben, Jan M.; Wieczorek, Dagmar; Gillessen-Kaesbach, Gabriele; Veltman, Joris A.; Brunner, Han G.; de Vries, Bert B. B. A.

    2011-01-01

    Bohring-Opitz syndrome is characterized by severe intellectual disability, distinctive facial features and multiple congenital malformations. We sequenced the exomes of three individuals with Bohring-Opitz syndrome and in each identified heterozygous de novo nonsense mutations in ASXL1, which is

  12. De novo mutations of KIAA2022 in females cause intellectual disability and intractable epilepsy

    DEFF Research Database (Denmark)

    de Lange, Iris M; Helbig, Katherine L; Weckhuysen, Sarah

    2016-01-01

    BACKGROUND: Mutations in the KIAA2022 gene have been reported in male patients with X-linked intellectual disability, and related female carriers were unaffected. Here, we report 14 female patients who carry a heterozygous de novo KIAA2022 mutation and share a phenotype characterised by intellect...

  13. Wound complications and surgical events in de novo heart transplant patients treated with everolimus

    DEFF Research Database (Denmark)

    Rashidi, Mitra; Esmaily, Sorosh; Fiane, Arnt E

    2016-01-01

    OBJECTIVES: The use of mammalian target of rapamycin (mTOR) inhibitors have been limited by adverse events (AE), including delayed wound healing. We retrospectively reviewed all AE and serious AE (SAE) in The Scandinavian heart transplant (HTx) everolimus (EVE) de novo trial with early calcineurin...

  14. Associations between Familial Rates of Psychiatric Disorders and De Novo Genetic Mutations in Autism

    Directory of Open Access Journals (Sweden)

    Kyleen Luhrs

    2017-01-01

    Full Text Available The purpose of this study was to examine the confluence of genetic and familial risk factors in children with Autism Spectrum Disorder (ASD with distinct de novo genetic events. We hypothesized that gene-disrupting mutations would be associated with reduced rates of familial psychiatric disorders relative to structural mutations. Participants included families of children with ASD in four groups: de novo duplication copy number variations (DUP, n=62, de novo deletion copy number variations (DEL, n=74, de novo likely gene-disrupting mutations (LGDM, n=267, and children without a known genetic etiology (NON, n=2111. Familial rates of psychiatric disorders were calculated from semistructured interviews. Results indicated overall increased rates of psychiatric disorders in DUP families compared to DEL and LGDM families, specific to paternal psychiatric histories, and particularly evident for depressive disorders. Higher rates of depressive disorders in maternal psychiatric histories were observed overall compared to paternal histories and higher rates of anxiety disorders were observed in paternal histories for LGDM families compared to DUP families. These findings support the notion of an additive contribution of genetic etiology and familial factors are associated with ASD risk and highlight critical need for continued work targeting these relationships.

  15. A recurrent de novo mutation in KCNC1 causes progressive myoclonus epilepsy

    DEFF Research Database (Denmark)

    Muona, M.; Berkovic, S. F.; Dibbens, L. M.

    2015-01-01

    Progressive myoclonus epilepsies (PMEs) are a group of rare, inherited disorders manifesting with action myoclonus, tonicclonic seizures and ataxia. We sequenced the exomes of 84 unrelated individuals with PME of unknown cause and molecularly solved 26 cases (31%). Remarkably, a recurrent de novo...

  16. The impact of employee satisfaction on productivity in Tiskarna Novo mesto, Ltd.

    Directory of Open Access Journals (Sweden)

    Simona Cimperman

    2016-06-01

    Full Text Available Research Question: Does employee satisfaction, impact on productivity? How are these two variables associated? What is the job satisfaction in Tiskarna Novo mesto, Ltd. What needs to be done to make employees more satisfied at work and, consequently, more productive? Purpose: The purpose of the study is to determine what are the factors that influence employee satisfaction Tiskarna Novo mesto, Ltd. and check the connection between work satisfaction and employee productivity. The aim of the research is to examine what is the level of job satisfaction of employees in Tiskarna Novo mesto, Ltd. And find our reasons and factors that prevent employees were satisfied in the workplace. Method: In this study we used a descriptive method and the method of combining the study of domestic and foreign literature. Pending the results we have come to interview employees in the Tiskarna Novo mesto, Ltd. Results: We conducted a survey among employees in Tiskarna Novo mesto, Ltd and we came to the conclusion that the employees are medium satisfied – the average grade point job satisfaction of employees was 3.1 (evaluated on a 5-point Likert scale. The worst assessed was factor in job satisfaction opportunity for advancement and educational opportunities. We have found out that factors like receiving praise and awards as well as good interpersonal relations are those that affect good on job satisfaction, on the other hand conflict is the one that reduces job satisfaction. The existence of links between work satisfaction and productivity were not found (r = -0.061. Organization: The organization and managers, it is important to know which are the factors by which employees are satisfied or dissatisfied. Results of the research will give managers a clear picture of the factors of satisfaction / dissatisfaction and opinion on productivity. Society: The employees it means a lot to have your job satisfaction and consequently they are more productive. Originality: The

  17. TRANSPORT OF PATIENTS FOR PRIMARY PTCA FROM GENERAL HOSPITAL NOVO MESTO TO LJUBLJANA IN 2002

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    Renata Okrajšek

    2004-12-01

    Full Text Available Background. The treatment of acute coronary syndrome (ACS with ST-segment elevation with primary percutaneous transluminal coronary angioplasty (PTCA is the best way to treat these patients. Primary PTCA is also practicable with patients who are admitted into institution without catheter laboratory. The transport of patients into the tertiary institution is safe, but it is important to keep the time of ischemia as short as possible and to reach the time interval of door-balloon as recommended by the guidelines. The ACS patients with ST-segment elevation that were directed into General Hospital Novo mesto after examination at the internistic emergency department have been redirected to KC Ljubljana for realization of PTCA since October 2001.Methods. A prospective analysis of patients with ACS with STsegment elevation, who had been transferred from General Hospital Novo mesto to KC Ljubljana in the period from January 1, 2002 to December 31, 2002 to have a primary PTCA, was performed. The analysis comprised the following: the time interval of handling the patients at Internistic department of General Hospital Novo mesto, the time of transport of patients to Ljubljana and total time interval from the arrival of patients to General Hospital Novo mesto to the first inflation of balloon in Ljubljana. We monitored the complications that occurred during the treatment of the patients.Results. In the above mentioned period 29 patients (24 males and 5 females were transported from the General Hospital Novo mesto to the KC Ljubljana to have a primary PTCA performed. The total time interval measured between the patients’ arrival to General Hospital Novo mesto to the first inflation of balloon in Ljubljana in the year 2002 was 145 minutes, which is 17 minutes better than in the previous period. The time interval recommended by the guidelines was achieved with four patients.Conclusions. By recognizing the problems that had encountered with directing the

  18. A prognostic scoring model for survival after locoregional therapy in de novo stage IV breast cancer.

    Science.gov (United States)

    Kommalapati, Anuhya; Tella, Sri Harsha; Goyal, Gaurav; Ganti, Apar Kishor; Krishnamurthy, Jairam; Tandra, Pavan Kumar

    2018-05-02

    The role of locoregional treatment (LRT) remains controversial in de novo stage IV breast cancer (BC). We sought to analyze the role of LRT and prognostic factors of overall survival (OS) in de novo stage IV BC patients treated with LRT utilizing the National Cancer Data Base (NCDB). The objective of the current study is to create and internally validate a prognostic scoring model to predict the long-term OS for de novo stage IV BC patients treated with LRT. We included de novo stage IV BC patients reported to NCDB between 2004 and 2015. Patients were divided into LRT and no-LRT subsets. We randomized LRT subset to training and validation cohorts. In the training cohort, a seventeen-point prognostic scoring system was developed based on the hazard ratios calculated using Cox-proportional method. We stratified both training and validation cohorts into two "groups" [group 1 (0-7 points) and group 2 (7-17 points)]. Kaplan-Meier method and log-rank test were used to compare OS between the two groups. Our prognostic score was validated internally by comparing the OS between the respective groups in both the training and validation cohorts. Among 67,978 patients, LRT subset (21,200) had better median OS as compared to that of no-LRT (45 vs. 24 months; p < 0.0001). The group 1 and group 2 in the training cohort showed a significant difference in the 3-year OS (p < 0.0001) (68 vs. 26%). On internal validation, comparable OS was seen between the respective groups in each cohort (p = 0.77). Our prognostic scoring system will help oncologists to predict the prognosis in de novo stage IV BC patients treated with LRT. Although firm treatment-related conclusions cannot be made due to the retrospective nature of the study, LRT appears to be associated with a better OS in specific subgroups.

  19. De Novo Heart Failure After Kidney Transplantation: Trends in Incidence and Outcomes.

    Science.gov (United States)

    Lenihan, Colin R; Liu, Sai; Deswal, Anita; Montez-Rath, Maria E; Winkelmayer, Wolfgang C

    2018-03-29

    Heart failure is an important cause of morbidity and mortality following kidney transplantation. Some studies in the general population have shown that the incidence of heart failure has decreased during the past 20 years. However, it is not currently known whether such a trend exists in the kidney transplantation population. Retrospective observational cohort study. Adult patients included in the US Renal Data System who underwent their first kidney transplantation in the United States between 1998 and 2010 with at least 6 months of continuous Medicare parts A and B coverage before transplantation and no prior evidence for a diagnosis of heart failure before kidney transplantation. Calendar year of transplantation and calendar year of posttransplantation heart failure diagnosis. De novo posttransplantation heart failure defined using International Classification of Diseases, Ninth Revision diagnosis codes and mortality following de novo posttransplantation heart failure diagnosis. Secular trends in de novo post-kidney transplantation heart failure were examined using Cox proportional hazards analysis. Within a study cohort of 48,771 patients, 7,269 developed de novo heart failure within 3 years of kidney transplantation, with a median time to heart failure of 0.76 years. The adjusted HR for heart failure with death as competing risk comparing patients who underwent transplantation in 2010 with those who underwent transplantation in 1998 was 0.69 (95% CI, 0.60-0.79). No temporal trend in mortality following a diagnosis of post-kidney transplantation heart failure was observed. Potential residual confounding from either incorrectly ascertained or unavailable confounders. The cohort was limited to Medicare beneficiaries. Adjusted for demographic and clinical characteristics, the risk for developing de novo post-kidney transplantation heart failure has declined significantly between 1998 and 2010, with no apparent change in subsequent mortality. Copyright © 2018

  20. Hominoid-specific de novo protein-coding genes originating from long non-coding RNAs.

    Directory of Open Access Journals (Sweden)

    Chen Xie

    2012-09-01

    Full Text Available Tinkering with pre-existing genes has long been known as a major way to create new genes. Recently, however, motherless protein-coding genes have been found to have emerged de novo from ancestral non-coding DNAs. How these genes originated is not well addressed to date. Here we identified 24 hominoid-specific de novo protein-coding genes with precise origination timing in vertebrate phylogeny. Strand-specific RNA-Seq analyses were performed in five rhesus macaque tissues (liver, prefrontal cortex, skeletal muscle, adipose, and testis, which were then integrated with public transcriptome data from human, chimpanzee, and rhesus macaque. On the basis of comparing the RNA expression profiles in the three species, we found that most of the hominoid-specific de novo protein-coding genes encoded polyadenylated non-coding RNAs in rhesus macaque or chimpanzee with a similar transcript structure and correlated tissue expression profile. According to the rule of parsimony, the majority of these hominoid-specific de novo protein-coding genes appear to have acquired a regulated transcript structure and expression profile before acquiring coding potential. Interestingly, although the expression profile was largely correlated, the coding genes in human often showed higher transcriptional abundance than their non-coding counterparts in rhesus macaque. The major findings we report in this manuscript are robust and insensitive to the parameters used in the identification and analysis of de novo genes. Our results suggest that at least a portion of long non-coding RNAs, especially those with active and regulated transcription, may serve as a birth pool for protein-coding genes, which are then further optimized at the transcriptional level.

  1. De Novo Insertions and Deletions of Predominantly Paternal Origin Are Associated with Autism Spectrum Disorder

    Directory of Open Access Journals (Sweden)

    Shan Dong

    2014-10-01

    Full Text Available Summary: Whole-exome sequencing (WES studies have demonstrated the contribution of de novo loss-of-function single-nucleotide variants (SNVs to autism spectrum disorder (ASD. However, challenges in the reliable detection of de novo insertions and deletions (indels have limited inclusion of these variants in prior analyses. By applying a robust indel detection method to WES data from 787 ASD families (2,963 individuals, we demonstrate that de novo frameshift indels contribute to ASD risk (OR = 1.6; 95% CI = 1.0–2.7; p = 0.03, are more common in female probands (p = 0.02, are enriched among genes encoding FMRP targets (p = 6 × 10−9, and arise predominantly on the paternal chromosome (p < 0.001. On the basis of mutation rates in probands versus unaffected siblings, we conclude that de novo frameshift indels contribute to risk in approximately 3% of individuals with ASD. Finally, by observing clustering of mutations in unrelated probands, we uncover two ASD-associated genes: KMT2E (MLL5, a chromatin regulator, and RIMS1, a regulator of synaptic vesicle release. : Insertions and deletions (indels have proven especially difficult to detect in exome sequencing data. Dong et al. now identify indels in exome data for 787 autism spectrum disorder (ASD families. They demonstrate association between de novo indels that alter the reading frame and ASD. Furthermore, by observing clustering of indels in unrelated probands, they uncover two additional ASD-associated genes: KMT2E (MLL5, a chromatin regulator, and RIMS1, a regulator of synaptic vesicle release.

  2. De novo synthesis of adenine nucleotides in different skeletal muscle fiber types

    International Nuclear Information System (INIS)

    Tullson, P.C.; John-Alder, H.B.; Hood, D.A.; Terjung, R.L.

    1988-01-01

    Management of adenine nucleotide catabolism differs among skeletal muscle fiber types. This study evaluated whether there are corresponding differences in the rates of de novo synthesis of adenine nucleotide among fiber type sections of skeletal muscle using an isolated perfused rat hindquarter preparation. Label incorporation into adenine nucleotides from the [1-14C]glycine precursor was determined and used to calculate synthesis rates based on the intracellular glycine specific radioactivity. Results show that intracellular glycine is closely related to the direct precursor pool. Rates of de novo synthesis were highest in fast-twitch red muscle (57.0 +/- 4.0, 58.2 +/- 4.4 nmol.h-1.g-1; deep red gastrocnemius and vastus lateralis), relatively high in slow-twitch red muscle (47.0 +/- 3.1; soleus), and low in fast-twitch white muscle (26.1 +/- 2.0 and 21.6 +/- 2.3; superficial white gastrocnemius and vastus lateralis). Rates for four mixed muscles were intermediate, ranging between 32.3 and 37.3. Specific de novo synthesis rates exhibited a strong correlation (r = 0.986) with muscle section citrate synthase activity. Turnover rates (de novo synthesis rate/adenine nucleotide pool size) were highest in high oxidative muscle (0.82-1.06%/h), lowest in low oxidative muscle (0.30-0.35%/h), and intermediate in mixed muscle (0.44-0.55%/h). Our results demonstrate that differences in adenine nucleotide management among fiber types extends to the process of de novo adenine nucleotide synthesis

  3. Efficient assembly of de novo human artificial chromosomes from large genomic loci

    Directory of Open Access Journals (Sweden)

    Stromberg Gregory

    2005-07-01

    Full Text Available Abstract Background Human Artificial Chromosomes (HACs are potentially useful vectors for gene transfer studies and for functional annotation of the genome because of their suitability for cloning, manipulating and transferring large segments of the genome. However, development of HACs for the transfer of large genomic loci into mammalian cells has been limited by difficulties in manipulating high-molecular weight DNA, as well as by the low overall frequencies of de novo HAC formation. Indeed, to date, only a small number of large (>100 kb genomic loci have been reported to be successfully packaged into de novo HACs. Results We have developed novel methodologies to enable efficient assembly of HAC vectors containing any genomic locus of interest. We report here the creation of a novel, bimolecular system based on bacterial artificial chromosomes (BACs for the construction of HACs incorporating any defined genomic region. We have utilized this vector system to rapidly design, construct and validate multiple de novo HACs containing large (100–200 kb genomic loci including therapeutically significant genes for human growth hormone (HGH, polycystic kidney disease (PKD1 and ß-globin. We report significant differences in the ability of different genomic loci to support de novo HAC formation, suggesting possible effects of cis-acting genomic elements. Finally, as a proof of principle, we have observed sustained ß-globin gene expression from HACs incorporating the entire 200 kb ß-globin genomic locus for over 90 days in the absence of selection. Conclusion Taken together, these results are significant for the development of HAC vector technology, as they enable high-throughput assembly and functional validation of HACs containing any large genomic locus. We have evaluated the impact of different genomic loci on the frequency of HAC formation and identified segments of genomic DNA that appear to facilitate de novo HAC formation. These genomic loci

  4. De novo triiodothyronine formation from thyrocytes activated by thyroid-stimulating hormone.

    Science.gov (United States)

    Citterio, Cintia E; Veluswamy, Balaji; Morgan, Sarah J; Galton, Valerie A; Banga, J Paul; Atkins, Stephen; Morishita, Yoshiaki; Neumann, Susanne; Latif, Rauf; Gershengorn, Marvin C; Smith, Terry J; Arvan, Peter

    2017-09-15

    The thyroid gland secretes primarily tetraiodothyronine (T 4 ), and some triiodothyronine (T 3 ). Under normal physiological circumstances, only one-fifth of circulating T 3 is directly released by the thyroid, but in states of hyperactivation of thyroid-stimulating hormone receptors (TSHRs), patients develop a syndrome of relative T 3 toxicosis. Thyroidal T 4 production results from iodination of thyroglobulin (TG) at residues Tyr 5 and Tyr 130 , whereas thyroidal T 3 production may originate in several different ways. In this study, the data demonstrate that within the carboxyl-terminal portion of mouse TG, T 3 is formed de novo independently of deiodination from T 4 We found that upon iodination in vitro , de novo T 3 formation in TG was decreased in mice lacking TSHRs. Conversely, de novo T 3 that can be formed upon iodination of TG secreted from PCCL3 (rat thyrocyte) cells was augmented from cells previously exposed to increased TSH, a TSHR agonist, a cAMP analog, or a TSHR-stimulating antibody. We present data suggesting that TSH-stimulated TG phosphorylation contributes to enhanced de novo T 3 formation. These effects were reversed within a few days after removal of the hyperstimulating conditions. Indeed, direct exposure of PCCL3 cells to human serum from two patients with Graves' disease, but not control sera, led to secretion of TG with an increased intrinsic ability to form T 3 upon in vitro iodination. Furthermore, TG secreted from human thyrocyte cultures hyperstimulated with TSH also showed an increased intrinsic ability to form T 3 Our data support the hypothesis that TG processing in the secretory pathway of TSHR-hyperstimulated thyrocytes alters the structure of the iodination substrate in a way that enhances de novo T 3 formation, contributing to the relative T 3 toxicosis of Graves' disease.

  5. Automated de novo phasing and model building of coiled-coil proteins.

    Science.gov (United States)

    Rämisch, Sebastian; Lizatović, Robert; André, Ingemar

    2015-03-01

    Models generated by de novo structure prediction can be very useful starting points for molecular replacement for systems where suitable structural homologues cannot be readily identified. Protein-protein complexes and de novo-designed proteins are examples of systems that can be challenging to phase. In this study, the potential of de novo models of protein complexes for use as starting points for molecular replacement is investigated. The approach is demonstrated using homomeric coiled-coil proteins, which are excellent model systems for oligomeric systems. Despite the stereotypical fold of coiled coils, initial phase estimation can be difficult and many structures have to be solved with experimental phasing. A method was developed for automatic structure determination of homomeric coiled coils from X-ray diffraction data. In a benchmark set of 24 coiled coils, ranging from dimers to pentamers with resolutions down to 2.5 Å, 22 systems were automatically solved, 11 of which had previously been solved by experimental phasing. The generated models contained 71-103% of the residues present in the deposited structures, had the correct sequence and had free R values that deviated on average by 0.01 from those of the respective reference structures. The electron-density maps were of sufficient quality that only minor manual editing was necessary to produce final structures. The method, named CCsolve, combines methods for de novo structure prediction, initial phase estimation and automated model building into one pipeline. CCsolve is robust against errors in the initial models and can readily be modified to make use of alternative crystallographic software. The results demonstrate the feasibility of de novo phasing of protein-protein complexes, an approach that could also be employed for other small systems beyond coiled coils.

  6. Genome sequencing of bacteria: sequencing, de novo assembly and rapid analysis using open source tools.

    Science.gov (United States)

    Kisand, Veljo; Lettieri, Teresa

    2013-04-01

    De novo genome sequencing of previously uncharacterized microorganisms has the potential to open up new frontiers in microbial genomics by providing insight into both functional capabilities and biodiversity. Until recently, Roche 454 pyrosequencing was the NGS method of choice for de novo assembly because it generates hundreds of thousands of long reads (tools for processing NGS data are increasingly free and open source and are often adopted for both their high quality and role in promoting academic freedom. The error rate of pyrosequencing the Alcanivorax borkumensis genome was such that thousands of insertions and deletions were artificially introduced into the finished genome. Despite a high coverage (~30 fold), it did not allow the reference genome to be fully mapped. Reads from regions with errors had low quality, low coverage, or were missing. The main defect of the reference mapping was the introduction of artificial indels into contigs through lower than 100% consensus and distracting gene calling due to artificial stop codons. No assembler was able to perform de novo assembly comparable to reference mapping. Automated annotation tools performed similarly on reference mapped and de novo draft genomes, and annotated most CDSs in the de novo assembled draft genomes. Free and open source software (FOSS) tools for assembly and annotation of NGS data are being developed rapidly to provide accurate results with less computational effort. Usability is not high priority and these tools currently do not allow the data to be processed without manual intervention. Despite this, genome assemblers now readily assemble medium short reads into long contigs (>97-98% genome coverage). A notable gap in pyrosequencing technology is the quality of base pair calling and conflicting base pairs between single reads at the same nucleotide position. Regardless, using draft whole genomes that are not finished and remain fragmented into tens of contigs allows one to characterize

  7. Balanço de carbono e nutrientes em plantio puro e misto de espécies florestais nativas no sudeste da Bahia Carbon and nutrient balance in pure and mixed stands of native tree species in Southeastern Bahia, Brazil

    Directory of Open Access Journals (Sweden)

    Antonio Carlos da Gama-Rodrigues

    2008-06-01

    Full Text Available A manutenção da produção florestal depende da quantidade e do fluxo de nutrientes no ecossistema, os quais são afetados pelas técnicas de manejo utilizadas. O objetivo deste trabalho foi avaliar diferenças na ciclagem e no balanço de C e nutrientes, em plantio puro e misto de espécies florestais nativas, bem como em fragmentos florestais de Mata Atlântica. O trabalho foi desenvolvido em solos de tabuleiro do sudeste da Bahia, Brasil, no período de agosto de 1994 a julho de 1995, em plantios, com 22 anos de idade, de pau-roxo, Peltogyne angustiflora; putumuju, Centrolobium robustum; arapati, Arapatiella psilophylla; arapaçu, Sclerolobium chrysophyllum; claraíba, Cordia trichotoma; e óleo-comumbá, Macrolobium latifolium. Como referências, foram utilizadas uma floresta secundária, praticamente em estado clímax, e uma capoeira de 40 anos de idade. As quantidades totais de carbono e nutrientes no sistema (solo + parte aérea + serapilheira variou marcadamente entre as espécies florestais. O plantio misto apresentou maior acúmulo desses elementos do que os plantios puros. O plantio misto apresentou maior intensidade de ciclagem bioquímica para todos os nutrientes do que a média dos plantios puros. Resultado similar ocorreu para a ciclagem biogeoquímica, à exceção de Ca. O balanço de C, P e K foi negativo em todas as coberturas florestais; entretanto, para N o balanço foi positivo. O balanço de Ca foi positivo apenas para o arapaçu, enquanto o de Mg foi negativo somente no putumuju e óleo-comumbá. O balanço mais negativo foi de P, seguido de K e Ca. O plantio misto apresentou balanço próximo à média dos plantios puros. Desse modo, o plantio misto mostrou-se mais adequado, por proporcionar, simultaneamente, maior eficiência da ciclagem bioquímica e biogeoquímica e balanços mais equilibrados de carbono e nutrientes.This study aimed to evaluate the differences in carbon and nutrient cycling and balance in two

  8. Candeias (Eremanthus sp.): espacialização e interações ambientais no município de Mariana (MG)

    OpenAIRE

    Faria, Maola Monique

    2012-01-01

    Os remanescentes florestais de Minas Gerais abrigam grande riqueza e diversidade de espécies vegetais nativas, dentre essas as espécies do gênero Eremanthus sp., conhecidas popularmente como candeia, se destacam. Esta se desenvolve sobre solos pouco férteis e rasos originando povoamentos puros, denominados de monodominantes. Sua ocorrência também é registrada dentro de florestas após alguma perturbação com consequente formação de clareiras, visto que essa é heliófila. A candeia apresenta alto...

  9. Transferência do fator caturra para o cultivar Mundo Novo de Coffea arabica Transfer of the CT gene to Mundo Novo cultivar

    Directory of Open Access Journals (Sweden)

    A. Carvalho

    1972-01-01

    Full Text Available No presente trabalho são relatados os estudos realizados visando à introdução do gene Ct (caturra que contribui para reduzir a altura da planta, no cultivar Mundo" Novo de Coffea arabica.Estudaram-se, em ensaios de produtividade, as populações Fv F.,, F3 e F4. Nessas populações e principalmente entre os descendentes dos "caféeiros H 2077-2-5 e H 2077-2-12, foram selecionadas plantas homozigotas para os alelos Ct e também para os alelos responsáveis pela cor do fruto xc ou Xc. Essas combinações foram denominadas 'Catuaí Amarelo' e 'Catuaí Vermelho', respectivamente, e suas características são apresentadas. Os novos cultivares vêm-se mostrando de interesse econômico para as regiões cafeeiras não somente pelo porte pequeno, mas também pela produtividade, pelo vigor vegetativo e pela precocidade.The successful transfer of the Ct gene for short internode to the tall cultivar of Coffea arábica'Mundo Novo' is reported. Individual selections were carried out in the F1, F2, F3 and F4 generations. It was found that early selection in the F2 generation was quite effective. A remarkably good correlation was found between productitivity of F2 plants and the yield of the F3 and F4 generations. Plants of the F4 generation have shown reasonable uniformity and high yield in several trials. The new selections showed to be early producers. Two new cultivars were released namely 'Catuaí Amarelo' and 'Catuaí Vermelho'. The former has yellow fruits whereas the latter has red fruits. The plants are much shorter that the ones of Mundo Novo. The new cultivars have a very strong secondary and tertiary branching. Because of these characteristics Catuaí Amarelo and Catuaí Vermelho are being planted in large scale replacing the tall cultivars.

  10. De novo mutations in the genome organizer CTCF cause intellectual disability

    DEFF Research Database (Denmark)

    Gregor, Anne; Oti, Martin; Kouwenhoven, Evelyn N

    2013-01-01

    An increasing number of genes involved in chromatin structure and epigenetic regulation has been implicated in a variety of developmental disorders, often including intellectual disability. By trio exome sequencing and subsequent mutational screening we now identified two de novo frameshift...... mutations and one de novo missense mutation in CTCF in individuals with intellectual disability, microcephaly, and growth retardation. Furthermore, an individual with a larger deletion including CTCF was identified. CTCF (CCCTC-binding factor) is one of the most important chromatin organizers in vertebrates...... and is involved in various chromatin regulation processes such as higher order of chromatin organization, enhancer function, and maintenance of three-dimensional chromatin structure. Transcriptome analyses in all three individuals with point mutations revealed deregulation of genes involved in signal transduction...

  11. Whole-Genome de novo Sequencing Of Quail And Grey Partridge

    DEFF Research Database (Denmark)

    Holm, Lars-Erik; Panitz, Frank; Burt, Dave

    2011-01-01

    The development in sequencing methods has made it possible to perform whole genome de novo sequencing of species without large commercial interests. Within the EU-financed QUANTOMICS project (KBBE-2A-222664), we have performed de novo sequencing of quail (Coturnix coturnix) and grey partridge...... (Perdix perdix) on a Genome Analyzer GAII (Illumina) using paired-end sequencing. The amount of generated sequences amounts to 8 to 9 Gb for each species. The analysis and assembly of the generated sequences is ongoing. Access to the whole genome sequence from these two species will enable enhanced...... comparative studies towards the chicken genome and will aid in identifying evolutionarily conserved sequences within the Galliformes. The obtained sequences from quail and partridge represent a beginning of generating the whole genome sequence for these species. The continuation of establishing the genome...

  12. NxRepair: error correction in de novo sequence assembly using Nextera mate pairs

    Directory of Open Access Journals (Sweden)

    Rebecca R. Murphy

    2015-06-01

    Full Text Available Scaffolding errors and incorrect repeat disambiguation during de novo assembly can result in large scale misassemblies in draft genomes. Nextera mate pair sequencing data provide additional information to resolve assembly ambiguities during scaffolding. Here, we introduce NxRepair, an open source toolkit for error correction in de novo assemblies that uses Nextera mate pair libraries to identify and correct large-scale errors. We show that NxRepair can identify and correct large scaffolding errors, without use of a reference sequence, resulting in quantitative improvements in the assembly quality. NxRepair can be downloaded from GitHub or PyPI, the Python Package Index; a tutorial and user documentation are also available.

  13. Trans-10, cis-12 conjugated linoleic acid decreases de novo lipid synthesis in human adipocytes

    DEFF Research Database (Denmark)

    Obsen, Thomas; Faergeman, Nils J; Chung, Soonkyu

    2012-01-01

    7-12 h, respectively. The mRNA levels of liver X receptor (LXR)α and sterol regulatory element binding protein (SREBP)-1c, transcription factors that regulate SCD-1, were decreased by 10,12 CLA within 5 h. These data suggest that the isomer-specific decrease in de novo lipid synthesis by 10,12 CLA......]-oleic or [(14)C]-linoleic acids. When using [(14)C]-acetic acid and [(14)C]-pyruvic acid as substrates, 30 μM 10,12 CLA, but not 9,11 CLA, decreased de novo synthesis of triglyceride, free FA, diacylglycerol, cholesterol esters, cardiolipin, phospholipids and ceramides within 3-24 h. Treatment with 30 μM 10...... is due, in part, to the rapid repression of lipogenic transcription factors that regulate MUFA synthesis, suggesting an anti-obesity mechanism unique to this trans FA....

  14. Integrative Analyses of De Novo Mutations Provide Deeper Biological Insights into Autism Spectrum Disorder

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    Atsushi Takata

    2018-01-01

    Full Text Available Recent studies have established important roles of de novo mutations (DNMs in autism spectrum disorders (ASDs. Here, we analyze DNMs in 262 ASD probands of Japanese origin and confirm the “de novo paradigm” of ASDs across ethnicities. Based on this consistency, we combine the lists of damaging DNMs in our and published ASD cohorts (total number of trios, 4,244 and perform integrative bioinformatics analyses. Besides replicating the findings of previous studies, our analyses highlight ATP-binding genes and fetal cerebellar/striatal circuits. Analysis of individual genes identified 61 genes enriched for damaging DNMs, including ten genes for which our dataset now contributes to statistical significance. Screening of compounds altering the expression of genes hit by damaging DNMs reveals a global downregulating effect of valproic acid, a known risk factor for ASDs, whereas cardiac glycosides upregulate these genes. Collectively, our integrative approach provides deeper biological and potential medical insights into ASDs.

  15. Alternative normalization methods demonstrate widespread cortical hypometabolism in untreated de novo Parkinson's disease

    DEFF Research Database (Denmark)

    Berti, Valentina; Polito, C; Borghammer, Per

    2012-01-01

    , recent studies suggested that conventional data normalization procedures may not always be valid, and demonstrated that alternative normalization strategies better allow detection of low magnitude changes. We hypothesized that these alternative normalization procedures would disclose more widespread...... metabolic alterations in de novo PD. METHODS: [18F]FDG PET scans of 26 untreated de novo PD patients (Hoehn & Yahr stage I-II) and 21 age-matched controls were compared using voxel-based analysis. Normalization was performed using gray matter (GM), white matter (WM) reference regions and Yakushev...... normalization. RESULTS: Compared to GM normalization, WM and Yakushev normalization procedures disclosed much larger cortical regions of relative hypometabolism in the PD group with extensive involvement of frontal and parieto-temporal-occipital cortices, and several subcortical structures. Furthermore...

  16. A de novo missense mutation of FGFR2 causes facial dysplasia syndrome in Holstein cattle

    DEFF Research Database (Denmark)

    Agerholm, Jørgen Steen; McEvoy, Fintan; Heegaard, Steffen

    2017-01-01

    was suspected as all recorded cases were progeny of the same sire. Detailed investigations were performed to characterize the syndrome and to reveal its cause. Results Seven malformed calves were submitted examination. All cases shared a common morphology with the most striking lesions being severe facial...... chromosome 26 where whole genome sequencing of a case-parent trio revealed two de novo variants perfectly associated with the disease: an intronic SNP in the DMBT1 gene and a single non-synonymous variant in the FGFR2 gene. This FGFR2 missense variant (c.927G>T) affects a gene encoding a member...... of the fibroblast growth factor receptor family, where amino acid sequence is highly conserved between members and across species. It is predicted to change an evolutionary conserved tryptophan into a cysteine residue (p.Trp309Cys). Both variant alleles were proven to result from de novo mutation events...

  17. A rare case of de novo gigantic ovarian abscess within an endometrioma.

    Science.gov (United States)

    Hameed, Aisha; Mehta, Vaishali; Sinha, Prabha

    2010-06-01

    We are reporting a rare case of de novo ovarian abscess in an endometrioma. Ovarian abscess within an endometrioma is a rare gynecological problem, but de novo abscess in the endometrioma is even rarer. Most of the ovarian abscesses develop in the endometriomas following interventions, e.g., aspiration, pelvic surgery, and oocyte retrieval. We are presenting a case of a spontaneous giant abscess in a large ovarian cyst in a nulliparous woman who presented with acute abdomen. Patient was treated in a district general hospital with multidisciplinary approach. Thirteen liters of the pus were drained. She has had a sub total (supra cervical) hysterectomy and bilateral salpingo-oophorectomy (BSO) performed. Histology of the abscess wall confirmed endometriotic nature of the cyst. Patient made an uneventful recovery and was discharged home on the 14th postoperative day. This case highlights that endometrioma and its complication can present as a surgical emergency and should be dealt as one.

  18. The significance of trilineage myelodysplasia in de novo acute myeloblastic leukemia: Clinical and laboratory features

    OpenAIRE

    Lima, CSP; Vassalo, J; LorandMetze, I; Bechelli, APP; Souza, CA

    1997-01-01

    A prospective study was undertaken to elucidate the clinical and laboratory differences between tie novo acute myeloid leukemia (AML) and AML with trilineage myelodysplasia (AML-TMDS). One hundred and seven patients with AML were diagnosed at the University Hospital between January 1987 and July 1992, and were followed until July 1995. TMDS was identified in 17 of them (16%). With regard to age and sex distribution no difference was found between AML patients with and without TMDS (p = 0.43, ...

  19. Perinatal Autopsy Findings in a Case of De Novo Hypohidrotic Ectodermal Dysplasia.

    Science.gov (United States)

    Chikkannaiah, Panduranga; Nagaraju, Smitha; Kangle, Rajit; Gosavi, Mansi

    2015-01-01

    Ectodermal dysplasia are group of inherited disorders involving the developmental defects of ectodermal structures like hair, teeth, nails, sweat glands, and others. X-linked recessive inheritance is most common. Here we describe perinatal autopsy findings in a case of de novo ectodermal dysplasia in a female fetus. To the best of our knowledge, this is the first fetal autopsy description in a case of ectodermal dysplasia.

  20. Demonstration of de novo synthesis of enzymes by density labelling with stable isotopes

    International Nuclear Information System (INIS)

    Huebner, G.; Hirschberg, K.

    1977-01-01

    The technique of in vivo density labelling of proteins with H 2 18 O and 2 H 2 O has been used to investigate hormonal regulation and developmental expression of enzymes in plant cells. Buoyant density data obtained from isopycnic equilibrium centrifugation demonstrated that the cytokinine-induced nitrate reductase activity and the gibberellic acid-induced phosphatase activity in isolated embryos of Agrostemma githago are activities of enzymes synthesized de novo. The increase in alanine-specific aminopeptidase in germinating A. githago seeds is not due to de novo synthesis but to the release of preformed enzyme. On the basis of this result it is possible to apply the enzyme aminopeptidase as an internal density standard in equilibrium centrifugation. Density labelling experiments on proteins in pea cotyledons have been used to study the change in the activity of acid phosphatase, alanine-specific aminopeptidase, and peroxidase during germination. The activities of these enzymes increase in cotyledons of Pisum sativum. Density labelling by 18 O and 2 H demonstrates de novo synthesis of these three enzymes. The differential time course of enzyme induction shows the advantage of using H 2 18 O as labelling substance in cases when the enzyme was synthesized immediately at the beginning of germination. At this stage of development the amino-acid pool available for synthesis is formed principally by means of hydrolysis of storage proteins. The incorporation of 2 H into the new proteins takes place in a measurable amount at a stage of growth in which the amino acids are also synthesized de novo. The enzyme acid phosphatase of pea cotyledons was chosen to demonstrate the possibility of using the density labelling technique to detect protein turnover. (author)

  1. Optimizing de novo common wheat transcriptome assembly using short-read RNA-Seq data

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    Duan Jialei

    2012-08-01

    Full Text Available Abstract Background Rapid advances in next-generation sequencing methods have provided new opportunities for transcriptome sequencing (RNA-Seq. The unprecedented sequencing depth provided by RNA-Seq makes it a powerful and cost-efficient method for transcriptome study, and it has been widely used in model organisms and non-model organisms to identify and quantify RNA. For non-model organisms lacking well-defined genomes, de novo assembly is typically required for downstream RNA-Seq analyses, including SNP discovery and identification of genes differentially expressed by phenotypes. Although RNA-Seq has been successfully used to sequence many non-model organisms, the results of de novo assembly from short reads can still be improved by using recent bioinformatic developments. Results In this study, we used 212.6 million pair-end reads, which accounted for 16.2 Gb, to assemble the hexaploid wheat transcriptome. Two state-of-the-art assemblers, Trinity and Trans-ABySS, which use the single and multiple k-mer methods, respectively, were used, and the whole de novo assembly process was divided into the following four steps: pre-assembly, merging different samples, removal of redundancy and scaffolding. We documented every detail of these steps and how these steps influenced assembly performance to gain insight into transcriptome assembly from short reads. After optimization, the assembled transcripts were comparable to Sanger-derived ESTs in terms of both continuity and accuracy. We also provided considerable new wheat transcript data to the community. Conclusions It is feasible to assemble the hexaploid wheat transcriptome from short reads. Special attention should be paid to dealing with multiple samples to balance the spectrum of expression levels and redundancy. To obtain an accurate overview of RNA profiling, removal of redundancy may be crucial in de novo assembly.

  2. Primary intraosseous squamous cell carcinoma of the mandible arising de novo.

    Science.gov (United States)

    Shamim, Thorakkal

    2009-07-01

    Primary intraosseous squamous cell carcinoma is an odontogenic tumour with aggressive behaviour usually noticed in 6th to 7th decades of life. The tumour is characterized by progressive swelling of the jaw, pain and loosening of teeth. Microscopically, the lesion is showing foci of keratinising cells separated by collagenous connective tissue stroma. A case of primary intraosseous squamous cell carcinoma of mandible arising de novo in a 40-year-old man is reported.

  3. De novo and salvage pathway precursor incorporation during DNA replication at the nuclear matrix

    International Nuclear Information System (INIS)

    Panzeter, P.L.

    1988-01-01

    Total nuclear DNA can be empirically subdivided into low salt-soluble (LS) DNA (75-80%), high salt-soluble (HS) DNA (18-23%), and nuclear matrix-associated (NM) DNA which remains tightly bound to the nuclear matrix (∼2%). The most-newly replicated DNA is that associated with the nuclear matrix in regenerating rat liver. Analyses of the DNA fractions after various pulse times revealed that the salvage and de novo pathway DNA precursors investigated were incorporated preferentially into NM-DNA at early pulse times, after which the radioactivity became progressively incorporated into HS- and LS-DNA, respectively. These results support two models of nuclear matrix-associated DNA replication, proposed previously, and a third model presented in this dissertation. In addition, the incorporation of de novo pathway precursors lagged significantly (> 10 minutes) behind the incorporation of precursors entering through the salvage pathway. Channeling of salvage pathway precursors to DNA replication sites would explain the more rapid uptake of salvage precursors into NM-DNA than de novo precursors. To investigate the possibility of this heretofore in vitro phenomenon, the incorporation of the salvage precursor, ( 3 H)deoxythymidine, and the de novo precursor, ( 14 C)orotic acid, into NM-DNA and dTTP was examined in regenerating rat liver. There was no significant difference between the incorporation pattern of ( 14 C)orotic acid into NM-DNA thymine and that of ( 14 C)orotic acid into soluble dTTP. Contrastingly, the salvage pathway precursor, ( 3 H)deoxythymidine, labeled NM-DNA before labeling the dTTP pool

  4. De novo complex intra chromosomal rearrangement after ICSI: characterisation by BACs micro array-CGH

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    Quimsiyeh Mazin

    2008-12-01

    Full Text Available Abstract Background In routine Assisted Reproductive Technology (ART men with severe oligozoospermia or azoospermia should be informed about the risk of de novo congenital or chromosomal abnormalities in ICSI program. Also the benefits of preimplantation or prenatal genetic diagnosis practice need to be explained to the couple. Methods From a routine ICSI attempt, using ejaculated sperm from male with severe oligozoospermia and having normal karyotype, a 30 years old pregnant woman was referred to prenatal diagnosis in the 17th week for bichorionic biamniotic twin gestation. Amniocentesis was performed because of the detection of an increased foetal nuchal translucency for one of the fetus by the sonographic examination during the 12th week of gestation (WG. Chromosome and DNA studies of the fetus were realized on cultured amniocytes Results Conventional, molecular cytogenetic and microarray CGH experiments allowed us to conclude that the fetus had a de novo pericentromeric inversion associated with a duplication of the 9p22.1-p24 chromosomal region, 46,XY,invdup(9(p22.1p24 [arrCGH 9p22.1p24 (RP11-130C19 → RP11-87O1x3]. As containing the critical 9p22 region, our case is in coincidence with the general phenotype features of the partial trisomy 9p syndrome with major growth retardation, microcephaly and microretrognathia. Conclusion This de novo complex chromosome rearrangement illustrates the possible risk of chromosome or gene defects in ICSI program and the contribution of array-CGH for mapping rapidly de novo chromosomal imbalance.

  5. Uridine monophosphate synthetase enables eukaryotic de novo NAD+ biosynthesis from quinolinic acid.

    Science.gov (United States)

    McReynolds, Melanie R; Wang, Wenqing; Holleran, Lauren M; Hanna-Rose, Wendy

    2017-07-07

    NAD + biosynthesis is an attractive and promising therapeutic target for influencing health span and obesity-related phenotypes as well as tumor growth. Full and effective use of this target for therapeutic benefit requires a complete understanding of NAD + biosynthetic pathways. Here, we report a previously unrecognized role for a conserved phosphoribosyltransferase in NAD + biosynthesis. Because a required quinolinic acid phosphoribosyltransferase (QPRTase) is not encoded in its genome, Caenorhabditis elegans are reported to lack a de novo NAD + biosynthetic pathway. However, all the genes of the kynurenine pathway required for quinolinic acid (QA) production from tryptophan are present. Thus, we investigated the presence of de novo NAD + biosynthesis in this organism. By combining isotope-tracing and genetic experiments, we have demonstrated the presence of an intact de novo biosynthesis pathway for NAD + from tryptophan via QA, highlighting the functional conservation of this important biosynthetic activity. Supplementation with kynurenine pathway intermediates also boosted NAD + levels and partially reversed NAD + -dependent phenotypes caused by mutation of pnc-1 , which encodes a nicotinamidase required for NAD + salvage biosynthesis, demonstrating contribution of de novo synthesis to NAD + homeostasis. By investigating candidate phosphoribosyltransferase genes in the genome, we determined that the conserved uridine monophosphate phosphoribosyltransferase (UMPS), which acts in pyrimidine biosynthesis, is required for NAD + biosynthesis in place of the missing QPRTase. We suggest that similar underground metabolic activity of UMPS may function in other organisms. This mechanism for NAD + biosynthesis creates novel possibilities for manipulating NAD + biosynthetic pathways, which is key for the future of therapeutics. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  6. Predicting survival of de novo metastatic breast cancer in Asian women: systematic review and validation study.

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    Hui Miao

    Full Text Available BACKGROUND: In Asia, up to 25% of breast cancer patients present with distant metastases at diagnosis. Given the heterogeneous survival probabilities of de novo metastatic breast cancer, individual outcome prediction is challenging. The aim of the study is to identify existing prognostic models for patients with de novo metastatic breast cancer and validate them in Asia. MATERIALS AND METHODS: We performed a systematic review to identify prediction models for metastatic breast cancer. Models were validated in 642 women with de novo metastatic breast cancer registered between 2000 and 2010 in the Singapore Malaysia Hospital Based Breast Cancer Registry. Survival curves for low, intermediate and high-risk groups according to each prognostic score were compared by log-rank test and discrimination of the models was assessed by concordance statistic (C-statistic. RESULTS: We identified 16 prediction models, seven of which were for patients with brain metastases only. Performance status, estrogen receptor status, metastatic site(s and disease-free interval were the most common predictors. We were able to validate nine prediction models. The capacity of the models to discriminate between poor and good survivors varied from poor to fair with C-statistics ranging from 0.50 (95% CI, 0.48-0.53 to 0.63 (95% CI, 0.60-0.66. CONCLUSION: The discriminatory performance of existing prediction models for de novo metastatic breast cancer in Asia is modest. Development of an Asian-specific prediction model is needed to improve prognostication and guide decision making.

  7. De novo assembly of human genomes with massively parallel short read sequencing

    DEFF Research Database (Denmark)

    Li, Ruiqiang; Zhu, Hongmei; Ruan, Jue

    2010-01-01

    genomes from short read sequences. We successfully assembled both the Asian and African human genome sequences, achieving an N50 contig size of 7.4 and 5.9 kilobases (kb) and scaffold of 446.3 and 61.9 kb, respectively. The development of this de novo short read assembly method creates new opportunities...... for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost-effective way....

  8. JTP-103237, a monoacylglycerol acyltransferase inhibitor, prevents fatty liver and suppresses both triglyceride synthesis and de novo lipogenesis

    Directory of Open Access Journals (Sweden)

    Chihiro Okuma

    2015-07-01

    Conclusion: In the present study, JTP-103237 prevented carbohydrate-induced fatty liver and suppressed both TG synthesis and de novo lipogenesis, suggesting MGAT inhibitor may prevent carbohydrate-induced metabolic disorders, including NAFLD, obesity and diabetes.

  9. Axonal regeneration and development of de novo axons from distal dendrites of adult feline commissural interneurons after a proximal axotomy

    DEFF Research Database (Denmark)

    Fenrich, Keith K; Skelton, Nicole; MacDermid, Victoria E

    2007-01-01

    Following proximal axotomy, several types of neurons sprout de novo axons from distal dendrites. These processes may represent a means of forming new circuits following spinal cord injury. However, it is not know whether mammalian spinal interneurons, axotomized as a result of a spinal cord injury......, develop de novo axons. Our goal was to determine whether spinal commissural interneurons (CINs), axotomized by 3-4-mm midsagittal transection at C3, form de novo axons from distal dendrites. All experiments were performed on adult cats. CINs in C3 were stained with extracellular injections of Neurobiotin...... at 4-5 weeks post injury. The somata of axotomized CINs were identified by the presence of immunoreactivity for the axonal growth-associated protein-43 (GAP-43). Nearly half of the CINs had de novo axons that emerged from distal dendrites. These axons lacked immunoreactivity for the dendritic protein...

  10. Building a Better Fragment Library for De Novo Protein Structure Prediction

    Science.gov (United States)

    de Oliveira, Saulo H. P.; Shi, Jiye; Deane, Charlotte M.

    2015-01-01

    Fragment-based approaches are the current standard for de novo protein structure prediction. These approaches rely on accurate and reliable fragment libraries to generate good structural models. In this work, we describe a novel method for structure fragment library generation and its application in fragment-based de novo protein structure prediction. The importance of correct testing procedures in assessing the quality of fragment libraries is demonstrated. In particular, the exclusion of homologs to the target from the libraries to correctly simulate a de novo protein structure prediction scenario, something which surprisingly is not always done. We demonstrate that fragments presenting different predominant predicted secondary structures should be treated differently during the fragment library generation step and that exhaustive and random search strategies should both be used. This information was used to develop a novel method, Flib. On a validation set of 41 structurally diverse proteins, Flib libraries presents both a higher precision and coverage than two of the state-of-the-art methods, NNMake and HHFrag. Flib also achieves better precision and coverage on the set of 275 protein domains used in the two previous experiments of the the Critical Assessment of Structure Prediction (CASP9 and CASP10). We compared Flib libraries against NNMake libraries in a structure prediction context. Of the 13 cases in which a correct answer was generated, Flib models were more accurate than NNMake models for 10. “Flib is available for download at: http://www.stats.ox.ac.uk/research/proteins/resources”. PMID:25901595

  11. De novo assembly of plant body plan: a step ahead of Deadpool.

    Science.gov (United States)

    Kareem, Abdul; Radhakrishnan, Dhanya; Sondhi, Yash; Aiyaz, Mohammed; Roy, Merin V; Sugimoto, Kaoru; Prasad, Kalika

    2016-08-01

    While in the movie Deadpool it is possible for a human to recreate an arm from scratch, in reality plants can even surpass that. Not only can they regenerate lost parts, but also the whole plant body can be reborn from a few existing cells. Despite the decades old realization that plant cells possess the ability to regenerate a complete shoot and root system, it is only now that the underlying mechanisms are being unraveled. De novo plant regeneration involves the initiation of regenerative mass, acquisition of the pluripotent state, reconstitution of stem cells and assembly of regulatory interactions. Recent studies have furthered our understanding on the making of a complete plant system in the absence of embryonic positional cues. We review the recent studies probing the molecular mechanisms of de novo plant regeneration in response to external inductive cues and our current knowledge of direct reprogramming of root to shoot and vice versa. We further discuss how de novo regeneration can be exploited to meet the demands of green culture industries and to serve as a general model to address the fundamental questions of regeneration across the plant kingdom.

  12. A rice gene of de novo origin negatively regulates pathogen-induced defense response.

    Directory of Open Access Journals (Sweden)

    Wenfei Xiao

    Full Text Available How defense genes originated with the evolution of their specific pathogen-responsive traits remains an important problem. It is generally known that a form of duplication can generate new genes, suggesting that a new gene usually evolves from an ancestral gene. However, we show that a new defense gene in plants may evolve by de novo origination, resulting in sophisticated disease-resistant functions in rice. Analyses of gene evolution showed that this new gene, OsDR10, had homologs only in the closest relative, Leersia genus, but not other subfamilies of the grass family; therefore, it is a rice tribe-specific gene that may have originated de novo in the tribe. We further show that this gene may evolve a highly conservative rice-specific function that contributes to the regulation difference between rice and other plant species in response to pathogen infections. Biologic analyses including gene silencing, pathologic analysis, and mutant characterization by transformation showed that the OsDR10-suppressed plants enhanced resistance to a broad spectrum of Xanthomonas oryzae pv. oryzae strains, which cause bacterial blight disease. This enhanced disease resistance was accompanied by increased accumulation of endogenous salicylic acid (SA and suppressed accumulation of endogenous jasmonic acid (JA as well as modified expression of a subset of defense-responsive genes functioning both upstream and downstream of SA and JA. These data and analyses provide fresh insights into the new biologic and evolutionary processes of a de novo gene recruited rapidly.

  13. De novo point mutations in patients diagnosed with ataxic cerebral palsy.

    Science.gov (United States)

    Parolin Schnekenberg, Ricardo; Perkins, Emma M; Miller, Jack W; Davies, Wayne I L; D'Adamo, Maria Cristina; Pessia, Mauro; Fawcett, Katherine A; Sims, David; Gillard, Elodie; Hudspith, Karl; Skehel, Paul; Williams, Jonathan; O'Regan, Mary; Jayawant, Sandeep; Jefferson, Rosalind; Hughes, Sarah; Lustenberger, Andrea; Ragoussis, Jiannis; Jackson, Mandy; Tucker, Stephen J; Németh, Andrea H

    2015-07-01

    Cerebral palsy is a sporadic disorder with multiple likely aetiologies, but frequently considered to be caused by birth asphyxia. Genetic investigations are rarely performed in patients with cerebral palsy and there is little proven evidence of genetic causes. As part of a large project investigating children with ataxia, we identified four patients in our cohort with a diagnosis of ataxic cerebral palsy. They were investigated using either targeted next generation sequencing or trio-based exome sequencing and were found to have mutations in three different genes, KCNC3, ITPR1 and SPTBN2. All the mutations were de novo and associated with increased paternal age. The mutations were shown to be pathogenic using a combination of bioinformatics analysis and in vitro model systems. This work is the first to report that the ataxic subtype of cerebral palsy can be caused by de novo dominant point mutations, which explains the sporadic nature of these cases. We conclude that at least some subtypes of cerebral palsy may be caused by de novo genetic mutations and patients with a clinical diagnosis of cerebral palsy should be genetically investigated before causation is ascribed to perinatal asphyxia or other aetiologies. © The Author (2015). Published by Oxford University Press on behalf of the Guarantors of Brain.

  14. Norgal: extraction and de novo assembly of mitochondrial DNA from whole-genome sequencing data.

    Science.gov (United States)

    Al-Nakeeb, Kosai; Petersen, Thomas Nordahl; Sicheritz-Pontén, Thomas

    2017-11-21

    Whole-genome sequencing (WGS) projects provide short read nucleotide sequences from nuclear and possibly organelle DNA depending on the source of origin. Mitochondrial DNA is present in animals and fungi, while plants contain DNA from both mitochondria and chloroplasts. Current techniques for separating organelle reads from nuclear reads in WGS data require full reference or partial seed sequences for assembling. Norgal (de Novo ORGAneLle extractor) avoids this requirement by identifying a high frequency subset of k-mers that are predominantly of mitochondrial origin and performing a de novo assembly on a subset of reads that contains these k-mers. The method was applied to WGS data from a panda, brown algae seaweed, butterfly and filamentous fungus. We were able to extract full circular mitochondrial genomes and obtained sequence identities to the reference sequences in the range from 98.5 to 99.5%. We also assembled the chloroplasts of grape vines and cucumbers using Norgal together with seed-based de novo assemblers. Norgal is a pipeline that can extract and assemble full or partial mitochondrial and chloroplast genomes from WGS short reads without prior knowledge. The program is available at: https://bitbucket.org/kosaidtu/norgal .

  15. Autism Spectrum Disorder in a Girl with a De Novo X;19 Balanced Translocation

    Science.gov (United States)

    Baruffi, Marcelo Razera; de Souza, Deise Helena; Bicudo da Silva, Rosana Aparecida; Ramos, Ester Silveira; Moretti-Ferreira, Danilo

    2012-01-01

    Balanced X-autosome translocations are rare, and female carriers are a clinically heterogeneous group of patients, with phenotypically normal women, history of recurrent miscarriage, gonadal dysfunction, X-linked disorders or congenital abnormalities, and/or developmental delay. We investigated a patient with a de novo X;19 translocation. The six-year-old girl has been evaluated due to hyperactivity, social interaction impairment, stereotypic and repetitive use of language with echolalia, failure to follow parents/caretakers orders, inconsolable outbursts, and persistent preoccupation with parts of objects. The girl has normal cognitive function. Her measurements are within normal range, and no other abnormalities were found during physical, neurological, or dysmorphological examinations. Conventional cytogenetic analysis showed a de novo balanced translocation, with the karyotype 46,X,t(X;19)(p21.2;q13.4). Replication banding showed a clear preference for inactivation of the normal X chromosome. The translocation was confirmed by FISH and Spectral Karyotyping (SKY). Although abnormal phenotypes associated with de novo balanced chromosomal rearrangements may be the result of disruption of a gene at one of the breakpoints, submicroscopic deletion or duplication, or a position effect, X; autosomal translocations are associated with additional unique risk factors including X-linked disorders, functional autosomal monosomy, or functional X chromosome disomy resulting from the complex X-inactivation process. PMID:23074688

  16. Autism Spectrum Disorder in a Girl with a De Novo X;19 Balanced Translocation

    Directory of Open Access Journals (Sweden)

    Marcelo Razera Baruffi

    2012-01-01

    Full Text Available Balanced X-autosome translocations are rare, and female carriers are a clinically heterogeneous group of patients, with phenotypically normal women, history of recurrent miscarriage, gonadal dysfunction, X-linked disorders or congenital abnormalities, and/or developmental delay. We investigated a patient with a de novo X;19 translocation. The six-year-old girl has been evaluated due to hyperactivity, social interaction impairment, stereotypic and repetitive use of language with echolalia, failure to follow parents/caretakers orders, inconsolable outbursts, and persistent preoccupation with parts of objects. The girl has normal cognitive function. Her measurements are within normal range, and no other abnormalities were found during physical, neurological, or dysmorphological examinations. Conventional cytogenetic analysis showed a de novo balanced translocation, with the karyotype 46,X,t(X;19(p21.2;q13.4. Replication banding showed a clear preference for inactivation of the normal X chromosome. The translocation was confirmed by FISH and Spectral Karyotyping (SKY. Although abnormal phenotypes associated with de novo balanced chromosomal rearrangements may be the result of disruption of a gene at one of the breakpoints, submicroscopic deletion or duplication, or a position effect, X; autosomal translocations are associated with additional unique risk factors including X-linked disorders, functional autosomal monosomy, or functional X chromosome disomy resulting from the complex X-inactivation process.

  17. Resveratrol induces growth inhibition and apoptosis in metastatic breast cancer cells via de novo ceramide signaling.

    Science.gov (United States)

    Scarlatti, Francesca; Sala, Giusy; Somenzi, Giulia; Signorelli, Paola; Sacchi, Nicoletta; Ghidoni, Riccardo

    2003-12-01

    Resveratrol (3,4',5-trans-trihydroxystilbene), a phytoalexin present in grapes and red wine, is emerging as a natural compound with potential anticancer properties. Here we show that resveratrol can induce growth inhibition and apoptosis in MDA-MB-231, a highly invasive and metastatic breast cancer cell line, in concomitance with a dramatic endogenous increase of growth inhibitory/proapoptotic ceramide. We found that accumulation of ceramide derives from both de novo ceramide synthesis and sphingomyelin hydrolysis. More specifically we demonstrated that ceramide accumulation induced by resveratrol can be traced to the activation of serine palmitoyltransferase (SPT), the key enzyme of de novo ceramide biosynthetic pathway, and neutral sphingomyelinase (nSMase), a main enzyme involved in the sphingomyelin/ceramide pathway. However, by using specific inhibitors of SPT, myriocin and L-cycloserine, and nSMase, gluthatione and manumycin, we found that only the SPT inhibitors could counteract the biological effects induced by resveratrol. Thus, resveratrol seems to exert its growth inhibitory/apoptotic effect on the metastatic breast cancer cell line MDA-MB-231 by activating the de novo ceramide synthesis pathway.

  18. Building a better fragment library for de novo protein structure prediction.

    Directory of Open Access Journals (Sweden)

    Saulo H P de Oliveira

    Full Text Available Fragment-based approaches are the current standard for de novo protein structure prediction. These approaches rely on accurate and reliable fragment libraries to generate good structural models. In this work, we describe a novel method for structure fragment library generation and its application in fragment-based de novo protein structure prediction. The importance of correct testing procedures in assessing the quality of fragment libraries is demonstrated. In particular, the exclusion of homologs to the target from the libraries to correctly simulate a de novo protein structure prediction scenario, something which surprisingly is not always done. We demonstrate that fragments presenting different predominant predicted secondary structures should be treated differently during the fragment library generation step and that exhaustive and random search strategies should both be used. This information was used to develop a novel method, Flib. On a validation set of 41 structurally diverse proteins, Flib libraries presents both a higher precision and coverage than two of the state-of-the-art methods, NNMake and HHFrag. Flib also achieves better precision and coverage on the set of 275 protein domains used in the two previous experiments of the the Critical Assessment of Structure Prediction (CASP9 and CASP10. We compared Flib libraries against NNMake libraries in a structure prediction context. Of the 13 cases in which a correct answer was generated, Flib models were more accurate than NNMake models for 10. "Flib is available for download at: http://www.stats.ox.ac.uk/research/proteins/resources".

  19. De novo and inherited private variants in MAP1B in periventricular nodular heterotopia.

    Science.gov (United States)

    Heinzen, Erin L; O'Neill, Adam C; Zhu, Xiaolin; Allen, Andrew S; Bahlo, Melanie; Chelly, Jamel; Dobyns, William B; Freytag, Saskia; Guerrini, Renzo; Leventer, Richard J; Poduri, Annapurna; Robertson, Stephen P; Walsh, Christopher A; Zhang, Mengqi

    2018-05-08

    Periventricular nodular heterotopia (PVNH) is a malformation of cortical development commonly associated with epilepsy. We exome sequenced 202 individuals with sporadic PVNH to identify novel genetic risk loci. We first performed a trio-based analysis and identified 219 de novo variants. Although no novel genes were implicated in this initial analysis, PVNH cases were found overall to have a significant excess of nonsynonymous de novo variants in intolerant genes (p = 3.27x10-7), suggesting a role for rare new alleles in genes yet to be associated with the condition. Using a gene-level collapsing analysis comparing cases and controls, we identified a genome-wide significant signal driven by four ultra-rare loss-of-function heterozygous variants in MAP1B, including one de novo variant. In at least one instance, the MAP1B variant was inherited from a parent with previously undiagnosed PVNH. The PVNH was frontally predominant and associated with perisylvian polymicrogyria. These results implicate MAP1B in PVNH. More broadly, our findings suggest that detrimental mutations likely arising in immediately preceding generations with incomplete penetrance may also be responsible for some apparently sporadic diseases.

  20. De novo FGF12 mutation in 2 patients with neonatal-onset epilepsy

    Science.gov (United States)

    Guella, Ilaria; Huh, Linda; McKenzie, Marna B.; Toyota, Eric B.; Bebin, E. Martina; Thompson, Michelle L.; Cooper, Gregory M.; Evans, Daniel M.; Buerki, Sarah E.; Adam, Shelin; Van Allen, Margot I.; Nelson, Tanya N.; Connolly, Mary B.; Farrer, Matthew J.

    2016-01-01

    Objective: We describe 2 additional patients with early-onset epilepsy with a de novo FGF12 mutation. Methods: Whole-exome sequencing was performed in 2 unrelated patients with early-onset epilepsy and their unaffected parents. Genetic variants were assessed by comparative trio analysis. Clinical evolution, EEG, and neuroimaging are described. The phenotype and response to treatment was reviewed and compared to affected siblings in the original report. Results: We identified the same FGF12 de novo mutation reported previously (c.G155A, p.R52H) in 2 additional patients with early-onset epilepsy. Similar to the original brothers described, both presented with tonic seizures in the first month of life. In the first patient, seizures responded to sodium channel blockers and her development was normal at 11 months. Patient 2 is a 15-year-old girl with treatment-resistant focal epilepsy, moderate intellectual disability, and autism. Carbamazepine (sodium channel blocker) was tried later in her course but not continued due to an allergic reaction. Conclusions: The identification of a recurrent de novo mutation in 2 additional unrelated probands with early-onset epilepsy supports the role of FGF12 p.R52H in disease pathogenesis. Affected carriers presented with similar early clinical phenotypes; however, this report expands the phenotype associated with this mutation which contrasts with the progressive course and early mortality of the siblings in the original report. PMID:27872899

  1. Modeling fructose-load-induced hepatic de-novo lipogenesis by model simplification

    Directory of Open Access Journals (Sweden)

    Richard J Allen

    2017-03-01

    Full Text Available Hepatic de-novo lipogenesis is a metabolic process implemented in the pathogenesis of type 2 diabetes. Clinically, the rate of this process can be ascertained by use of labeled acetate and stimulation by fructose administration. A systems pharmacology model of this process is desirable because it facilitates the description, analysis, and prediction of this experiment. Due to the multiple enzymes involved in de-novo lipogenesis, and the limited data, it is desirable to use single functional expressions to encapsulate the flux between multiple enzymes. To accomplish this we developed a novel simplification technique which uses the available information about the properties of the individual enzymes to bound the parameters of a single governing ‘transfer function’. This method should be applicable to any model with linear chains of enzymes that are well stimulated. We validated this approach with computational simulations and analytical justification in a limiting case. Using this technique we generated a simple model of hepatic de-novo lipogenesis in these experimental conditions that matched prior data. This model can be used to assess pharmacological intervention at specific points on this pathway. We have demonstrated this with prospective simulation of acetyl-CoA carboxylase inhibition. This simplification technique suggests how the constituent properties of an enzymatic chain of reactions gives rise to the sensitivity (to substrate of the pathway as a whole.

  2. Modeling fructose-load-induced hepatic de-novo lipogenesis by model simplification.

    Science.gov (United States)

    Allen, Richard J; Musante, Cynthia J

    2017-01-01

    Hepatic de-novo lipogenesis is a metabolic process implemented in the pathogenesis of type 2 diabetes. Clinically, the rate of this process can be ascertained by use of labeled acetate and stimulation by fructose administration. A systems pharmacology model of this process is desirable because it facilitates the description, analysis, and prediction of this experiment. Due to the multiple enzymes involved in de-novo lipogenesis, and the limited data, it is desirable to use single functional expressions to encapsulate the flux between multiple enzymes. To accomplish this we developed a novel simplification technique which uses the available information about the properties of the individual enzymes to bound the parameters of a single governing 'transfer function'. This method should be applicable to any model with linear chains of enzymes that are well stimulated. We validated this approach with computational simulations and analytical justification in a limiting case. Using this technique we generated a simple model of hepatic de-novo lipogenesis in these experimental conditions that matched prior data. This model can be used to assess pharmacological intervention at specific points on this pathway. We have demonstrated this with prospective simulation of acetyl-CoA carboxylase inhibition. This simplification technique suggests how the constituent properties of an enzymatic chain of reactions gives rise to the sensitivity (to substrate) of the pathway as a whole.

  3. De novo mutation in the dopamine transporter gene associates dopamine dysfunction with autism spectrum disorder.

    Science.gov (United States)

    Hamilton, P J; Campbell, N G; Sharma, S; Erreger, K; Herborg Hansen, F; Saunders, C; Belovich, A N; Sahai, M A; Cook, E H; Gether, U; McHaourab, H S; Matthies, H J G; Sutcliffe, J S; Galli, A

    2013-12-01

    De novo genetic variation is an important class of risk factors for autism spectrum disorder (ASD). Recently, whole-exome sequencing of ASD families has identified a novel de novo missense mutation in the human dopamine (DA) transporter (hDAT) gene, which results in a Thr to Met substitution at site 356 (hDAT T356M). The dopamine transporter (DAT) is a presynaptic membrane protein that regulates dopaminergic tone in the central nervous system by mediating the high-affinity reuptake of synaptically released DA, making it a crucial regulator of DA homeostasis. Here, we report the first functional, structural and behavioral characterization of an ASD-associated de novo mutation in the hDAT. We demonstrate that the hDAT T356M displays anomalous function, characterized as a persistent reverse transport of DA (substrate efflux). Importantly, in the bacterial homolog leucine transporter, substitution of A289 (the homologous site to T356) with a Met promotes an outward-facing conformation upon substrate binding. In the substrate-bound state, an outward-facing transporter conformation is required for substrate efflux. In Drosophila melanogaster, the expression of hDAT T356M in DA neurons-lacking Drosophila DAT leads to hyperlocomotion, a trait associated with DA dysfunction and ASD. Taken together, our findings demonstrate that alterations in DA homeostasis, mediated by aberrant DAT function, may confer risk for ASD and related neuropsychiatric conditions.

  4. De novo and rare inherited copy-number variations in the hemiplegic form of cerebral palsy.

    Science.gov (United States)

    Zarrei, Mehdi; Fehlings, Darcy L; Mawjee, Karizma; Switzer, Lauren; Thiruvahindrapuram, Bhooma; Walker, Susan; Merico, Daniele; Casallo, Guillermo; Uddin, Mohammed; MacDonald, Jeffrey R; Gazzellone, Matthew J; Higginbotham, Edward J; Campbell, Craig; deVeber, Gabrielle; Frid, Pam; Gorter, Jan Willem; Hunt, Carolyn; Kawamura, Anne; Kim, Marie; McCormick, Anna; Mesterman, Ronit; Samdup, Dawa; Marshall, Christian R; Stavropoulos, Dimitri J; Wintle, Richard F; Scherer, Stephen W

    2018-02-01

    PurposeHemiplegia is a subtype of cerebral palsy (CP) in which one side of the body is affected. Our earlier study of unselected children with CP demonstrated de novo and clinically relevant rare inherited genomic copy-number variations (CNVs) in 9.6% of participants. Here, we examined the prevalence and types of CNVs specifically in hemiplegic CP.MethodsWe genotyped 97 unrelated probands with hemiplegic CP and their parents. We compared their CNVs to those of 10,851 population controls, in order to identify rare CNVs (<0.1% frequency) that might be relevant to CP. We also sequenced exomes of "CNV-positive" trios.ResultsWe detected de novo CNVs and/or sex chromosome abnormalities in 7/97 (7.2%) of probands, impacting important developmental genes such as GRIK2, LAMA1, DMD, PTPRM, and DIP2C. In 18/97 individuals (18.6%), rare inherited CNVs were found, affecting loci associated with known genomic disorders (17p12, 22q11.21) or involving genes linked to neurodevelopmental disorders.ConclusionWe found an increased rate of de novo CNVs in the hemiplegic CP subtype (7.2%) compared to controls (1%). This result is similar to that for an unselected CP group. Combined with rare inherited CNVs, the genomic data impacts the understanding of the potential etiology of hemiplegic CP in 23/97 (23.7%) of participants.

  5. Use of transient elastography to predict de novo recurrence after radiofrequency ablation for hepatocellular carcinoma.

    Science.gov (United States)

    Lee, Sang Hoon; Kim, Seung Up; Jang, Jeong Won; Bae, Si Hyun; Lee, Sanghun; Kim, Beom Kyung; Park, Jun Yong; Kim, Do Young; Ahn, Sang Hoon; Han, Kwang-Hyub

    2015-01-01

    Liver stiffness (LS) measurement using transient elastography can accurately assess the degree of liver fibrosis, which is associated with the risk of the development of hepatocellular carcinoma (HCC). We investigated whether LS values could predict HCC de novo recurrence after radiofrequency ablation (RFA). This retrospective, multicenter study analyzed 111 patients with HCC who underwent RFA and LS measurement using transient elastography between May 2005 and April 2011. All patients were followed until March 2013 to monitor for HCC recurrence. This study included 76 men and 35 women with a mean age of 62.4 years, and the mean LS value was 21.2 kPa. During the follow-up period (median 22.4 months), 47 (42.3%) patients experienced HCC de novo recurrence, and 18 (16.2%) died. Patients with recurrence had significantly more frequent liver cirrhosis, more frequent history of previous treatment for HCC, higher total bilirubin, larger spleen size, larger total tumor size, higher tumor number, higher LS values, and lower platelet counts than those without recurrence (all P13.0 kPa were at significantly greater risk for recurrence after RFA, with a hazard ratio (HR) of 3.115 (95% confidence interval [CI], 1.238-7.842, Pmeasurement is a useful predictor of HCC de novo recurrence and overall survival after RFA.

  6. Cognitive impairment is associated with Hoehn and Yahr stages in early, de novo Parkinson disease patients.

    Science.gov (United States)

    Siciliano, Mattia; De Micco, Rosa; Trojano, Luigi; De Stefano, Manuela; Baiano, Chiara; Passaniti, Carla; De Mase, Antonio; Russo, Antonio; Tedeschi, Gioacchino; Tessitore, Alessandro

    2017-08-01

    The relationship between motor impairment and cognitive deterioration has long been described in Parkinson's disease (PD). The aim of the study was to compare cognitive performance of de novo PD patients in relation to the motor impairment severity according to Hoehn and Yahr (HY) stages. Forty de novo PD patients at HY stage I and 40 patients at HY stage II completed a standardized neuropsychological battery. A multivariate analysis of covariance was used to compare cognitive performance between HY groups. Odds ratios (ORs) were employed to explore the risk of cognitive impairment between HY stages. Finally, the prevalence of mild cognitive impairment (MCI) was estimated for patients in HY stage I and II. Patients at HY stage I obtained better scores on neuropsychological tests than patients at HY stage II (p = 0.001). Univariate analysis of covariance revealed significant differences between HY stages on Rey's auditory verbal learning test -immediate recall (p cognitive impairment were greater for HY stage II than stage I group. MCI occurred in 7.5% of patients in HY stage I, and in 42.5% of patients in HY stage II. In de novo PD patients, the severity of motor impairment at the diagnosis is associated to cognitive deficits and higher risk of MCI. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. De novo-based transcriptome profiling of male-sterile and fertile watermelon lines.

    Science.gov (United States)

    Rhee, Sun-Ju; Kwon, Taehyung; Seo, Minseok; Jang, Yoon Jeong; Sim, Tae Yong; Cho, Seoae; Han, Sang-Wook; Lee, Gung Pyo

    2017-01-01

    The whole-genome sequence of watermelon (Citrullus lanatus (Thunb.) Matsum. & Nakai), a valuable horticultural crop worldwide, was released in 2013. Here, we compared a de novo-based approach (DBA) to a reference-based approach (RBA) using RNA-seq data, to aid in efforts to improve the annotation of the watermelon reference genome and to obtain biological insight into male-sterility in watermelon. We applied these techniques to available data from two watermelon lines: the male-sterile line DAH3615-MS and the male-fertile line DAH3615. Using DBA, we newly annotated 855 watermelon transcripts, and found gene functional clusters predicted to be related to stimulus responses, nucleic acid binding, transmembrane transport, homeostasis, and Golgi/vesicles. Among the DBA-annotated transcripts, 138 de novo-exclusive differentially-expressed genes (DEDEGs) related to male sterility were detected. Out of 33 randomly selected newly annotated transcripts and DEDEGs, 32 were validated by RT-qPCR. This study demonstrates the usefulness and reliability of the de novo transcriptome assembly in watermelon, and provides new insights for researchers exploring transcriptional blueprints with regard to the male sterility.

  8. Photoreactivation of conversion and de novo suppressor mutation in Escherichia coli

    Energy Technology Data Exchange (ETDEWEB)

    Bockrath, R C; Plamer, J E [Indiana Univ., Indianapolis (USA). Dept. of Microbiology

    1977-04-01

    Studies of mutagenesis and photoreactivation in various E.coli strains have shown that conversion mutation of a mutant containing an amber suppressor to one containing an ochre suppressor is sensitive to photoreactivation. Direct photoreactivation by photoreactivating light (PRL) after uv mutagenesis reduced mutation frequencies by a factor of about 2 for each minute of exposure during the first 5 to 8 min of exposure for cells with normal repair capacity. Conversion and potential de novo suppressor mutations were about equally sensitive. For conversion, the sensitivities to PRL were identical in the repair-normal and excisions-repair-deficient strains. For de novo suppressor mutation, the rate of mutation frequency reduction by PRL in the repair-deficient strain was about one-half that in the other strains. The results suggest that ultraviolet radiation produces both de novo suppressor mutation and conversion at the sup(E,B) locus by photoreversible pyrimidine dimers in the DNA. The causative dimers could be Thy()Cyt dimers in the transcribed strand or the non-transcribed strand, respectively.

  9. Similar prognosis of transformed and de novo diffuse large B-cell lymphomas in patients treated with immunochemotherapy.

    Science.gov (United States)

    Sorigue, Marc; Garcia, Olga; Baptista, Maria Joao; Sancho, Juan-Manuel; Tapia, Gustavo; Mate, José Luis; Feliu, Evarist; Navarro, José-Tomás; Ribera, Josep-Maria

    2017-03-22

    The prognosis of diffuse large B-cell lymphomas (DLBCL) transformed from indolent lymphoma (TL) has been considered poorer than that of de novo DLBCL. However, it seems to have improved since the introduction of rituximab. We compared the characteristics (including the cell-of-origin), and the prognosis of 29 patients with TL and 101 with de novo DLBCL treated with immunochemotherapy. Patients with TL and de novo DLBCL had similar characteristics. All TL cases evolving from follicular lymphoma were germinal-center B-cell-like, while those TL from marginal zone lymphoma or chronic lymphocytic leukemia were non-germinal-center B-cell-like. The complete response rate was similar in TL and de novo DLBCL (62 vs. 66%, P=.825). The 5-year overall and progression-free survival probabilities (95% CI) were 59% (40-78) and 41% (22-60) for TL and 63% (53-73) and 60% (50-70) for de novo DLBCL, respectively (P=.732 for overall survival and P=.169 for progression-free survival). In this study, the prognosis of TL and de novo DLBCL treated with immunochemotherapy was similar. The role of intensification with stem cell transplantation in the management of TL may be questionable in the rituximab era. Copyright © 2016 Elsevier España, S.L.U. All rights reserved.

  10. An 11bp region with stem formation potential is essential for de novo DNA methylation of the RPS element.

    Directory of Open Access Journals (Sweden)

    Matthew Gentry

    Full Text Available The initiation of DNA methylation in Arabidopsis is controlled by the RNA-directed DNA methylation (RdDM pathway that uses 24nt siRNAs to recruit de novo methyltransferase DRM2 to the target site. We previously described the REPETITIVE PETUNIA SEQUENCE (RPS fragment that acts as a hot spot for de novo methylation, for which it requires the cooperative activity of all three methyltransferases MET1, CMT3 and DRM2, but not the RdDM pathway. RPS contains two identical 11nt elements in inverted orientation, interrupted by a 18nt spacer, which resembles the features of a stemloop structure. The analysis of deletion/substitution derivatives of this region showed that deletion of one 11nt element RPS is sufficient to eliminate de novo methylation of RPS. In addition, deletion of a 10nt region directly adjacent to one of the 11nt elements, significantly reduced de novo methylation. When both 11nt regions were replaced by two 11nt elements with altered DNA sequence but unchanged inverted repeat homology, DNA methylation was not affected, indicating that de novo methylation was not targeted to a specific DNA sequence element. These data suggest that de novo DNA methylation is attracted by a secondary structure to which the two 11nt elements contribute, and that the adjacent 10nt region influences the stability of this structure. This resembles the recognition of structural features by DNA methyltransferases in animals and suggests that similar mechanisms exist in plants.

  11. Heterologous aggregates promote de novo prion appearance via more than one mechanism.

    Directory of Open Access Journals (Sweden)

    Fatih Arslan

    2015-01-01

    Full Text Available Prions are self-perpetuating conformational variants of particular proteins. In yeast, prions cause heritable phenotypic traits. Most known yeast prions contain a glutamine (Q/asparagine (N-rich region in their prion domains. [PSI+], the prion form of Sup35, appears de novo at dramatically enhanced rates following transient overproduction of Sup35 in the presence of [PIN+], the prion form of Rnq1. Here, we establish the temporal de novo appearance of Sup35 aggregates during such overexpression in relation to other cellular proteins. Fluorescently-labeled Sup35 initially forms one or a few dots when overexpressed in [PIN+] cells. One of the dots is perivacuolar, colocalizes with the aggregated Rnq1 dot and grows into peripheral rings/lines, some of which also colocalize with Rnq1. Sup35 dots that are not near the vacuole do not always colocalize with Rnq1 and disappear by the time rings start to grow. Bimolecular fluorescence complementation failed to detect any interaction between Sup35-VN and Rnq1-VC in [PSI+][PIN+] cells. In contrast, all Sup35 aggregates, whether newly induced or in established [PSI+], completely colocalize with the molecular chaperones Hsp104, Sis1, Ssa1 and eukaryotic release factor Sup45. In the absence of [PIN+], overexpressed aggregating proteins such as the Q/N-rich Pin4C or the non-Q/N-rich Mod5 can also promote the de novo appearance of [PSI+]. Similar to Rnq1, overexpressed Pin4C transiently colocalizes with newly appearing Sup35 aggregates. However, no interaction was detected between Mod5 and Sup35 during [PSI+] induction in the absence of [PIN+]. While the colocalization of Sup35 and aggregates of Rnq1 or Pin4C are consistent with the model that the heterologous aggregates cross-seed the de novo appearance of [PSI+], the lack of interaction between Mod5 and Sup35 leaves open the possibility of other mechanisms. We also show that Hsp104 is required in the de novo appearance of [PSI+] aggregates in a [PIN

  12. Characterization of Substrates Elaborated with Organic Residues to Produce Forest Species Seedlings Caracterização de substratos para produção de mudas de espécies florestais elaborados a partir de resíduos orgânicos

    Directory of Open Access Journals (Sweden)

    Shizuo Maeda

    2010-06-01

    Full Text Available Considering the need for viable options for destination of waste from agricultural and agriindustries activities waste from logging and brewing industries and goat dregs previously composted, with potential for
    use as substrates for the production of seedlings of trees were characterized chemically and physically. The treatments had consisted of the following mixtures: S1 commercial product for substratum (Plantmax® Florestal + pinus bark partially decomposed - PB (1:1; S2 residue of malt with wooden sawdust - WS (1:4; S3 cellulosic
    mud with WS (1:1; S4 mixture of treatment S3 product with PB (1:1; S5 black-liquor with WS (4:1; S6 blackliquor with WS (3:2; S7 mixture of the product of treatment 6 with PB (1:1; S8 goat dregs. The following variable were evaluated: pH CaCl2; P, C, N, K, Ca, Mg, Al, H+Al and Na concentrations; CEC, Al saturation and C/N; total porosity, macroporosity, microporosity, density and available water. The substrates made with mixtures of Plantmax Florestal® + PB (1:1; residue of malt with wooden sawdust - WS (1:4; cellulosic mud with WS (1:1 mixed with PB (1:1 and goat dreg composted can be used in the production of seedlings of forest species tolerant to acidity, adopting the protocols of management recommended, both for irrigation as for fertilization.Considerando a necessidade de viabilizar opções de destinação de resíduos das atividades agropecuárias e agroindustriais, caracterizaram-se química e fisicamente resíduos das indústrias madeireira e cervejeira e da caprinocultura previamente compostados, com potencial para utilização como substratos para produção de mudas de espécies florestais. Foram avaliadas as seguintes  combinações (v:v: S1 substrato comercial (Plantmax Florestal® + casca de pínus parcialmente decomposta (CP (1:1; S2 bagaço de malte + serragem (1:4; S3 lodo celulósico + serragem (1:1; S4 composto do tratamento 3 + CP (1:1; S5 lixívia celulósica + serragem (4:1; S6

  13. Fauna de répteis dos remanescentes florestais e cultivos agrícolas da Fazenda Cambuhy, municípios de Matão, Nova Europa e Tabatinga, região Noroeste do estado de São Paulo

    Directory of Open Access Journals (Sweden)

    Ana Bárbara Barros

    2017-02-01

    Full Text Available http://dx.doi.org/10.5007/2175-7925.2017v30n1p79 A região Noroeste é a mais desmatada e com menor concentração de Unidades de Conservação do estado de São Paulo. Apesar dos avanços científicos recentes, ainda existem lacunas de conhecimento de herpetofauna. O presente estudo teve como objetivo fornecer informações sobre riqueza, abundância e uso do habitat dos répteis da Fazenda Cambuhy, que abrange os municípios de Matão, Nova Europa e Tabatinga. As amostragens ocorreram entre os anos de 2013 a 2015, utilizando-se quatro metodologias: armadilhas de interceptação e queda, procura visual limitada por tempo, procura em estradas e encontros ocasionais. Foram incluídos também os registros disponíveis em coleções científicas e na literatura. Foram registradas 46 espécies de répteis pertencentes aos grupos Squamata e Crocodylia. As espécies mais frequentes foram Salvator merianae (N = 55, espécie mais abundante em todos os ambientes amostrados, Notomabuya frenata (N = 14, amostrada somente nas florestas e Ameiva ameiva (N = 4, registrada nos ambientes antrópicos e florestais. A composição de espécies registrada reflete o posicionamento da área de estudo, apresentando a maioria das espécies associadas aos biomas Cerrado e Mata Atlântica. A riqueza de répteis da Fazenda Cambuhy representa 21% da riqueza de répteis do estado, sendo de grande significância para conservação da herpetofauna da região Noroeste do estado de São Paulo.

  14. NOVO SISTEMA DE SEMEADURA CONSERVACIONISTA MULTIFUNCIONAL PARA A AGRICULTURA FAMILIAR: NOVO DRAGÃO/ NEW CONSERVATIONIST SYSTEM SEEDING FOR SMALL FARMS WITH MULTIFUNCTIONAL NEW DRAGON

    Directory of Open Access Journals (Sweden)

    Daniel ALBIERO

    2010-11-01

    Full Text Available A agricultura familiar exerce papel importante na agricultura brasileira, sendo responsável por grande parcela da produção nacional de alimentos. No entanto não possui muitos equipamentos específicos para a semeadura. O objetivo principal deste trabalho foi o desenvolvimento e testes de um novo sistema de semeadura conservacionista para a agricultura familiar através de uma máquina multifuncional. Uma nova semeadora construída na filosofia de plantio em faixas com “Paraplow” Rotativo foi testada em campo em experimentos sob condições reais. Como resultado obteve-se um protótipo com bom desempenho na semeadura de soja, de fácil operação e manutenção, e principalmente adaptado às necessidades operacionais da agricultura familiar.Palavras-chaves: Sistema de semeadura, agricultura familiar, semedora multifuncional.

  15. Da família patriarcal à contemporânea. Entre o vellho e o novo: o surgimento dos novos arranjos familiares

    OpenAIRE

    Móas, Luciane da Costa

    2012-01-01

    O presente artigo propõe uma dupla abordagem da família levando em consideração o caráter socioantropológico e também histórico-evolutivo da legislação brasileira. Tem como objetivo interrogar a ideia de crise na ou da família em razão das mudanças verificadas em sua constituição: abandonou-se o modelo patriarcal, único existente no passado, que cedeu o passo aos modelos diversos, dos quais se originaram os novos arranjos familiares. O texto cuida da família como o fenômeno social que nos é m...

  16. "A poesia dos simples": arte popular e nação no Estado Novo "The poetry of the simple": popular art and nation in the Estado Novo

    Directory of Open Access Journals (Sweden)

    Vera Marques Alves

    2007-05-01

    Full Text Available Nos anos 30 e 40 do século XX, o Secretariado da Propaganda Nacional - órgão máximo da propaganda do regime de Salazar - desenvolveu um largo conjunto de iniciativas folcloristas que marcaram a memória crítica do Estado Novo. Este artigo sonda os limites de uma interpretação que reduz tal política a um instrumento de domesticação do povo, mostrando que é nos mecanismos de afirmação da nação, dentro e fora das fronteiras portuguesas, que podemos encontrar a explicação mais pertinente para a campanha etnográfica então empreendida. E é em função de tal proposta que abordaremos ainda os processos de manipulação e selecção dos materiais da cultura popular aí implicados, mostrando como, através dos mesmos, o SPN;/;SNI veiculou um retrato do país baseado na imagem do povo português enquanto camponês-esteta.In the 1930’ and 1940’ the Secretariado da Propaganda Nacional - the propaganda head office of Salazar’s dictatorship - promoted several folkloristic events, which became a core element of the Estado Novo current memory. This paper shows how the Secretariado‘s ethnographic campaign relates mostly with the politics of national identity building developed inside the Portuguese borders and in the international arena. In this context, I examine the selective approach to the folk culture materials evolved in those pratics. I also try to illuminate the ways by witch such materials were used to create a representation of the Portuguese folk as a people of artist-peasants, and of Portugal as a pacific and lovable country.

  17. Contrôle genético dos "frutos chochos" no Café "Mundo Novo" Manofactorial inheritance of "empty-locule" in the Mundo Novo coffee

    Directory of Open Access Journals (Sweden)

    A. J. T. Mendes

    1955-01-01

    Full Text Available 1. Decorre do presente trabalho que no Café Mundo Novo há dois grupos distintos de plantas : a de baixa ocorrência de frutos chochos; b de alta ocorrência de frutos chochos. 2. Há evidências de que a existência de 2 grupos distintos de plantas é devida a um par de fatores genéticos Dd. As plantas onde é baixa a ocorrência de frutos chochos são de constituição genética DD. As demais são Dd. Não há o grupo dd, pois que a combinação endosperma ddd e embrião dd é letal. 3. Segundo a hipótese, a letalidade dos fatores dd se manifesta quando o endosperma tem 2 a 3 mm de diâmetro; nesse ponto estaciona o crescimento e êle se transforma num disco (donde o símbolo d para o gen em questão. Raras vêzes a ação letal se manifesta antes dêsse estado e então nada ou quase nada resta do endosperma. Outras vezes a ação letal é tardia: o endosperma se desenvolve em semente mas esta não germina. 4. As populações de café Mundo Novo que estão se formando no Estado de São Paulo terão diferentes proporções de plantas com e sem o defeito das lojas vazias, dependendo isso da fonte onde se procurarem as sementes. 5. Limitando-se a selecionar as plantas Mundo Novo dentro do grupo de baixa ocorrência de chochos o melhorista encontra base científica para ehminar um notório defeito da variedade.It was shown in a recent paper that the occurrence of empty locules in coffee fruits of the variety Mundo Novo (Coffea arabica L. is due to an arrest in the endosperm development that takes place at a definite stage, leading to the formation of a small disc ; this rudimentary type of endosperm has been called "discoid endosperm". A suggestion was then made that this process might be controlled by genetic factors. Under this assumption, normal plants were DD; plants in which the defect occurred, Dd, and the homozygous, recessive form was lethal. The high correlation between discoid endosperm and empty locules permitted a clear

  18. CIPESC® Curitiba: o trabalho da enfermagem no Distrito Bairro Novo CIPESC® Curitiba: el trabajo de enfermería en el Districto Bairro Novo CIPESC® Curitiba: the work of nursing at Bairro Novo District

    Directory of Open Access Journals (Sweden)

    Denise Maria Altino

    2006-08-01

    Full Text Available Curitiba implantou em rede o sistema Classificação Internacional das Práticas de Enfermagem em Saúde Coletiva - CIPESC®. O presente estudo objetivou identificar as atividades exercidas pelos profissionais de enfermagem nas unidades de saúde do distrito Bairro Novo de Curitiba. Trata-se de uma pesquisa descritiva em que foram entrevistados auxiliares e enfermeiras utilizando-se de um check-list. Os resultados mostram que: o acolhimento é realizado por todos; as auxiliares se ocupam mais das atividades assistencial-procedimentais; a totalidade das enfermeiras realiza consulta de enfermagem diariamente, recorrendo ao prontuário eletrônico de base CIPESC®. Conclui-se que, excetuando-se as atividades de pesquisa, houve intensificação e ampliação das atividades assistenciais sistematizadas e embasadas no trabalho cotidiano da enfermagem, intra e extramuros.Curitiba implantó el sistema Clasificación Internacional de las Prácticas de Enfermería en Salud Colectiva - CIPESC®. El presente estudio objetivó identificar las actividades ejercidas por personal de enfermería en la red de atención básica de la salud del distrito Bairro Novo, Curitiba. Ha hecho una investigación junto a los trabajadores de enfermería, recorriendo-se a check-list. Los resultados mostrarán: todos realizan el acogimiento; las auxiliares de enfermería se ocupan más de las actividades asistencial-procedimentales; todas las enfermeras realizan consulta de enfermería diariamente, utilizando-se del prontuario electrónico bases CIPESC®. En conclusión, excepto las actividades del investigación, hube intensificación y ampliación de las actividades asistenciales, que se ubican sistematizadas e embasadas en el trabajo cotidiano de la enfermería, así como la educación y planeamiento.Curitiba has been utilized system CIPESC® - International Nursing Practice Classification in Collective Health. This study goal identifies the activities of nursing staff in

  19. Identification of a novel Plasmopara halstedii elicitor protein combining de novo peptide sequencing algorithms and RACE-PCR

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    Madlung Johannes

    2010-05-01

    Full Text Available Abstract Background Often high-quality MS/MS spectra of tryptic peptides do not match to any database entry because of only partially sequenced genomes and therefore, protein identification requires de novo peptide sequencing. To achieve protein identification of the economically important but still unsequenced plant pathogenic oomycete Plasmopara halstedii, we first evaluated the performance of three different de novo peptide sequencing algorithms applied to a protein digests of standard proteins using a quadrupole TOF (QStar Pulsar i. Results The performance order of the algorithms was PEAKS online > PepNovo > CompNovo. In summary, PEAKS online correctly predicted 45% of measured peptides for a protein test data set. All three de novo peptide sequencing algorithms were used to identify MS/MS spectra of tryptic peptides of an unknown 57 kDa protein of P. halstedii. We found ten de novo sequenced peptides that showed homology to a Phytophthora infestans protein, a closely related organism of P. halstedii. Employing a second complementary approach, verification of peptide prediction and protein identification was performed by creation of degenerate primers for RACE-PCR and led to an ORF of 1,589 bp for a hypothetical phosphoenolpyruvate carboxykinase. Conclusions Our study demonstrated that identification of proteins within minute amounts of sample material improved significantly by combining sensitive LC-MS methods with different de novo peptide sequencing algorithms. In addition, this is the first study that verified protein prediction from MS data by also employing a second complementary approach, in which RACE-PCR led to identification of a novel elicitor protein in P. halstedii.

  20. Sensitivity-Informed De Novo Programming for Many-Objective Water Portfolio Planning Under Uncertainty

    Science.gov (United States)

    Kasprzyk, J. R.; Reed, P. M.; Kirsch, B. R.; Characklis, G. W.

    2009-12-01

    Risk-based water supply management presents severe cognitive, computational, and social challenges to planning in a changing world. Decision aiding frameworks must confront the cognitive biases implicit to risk, the severe uncertainties associated with long term planning horizons, and the consequent ambiguities that shape how we define and solve water resources planning and management problems. This paper proposes and demonstrates a new interactive framework for sensitivity informed de novo programming. The theoretical focus of our many-objective de novo programming is to promote learning and evolving problem formulations to enhance risk-based decision making. We have demonstrated our proposed de novo programming framework using a case study for a single city’s water supply in the Lower Rio Grande Valley (LRGV) in Texas. Key decisions in this case study include the purchase of permanent rights to reservoir inflows and anticipatory thresholds for acquiring transfers of water through optioning and spot leases. A 10-year Monte Carlo simulation driven by historical data is used to provide performance metrics for the supply portfolios. The three major components of our methodology include Sobol globoal sensitivity analysis, many-objective evolutionary optimization and interactive tradeoff visualization. The interplay between these components allows us to evaluate alternative design metrics, their decision variable controls and the consequent system vulnerabilities. Our LRGV case study measures water supply portfolios’ efficiency, reliability, and utilization of transfers in the water supply market. The sensitivity analysis is used interactively over interannual, annual, and monthly time scales to indicate how the problem controls change as a function of the timescale of interest. These results have been used then to improve our exploration and understanding of LRGV costs, vulnerabilities, and the water portfolios’ critical reliability constraints. These results

  1. De Novo Assembly and Characterization of the Transcriptome of Grasshopper Shirakiacris shirakii

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    Zhongying Qiu

    2016-07-01

    Full Text Available Background: The grasshopper Shirakiacris shirakii is an important agricultural pest and feeds mainly on gramineous plants, thereby causing economic damage to a wide range of crops. However, genomic information on this species is extremely limited thus far, and transcriptome data relevant to insecticide resistance and pest control are also not available. Methods: The transcriptome of S. shirakii was sequenced using the Illumina HiSeq platform, and we de novo assembled the transcriptome. Results: Its sequencing produced a total of 105,408,878 clean reads, and the de novo assembly revealed 74,657 unigenes with an average length of 680 bp and N50 of 1057 bp. A total of 28,173 unigenes were annotated for the NCBI non-redundant protein sequences (Nr, NCBI non-redundant nucleotide sequences (Nt, a manually-annotated and reviewed protein sequence database (Swiss-Prot, Gene Ontology (GO and Kyoto Encyclopedia of Genes and Genomes (KEGG databases. Based on the Nr annotation results, we manually identified 79 unigenes encoding cytochrome P450 monooxygenases (P450s, 36 unigenes encoding carboxylesterases (CarEs and 36 unigenes encoding glutathione S-transferases (GSTs in S. shirakii. Core RNAi components relevant to miroRNA, siRNA and piRNA pathways, including Pasha, Loquacious, Argonaute-1, Argonaute-2, Argonaute-3, Zucchini, Aubergine, enhanced RNAi-1 and Piwi, were expressed in S. shirakii. We also identified five unigenes that were homologous to the Sid-1 gene. In addition, the analysis of differential gene expressions revealed that a total of 19,764 unigenes were up-regulated and 4185 unigenes were down-regulated in larvae. In total, we predicted 7504 simple sequence repeats (SSRs from 74,657 unigenes. Conclusions: The comprehensive de novo transcriptomic data of S. shirakii will offer a series of valuable molecular resources for better studying insecticide resistance, RNAi and molecular marker discovery in the transcriptome.

  2. BayesMotif: de novo protein sorting motif discovery from impure datasets.

    Science.gov (United States)

    Hu, Jianjun; Zhang, Fan

    2010-01-18

    Protein sorting is the process that newly synthesized proteins are transported to their target locations within or outside of the cell. This process is precisely regulated by protein sorting signals in different forms. A major category of sorting signals are amino acid sub-sequences usually located at the N-terminals or C-terminals of protein sequences. Genome-wide experimental identification of protein sorting signals is extremely time-consuming and costly. Effective computational algorithms for de novo discovery of protein sorting signals is needed to improve the understanding of protein sorting mechanisms. We formulated the protein sorting motif discovery problem as a classification problem and proposed a Bayesian classifier based algorithm (BayesMotif) for de novo identification of a common type of protein sorting motifs in which a highly conserved anchor is present along with a less conserved motif regions. A false positive removal procedure is developed to iteratively remove sequences that are unlikely to contain true motifs so that the algorithm can identify motifs from impure input sequences. Experiments on both implanted motif datasets and real-world datasets showed that the enhanced BayesMotif algorithm can identify anchored sorting motifs from pure or impure protein sequence dataset. It also shows that the false positive removal procedure can help to identify true motifs even when there is only 20% of the input sequences containing true motif instances. We proposed BayesMotif, a novel Bayesian classification based algorithm for de novo discovery of a special category of anchored protein sorting motifs from impure datasets. Compared to conventional motif discovery algorithms such as MEME, our algorithm can find less-conserved motifs with short highly conserved anchors. Our algorithm also has the advantage of easy incorporation of additional meta-sequence features such as hydrophobicity or charge of the motifs which may help to overcome the limitations of

  3. New experimental model for training in videosurgery Novo modelo experimental para treinamento em videocirurgia

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    Danilo Malta Batista

    2012-10-01

    Full Text Available PURPOSE: To develop a new experimental model of lower cost for training in videosurgery. METHODS: This project was performed at the Nucleus of Experimental Surgery of the Bahiana School of Medicine and Public Health, based on previous models described in the literature and under the supervision of the full professor of Operative Technique and Experimental Surgery II. It was made a model cube-shaped, made of wood, with holes distributed in various locations, rubber stoppers for the holes and lined externally with carpet, and internally with laminate. RESULTS: The new experimental model is of low cost and reproduces quite faithfully several videosurgical procedures. CONCLUSION: Medical schools interested in the subject may adopt the new model for training in videosurgery without the need of high costs for making and using these models.OBJETIVO: Desenvolver um novo modelo experimental de baixo custo para treinamento em videocirurgia MÉTODOS: Este projeto foi conduzido no Núcleo de Cirurgia Experimental da Escola Bahiana de Medicina e Saúde Pública, baseado em modelos prévios descritos na literatura e sob a supervisão do professor titular de Técnica Operatória e Cirurgia Experimental II. Foi feito um modelo em formato de cubo, de madeira, com furos distribuídos em vários locais, tampas de borracha para os orifícios e forrado externamente com carpete e internamente com laminado. RESULTADOS: O novo modelo experimental desenvolvido é de baixo custo e reproduz de forma bastante fiel diversos procedimentos videocirúrgicos. CONCLUSÃO: Faculdades médicas interessadas no tema poderão adotar o novo modelo para o treinamento em videocirurgia sem que sejam necessários gastos elevados para a confecção e o uso desses modelos.

  4. Locoregional symptoms in patients with de novo metastatic prostate cancer: Morbidity, management, and disease outcome.

    Science.gov (United States)

    Patrikidou, Anna; Brureau, Laurent; Casenave, Julien; Albiges, Laurence; Di Palma, Mario; Patard, Jean-Jacques; Baumert, Hervé; Blanchard, Pierre; Bossi, Alberto; Kitikidou, Kyriaki; Massard, Christophe; Fizazi, Karim; Blanchet, Pascal; Loriot, Yohann

    2015-05-01

    The paradigm change observed over the last few years in several solid tumors emphasizes the value of locoregional treatment in the presence of metastatic disease, currently ignored in de novo prostate cancer (CaP). We investigated the effect of the primary tumor that is left untreated on prostate cancer-specific morbidity and mortality, time to castration resistance, and overall survival (OS). We performed a bicentric cohort study. The overall population included de novo metastatic CaP managed at the Genito-Urinary Oncology Unit of the Gustave Roussy Institute and the Urology Clinic of the University Hospital of Pointe-à-Pitre, France. Descriptive statistical and outcome analyses were performed in the overall cohort and also separately in the N+M0 and M+subgroups. The overall cohort included 263 patients. Approximately two-thirds of patients (64%) presented with locoregional symptoms at diagnosis, and 78% throughout the disease. Of the symptomatic patients, 59% required a locoregional procedure. Median OS of patients with locoregional symptoms at diagnosis was shorter than in those who were asymptomatic (47 vs. 86 mo, P = 0.0007); this difference was maintained in the N+M0 and M+subgroups. Median OS and time to castration resistance showed a nonsignificant trend in favor of patients undergoing a locoregional treatment at diagnosis. The presence of symptoms due to locoregional disease in de novo metastatic CaP entails significant morbidity and even mortality and requires active management. Randomized prospective trials are needed to evaluate the role of initial definite locoregional treatment in these patients. Copyright © 2015 Elsevier Inc. All rights reserved.

  5. Developing de novo human artificial chromosomes in embryonic stem cells using HSV-1 amplicon technology.

    Science.gov (United States)

    Moralli, Daniela; Monaco, Zoia L

    2015-02-01

    De novo artificial chromosomes expressing genes have been generated in human embryonic stem cells (hESc) and are maintained following differentiation into other cell types. Human artificial chromosomes (HAC) are small, functional, extrachromosomal elements, which behave as normal chromosomes in human cells. De novo HAC are generated following delivery of alpha satellite DNA into target cells. HAC are characterized by high levels of mitotic stability and are used as models to study centromere formation and chromosome organisation. They are successful and effective as gene expression vectors since they remain autonomous and can accommodate larger genes and regulatory regions for long-term expression studies in cells unlike other viral gene delivery vectors currently used. Transferring the essential DNA sequences for HAC formation intact across the cell membrane has been challenging for a number of years. A highly efficient delivery system based on HSV-1 amplicons has been used to target DNA directly to the ES cell nucleus and HAC stably generated in human embryonic stem cells (hESc) at high frequency. HAC were detected using an improved protocol for hESc chromosome harvesting, which consistently produced high-quality metaphase spreads that could routinely detect HAC in hESc. In tumour cells, the input DNA often integrated in the host chromosomes, but in the host ES genome, it remained intact. The hESc containing the HAC formed embryoid bodies, generated teratoma in mice, and differentiated into neuronal cells where the HAC were maintained. The HAC structure and chromatin composition was similar to the endogenous hESc chromosomes. This review will discuss the technological advances in HAC vector delivery using HSV-1 amplicons and the improvements in the identification of de novo HAC in hESc.

  6. Facebook - Um novo espaço autobiográfico?

    Directory of Open Access Journals (Sweden)

    Maria Tereza Lima

    2015-07-01

    Full Text Available O arigo "Facebook - Um novo espaço autobiográfico?" tem como objetivo central investigar como a perspectiva autobiográfica e biográfica se configura em uma rede social. Levando em consideração esse novo espaço de exteriorização da memória, analisamos as escolhas de uma pessoa ao postar os mais diversos gêneros textuais no Facebook e verificamos até que ponto tais fragmentos textuais narram a história de um indivíduo. Quais textos são postados? O que foi escolhido e o que foi excluído desse perfil? O autor trava um pacto de leitura com o leitor? Se levarmos em consideração que os textos postados nessa rede social são textos produzidos pelo próprio autor do perfil e de autores diversos, como configuraremos esses espaços virtuais? Autobiográficos e biográficos? Quem escreve a página virtual é o próprio autor do perfil ou múltiplos autores? Com as redes sociais, surge um novo modelo de autobiografia e de biógrafo? Esses e tantos outros questionamentos nortearam nossas investigações e permitiram-nos conhecer um pouco mais sobre as estratégias autobiográficas dos autores virtuais contemporâneos.

  7. ESTADO E NOVOS AGENTES SOCIAIS NA RECONSTRUÇÃO DO ESPAÇO

    Directory of Open Access Journals (Sweden)

    Cláudio Barbosa da Costa

    2006-07-01

    Full Text Available Este estudo tem como objetivo principal sistematizar novas questões referentes à complexidade das ações dos agentes sociais na construção do espaço contemporâneo, e que vem interferindo, de maneira significativa, na forma como o Estado vem realizando o processo de intervenção no território. Os eixos analíticos do estudo serão constituídos pelo novo patamar de acumulação que constitui a globalização, os grandes agentes econômicos internacionais e as novas referências da chamada lógica civilizatória, na qual emergem sujeitos sociais que ao buscarem romper com idéia dominante de desenvolvimento e de crescimento, vêm construindo novas formas de lidar com a natureza, com o território e com o trabalho, estabelecendo a alteridade, a partir da luta pela sua legitimidade. A compreensão teórica dos novos movimentos sociais possibilitou um melhor entendimento do papel histórico destes agentes na construção contemporânea do espaço e das suas relações com o vetor ecológico e o desenvolvimento sustentável. Para finalizar, realizamos uma análise histórica das intervenções do Estado brasileiro na construção do território nacional, buscando identificar a complexidade dos agentes da sociedade civil, e as possibilidades e os limites da constituição de um projeto geopolítico através de um novo pacto social, que resguardando as diferenças, consideram-se as territorialidades dos setores sociais historicamente excluídos do processo de

  8. De novo analysis of transcriptome dynamics in the migratory locust during the development of phase traits.

    Directory of Open Access Journals (Sweden)

    Shuang Chen

    Full Text Available Locusts exhibit remarkable density-dependent phenotype (phase changes from the solitary to the gregarious, making them one of the most destructive agricultural pests. This phenotype polyphenism arises from a single genome and diverse transcriptomes in different conditions. Here we report a de novo transcriptome for the migratory locust and a comprehensive, representative core gene set. We carried out assembly of 21.5 Gb Illumina reads, generated 72,977 transcripts with N50 2,275 bp and identified 11,490 locust protein-coding genes. Comparative genomics analysis with eight other sequenced insects was carried out to identify the genomic divergence between hemimetabolous and holometabolous insects for the first time and 18 genes relevant to development was found. We further utilized the quantitative feature of RNA-seq to measure and compare gene expression among libraries. We first discovered how divergence in gene expression between two phases progresses as locusts develop and identified 242 transcripts as candidates for phase marker genes. Together with the detailed analysis of deep sequencing data of the 4(th instar, we discovered a phase-dependent divergence of biological investment in the molecular level. Solitary locusts have higher activity in biosynthetic pathways while gregarious locusts show higher activity in environmental interaction, in which genes and pathways associated with regulation of neurotransmitter activities, such as neurotransmitter receptors, synthetase, transporters, and GPCR signaling pathways, are strongly involved. Our study, as the largest de novo transcriptome to date, with optimization of sequencing and assembly strategy, can further facilitate the application of de novo transcriptome. The locust transcriptome enriches genetic resources for hemimetabolous insects and our understanding of the origin of insect metamorphosis. Most importantly, we identified genes and pathways that might be involved in locust development

  9. When less is more: 'slicing' sequencing data improves read decoding accuracy and de novo assembly quality.

    Science.gov (United States)

    Lonardi, Stefano; Mirebrahim, Hamid; Wanamaker, Steve; Alpert, Matthew; Ciardo, Gianfranco; Duma, Denisa; Close, Timothy J

    2015-09-15

    As the invention of DNA sequencing in the 70s, computational biologists have had to deal with the problem of de novo genome assembly with limited (or insufficient) depth of sequencing. In this work, we investigate the opposite problem, that is, the challenge of dealing with excessive depth of sequencing. We explore the effect of ultra-deep sequencing data in two domains: (i) the problem of decoding reads to bacterial artificial chromosome (BAC) clones (in the context of the combinatorial pooling design we have recently proposed), and (ii) the problem of de novo assembly of BAC clones. Using real ultra-deep sequencing data, we show that when the depth of sequencing increases over a certain threshold, sequencing errors make these two problems harder and harder (instead of easier, as one would expect with error-free data), and as a consequence the quality of the solution degrades with more and more data. For the first problem, we propose an effective solution based on 'divide and conquer': we 'slice' a large dataset into smaller samples of optimal size, decode each slice independently, and then merge the results. Experimental results on over 15 000 barley BACs and over 4000 cowpea BACs demonstrate a significant improvement in the quality of the decoding and the final assembly. For the second problem, we show for the first time that modern de novo assemblers cannot take advantage of ultra-deep sequencing data. Python scripts to process slices and resolve decoding conflicts are available from http://goo.gl/YXgdHT; software Hashfilter can be downloaded from http://goo.gl/MIyZHs stelo@cs.ucr.edu or timothy.close@ucr.edu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  10. Sequential search leads to faster, more efficient fragment-based de novo protein structure prediction.

    Science.gov (United States)

    de Oliveira, Saulo H P; Law, Eleanor C; Shi, Jiye; Deane, Charlotte M

    2018-04-01

    Most current de novo structure prediction methods randomly sample protein conformations and thus require large amounts of computational resource. Here, we consider a sequential sampling strategy, building on ideas from recent experimental work which shows that many proteins fold cotranslationally. We have investigated whether a pseudo-greedy search approach, which begins sequentially from one of the termini, can improve the performance and accuracy of de novo protein structure prediction. We observed that our sequential approach converges when fewer than 20 000 decoys have been produced, fewer than commonly expected. Using our software, SAINT2, we also compared the run time and quality of models produced in a sequential fashion against a standard, non-sequential approach. Sequential prediction produces an individual decoy 1.5-2.5 times faster than non-sequential prediction. When considering the quality of the best model, sequential prediction led to a better model being produced for 31 out of 41 soluble protein validation cases and for 18 out of 24 transmembrane protein cases. Correct models (TM-Score > 0.5) were produced for 29 of these cases by the sequential mode and for only 22 by the non-sequential mode. Our comparison reveals that a sequential search strategy can be used to drastically reduce computational time of de novo protein structure prediction and improve accuracy. Data are available for download from: http://opig.stats.ox.ac.uk/resources. SAINT2 is available for download from: https://github.com/sauloho/SAINT2. saulo.deoliveira@dtc.ox.ac.uk. Supplementary data are available at Bioinformatics online.

  11. Optimizing and benchmarking de novo transcriptome sequencing: from library preparation to assembly evaluation.

    Science.gov (United States)

    Hara, Yuichiro; Tatsumi, Kaori; Yoshida, Michio; Kajikawa, Eriko; Kiyonari, Hiroshi; Kuraku, Shigehiro

    2015-11-18

    RNA-seq enables gene expression profiling in selected spatiotemporal windows and yields massive sequence information with relatively low cost and time investment, even for non-model species. However, there remains a large room for optimizing its workflow, in order to take full advantage of continuously developing sequencing capacity. Transcriptome sequencing for three embryonic stages of Madagascar ground gecko (Paroedura picta) was performed with the Illumina platform. The output reads were assembled de novo for reconstructing transcript sequences. In order to evaluate the completeness of transcriptome assemblies, we prepared a reference gene set consisting of vertebrate one-to-one orthologs. To take advantage of increased read length of >150 nt, we demonstrated shortened RNA fragmentation time, which resulted in a dramatic shift of insert size distribution. To evaluate products of multiple de novo assembly runs incorporating reads with different RNA sources, read lengths, and insert sizes, we introduce a new reference gene set, core vertebrate genes (CVG), consisting of 233 genes that are shared as one-to-one orthologs by all vertebrate genomes examined (29 species)., The completeness assessment performed by the computational pipelines CEGMA and BUSCO referring to CVG, demonstrated higher accuracy and resolution than with the gene set previously established for this purpose. As a result of the assessment with CVG, we have derived the most comprehensive transcript sequence set of the Madagascar ground gecko by means of assembling individual libraries followed by clustering the assembled sequences based on their overall similarities. Our results provide several insights into optimizing de novo RNA-seq workflow, including the coordination between library insert size and read length, which manifested in improved connectivity of assemblies. The approach and assembly assessment with CVG demonstrated here would be applicable to transcriptome analysis of other species as

  12. A «educação nova» e o estado novo

    OpenAIRE

    Alho, Albérico Afonso Costa

    2008-01-01

    A reforma do ensino técnico foi filha das mudanças que espreitavam no Portugal do pós-guerra. Apesar do espartilho imposto à liberdade de expressão, quase todos os sectores sociais vão tomar posição sobre os novos caminhos enunciados para o ensino profissional. Das associações patronais aos sectores oposicionistas, ninguém ficou indiferente às novas propostas que emergiam da reforma.

  13. Anterior abdominal wall leiomyoma arising de novo in a fertile women: A case report

    International Nuclear Information System (INIS)

    Cho, Je Young; Woo, Ji Young; Hong, Hye Suk; Yang, Ik; Lee, Yul; Hwang, Ji Young; Kim, Han Myun; Shin, Mi Kyung

    2016-01-01

    Abdominal wall leiomyoma arising de novo is very rare, hence the reported imaging findings of this disease are also rare. We reported the case of a 33-year-old woman who presented with an abdominal wall mass without antecedent gynecological surgeries. The initial abdominal computed tomography (CT) showed thickening of the left rectus abdominis and the loss of intervening fat between the rectus abdominis and the lateral abdominal muscles. After 8 months, the follow-up contrast-enhanced CT and ultrasonography (US) showed a lentiform-shaped mass with isodensity to the adjacent muscles. The US-guided biopsy was consistent with leiomyoma

  14. Anterior abdominal wall leiomyoma arising de novo in a fertile women: A case report

    Energy Technology Data Exchange (ETDEWEB)

    Cho, Je Young; Woo, Ji Young; Hong, Hye Suk; Yang, Ik; Lee, Yul; Hwang, Ji Young; Kim, Han Myun; Shin, Mi Kyung [Hallym University College of Medicine, Kangnam Sacred Heart Hospital, Seoul (Korea, Republic of)

    2016-01-15

    Abdominal wall leiomyoma arising de novo is very rare, hence the reported imaging findings of this disease are also rare. We reported the case of a 33-year-old woman who presented with an abdominal wall mass without antecedent gynecological surgeries. The initial abdominal computed tomography (CT) showed thickening of the left rectus abdominis and the loss of intervening fat between the rectus abdominis and the lateral abdominal muscles. After 8 months, the follow-up contrast-enhanced CT and ultrasonography (US) showed a lentiform-shaped mass with isodensity to the adjacent muscles. The US-guided biopsy was consistent with leiomyoma.

  15. Chromosome aberrations and oncogene alterations in atomic bomb related leukemias - different mechanisms from de novo leukemias

    International Nuclear Information System (INIS)

    Tanaka, K.; Tanaka, H.; Kamada, N.

    2003-01-01

    It is well known that leukemia occurred more frequently among atomic bomb survivors. In 132 atomic bomb related ( AB- related) leukemia patients during 1978-1999, 33 acute myeloid leukemia (AML)/myelodysplastic syndrome (MDS) patients had their exposure doses of more than 1Gy (DS86). Chromosome aberrations of the 33 patients were compared with those from 588 de novo AML/MDS patients who had been bone before August 1945 as control. No FAB M3 patient was observed in the exposed group. Most AB-related AML preceded a long term of MDS stage. Twenty seven of the 33 patients showed complex types of chromosome aberrations with more than three chromosomes involving chromosomes 5,7 and 11. The number of chromosomes abnormality per cell in the AB-related leukemia was 3.78 while 0.92 in de novo leukemia. Only one of the 33 patients had normal karyotype, while 44.1% in de novo leukemia patients. Translocations of chromosome 11 at 11q13 to 11q23 and deletion/ loss of chromosome 20 were frequently observed in AB-related leukemia. No leukemia-type specific translocations such as t(8;21),t(15;17) and 11q23 were found in the 33 AB-related leukemia patients. Furthermore, molecular analyses using FISH and PCR-SSCP revealed the presence of breakpoint located outside of MLL gene in the patients with translocations at 11q22-23 and DNA base derangements of RUNT domain of AML1(CBF β 2)gene with AML/MDS patients without t(8;21) and with a high dose of exposure. These results suggest that AB-related leukemia derives from an exposed pluripotent hematopoietic stem cell which has been preserved for a long time in the bone marrow, expressing high genetic instability such as microsatellite instability. On the other hand, de novo leukemia develops from a committed hematopoietic stem cell and shows simple and leukemia-type specific chromosome aberrations. These findings are important for understanding mechanisms for radiation-induced leukemia

  16. Everolimus Initiation With Early Calcineurin Inhibitor Withdrawal in De Novo Heart Transplant Recipients

    DEFF Research Database (Denmark)

    Andreassen, A K; Andersson, B; Gustafsson, F

    2016-01-01

    In a randomized, open-label trial, de novo heart transplant recipients were randomized to everolimus (3-6 ng/mL) with reduced-exposure calcineurin inhibitor (CNI; cyclosporine) to weeks 7-11 after transplant, followed by increased everolimus exposure (target 6-10 ng/mL) with cyclosporine withdrawal...... events occurred in 37.3% and 19.6% of everolimus- and CNI-treated patients, respectively (p = 0.078). These results suggest that early CNI withdrawal after heart transplantation supported by everolimus, mycophenolic acid and steroids with lymphocyte-depleting induction is safe at intermediate follow...

  17. A Psicologia no novo contexto mundial Psychology in the new world context

    Directory of Open Access Journals (Sweden)

    Carla Faria Leitão

    2003-12-01

    Full Text Available Profundas alterações no mundo contemporâneo criaram um novo contexto de produção científica, caracterizado pela desconstrução de antigas teorias e pela construção de uma nova rede de conhecimentos. Neste artigo, analisamos algumas teorias recentemente desenvolvidas nas ciências sociais e na filosofia que compõem esta rede: as teorias pós-modernas, as teorias da modernização reflexiva e a teoria da Revolução da Tecnologia da Informação. Visamos com isto munir os psicólogos de conhecimentos advindos de outros campos disciplinares que sirvam como ponto de partida para a análise das mudanças subjetivas introduzidas pelo novo cenário mundial. Argumentamos que a psicologia ainda observa o homem contemporâneo a partir de categorias tradicionais, desconsiderando que transformações sociais profundas geram impactos psicológicos não menos profundos e dificilmente captáveis a partir de antigos referenciais. Concluímos que um conhecimento mais aprofundado das transformações radicais em curso no mundo atual pode ajudar os psicólogos a rever suas antigas certezas a respeito do homem e a aventurar novos olhares sobre os também novos fenômenos humanos.Profound changes in the contemporary world have created a new context for scientific work, characterised by the deconstruction of old theories and the construction of a new network of knowledge. In this article, we analyse a few theories recently developed in the social sciences and in philosophy that make up this network: post-modernist theories, reflexive modernisation theories and Information Technology Revolution theory. In this way, we aim to provide psychologists with insights produced in other fields of knowledge that can serve as a starting point for the analysis of the subjective changes introduced by the new global scenario. We argue that psychology still observes contemporary man on the basis of traditional categories, ignoring the fact that profound social changes

  18. Novos táxons de Lamiinae (Coleoptera, Cerambycidae da América do Sul

    Directory of Open Access Journals (Sweden)

    Maria Helena M. Galileo

    2012-06-01

    Full Text Available Novos táxons descritos: Acanthoderini, Nesozineus osorioensis sp. nov., do Brasil (Rio Grande do Sul; Calliini, Drycothaea clara sp. nov., do Brasil (Rondônia e Drycothaea hovorei sp. nov., do Equador (Napo; Forsteriini, Itacolomi gen. nov., espécie-tipo I. letiziae sp. nov., do Brasil (Minas Gerais; Yapyguara gen. nov., espécie-tipo Y. fusca sp. nov., da Bolívia (Santa Cruz; Xenofreini, Xenofrea zischkai sp. nov., do Equador (Napo e da Bolívia (Santa Cruz.

  19. Identification of de Novo Fanconi Anemia in Younger Patients With Newly Diagnosed Acute Myeloid Leukemia

    Science.gov (United States)

    2016-05-13

    Childhood Acute Erythroleukemia (M6); Childhood Acute Megakaryocytic Leukemia (M7); Childhood Acute Minimally Differentiated Myeloid Leukemia (M0); Childhood Acute Monoblastic Leukemia (M5a); Childhood Acute Monocytic Leukemia (M5b); Childhood Acute Myeloblastic Leukemia With Maturation (M2); Childhood Acute Myeloblastic Leukemia Without Maturation (M1); Childhood Acute Myelomonocytic Leukemia (M4); Childhood Myelodysplastic Syndromes; Chronic Myelomonocytic Leukemia; de Novo Myelodysplastic Syndromes; Fanconi Anemia; Refractory Anemia; Refractory Anemia With Excess Blasts; Refractory Anemia With Excess Blasts in Transformation; Refractory Anemia With Ringed Sideroblasts; Secondary Myelodysplastic Syndromes; Untreated Childhood Acute Myeloid Leukemia and Other Myeloid Malignancies

  20. De novo assembly of plant body plan: a step ahead of Deadpool

    OpenAIRE

    Kareem, Abdul; Radhakrishnan, Dhanya; Sondhi, Yash; Aiyaz, Mohammed; Roy, Merin V.; Sugimoto, Kaoru; Prasad, Kalika

    2016-01-01

    Abstract While in the movie Deadpool it is possible for a human to recreate an arm from scratch, in reality plants can even surpass that. Not only can they regenerate lost parts, but also the whole plant body can be reborn from a few existing cells. Despite the decades old realization that plant cells possess the ability to regenerate a complete?shoot and root system, it is only now that the underlying mechanisms are being unraveled. De novo plant regeneration involves the initiation of regen...

  1. O Estado Novo, o rádio e seus órgãos reguladores

    Directory of Open Access Journals (Sweden)

    Othon Jambeiro

    2003-01-01

    Full Text Available This paper analyses the Brazilian broadcasting regulation in the 1935-1945 period, including the Estado Novo coup d'etat preparation, its implementation, consolidation and fall. It is taken into account the historical context and the national and international changes which occured in that period. It also analyses the rules for broadcasting and mass communication media, particularly on control issues. Functions, structure and acting of the Departmento de Imprensa e Propaganda - DIP area studied, in the perspective of understanding the role of the most important intelligence agency of the Vargas government.

  2. De novo development of eosinophilic myocarditis with left ventricular assist device support as bridge to transplant.

    Science.gov (United States)

    Pereira, Naveen L; Park, Soon J; Daly, Richard C; Kushwaha, Sudhir S; Edwards, William D

    2010-10-01

    The de novo development of myocarditis during left ventricular assist device support for dilated cardiomyopathy has not been previously described. We report a case of severe eosinophilic myocarditis associated with the use of leukotriene-receptor antagonist montelukast that developed during left ventricular assist device support accompanied by intra-device thrombus formation that was hemodynamically tolerated and subsequently discovered in the explanted heart. There may be no visible change in cardiac function as assessed by echocardiography, but the diagnosis should be entertained with the development of peripheral eosinophilia. Copyright © 2010 The Society of Thoracic Surgeons. Published by Elsevier Inc. All rights reserved.

  3. De novo transcriptome assembly associated with fumonisin production by the rice pathogen Fusarium fujikuroi

    Directory of Open Access Journals (Sweden)

    Keerthi S. Guruge

    2018-06-01

    Full Text Available The present study employed a next-generation sequencing method to assemble a de novo transcriptome database designed to distinguish gene expression changes exhibited by the fumonisin-producing fungus Fusarium fujikuroi when grown under ‘fumonisin-producing’ compared to ‘non-fumonisin-producing’ conditions. The raw data of this study have been deposited at DNA Data Bank of Japan (DDBJ under the accession ID DRA006146. Keywords: Fusarium fujikuroi, Fumonisin, Next-generation sequencing, Transcriptome, Gene-expression

  4. Analysis of the NovoTwist pen needle in comparison with conventional screw-thread needles.

    Science.gov (United States)

    Aye, Tandy

    2011-11-01

    Administration of insulin via a pen device may be advantageous over a vial and syringe system. Hofman and colleagues introduce a new insulin pen needle, the NovoTwist, to simplify injections to a small group of children and adolescents. Their overall preferences and evaluation of the handling of the needle are reported in the study. This new needle has the potential to ease administration of insulin via a pen device that may increase both the use of a pen device and adherence to insulin therapy. © 2011 Diabetes Technology Society.

  5. A de novo designed monomeric, compact three helix bundle protein on a carbohydrate template

    DEFF Research Database (Denmark)

    Malik, Leila; Nygård, Jesper; Christensen, Niels Johan

    2015-01-01

    De novo design and chemical synthesis of proteins and of other artificial structures, which mimic them, is a central strategy for understanding protein folding and for accessing proteins with novel functions. We have previously described carbohydrates as templates for the assembly of artificial...... the template could facilitate protein folding. Here we report the design and synthesis of 3-helix bundle carboproteins on deoxy-hexopyranosides. The carboproteins were analyzed by CD, AUC, SAXS, and NMR, which revealed the formation of the first compact, and folded monomeric carboprotein distinctly different...

  6. De-novo discovery of differentially abundant transcription factor binding sites including their positional preference.

    Science.gov (United States)

    Keilwagen, Jens; Grau, Jan; Paponov, Ivan A; Posch, Stefan; Strickert, Marc; Grosse, Ivo

    2011-02-10

    Transcription factors are a main component of gene regulation as they activate or repress gene expression by binding to specific binding sites in promoters. The de-novo discovery of transcription factor binding sites in target regions obtained by wet-lab experiments is a challenging problem in computational biology, which has not been fully solved yet. Here, we present a de-novo motif discovery tool called Dispom for finding differentially abundant transcription factor binding sites that models existing positional preferences of binding sites and adjusts the length of the motif in the learning process. Evaluating Dispom, we find that its prediction performance is superior to existing tools for de-novo motif discovery for 18 benchmark data sets with planted binding sites, and for a metazoan compendium based on experimental data from micro-array, ChIP-chip, ChIP-DSL, and DamID as well as Gene Ontology data. Finally, we apply Dispom to find binding sites differentially abundant in promoters of auxin-responsive genes extracted from Arabidopsis thaliana microarray data, and we find a motif that can be interpreted as a refined auxin responsive element predominately positioned in the 250-bp region upstream of the transcription start site. Using an independent data set of auxin-responsive genes, we find in genome-wide predictions that the refined motif is more specific for auxin-responsive genes than the canonical auxin-responsive element. In general, Dispom can be used to find differentially abundant motifs in sequences of any origin. However, the positional distribution learned by Dispom is especially beneficial if all sequences are aligned to some anchor point like the transcription start site in case of promoter sequences. We demonstrate that the combination of searching for differentially abundant motifs and inferring a position distribution from the data is beneficial for de-novo motif discovery. Hence, we make the tool freely available as a component of the open

  7. S1P Signaling and De Novo Biosynthesis in Blood Pressure Homeostasis

    Science.gov (United States)

    Cantalupo, Anna

    2016-01-01

    Initially discovered as abundant components of eukaryotic cell membranes, sphingolipids are now recognized as important bioactive signaling molecules that modulate a variety of cellular functions, including those relevant to cancer and immunologic, inflammatory, and cardiovascular disorders. In this review, we discuss recent advances in our understanding of the role of sphingosine-1-phosphate (S1P) receptors in the regulation of vascular function, and focus on how de novo biosynthesized sphingolipids play a role in blood pressure homeostasis. The therapeutic potential of new drugs that target S1P signaling is also discussed. PMID:27317800

  8. Visões do Novo Mundo na pintura religiosa da Renascença

    Directory of Open Access Journals (Sweden)

    Yobenj Aucardo Chicangana-Bayona

    2013-06-01

    Full Text Available Este artigo aborda o estudo dos elementos familiares aos exploradores europeus que estabeleceram suas primeiras coordenadas a partir de analogias com o Paraíso e com Cocanha para assimilar e interpretar pictoricamente o Novo Mundo, uma realidade antes desconhecida, e integrá-la à cultura ocidental. Assim, o Cristianismo é muito importante, porque vai oferecer o referencial - em um primeiro momento - para estabelecer a imagem do índio em episódios religiosos da cultura ocidental europeia. Uma imagem que ora será positiva, vinculada ao paraíso, e ora negativa, sendo vinculada ao inferno.

  9. A inclusão na perspectiva do novo paradigma da ciência

    Directory of Open Access Journals (Sweden)

    Reinoldo Marqueza

    2011-12-01

    Full Text Available O estudo aborda o processo de transição paradigmática da ciência moderna para a ciência pós-moderna. Salienta as características do paradigma atual, a crise desse paradigma e aponta os contornos do paradigma emergente na perspectiva do sociólogo Boaventura Sousa Santos. Refere a Educação Inclusiva como um novo processo de produção e de apropriação do conhecimento e como uma nova forma de estar na relação.Palavras-chave: Paradigma. Conhecimento. Educação Inclusiva.

  10. Novos biomateriais poliméricos para implantes ósseos

    OpenAIRE

    Ferreira, Sara Cristina Silva

    2016-01-01

    Os danos dos tecidos ósseos representam um problema importante de saúde em todo o mundo. Um dos componentes principais utilizados em engenharia de tecidos são os materiais de suporte, estruturas 3D formadas por matrizes porosas, que visam proporcionar o desenvolvimento do novo tecido. Muitas das matrizes poliméricas porosas (espumas) utilizadas em aplicações médicas são constituídas por poliuretanos, sendo estes produzidos a partir de isocianatos (produtos tóxicos) e polióis. Assim, surge a n...

  11. SV2: accurate structural variation genotyping and de novo mutation detection from whole genomes.

    Science.gov (United States)

    Antaki, Danny; Brandler, William M; Sebat, Jonathan

    2018-05-15

    Structural variation (SV) detection from short-read whole genome sequencing is error prone, presenting significant challenges for population or family-based studies of disease. Here, we describe SV2, a machine-learning algorithm for genotyping deletions and duplications from paired-end sequencing data. SV2 can rapidly integrate variant calls from multiple structural variant discovery algorithms into a unified call set with high genotyping accuracy and capability to detect de novo mutations. SV2 is freely available on GitHub (https://github.com/dantaki/SV2). jsebat@ucsd.edu. Supplementary data are available at Bioinformatics online.

  12. A comprehensive cytogenetic classification of 1466 Chinese patients with de novo acute lymphoblastic leukemia.

    Science.gov (United States)

    Li, Xin; Li, Juan; Hu, Yanjie; Xie, Wei; Du, Wen; Liu, Wei; Li, Xiaoqing; Chen, Xiangjun; Li, Hongrui; Wang, Junfeng; Zhang, Lannan; Huang, Shiang

    2012-06-01

    Cytogenetics and molecular cytogenetics of 1466 Chinese patients with de novo acute lymphoblastic leukemia (ALL) were studied. Cytogenetic results were available in 1175 patients. Cross-correlations of 23 subclasses of cytogenetic abnormalities were described. Childhood cases had higher incidences of normal karyotype, t(1;19), +8, 12q-, +21, +22 and high hyperdiploidy with 51-65 chromosomes, and lower incidences of t(9;22) and -5/5q- than adult ones (all pcytogenetic subclasses with immunophenotyping subgroups of ALL were studied. Our study presents the cytogenetic characteristics of a large series of Chinese ALL patients. Copyright © 2011 Elsevier Ltd. All rights reserved.

  13. A Presença da Gastronomia Alemã na Hotelaria de Novo Hamburgo, RS

    OpenAIRE

    mary sandra ashton; Ana Cristina Müller

    2013-01-01

    Esse estudo tem por objetivo investigar os elementos e características da gastronomia alemã presentes nos serviços hoteleiros de Novo Hamburgo. Tem ênfase na gastronomia, evidenciando e (re) conhecendo os hábitos e costumes alimentares trazidos pela imigração germânica e sua relação com a oferta de alimentos nos hotéis da cidade, como diferencial no quesito turismo cultural. Para tanto, foram utilizados autores reconhe...

  14. Emergence, Retention and Selection: A Trilogy of Origination for Functional De Novo Proteins from Ancestral LncRNAs in Primates.

    Directory of Open Access Journals (Sweden)

    Jia-Yu Chen

    2015-07-01

    Full Text Available While some human-specific protein-coding genes have been proposed to originate from ancestral lncRNAs, the transition process remains poorly understood. Here we identified 64 hominoid-specific de novo genes and report a mechanism for the origination of functional de novo proteins from ancestral lncRNAs with precise splicing structures and specific tissue expression profiles. Whole-genome sequencing of dozens of rhesus macaque animals revealed that these lncRNAs are generally not more selectively constrained than other lncRNA loci. The existence of these newly-originated de novo proteins is also not beyond anticipation under neutral expectation, as they generally have longer theoretical lifespan than their current age, due to their GC-rich sequence property enabling stable ORFs with lower chance of non-sense mutations. Interestingly, although the emergence and retention of these de novo genes are likely driven by neutral forces, population genetics study in 67 human individuals and 82 macaque animals revealed signatures of purifying selection on these genes specifically in human population, indicating a proportion of these newly-originated proteins are already functional in human. We thus propose a mechanism for creation of functional de novo proteins from ancestral lncRNAs during the primate evolution, which may contribute to human-specific genetic novelties by taking advantage of existed genomic contexts.

  15. Critical importance of the de novo pyrimidine biosynthesis pathway for Trypanosoma cruzi growth in the mammalian host cell cytoplasm

    International Nuclear Information System (INIS)

    Hashimoto, Muneaki; Morales, Jorge; Fukai, Yoshihisa; Suzuki, Shigeo; Takamiya, Shinzaburo; Tsubouchi, Akiko; Inoue, Syou; Inoue, Masayuki; Kita, Kiyoshi; Harada, Shigeharu; Tanaka, Akiko; Aoki, Takashi; Nara, Takeshi

    2012-01-01

    Highlights: ► We established Trypanosoma cruzi lacking the gene for carbamoyl phosphate synthetase II. ► Disruption of the cpsII gene significantly reduced the growth of epimastigotes. ► In particular, the CPSII-null mutant severely retarded intracellular growth. ► The de novo pyrimidine pathway is critical for the parasite growth in the host cell. -- Abstract: The intracellular parasitic protist Trypanosoma cruzi is the causative agent of Chagas disease in Latin America. In general, pyrimidine nucleotides are supplied by both de novo biosynthesis and salvage pathways. While epimastigotes—an insect form—possess both activities, amastigotes—an intracellular replicating form of T. cruzi—are unable to mediate the uptake of pyrimidine. However, the requirement of de novo pyrimidine biosynthesis for parasite growth and survival has not yet been elucidated. Carbamoyl-phosphate synthetase II (CPSII) is the first and rate-limiting enzyme of the de novo biosynthetic pathway, and increased CPSII activity is associated with the rapid proliferation of tumor cells. In the present study, we showed that disruption of the T. cruzicpsII gene significantly reduced parasite growth. In particular, the growth of amastigotes lacking the cpsII gene was severely suppressed. Thus, the de novo pyrimidine pathway is important for proliferation of T. cruzi in the host cell cytoplasm and represents a promising target for chemotherapy against Chagas disease.

  16. Whole Exome Sequencing for a Patient with Rubinstein-Taybi Syndrome Reveals de Novo Variants besides an Overt CREBBP Mutation

    Directory of Open Access Journals (Sweden)

    Hee Jeong Yoo

    2015-03-01

    Full Text Available Rubinstein-Taybi syndrome (RSTS is a rare condition with a prevalence of 1 in 125,000–720,000 births and characterized by clinical features that include facial, dental, and limb dysmorphology and growth retardation. Most cases of RSTS occur sporadically and are caused by de novo mutations. Cytogenetic or molecular abnormalities are detected in only 55% of RSTS cases. Previous genetic studies have yielded inconsistent results due to the variety of methods used for genetic analysis. The purpose of this study was to use whole exome sequencing (WES to evaluate the genetic causes of RSTS in a young girl presenting with an Autism phenotype. We used the Autism diagnostic observation schedule (ADOS and Autism diagnostic interview revised (ADI-R to confirm her diagnosis of Autism. In addition, various questionnaires were used to evaluate other psychiatric features. We used WES to analyze the DNA sequences of the patient and her parents and to search for de novo variants. The patient showed all the typical features of Autism, WES revealed a de novo frameshift mutation in CREBBP and de novo sequence variants in TNC and IGFALS genes. Mutations in the CREBBP gene have been extensively reported in RSTS patients, while potential missense mutations in TNC and IGFALS genes have not previously been associated with RSTS. The TNC and IGFALS genes are involved in central nervous system development and growth. It is possible for patients with RSTS to have additional de novo variants that could account for previously unexplained phenotypes.

  17. A case of de novo duplication of 15q24-q26.3

    Directory of Open Access Journals (Sweden)

    Hye Ran Kim

    2011-06-01

    Full Text Available Distal duplication, or trisomy 15q, is an extremely rare chromosomal disorder characterized by prenatal and postnatal overgrowth, mental retardation, and craniofacial malformations. Additional abnormalities typically include an unusually short neck, malformations of the fingers and toes, scoliosis and skeletal malformations, genital abnormalities, particularly in affected males, and, in some cases, cardiac defects. The range and severity of symptoms and physical findings may vary from case to case, depending upon the length and location of the duplicated portion of chromosome 15q. Most reported cases of duplication of the long arm of chromosome 15 frequently have more than one segmental imbalance resulting from unbalanced translocations involving chromosome 15 and deletions in another chromosome, as well as other structural chromosomal abnormalities. We report a female newborn with a de novo duplication, 15q24- q26.3, showing intrauterine overgrowth, a narrow asymmetric face with down-slanting palpebral fissures, a large, prominent nose, and micrognathia, arachnodactyly, camptodactyly, congenital heart disease, hydronephrosis, and hydroureter. Chromosomal analysis showed a 46,XX,inv(9(p12q13,dup(15(q24q26.3. Array comparative genomic hybridization analysis revealed a gain of 42 clones on 15q24-q26.3. This case represents the only reported patient with a de novo 15q24-q26.3 duplication that did not result from an unbalanced translocation and did not have a concomitant monosomic component in Korea.

  18. De novo transcriptome assembly of drought tolerant CAM plants, Agave deserti and Agave tequilana.

    Science.gov (United States)

    Gross, Stephen M; Martin, Jeffrey A; Simpson, June; Abraham-Juarez, María Jazmín; Wang, Zhong; Visel, Axel

    2013-08-19

    Agaves are succulent monocotyledonous plants native to xeric environments of North America. Because of their adaptations to their environment, including crassulacean acid metabolism (CAM, a water-efficient form of photosynthesis), and existing technologies for ethanol production, agaves have gained attention both as potential lignocellulosic bioenergy feedstocks and models for exploring plant responses to abiotic stress. However, the lack of comprehensive Agave sequence datasets limits the scope of investigations into the molecular-genetic basis of Agave traits. Here, we present comprehensive, high quality de novo transcriptome assemblies of two Agave species, A. tequilana and A. deserti, built from short-read RNA-seq data. Our analyses support completeness and accuracy of the de novo transcriptome assemblies, with each species having a minimum of approximately 35,000 protein-coding genes. Comparison of agave proteomes to those of additional plant species identifies biological functions of gene families displaying sequence divergence in agave species. Additionally, a focus on the transcriptomics of the A. deserti juvenile leaf confirms evolutionary conservation of monocotyledonous leaf physiology and development along the proximal-distal axis. Our work presents a comprehensive transcriptome resource for two Agave species and provides insight into their biology and physiology. These resources are a foundation for further investigation of agave biology and their improvement for bioenergy development.

  19. Delayed manifestation and transmission bias of de novo chromosome mutations. Their relevance for radiation health effect

    International Nuclear Information System (INIS)

    Sasaki, Masao S.

    2006-01-01

    The origin and transmission of de novo chromosome mutations were reviewed on the basis of our chromosome studies in retinoblastoma patients and male infertility. In a series of 264 sporadic retinoblastoma families, gross chromosome rearrangements involving the RB1 locus were identified in 23 cases (8.7%), of which 16 were non-mosaic and 7 were mosaic mutations. The newly formed chromosome mutations, whether they were non-mosaic or mosaic, had a strong bias towards paternally derived chromosome, indicating that they shared a common mechanism where a pre-mutational event or instability is carried over to zygote by sperm and manifested as gross chromosome mutation at the early stages of development. The de novo chromosome mutations are preferentially transmitted through female carriers. This transmission bias is consistent with the finding of higher frequencies of translocation carriers in infertile men (7.69% versus 0.27% in general populations) in whom meiotic progression is severely suppressed, possibly through activation of meiotic checkpoints. Such a meiotic surveillance mechanism may minimize the spreading of newly-arisen chromosome mutations in populations. A quantitative model of meiotic surveillance mechanism is proposed and successfully applied to the published data on ''humped'' dose-response curves for radiation-induced spermatogonial reciprocal translocations in several mammalian species. (author)

  20. De novo biosynthesis of vanillin in fission yeast (Schizosaccharomyces pombe) and baker's yeast (Saccharomyces cerevisiae).

    Science.gov (United States)

    Hansen, Esben H; Møller, Birger Lindberg; Kock, Gertrud R; Bünner, Camilla M; Kristensen, Charlotte; Jensen, Ole R; Okkels, Finn T; Olsen, Carl E; Motawia, Mohammed S; Hansen, Jørgen

    2009-05-01

    Vanillin is one of the world's most important flavor compounds, with a global market of 180 million dollars. Natural vanillin is derived from the cured seed pods of the vanilla orchid (Vanilla planifolia), but most of the world's vanillin is synthesized from petrochemicals or wood pulp lignins. We have established a true de novo biosynthetic pathway for vanillin production from glucose in Schizosaccharomyces pombe, also known as fission yeast or African beer yeast, as well as in baker's yeast, Saccharomyces cerevisiae. Productivities were 65 and 45 mg/liter, after introduction of three and four heterologous genes, respectively. The engineered pathways involve incorporation of 3-dehydroshikimate dehydratase from the dung mold Podospora pauciseta, an aromatic carboxylic acid reductase (ACAR) from a bacterium of the Nocardia genus, and an O-methyltransferase from Homo sapiens. In S. cerevisiae, the ACAR enzyme required activation by phosphopantetheinylation, and this was achieved by coexpression of a Corynebacterium glutamicum phosphopantetheinyl transferase. Prevention of reduction of vanillin to vanillyl alcohol was achieved by knockout of the host alcohol dehydrogenase ADH6. In S. pombe, the biosynthesis was further improved by introduction of an Arabidopsis thaliana family 1 UDP-glycosyltransferase, converting vanillin into vanillin beta-D-glucoside, which is not toxic to the yeast cells and thus may be accumulated in larger amounts. These de novo pathways represent the first examples of one-cell microbial generation of these valuable compounds from glucose. S. pombe yeast has not previously been metabolically engineered to produce any valuable, industrially scalable, white biotech commodity.

  1. The significance of trilineage myelodysplasia in de novo acute myeloblastic leukemia: clinical and laboratory features.

    Science.gov (United States)

    Lima, C S; Vassalo, J; Lorand-Metze, I; Bechelli, A P; Souza, C A

    1997-01-01

    A prospective study was undertaken to elucidate the clinical and laboratory differences between de novo acute myeloid leukemia (AML) and AML with trilineage myelodysplasia (AML-TMDS). One hundred and seven patients with AML were diagnosed at the University Hospital between January 1987 and July 1992, and were followed until July 1995. TMDS was identified in 17 of them (16%). With regard to age and sex distribution no difference was found between AML patients with and without TMDS (p = 0.43, p = 0.54, respectively). The duration of symptoms at presentation in AML-TMDS was similar to those observed in de novo AML (p = 0.29). Hemoglobin values and platelet counts were similar in both groups of patients (p = 0.45, p = 0.44, respectively). However, peripheral white blood cell and neutrophil counts, as well as blast counts in AML-TMDS patients were lower than those observed in AML without TMDS patients (p leukemia transformation occurs in a more undifferentiated pluripotent stem cell, leading to a dysplastic residual hemopoiesis besides the blast proliferation; 2) the incidence of TMDS in our group of patients did not influence the clinical outcome after treatment of the disease.

  2. Customizable de novo design strategies for DOCK: Application to HIVgp41 and other therapeutic targets.

    Science.gov (United States)

    Allen, William J; Fochtman, Brian C; Balius, Trent E; Rizzo, Robert C

    2017-11-15

    De novo design can be used to explore vast areas of chemical space in computational lead discovery. As a complement to virtual screening, from-scratch construction of molecules is not limited to compounds in pre-existing vendor catalogs. Here, we present an iterative fragment growth method, integrated into the program DOCK, in which new molecules are built using rules for allowable connections based on known molecules. The method leverages DOCK's advanced scoring and pruning approaches and users can define very specific criteria in terms of properties or features to customize growth toward a particular region of chemical space. The code was validated using three increasingly difficult classes of calculations: (1) Rebuilding known X-ray ligands taken from 663 complexes using only their component parts (focused libraries), (2) construction of new ligands in 57 drug target sites using a library derived from ∼13M drug-like compounds (generic libraries), and (3) application to a challenging protein-protein interface on the viral drug target HIVgp41. The computational testing confirms that the de novo DOCK routines are robust and working as envisioned, and the compelling results highlight the potential utility for designing new molecules against a wide variety of important protein targets. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  3. Adopting De Novo Programming Approach on IC Design Service Firms Resources Integration

    Directory of Open Access Journals (Sweden)

    James K. C. Chen

    2014-01-01

    Full Text Available The semiconductor industry has very important position in computer industry, ICT field, and new electronic technology developing. The IC design service is one of key factor of semiconductor industry development. There are more than 365 IC design service firms have been established around Hsinchu Science Park in Taiwan. Building an efficient planning model for IC design service firm resources integrating is very interest issue. This study aims to construct a planning model for IC design service firm implementation resources integration. This study uses the De Novo programming as an approach of criteria alternative to achieve optimal resource allocation on IC design firm. Results show the IC design service firm should conduct open innovation concept and utilizes design outsourcing obtains cost down and enhance IC design service business performance. This plan model of De Novo programming is not only for IC design service firm and also can apply to the other industrial implementation strategic alliance/integrating resource. This plan model is a universal model for the others industries field.

  4. Therapeutic equivalence and pharmacokinetics of generic tacrolimus formulation in de novo kidney transplant patients.

    Science.gov (United States)

    Min, Sang-Il; Ha, Jongwon; Kim, Yon Su; Ahn, Sang Hyun; Park, Taejin; Park, Dae Do; Kim, Suh Min; Min, Seung-Kee; Hong, Hyejin; Ahn, Curie; Kim, Sang Joon

    2013-12-01

    There is a growing concern about the therapeutic equivalence of the generic tacrolimus formulation (GEN Tacrolimus) to the reference tacrolimus (REF Tacrolimus) in solid organ transplantation. A prospective, randomized study of 126 de novo renal transplant patients was conducted to compare the efficacy, safety and pharmacokinetic (PK) profiles between GEN tacrolimus (n = 63) and REF tacrolimus (n = 63). The PK of tacrolimus was evaluated on Day 10 and 6 months under steady-state condition. Crossover study was carried out in 66 patients at 6 months. On Day 10, 117 patients completed PK profiles (54 GEN tacrolimus and 63 REF tacrolimus) and GEN tacrolimus showed comparable C(0) (9.8 ± 2.5 versus 9.7 ± 3.0 ng/mL, P = 0.80) but significantly higher dose-normalized C(max) (309.1 ± 191.9 versus 192.5 ± 95.2 ng/mL/mg/kg, P PK profiles evaluated at 9 months showed that generic substitution also resulted in an 'early and high C(max)'. Efficacy and safety data were comparable over the 9-month study period. Therapeutic equivalence and the PK of GEN tacrolimus should be evaluated in patients undergoing de novo renal transplantation.

  5. De novo mutations in ATP1A3 cause alternating hemiplegia of childhood

    Science.gov (United States)

    Heinzen, Erin L.; Swoboda, Kathryn J.; Hitomi, Yuki; Gurrieri, Fiorella; Nicole, Sophie; de Vries, Boukje; Tiziano, F. Danilo; Fontaine, Bertrand; Walley, Nicole M.; Heavin, Sinéad; Panagiotakaki, Eleni; Fiori, Stefania; Abiusi, Emanuela; Di Pietro, Lorena; Sweney, Matthew T.; Newcomb, Tara M.; Viollet, Louis; Huff, Chad; Jorde, Lynn B.; Reyna, Sandra P.; Murphy, Kelley J.; Shianna, Kevin V.; Gumbs, Curtis E.; Little, Latasha; Silver, Kenneth; Ptác̆ek, Louis J.; Haan, Joost; Ferrari, Michel D.; Bye, Ann M.; Herkes, Geoffrey K.; Whitelaw, Charlotte M.; Webb, David; Lynch, Bryan J.; Uldall, Peter; King, Mary D.; Scheffer, Ingrid E.; Neri, Giovanni; Arzimanoglou, Alexis; van den Maagdenberg, Arn M.J.M.; Sisodiya, Sanjay M.; Mikati, Mohamad A.; Goldstein, David B.; Nicole, Sophie; Gurrieri, Fiorella; Neri, Giovanni; de Vries, Boukje; Koelewijn, Stephany; Kamphorst, Jessica; Geilenkirchen, Marije; Pelzer, Nadine; Laan, Laura; Haan, Joost; Ferrari, Michel; van den Maagdenberg, Arn; Zucca, Claudio; Bassi, Maria Teresa; Franchini, Filippo; Vavassori, Rosaria; Giannotta, Melania; Gobbi, Giuseppe; Granata, Tiziana; Nardocci, Nardo; De Grandis, Elisa; Veneselli, Edvige; Stagnaro, Michela; Gurrieri, Fiorella; Neri, Giovanni; Vigevano, Federico; Panagiotakaki, Eleni; Oechsler, Claudia; Arzimanoglou, Alexis; Nicole, Sophie; Giannotta, Melania; Gobbi, Giuseppe; Ninan, Miriam; Neville, Brian; Ebinger, Friedrich; Fons, Carmen; Campistol, Jaume; Kemlink, David; Nevsimalova, Sona; Laan, Laura; Peeters-Scholte, Cacha; van den Maagdenberg, Arn; Casaer, Paul; Casari, Giorgio; Sange, Guenter; Spiel, Georg; Boneschi, Filippo Martinelli; Zucca, Claudio; Bassi, Maria Teresa; Schyns, Tsveta; Crawley, Francis; Poncelin, Dominique; Vavassori, Rosaria

    2012-01-01

    Alternating hemiplegia of childhood (AHC) is a rare, severe neurodevelopmental syndrome characterized by recurrent hemiplegic episodes and distinct neurologic manifestations. AHC is usually a sporadic disorder with unknown etiology. Using exome sequencing of seven patients with AHC, and their unaffected parents, we identified de novo nonsynonymous mutations in ATP1A3 in all seven AHC patients. Subsequent sequence analysis of ATP1A3 in 98 additional patients revealed that 78% of AHC cases have a likely causal ATP1A3 mutation, including one inherited mutation in a familial case of AHC. Remarkably, six ATP1A3 mutations explain the majority of patients, including one observed in 36 patients. Unlike ATP1A3 mutations that cause rapid-onset-dystonia-parkinsonism, AHC-causing mutations revealed consistent reductions in ATPase activity without effects on protein expression. This work identifies de novo ATP1A3 mutations as the primary cause of AHC, and offers insight into disease pathophysiology by expanding the spectrum of phenotypes associated with mutations in this gene. PMID:22842232

  6. Colorimetry provides a rapid objective measurement of de novo hair growth rate in mice.

    Science.gov (United States)

    Tzung, Tien-Yi; Yang, Chia-Yi; Huang, Yung-Chang; Kao, Fu-Jen

    2009-11-01

    Depilated mice have been used as a test platform for hair growth-regulating agents. However, currently available assessment tools for hair growth in mice are less than ideal. Tristimulus colorimetry of the fur color of depilated agouti, albino, and black mice with L*, a*, and b* values were performed daily until the full growth of pelage. Using light-emitting diode (LED) irradiation (650 and 890 nm) with a daily dose of 3.5 J/cm(2) as hair growth regulators, the hair growth rates observed by the global assessment were compared with those derived from colorimetry. In contrast to a* and b* values, L* values changed more drastically over time in the anagen phase regardless of fur color. Unlike the inhibitory effect of 650 nm irradiation, LED of 890 nm promoted de novo hair regrowth in mice. The difference in hair growth rates detected by colorimetry paralleled the observation made by the global assessment. The L* value of fur color obtained by tristimulus colorimetry was a sensitive yet quantitative indicator of de novo hair growth, and could be used to project the hair growth rate in mice.

  7. De novo transcriptome assembly of two different peach cultivars grown in Korea

    Directory of Open Access Journals (Sweden)

    Yeonhwa Jo

    2015-12-01

    Full Text Available Peach (Prunus persica is one of the most popular stone fruits worldwide. Next generation sequencing (NGS has facilitated genome and transcriptome analyses of several stone fruit trees. In this study, we conducted de novo transcriptome analyses of two peach cultivars grown in Korea. Leaves of two cultivars, referred to as Jangtaek and Mibaek, were harvested and used for library preparation. The two prepared libraries were paired-end sequenced by the HiSeq2000 system. We obtained 8.14 GB and 9.62 GB sequence data from Jangtaek and Mibaek (NCBI accession numbers: SRS1056585 and SRS1056587, respectively. The Trinity program was used to assemble two transcriptomes de novo, resulting in 110,477 (Jangtaek and 136,196 (Mibaek transcripts. TransDecoder identified possible coding regions in assembled transcripts. The identified proteins were subjected to BLASTP search against NCBI's non-redundant database for functional annotation. This study provides transcriptome data for two peach cultivars, which might be useful for genetic marker development and comparative transcriptome analyses.

  8. De novo generation of infectious prions with bacterially expressed recombinant prion protein.

    Science.gov (United States)

    Zhang, Zhihong; Zhang, Yi; Wang, Fei; Wang, Xinhe; Xu, Yuanyuan; Yang, Huaiyi; Yu, Guohua; Yuan, Chonggang; Ma, Jiyan

    2013-12-01

    The prion hypothesis is strongly supported by the fact that prion infectivity and the pathogenic conformer of prion protein (PrP) are simultaneously propagated in vitro by the serial protein misfolding cyclic amplification (sPMCA). However, due to sPMCA's enormous amplification power, whether an infectious prion can be formed de novo with bacterially expressed recombinant PrP (rPrP) remains to be satisfactorily resolved. To address this question, we performed unseeded sPMCA with rPrP in a laboratory that has never been exposed to any native prions. Two types of proteinase K (PK)-resistant and self-perpetuating recombinant PrP conformers (rPrP-res) with PK-resistant cores of 17 or 14 kDa were generated. A bioassay revealed that rPrP-res(17kDa) was highly infectious, causing prion disease in wild-type mice with an average survival time of about 172 d. In contrast, rPrP-res(14kDa) completely failed to induce any disease. Our findings reveal that sPMCA is sufficient to initiate various self-perpetuating PK-resistant rPrP conformers, but not all of them possess in vivo infectivity. Moreover, generating an infectious prion in a prion-free environment establishes that an infectious prion can be formed de novo with bacterially expressed rPrP.

  9. De novo formation of nucleoli in developing mouse embryos originating from enucleolated zygotes.

    Science.gov (United States)

    Kyogoku, Hirohisa; Fulka, Josef; Wakayama, Teruhiko; Miyano, Takashi

    2014-06-01

    The large, compact oocyte nucleoli, sometimes referred to as nucleolus precursor bodies (NPBs), are essential for embryonic development in mammals; in their absence, the oocytes complete maturation and can be fertilized, but no nucleoli are formed in the zygote or embryo, leading to developmental failure. It has been convincingly documented that zygotes inherit the oocyte nucleolar material and form NPBs again in pronuclei. It is commonly accepted that during early embryonic development, the original compact zygote NPBs gradually transform into reticulated nucleoli of somatic cells. Here, we show that zygote NPBs are not required for embryonic and full-term development in the mouse. When NPBs were removed from late-stage zygotes by micromanipulation, the enucleolated zygotes developed to the blastocyst stage and, after transfer to recipients, live pups were obtained. We also describe de novo formation of nucleoli in developing embryos. After removal of NPBs from zygotes, they formed new nucleoli after several divisions. These results indicate that the zygote NPBs are not used in embryonic development and that the nucleoli in developing embryos originate from de novo synthesized materials. © 2014. Published by The Company of Biologists Ltd.

  10. Brain metabolic correlates of dopaminergic degeneration in de novo idiopathic Parkinson's disease

    International Nuclear Information System (INIS)

    Berti, Valentina; Polito, Cristina; Vanzi, Eleonora; Cristofaro, Maria Teresa de; Pellicano, Giannantonio; Mungai, Francesco; Formiconi, Andreas Robert; Pupi, Alberto; Ramat, Silvia; Marini, Paolo; Sorbi, Sandro

    2010-01-01

    The aim of the present study was to evaluate the reciprocal relationships between motor impairment, dopaminergic dysfunction, and cerebral metabolism (rCMRglc) in de novo Parkinson's disease (PD) patients. Twenty-six de novo untreated PD patients were scanned with 123 I-FP-CIT SPECT and 18 F-FDG PET. The dopaminergic impairment was measured with putaminal 123 I-FP-CIT binding potential (BP), estimated with two different techniques: an iterative reconstruction algorithm (BP OSEM ) and the least-squares (LS) method (BP LS ). Statistical parametric mapping (SPM) multiple regression analyses were performed to determine the specific brain regions in which UPDRS III scores and putaminal BP values correlated with rCMRglc. The SPM results showed a negative correlation between UPDRS III and rCMRglc in premotor cortex, and a positive correlation between BP OSEM and rCMRglc in premotor and dorsolateral prefrontal cortex, not surviving at multiple comparison correction. Instead, there was a positive significant correlation between putaminal BP LS and rCMRglc in premotor, dorsolateral prefrontal, anterior prefrontal, and orbitofrontal cortex (p LS is an efficient parameter for exploring the correlations between PD severity and rCMRglc cortical changes. The correlation between dopaminergic degeneration and rCMRglc in several prefrontal regions likely represents the cortical functional correlate of the dysfunction in the motor basal ganglia-cortical circuit in PD. This finding suggests focusing on the metabolic course of these areas to follow PD progression and to analyze treatment effects. (orig.)

  11. A de novo nonsense PDGFB mutation causing idiopathic basal ganglia calcification with laryngeal dystonia.

    Science.gov (United States)

    Nicolas, Gaël; Jacquin, Agnès; Thauvin-Robinet, Christel; Rovelet-Lecrux, Anne; Rouaud, Olivier; Pottier, Cyril; Aubriot-Lorton, Marie-Hélène; Rousseau, Stéphane; Wallon, David; Duvillard, Christian; Béjot, Yannick; Frébourg, Thierry; Giroud, Maurice; Campion, Dominique; Hannequin, Didier

    2014-10-01

    Idiopathic basal ganglia calcification (IBGC) is characterized by brain calcification and a wide variety of neurologic and psychiatric symptoms. In families with autosomal dominant inheritance, three causative genes have been identified: SLC20A2, PDGFRB, and, very recently, PDGFB. Whereas in clinical practice sporadic presentation of IBGC is frequent, well-documented reports of true sporadic occurrence are rare. We report the case of a 20-year-old woman who presented laryngeal dystonia revealing IBGC. Her healthy parents' CT scans were both normal. We identified in the proband a new nonsense mutation in exon 4 of PDGFB, c.439C>T (p.Gln147*), which was absent from the parents' DNA. This mutation may result in a loss-of-function of PDGF-B, which has been shown to cause IBGC in humans and to disrupt the blood-brain barrier in mice, resulting in brain calcification. The c.439C>T mutation is located between two previously reported nonsense mutations, c.433C>T (p.Gln145*) and c.445C>T (p.Arg149*), on a region that could be a hot spot for de novo mutations. We present the first full demonstration of the de novo occurrence of an IBGC-causative mutation in a sporadic case.

  12. De novo biosynthesis of volatiles induced by insect herbivory in cotton plants

    International Nuclear Information System (INIS)

    Pare, P.W.; Tumlinson, J.H.

    1997-01-01

    In response to insect feeding on the leaves, cotton (Gossypium hirsutum L.) plants release elevated levels of volatiles, which can serve as a chemical signal that attracts natural enemies of the herbivore to the damaged plant. Pulse-labeling experiments with [13C]CO2 demonstrated that many of the volatiles released, including the acyclic terpenes (E,E)-alpha-farnesene, (E)-beta-farnesene, (E)-beta-ocimene, linalool,(E)-4,8-dimethyl-1,3,7-nonatriene, and (E,E)-4,8,12-trimethyl-1,3,7,11-tridecatetrane, as well as the shikimate pathway product indole, are biosynthesized de novo following insect damage. However, other volatile constituents, including several cyclic terpenes, butyrates, and green leaf volatiles of the lipoxygenase pathway are released from storage or synthesized from stored intermediates. Analysis of volatiles from artificially damaged plants, with and without beet armyworm (Spodoptera exigua Hubner) oral secretions exogenously applied to the leaves, as well as volatiles from beet armyworm-damaged and -undamaged control plants, demonstrated that the application of caterpillar oral secretions increased both the production and release of several volatiles that are synthesized de novo in response to insect feeding. These results establish that the plant plays an active and dynamic role in mediating the interaction between herbivores and natural enemies of herbivores

  13. Visualizing the origins of selfish de novo mutations in individual seminiferous tubules of human testes.

    Science.gov (United States)

    Maher, Geoffrey J; McGowan, Simon J; Giannoulatou, Eleni; Verrill, Clare; Goriely, Anne; Wilkie, Andrew O M

    2016-03-01

    De novo point mutations arise predominantly in the male germline and increase in frequency with age, but it has not previously been possible to locate specific, identifiable mutations directly within the seminiferous tubules of human testes. Using microdissection of tubules exhibiting altered expression of the spermatogonial markers MAGEA4, FGFR3, and phospho-AKT, whole genome amplification, and DNA sequencing, we establish an in situ strategy for discovery and analysis of pathogenic de novo mutations. In 14 testes from men aged 39-90 y, we identified 11 distinct gain-of-function mutations in five genes (fibroblast growth factor receptors FGFR2 and FGFR3, tyrosine phosphatase PTPN11, and RAS oncogene homologs HRAS and KRAS) from 16 of 22 tubules analyzed; all mutations have known associations with severe diseases, ranging from congenital or perinatal lethal disorders to somatically acquired cancers. These results support proposed selfish selection of spermatogonial mutations affecting growth factor receptor-RAS signaling, highlight its prevalence in older men, and enable direct visualization of the microscopic anatomy of elongated mutant clones.

  14. Concept of combinatorial de novo design of drug-like molecules by particle swarm optimization.

    Science.gov (United States)

    Hartenfeller, Markus; Proschak, Ewgenij; Schüller, Andreas; Schneider, Gisbert

    2008-07-01

    We present a fast stochastic optimization algorithm for fragment-based molecular de novo design (COLIBREE, Combinatorial Library Breeding). The search strategy is based on a discrete version of particle swarm optimization. Molecules are represented by a scaffold, which remains constant during optimization, and variable linkers and side chains. Different linkers represent virtual chemical reactions. Side-chain building blocks were obtained from pseudo-retrosynthetic dissection of large compound databases. Here, ligand-based design was performed using chemically advanced template search (CATS) topological pharmacophore similarity to reference ligands as fitness function. A weighting scheme was included for particle swarm optimization-based molecular design, which permits the use of many reference ligands and allows for positive and negative design to be performed simultaneously. In a case study, the approach was applied to the de novo design of potential peroxisome proliferator-activated receptor subtype-selective agonists. The results demonstrate the ability of the technique to cope with large combinatorial chemistry spaces and its applicability to focused library design. The technique was able to perform exploitation of a known scheme and at the same time explorative search for novel ligands within the framework of a given molecular core structure. It thereby represents a practical solution for compound screening in the early hit and lead finding phase of a drug discovery project.

  15. A multi-method approach toward de novo glycan characterization: a Man-5 case study.

    Science.gov (United States)

    Prien, Justin M; Prater, Bradley D; Cockrill, Steven L

    2010-05-01

    Regulatory agencies' expectations for biotherapeutic approval are becoming more stringent with regard to product characterization, where minor species as low as 0.1% of a given profile are typically identified. The mission of this manuscript is to demonstrate a multi-method approach toward de novo glycan characterization and quantitation, including minor species at or approaching the 0.1% benchmark. Recently, unexpected isomers of the Man(5)GlcNAc(2) (M(5)) were reported (Prien JM, Ashline DJ, Lapadula AJ, Zhang H, Reinhold VN. 2009. The high mannose glycans from bovine ribonuclease B isomer characterization by ion trap mass spectrometry (MS). J Am Soc Mass Spectrom. 20:539-556). In the current study, quantitative analysis of these isomers found in commercial M(5) standard demonstrated that they are in low abundance (2-aminobenzoic acid to detect and chromatographically resolve multiple M(5) isomers in bovine ribonuclease B. With this multi-method approach, we have the capabilities to comprehensively characterize a biotherapeutic's glycan array in a de novo manner, including structural isomers at >/=0.1% of the total chromatographic peak area.

  16. Damaging de novo mutations diminish motor skills in children on the autism spectrum.

    Science.gov (United States)

    Buja, Andreas; Volfovsky, Natalia; Krieger, Abba M; Lord, Catherine; Lash, Alex E; Wigler, Michael; Iossifov, Ivan

    2018-02-20

    In individuals with autism spectrum disorder (ASD), de novo mutations have previously been shown to be significantly correlated with lower IQ but not with the core characteristics of ASD: deficits in social communication and interaction and restricted interests and repetitive patterns of behavior. We extend these findings by demonstrating in the Simons Simplex Collection that damaging de novo mutations in ASD individuals are also significantly and convincingly correlated with measures of impaired motor skills. This correlation is not explained by a correlation between IQ and motor skills. We find that IQ and motor skills are distinctly associated with damaging mutations and, in particular, that motor skills are a more sensitive indicator of mutational severity than is IQ, as judged by mutational type and target gene. We use this finding to propose a combined classification of phenotypic severity: mild (little impairment of either), moderate (impairment mainly to motor skills), and severe (impairment of both IQ and motor skills). Copyright © 2018 the Author(s). Published by PNAS.

  17. REQUALIFICAÇÃO URBANA E DESPEJOS EM CENTROS NOVO E ANTIGO DE SALVADOR

    Directory of Open Access Journals (Sweden)

    John Gledhill

    Full Text Available A cidade de Salvador replica o processo de “acumulação por espoliação”, característico de um urbanismo neoliberal em todo o mundo. Neste artigo, comparamos como atua a lógica da requalificação urbana em duas zonas da cidade. A primeira é uma grande e historicamente combativa favela localizada na região que tem se tornado o mais moderno “novo centro” da cidade. Nela, a chave dos problemas são os novos projetos de mobilidade urbana e a construção de condomínios para outras classes sociais. A segunda zona é o centro colonial da cidade, que experimenta uma nova fase de gentrificação. Ali, as políticas de patrimônio histórico se encontram com outras políticas, transformando os remanescentes espaços públicos da cidade neoliberal securitizada em zonas mais seguras para turistas e residentes mais ricos. Enfatizamos o valor de um entendimento etnograficamente fundamentado para compreender o que essas mudanças significam para moradores pobres da cidade, assim como a complexidade, a heterogeneidade e a ambiguidade de suas diferentes reações.

  18. De novo mutations in HCN1 cause early infantile epileptic encephalopathy.

    Science.gov (United States)

    Nava, Caroline; Dalle, Carine; Rastetter, Agnès; Striano, Pasquale; de Kovel, Carolien G F; Nabbout, Rima; Cancès, Claude; Ville, Dorothée; Brilstra, Eva H; Gobbi, Giuseppe; Raffo, Emmanuel; Bouteiller, Delphine; Marie, Yannick; Trouillard, Oriane; Robbiano, Angela; Keren, Boris; Agher, Dahbia; Roze, Emmanuel; Lesage, Suzanne; Nicolas, Aude; Brice, Alexis; Baulac, Michel; Vogt, Cornelia; El Hajj, Nady; Schneider, Eberhard; Suls, Arvid; Weckhuysen, Sarah; Gormley, Padhraig; Lehesjoki, Anna-Elina; De Jonghe, Peter; Helbig, Ingo; Baulac, Stéphanie; Zara, Federico; Koeleman, Bobby P C; Haaf, Thomas; LeGuern, Eric; Depienne, Christel

    2014-06-01

    Hyperpolarization-activated, cyclic nucleotide-gated (HCN) channels contribute to cationic Ih current in neurons and regulate the excitability of neuronal networks. Studies in rat models have shown that the Hcn1 gene has a key role in epilepsy, but clinical evidence implicating HCN1 mutations in human epilepsy is lacking. We carried out exome sequencing for parent-offspring trios with fever-sensitive, intractable epileptic encephalopathy, leading to the discovery of two de novo missense HCN1 mutations. Screening of follow-up cohorts comprising 157 cases in total identified 4 additional amino acid substitutions. Patch-clamp recordings of Ih currents in cells expressing wild-type or mutant human HCN1 channels showed that the mutations had striking but divergent effects on homomeric channels. Individuals with mutations had clinical features resembling those of Dravet syndrome with progression toward atypical absences, intellectual disability and autistic traits. These findings provide clear evidence that de novo HCN1 point mutations cause a recognizable early-onset epileptic encephalopathy in humans.

  19. De Novo Advanced Adult-Onset Offending: New Evidence from a Population of Federal Correctional Clients.

    Science.gov (United States)

    DeLisi, Matt; Tahja, Katherine N; Drury, Alan J; Elbert, Michael J; Caropreso, Daniel E; Heinrichs, Timothy

    2018-01-01

    Adult antisocial behavior is almost always predated by delinquency during childhood or adolescence; however, there is also evidence of adult-onset criminal offending. This study examined this controversial subgroup of offenders using self-reported and official data from a total population of federal correctional clients selected from the Midwestern United States. Difference of means t-tests, chi-square tests, and logistic regression models found that 11.7% of clients had an adult onset of offending and 2.7% of clients (n = 23) had an onset occurring at age 60 years or older. This group-introduced as de novo advanced adult-onset offenders-had high socioeconomic status, mixed evidence of adverse childhood experiences, and virtually no usage of drugs with the exception of alcohol. These offenders were primarily convicted of social security and white-collar crimes and evinced remarkably low psychopathology and criminal risk. More research is needed to replicate the phenomenon of de novo advanced adult-onset offending. © 2017 American Academy of Forensic Sciences.

  20. Developmental and adult-specific processes contribute to de novo neuromuscular regeneration in the lizard tail.

    Science.gov (United States)

    Tokuyama, Minami A; Xu, Cindy; Fisher, Rebecca E; Wilson-Rawls, Jeanne; Kusumi, Kenro; Newbern, Jason M

    2018-01-15

    Peripheral nerves exhibit robust regenerative capabilities in response to selective injury among amniotes, but the regeneration of entire muscle groups following volumetric muscle loss is limited in birds and mammals. In contrast, lizards possess the remarkable ability to regenerate extensive de novo muscle after tail loss. However, the mechanisms underlying reformation of the entire neuromuscular system in the regenerating lizard tail are not completely understood. We have tested whether the regeneration of the peripheral nerve and neuromuscular junctions (NMJs) recapitulate processes observed during normal neuromuscular development in the green anole, Anolis carolinensis. Our data confirm robust axonal outgrowth during early stages of tail regeneration and subsequent NMJ formation within weeks of autotomy. Interestingly, NMJs are overproduced as evidenced by a persistent increase in NMJ density 120 and 250 days post autotomy (DPA). Substantial Myelin Basic Protein (MBP) expression could also be detected along regenerating nerves indicating that the ability of Schwann cells to myelinate newly formed axons remained intact. Overall, our data suggest that the mechanism of de novo nerve and NMJ reformation parallel, in part, those observed during neuromuscular development. However, the prolonged increase in NMJ number and aberrant muscle differentiation hint at processes specific to the adult response. An examination of the coordinated exchange between peripheral nerves, Schwann cells, and newly synthesized muscle of the regenerating neuromuscular system may assist in the identification of candidate molecules that promote neuromuscular recovery in organisms incapable of a robust regenerative response. Copyright © 2017 Elsevier Inc. All rights reserved.

  1. Evaluation of the impact of RNA preservation methods of spiders for de novo transcriptome assembly.

    Science.gov (United States)

    Kono, Nobuaki; Nakamura, Hiroyuki; Ito, Yusuke; Tomita, Masaru; Arakawa, Kazuharu

    2016-05-01

    With advances in high-throughput sequencing technologies, de novo transcriptome sequencing and assembly has become a cost-effective method to obtain comprehensive genetic information of a species of interest, especially in nonmodel species with large genomes such as spiders. However, high-quality RNA is essential for successful sequencing, and sample preservation conditions require careful consideration for the effective storage of field-collected samples. To this end, we report a streamlined feasibility study of various storage conditions and their effects on de novo transcriptome assembly results. The storage parameters considered include temperatures ranging from room temperature to -80°C; preservatives, including ethanol, RNAlater, TRIzol and RNAlater-ICE; and sample submersion states. As a result, intact RNA was extracted and assembly was successful when samples were preserved at low temperatures regardless of the type of preservative used. The assemblies as well as the gene expression profiles were shown to be robust to RNA degradation, when 30 million 150-bp paired-end reads are obtained. The parameters for sample storage, RNA extraction, library preparation, sequencing and in silico assembly considered in this work provide a guideline for the study of field-collected samples of spiders. © 2015 John Wiley & Sons Ltd.

  2. The Folding of de Novo Designed Protein DS119 via Molecular Dynamics Simulations

    Directory of Open Access Journals (Sweden)

    Moye Wang

    2016-04-01

    Full Text Available As they are not subjected to natural selection process, de novo designed proteins usually fold in a manner different from natural proteins. Recently, a de novo designed mini-protein DS119, with a βαβ motif and 36 amino acids, has folded unusually slowly in experiments, and transient dimers have been detected in the folding process. Here, by means of all-atom replica exchange molecular dynamics (REMD simulations, several comparably stable intermediate states were observed on the folding free-energy landscape of DS119. Conventional molecular dynamics (CMD simulations showed that when two unfolded DS119 proteins bound together, most binding sites of dimeric aggregates were located at the N-terminal segment, especially residues 5–10, which were supposed to form β-sheet with its own C-terminal segment. Furthermore, a large percentage of individual proteins in the dimeric aggregates adopted conformations similar to those in the intermediate states observed in REMD simulations. These results indicate that, during the folding process, DS119 can easily become trapped in intermediate states. Then, with diffusion, a transient dimer would be formed and stabilized with the binding interface located at N-terminals. This means that it could not quickly fold to the native structure. The complicated folding manner of DS119 implies the important influence of natural selection on protein-folding kinetics, and more improvement should be achieved in rational protein design.

  3. De novo centriole formation in human cells is error-prone and does not require SAS-6 self-assembly.

    Science.gov (United States)

    Wang, Won-Jing; Acehan, Devrim; Kao, Chien-Han; Jane, Wann-Neng; Uryu, Kunihiro; Tsou, Meng-Fu Bryan

    2015-11-26

    Vertebrate centrioles normally propagate through duplication, but in the absence of preexisting centrioles, de novo synthesis can occur. Consistently, centriole formation is thought to strictly rely on self-assembly, involving self-oligomerization of the centriolar protein SAS-6. Here, through reconstitution of de novo synthesis in human cells, we surprisingly found that normal looking centrioles capable of duplication and ciliation can arise in the absence of SAS-6 self-oligomerization. Moreover, whereas canonically duplicated centrioles always form correctly, de novo centrioles are prone to structural errors, even in the presence of SAS-6 self-oligomerization. These results indicate that centriole biogenesis does not strictly depend on SAS-6 self-assembly, and may require preexisting centrioles to ensure structural accuracy, fundamentally deviating from the current paradigm.

  4. Lethal Ultra-Early Subarachnoid Hemorrhage Due to Rupture of De Novo Aneurysm 5 Months After Primary Aneurysmatic Subarachnoid Hemorrhage.

    Science.gov (United States)

    Walter, Johannes; Unterberg, Andreas W; Zweckberger, Klaus

    2018-05-01

    Approximately 1% of all patients surviving rupture of a cerebral aneurysm suffer from a second aneurysmatic subarachnoid hemorrhage later in their lives, 61% of which are caused by rupture of a de novo aneurysm. Latency between bleedings is usually many years, and younger patients tend to achieve better outcomes from a second subarachnoid hemorrhage. We report an unusual case of lethal ultra-early rupture of a de novo aneurysm of the anterior communicating artery only 5 months after the initial subarachnoid hemorrhage and complete coiling in a young, healthy male patient. Despite complete aneurysm obliteration, young age, and good recovery, patients may be subjected to secondary subarachnoid hemorrhages from de novo aneurysms after only a few months of the initial bleeding. Early-control magnetic resonance angiography might hence be advisable. Copyright © 2018 Elsevier Inc. All rights reserved.

  5. Integration of CpG-free DNA induces de novo methylation of CpG islands in pluripotent stem cells

    KAUST Repository

    Takahashi, Yuta

    2017-05-05

    CpG islands (CGIs) are primarily promoter-associated genomic regions and are mostly unmethylated within highly methylated mammalian genomes. The mechanisms by which CGIs are protected from de novo methylation remain elusive. Here we show that insertion of CpG-free DNA into targeted CGIs induces de novo methylation of the entire CGI in human pluripotent stem cells (PSCs). The methylation status is stably maintained even after CpG-free DNA removal, extensive passaging, and differentiation. By targeting the DNA mismatch repair gene MLH1 CGI, we could generate a PSC model of a cancer-related epimutation. Furthermore, we successfully corrected aberrant imprinting in induced PSCs derived from an Angelman syndrome patient. Our results provide insights into how CpG-free DNA induces de novo CGI methylation and broaden the application of targeted epigenome editing for a better understanding of human development and disease.

  6. Autosomal dominant cutis laxa with progeroid features due to a novel, de novo mutation in ALDH18A1.

    Science.gov (United States)

    Bhola, Priya T; Hartley, Taila; Bareke, Eric; Boycott, Kym M; Nikkel, Sarah M; Dyment, David A

    2017-06-01

    De novo dominant mutations in the aldehyde dehydrogenase 18 family member A1 (ALDH18A1) gene have recently been shown to cause autosomal dominant cutis laxa with progeroid features (MIM 616603). To date, all de novo dominant mutations have been found in a single highly conserved amino acid residue at position p.Arg138. We report an 8-year-old male with a clinical diagnosis of autosomal dominant cutis laxa (ADCL) with progeroid features and a novel de novo missense mutation in ALDH18A1 (NM_002860.3: c.377G>A (p.Arg126His)). This is the first report of an individual with ALDH18A1-ADCL due to a substitution at a residue other than p.Arg138. Knowledge of the complete spectrum of dominant-acting mutations that cause this rare syndrome will have implications for molecular diagnosis and genetic counselling of these families.

  7. Human native lipoprotein-induced de novo DNA methylation is associated with repression of inflammatory genes in THP-1 macrophages.

    Science.gov (United States)

    Rangel-Salazar, Rubén; Wickström-Lindholm, Marie; Aguilar-Salinas, Carlos A; Alvarado-Caudillo, Yolanda; Døssing, Kristina B V; Esteller, Manel; Labourier, Emmanuel; Lund, Gertrud; Nielsen, Finn C; Rodríguez-Ríos, Dalia; Solís-Martínez, Martha O; Wrobel, Katarzyna; Wrobel, Kazimierz; Zaina, Silvio

    2011-11-25

    We previously showed that a VLDL- and LDL-rich mix of human native lipoproteins induces a set of repressive epigenetic marks, i.e. de novo DNA methylation, histone 4 hypoacetylation and histone 4 lysine 20 (H4K20) hypermethylation in THP-1 macrophages. Here, we: 1) ask what gene expression changes accompany these epigenetic responses; 2) test the involvement of candidate factors mediating the latter. We exploited genome expression arrays to identify target genes for lipoprotein-induced silencing, in addition to RNAi and expression studies to test the involvement of candidate mediating factors. The study was conducted in human THP-1 macrophages. Native lipoprotein-induced de novo DNA methylation was associated with a general repression of various critical genes for macrophage function, including pro-inflammatory genes. Lipoproteins showed differential effects on epigenetic marks, as de novo DNA methylation was induced by VLDL and to a lesser extent by LDL, but not by HDL, and VLDL induced H4K20 hypermethylation, while HDL caused H4 deacetylation. The analysis of candidate factors mediating VLDL-induced DNA hypermethylation revealed that this response was: 1) surprisingly, mediated exclusively by the canonical maintenance DNA methyltransferase DNMT1, and 2) independent of the Dicer/micro-RNA pathway. Our work provides novel insights into epigenetic gene regulation by native lipoproteins. Furthermore, we provide an example of DNMT1 acting as a de novo DNA methyltransferase independently of canonical de novo enzymes, and show proof of principle that de novo DNA methylation can occur independently of a functional Dicer/micro-RNA pathway in mammals.

  8. Human native lipoprotein-induced de novo DNA methylation is associated with repression of inflammatory genes in THP-1 macrophages

    Directory of Open Access Journals (Sweden)

    Rangel-Salazar Rubén

    2011-11-01

    Full Text Available Abstract Background We previously showed that a VLDL- and LDL-rich mix of human native lipoproteins induces a set of repressive epigenetic marks, i.e. de novo DNA methylation, histone 4 hypoacetylation and histone 4 lysine 20 (H4K20 hypermethylation in THP-1 macrophages. Here, we: 1 ask what gene expression changes accompany these epigenetic responses; 2 test the involvement of candidate factors mediating the latter. We exploited genome expression arrays to identify target genes for lipoprotein-induced silencing, in addition to RNAi and expression studies to test the involvement of candidate mediating factors. The study was conducted in human THP-1 macrophages. Results Native lipoprotein-induced de novo DNA methylation was associated with a general repression of various critical genes for macrophage function, including pro-inflammatory genes. Lipoproteins showed differential effects on epigenetic marks, as de novo DNA methylation was induced by VLDL and to a lesser extent by LDL, but not by HDL, and VLDL induced H4K20 hypermethylation, while HDL caused H4 deacetylation. The analysis of candidate factors mediating VLDL-induced DNA hypermethylation revealed that this response was: 1 surprisingly, mediated exclusively by the canonical maintenance DNA methyltransferase DNMT1, and 2 independent of the Dicer/micro-RNA pathway. Conclusions Our work provides novel insights into epigenetic gene regulation by native lipoproteins. Furthermore, we provide an example of DNMT1 acting as a de novo DNA methyltransferase independently of canonical de novo enzymes, and show proof of principle that de novo DNA methylation can occur independently of a functional Dicer/micro-RNA pathway in mammals.

  9. De novo status epilepticus is associated with adverse outcome: An 11-year retrospective study in Hong Kong.

    Science.gov (United States)

    Lui, Hoi Ki Kate; Hui, Kwok Fai; Fong, Wing Chi; Ip, Chun Tak; Lui, Hiu Tung Colin

    2016-08-01

    To identify predictors of poor clinical outcome in patients presenting to the intensive care units with status epilepticus (SE), in particular for patients presenting with de novo status epileptics. A retrospective review was performed on patients admitted to the intensive care units with status epilepticus in two hospitals in Hong Kong over an 11-year period from 2003 to 2013. A total of 87 SE cases were analyzed. The mean age of patients was 49.3 years (SD 14.9 years). Eighteen subjects (20.7%) had breakthrough seizure, which was the most common etiology for the status epilepticus episodes. Seventy-eight subjects (89.7%) had convulsive status epilepticus (CSE) and 9 subjects (10.3%) had non-convulsive status epilepticus (NCSE) on presentation. The 30-day mortality rate of all subjects was 18.4%. Non-convulsive status epilepticus was more common in patients with de novo status epilepticus when compared to those with existing history of epilepsy (15.5% Vs. 0%, p=0.03). Patients with de novo status epilepticus were older (52 Vs 43, p=0.009). De novo status epilepticus was associated with longer status duration (median 2.5 days, IQR 5 days), longer ICU stay (median 7.5 days, IQR 9 days) and poorer outcome (OR 4.15, 95% CI 1.53-11.2). For patients presenting to intensive care units with status epilepticus, those with de novo status epileptics were older and were more likely to develop non-convulsive status epilepticus. De novo status epilepticus was associated with poorer outcome. Continuous EEG monitoring would help identifying NCSE and potentially help improving clinical outcomes. Copyright © 2016 British Epilepsy Association. Published by Elsevier Ltd. All rights reserved.

  10. Utilization of marble from Bejui mine - Currais Novos/RN in ceramic mass; Analise da incorporacao de marmore da mina Brejui - Currais Novos/RN na massa ceramica

    Energy Technology Data Exchange (ETDEWEB)

    Farias, D.S.U. de; Souza, M.M. de; Almeida, A.B.D. de; Lima, T.C. de; Nobrega, L.F.P. de M. [Instituto Federal de Ciencia e Tecnologia do Rio Grande do Norte (IFRN), Natal, RN (Brazil); Mendes, L.B., E-mail: debora_suf_00@hotmail.com [Fundacao de Apoio a Pesquisa do Rio Grande do Norte (FAPERN), Natal RN (Brazil)

    2016-07-01

    Mining in Mine Brejui, in Currais Novos - RN, is related to the extraction of scheelite, however the marble of the region is not fully tapped. Aiming to provide a utility to this carbonate rock very abundant in the Serido region, this work is to evaluate, from its chemical and other tests, the addition of marble in the ceramic mass. For the analysis, the samples were collected, then comminuted and sieved to #200 and, right after, characterized by fluorescence X-ray method (FRX). The results indicate a high concentration of CaO (95%), a flux element, and very low content of Fe{sub 2}O{sub 3} and SO{sub 3} (less than 0.6%). After produced the samples, there were performed the water absorption tests and linear shrinkage, which has indicate satisfactory results and classifying them as porcelain. Therefore, with the significant potential of the marble, other laboratory tests may be performed to analyze its incorporation in the formulation of ceramic bodies, being economically viable and adding proper use and commercial value to the rock. (author)

  11. Produtividade e rendimento das duas classes de plantas existentes no Café "Mundo Novo" Fruit and seed yields of two classes of Mundo Novo coffee plants

    Directory of Open Access Journals (Sweden)

    A. J. T. Mendes

    1955-01-01

    Full Text Available Dados já publicados sobre produção de frutos e rendimento em sementes, de progênies do café Mundo Novo, foram reclassificados com base na existência de duas classes distintas de plantas : a aquelas heterozigotas (Dd, em que há ocorrência de endosperma discóide e conseqüente formação de maior quantidade de frutos chochos ; e b aquelas homozigotas (DD em que o endosperma é normal e por conseguinte os frutos são normais. Verificou-se que o peso da produção em frutos das plantas Dd é, em média, maior que o das plantas DD. A ocorrência do endosperma discóide, no entanto, acarreta um rendimento menor em sementes, para igual peso de frutos. O resultado final em peso de sementes chega a pender em favor das plantas DD, sem, no entanto, haver uma diferença estatisticamente significativa. A existência de plantas Dd nos cafezais é, portanto, prejudicial, uma vez que, para produzir mais frutos elas retiram maior quantidade de elementos minerais do solo ; a maior produção exige maior mão de obra na colheita ; e o pêso do produto final, café beneficiado, não é compensador, pois não é superior ao das plantas DD. As fontes de sementes são várias, atualmente ; se o fornecedor não faz qualquer seleção, as plantas com o defeito tendem a diminuir ; se o fornecedor, imaginando que faz seleção, escolhe as plantas aparentemente mais produtivas, o defeito aumentará na nova plantação ; se o fornecedor das sementes leva em consideração a produtividade e ao mesmo tempo a não ocorrência de frutos chochos, a nova plantação estará pràticamente isenta do defeito. Sómente as sementes certificadas pelo Instituto Agronômico apresentam a garantia de produzir exclusivamente plantas DD.Evidence presented in previous papers indicated that two classes of plants are present in ordinary populations of Mundo Novo coffee (Coffea arabica L. : a heterozygotes (Dd in which the occurrence of "discoid endosperm" is responsible for the

  12. A SA8000 e a responsabilidade social das empresas: a emergência de um novo paradigma?

    OpenAIRE

    Lopes, Ana Catarina Marques Figueiredo Caetano

    2004-01-01

    Mestrado em Desenvolvimento e Cooperação Internacional A Responsabilidade Social das Empresas, não é um tema novo. Durante muito tempo foi discutido e interpretado no âmbito do debate sobre as responsabilidades que uma empresa deve assumir para além daquelas que tem perante os seus accionistas, e das impostas por lei. Hoje, observamos a emergência de um novo paradigma assente no reconhecimento que o sector privado não só pode, mas deve, fazer mais para combater a pobreza, preservar o meio ...

  13. NOVOS PRODUTOS SOB O ENFOQUE DO SISTEMA DE CONSUMO E A ORIENTAÇÃO PARA O MERCADO

    OpenAIRE

    Mauro Calixta Tavares; Valéria Braga Pinto

    2009-01-01

    A orientação para o mercado tem sido abordada com suas possíveis implicações na estrutura, processos, pessoas, desenvolvimento de novos produtos, inovação e flexibilidade estratégica, entre outras possibilidades. O foco do presente capítulo é sobre sua relação com novos produtos sob a perspectiva de sistema de consumo. A partir de um estudo exploratório, os alunos de um programa de MBA, divididos em grupos, realizaram um trabalho envolvendo o consumo de vários produtos e serviços sob a perspe...

  14. Para além do lumpen-indigenismo: novos aspectos informacionais da política indigenista brasileira

    Directory of Open Access Journals (Sweden)

    Rodrigo Piquet Saboia de Mello

    2017-06-01

    Full Text Available O artigo em tela propõe uma releitura do artigo intitulado “O lumpen-indigenismo do estado brasileiro” do antropólogo Jorge Pozzobon tendo por objetivo reelaborar alguns conceitos e propostas do autor em tempo outrora, assim como estabelecer uma ponte para os novos fenômenos informacionais que advém do conjunto político-jurídico hodierno, assim como no fortalecimento do protagonismo indígena na construção de novos modelos de participação e gerenciamento da informação indígena.

  15. Estudo do mecanismo de ação de novos compostos de ruténio com atividade antitumoral

    OpenAIRE

    Carvalho, Andreia Catarina Guerreiro Morais de

    2017-01-01

    Tese de mestrado, Bioquímica (Bioquímica Médica), Universidade de Lisboa, Faculdade de Ciências, 2017 A quimioterapia é um tratamento tradicional do cancro. Sua alta toxicidade, afetando tecidos saudáveis, e a resistência intrínseca a fármacos são obstáculos que precisam de ser superados. Desta forma, a identificação de novos agentes quimioterapêuticos é fundamental para novos progressos no tratamento do cancro. Uma abordagem inclui complexos de ruténio, que foram reconhecidos como uma alt...

  16. Seleção de ideótipos de espécies florestais de múltiplo uso em planícies fluviais do Baixo Amazonas, Pará Selection of multipurpose forest species ideotypes of the floodplains in the Low Amazon Basin, Pará

    Directory of Open Access Journals (Sweden)

    Gladys Beatriz Martínez

    2010-03-01

    Full Text Available A pesquisa objetivou selecionar ideótipos arbóreos de múltiplo uso, baseado em informações etnobotânicas de comunidades ribeirinhas de planícies fluviais do Baixo Amazonas, Pará, para uso em sistemas silvipastoris. Como essas áreas foram antropizadas pela agricultura seguida da pecuária, esses sistemas são considerados alternativas viáveis para sua recuperação. Por meio de pesquisa participativa junto aos ribeirinhos, foi utilizado um questionário semi-estruturado para determinar as espécies arbóreas de maior importância para essas populações, enfocando sua finalidade e formas de uso, consumidor destino e a abundância nas comunidades estudadas. As espécies florestais de interesse dos ribeirinhos concentraram-se nas frutíferas, para alimentação humana e animal, seguidas daquelas com função madeireira. Em sua grande maioria, essas espécies são utilizadas internamente na propriedade, não gerando produtos excedentes e foram consideradas, pelos entrevistados como de “grande" abundância na região.The objective of this research was to select multipurpose arboreal ideotypes for use in silvipastoral systems. Selection of ideotypes was based on ethnobotanical information from riverside communities of Lower Amazon river floodplains, in Pará. Since these areas had been impacted by agriculture followed by ranching, the silvipastoral systems are considered viable alternatives for recuperating them. Through participatory research among the riverside inhabitants, a semi-structured questionnaire was used to determine the tree species of greatest importance to those populations, with focus on their purpose and forms of use, consumer destination and abundance in the communities studied. The forest species of interest to riverside people are most often fruit-producing species for human and animal food, followed by those for timber. The great majority of these species are employed internally on the property. They do not generate

  17. Analysis of pyrimidine synthesis "de novo" intermediates in urine and dried urine filter- paper strips with HPLC-electrospray tandem mass spectrometry

    NARCIS (Netherlands)

    van Kuilenburg, André B. P.; van Lenthe, Henk; Löffler, Monika; van Gennip, Albert H.

    2004-01-01

    BACKGROUND: The concentrations of the pyrimidine "de novo" metabolites and their degradation products in urine are useful indicators for the diagnosis of an inborn error of the pyrimidine de novo pathway or a urea-cycle defect. Until now, no procedure was available that allowed the analysis of all

  18. De novo origin of VCY2 from autosome to Y-transposed amplicon.

    Directory of Open Access Journals (Sweden)

    Peng-Rong Cao

    Full Text Available The formation of new genes is a primary driving force of evolution in all organisms. The de novo evolution of new genes from non-protein-coding genomic regions is emerging as an important additional mechanism for novel gene creation. Y chromosomes underlie sex determination in mammals and contain genes that are required for male-specific functions. In this study, a search was undertaken for Y chromosome de novo genes derived from non-protein-coding sequences. The Y chromosome orphan gene variable charge, Y-linked (VCY2, is an autosome-derived gene that has sequence similarity to large autosomal fragments but lacks an autosomal protein-coding homolog. VCY2 locates in the amplicon containing long DNA fragments that were transposed from autosomes to the Y chromosome before the ape-monkey split. We confirmed that VCY2 cannot be encoded by autosomes due to the presence of multiple disablers that disrupt the open reading frame, such as the absence of start or stop codons and the presence of premature stop codons. Similar observations have been made for homologs in the autosomes of the chimpanzee, gorilla, rhesus macaque, baboon and out-group marmoset, which suggests that there was a non-protein-coding ancestral VCY2 that was common to apes and monkeys that predated the transposition event. Furthermore, while protein-coding orthologs are absent, a putative non-protein-coding VCY2 with conserved disablers was identified in the rhesus macaque Y chromosome male-specific region. This finding implies that VCY2 might have not acquired its protein-coding ability before the ape-monkey split. VCY2 encodes a testis-specific expressed protein and is involved in the pathologic process of male infertility, and the acquisition of this gene might improve male fertility. This is the first evidence that de novo genes can be generated from transposed autosomal non-protein-coding segments, and this evidence provides novel insights into the evolutionary history of the Y

  19. De novo hepatic steatosis drives atherogenic risk in liver transplantation recipients.

    Science.gov (United States)

    Idowu, Michael O; Chhatrala, Ravi; Siddiqui, M Bilal; Driscoll, Carolyn; Stravitz, R Todd; Sanyal, Arun J; Bhati, Chandra; Sargeant, Carol; Luketic, Velimir A; Sterling, Richard K; Contos, Melissa; Matherly, Scott; Puri, Puneet; Siddiqui, M Shadab

    2015-11-01

    Nonalcoholic fatty liver disease is associated with cardiovascular disease (CVD) in the general population. Despite a high prevalence of de novo hepatic steatosis after liver transplantation (LT), there are no data exploring the association between hepatic steatosis after LT and atherogenic risk. The aim of the study was to explore the impact of hepatic steatosis on serum atherogenic markers in liver transplantation recipients (LTRs). Biomarkers of CVD risk were compared in 89 LTRs with no known history of dyslipidemia, ischemic heart disease, or graft cirrhosis. To avoid potential confounders, LTRs on oral hypoglycemic agents, exogenous insulin, corticosteroids, or lipid-lowering therapy were excluded. Only patients for whom histological assessment was available after LT were included in the study. Thirty-five LTRs had de novo hepatic steatosis after LT, whereas 54 did not. Both cohorts were similar with regards to age, sex, ethnicity, and follow-up from LT. Additionally, the traditional lipid profile was similar between the 2 cohorts. LTRs with hepatic steatosis had higher serum concentrations of small-dense low-density lipoprotein cholesterol (sdLDL-C; 34.8 ± 16.9 versus 22.7 ± 11.2 mg/dL; P hepatic steatosis had higher serum insulin concentrations (27.8 ± 41.8 versus 11.7 ± 7.8 uU/mL; P Steatosis grade was directly related to sdLDL-C, sdLDL-P, insulin, VLDL-P, and VLDL-size. In multivariate analysis, the association between steatosis grade and sdLDL-C (β = 0.03; P = 0.029), VLDL-size (β = 0.316; P = 0.04), and low-density lipoprotein particle size (β = -0.27; P = 0.05) was independent of sex, body mass index, age, diabetes mellitus, time from transplant, and indication for LT. In conclusion, de novo hepatic steatosis after LT is associated with atherogenic lipoproteins and independent of traditional CVD risk factors. © 2015 American Association for the Study of Liver Diseases.

  20. De Novo Nodal Diffuse Large B-Cell Lymphoma: Identification of Biologic Prognostic Factors

    International Nuclear Information System (INIS)

    Abd El-Hameed, A.

    2005-01-01

    Diffuse large B-cell Lymphoma (DLBCL) represents the most frequent type of non-Hodgkin lymphoma (NHL). Although combination chemotherapy has improved the outcome, long-term cure is now possible for approximately 50% of all patients. making the search for parameters identifying patients at high risk particularly needed. The presence of bcl-2 gene rearrangement in de novo DLBCL suggests a possible follicle center cell origin and perhaps a distinct clinical behavior. This study investigated the frequency and prognostic significance of t( 14; 18) translocation and bcl-2 protein overexpression in a cohort of patients with de novo nodal DLBCL who where uniformly evaluated and treated. Material and Methods: A total of 40 patients with de novo nodal DLBCL treated at National Cancer Institute (NCI), Cairo University were investigated. Formal infixed, paraffin-embedded sections were analyzed for: I) bcl-2 gene rearrangement including major break point region (mbr) and minor cluster region (mcr) by polymerase chain reaction (PCR). and 2) bcl-2 protein expression by immunohistochemistry using Dako 124 clone. Results were correlated with the clinical features and subsequent clinical course. Bcl-2 gene rearrangement was detected in 8 cases (20%). 2 cases at mbr, and 6 cases at mcr. Bcl-2 protein (> I 0%) was expressed in 24 cases (60%), irrespective of the presence of t( 14; 18) translocation. The t( 14; 18), and bcl-2 protein overexpression were more frequently associated with failure to achieve a complete response to therapy (ρ=0.008. and 0.04. respectively). DLBCL patients with t(14;18), and bcl-2 protein expression had a significantly reduced 5-year disease free survival (ρ=0.04, and 0.01, respectively). The t( 14; 18) translocation, and bcl-2 protein expression define a group of DLBCL patients with a poor prognosis, and could be used to tailor treatment, and to identify candidates for therapeutic approaches. Geographic differences in t(14;18) may be related to the

  1. De novo formation of left-right asymmetry by posterior tilt of nodal cilia.

    Directory of Open Access Journals (Sweden)

    Shigenori Nonaka

    2005-08-01

    Full Text Available In the developing mouse embryo, leftward fluid flow on the ventral side of the node determines left-right (L-R asymmetry. However, the mechanism by which the rotational movement of node cilia can generate a unidirectional flow remains hypothetical. Here we have addressed this question by motion and morphological analyses of the node cilia and by fluid dynamic model experiments. We found that the cilia stand, not perpendicular to the node surface, but tilted posteriorly. We further confirmed that such posterior tilt can produce leftward flow in model experiments. These results strongly suggest that L-R asymmetry is not the descendant of pre-existing L-R asymmetry within each cell but is generated de novo by combining three sources of spatial information: antero-posterior and dorso-ventral axes, and the chirality of ciliary movement.

  2. A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors

    Directory of Open Access Journals (Sweden)

    Donald M. Bryant

    2017-01-01

    Full Text Available Mammals have extremely limited regenerative capabilities; however, axolotls are profoundly regenerative and can replace entire limbs. The mechanisms underlying limb regeneration remain poorly understood, partly because the enormous and incompletely sequenced genomes of axolotls have hindered the study of genes facilitating regeneration. We assembled and annotated a de novo transcriptome using RNA-sequencing profiles for a broad spectrum of tissues that is estimated to have near-complete sequence information for 88% of axolotl genes. We devised expression analyses that identified the axolotl orthologs of cirbp and kazald1 as highly expressed and enriched in blastemas. Using morpholino anti-sense oligonucleotides, we find evidence that cirbp plays a cytoprotective role during limb regeneration whereas manipulation of kazald1 expression disrupts regeneration. Our transcriptome and annotation resources greatly complement previous transcriptomic studies and will be a valuable resource for future research in regenerative biology.

  3. De Novo transcriptome assembly of Zingiber officinale cv. Suruchi of Odisha.

    Science.gov (United States)

    Gaur, Mahendra; Das, Aradhana; Sahoo, Rajesh Kumar; Kar, Basudeba; Nayak, Sanghamitra; Subudhi, Enketeswara

    2016-09-01

    Zingiber officinale Rosc., known as ginger, is an Asian crop, popularly used in every household kitchen and commercially used in bakery, beverage, food and pharmaceutical industries. The present study deals with de novo transcriptome assembly of an elite ginger cultivar Suruchi by next generation sequencing methodology. From the analysis 10.9 GB raw data was obtained which can be available in NCBI accession number SAMN03761185. We identified 41,969 transcripts using Trinity RNA-Seq from ginger rhizome of Suruchi variety from Odisha. The transcript length varied from 300 bp to 8404 bp with a total length of 3,96,40,526 bp and N50 of 1251 bp. To the best of our knowledge, this is the first transcriptome data of an elite ginger cultivar Suruchi released for Odisha state of India which will help molecular biologists to develop genetic markers for identification of cultivars.

  4. The sequence and de novo assembly of the giant panda genome

    Science.gov (United States)

    Li, Ruiqiang; Fan, Wei; Tian, Geng; Zhu, Hongmei; He, Lin; Cai, Jing; Huang, Quanfei; Cai, Qingle; Li, Bo; Bai, Yinqi; Zhang, Zhihe; Zhang, Yaping; Wang, Wen; Li, Jun; Wei, Fuwen; Li, Heng; Jian, Min; Li, Jianwen; Zhang, Zhaolei; Nielsen, Rasmus; Li, Dawei; Gu, Wanjun; Yang, Zhentao; Xuan, Zhaoling; Ryder, Oliver A.; Leung, Frederick Chi-Ching; Zhou, Yan; Cao, Jianjun; Sun, Xiao; Fu, Yonggui; Fang, Xiaodong; Guo, Xiaosen; Wang, Bo; Hou, Rong; Shen, Fujun; Mu, Bo; Ni, Peixiang; Lin, Runmao; Qian, Wubin; Wang, Guodong; Yu, Chang; Nie, Wenhui; Wang, Jinhuan; Wu, Zhigang; Liang, Huiqing; Min, Jiumeng; Wu, Qi; Cheng, Shifeng; Ruan, Jue; Wang, Mingwei; Shi, Zhongbin; Wen, Ming; Liu, Binghang; Ren, Xiaoli; Zheng, Huisong; Dong, Dong; Cook, Kathleen; Shan, Gao; Zhang, Hao; Kosiol, Carolin; Xie, Xueying; Lu, Zuhong; Zheng, Hancheng; Li, Yingrui; Steiner, Cynthia C.; Lam, Tommy Tsan-Yuk; Lin, Siyuan; Zhang, Qinghui; Li, Guoqing; Tian, Jing; Gong, Timing; Liu, Hongde; Zhang, Dejin; Fang, Lin; Ye, Chen; Zhang, Juanbin; Hu, Wenbo; Xu, Anlong; Ren, Yuanyuan; Zhang, Guojie; Bruford, Michael W.; Li, Qibin; Ma, Lijia; Guo, Yiran; An, Na; Hu, Yujie; Zheng, Yang; Shi, Yongyong; Li, Zhiqiang; Liu, Qing; Chen, Yanling; Zhao, Jing; Qu, Ning; Zhao, Shancen; Tian, Feng; Wang, Xiaoling; Wang, Haiyin; Xu, Lizhi; Liu, Xiao; Vinar, Tomas; Wang, Yajun; Lam, Tak-Wah; Yiu, Siu-Ming; Liu, Shiping; Zhang, Hemin; Li, Desheng; Huang, Yan; Wang, Xia; Yang, Guohua; Jiang, Zhi; Wang, Junyi; Qin, Nan; Li, Li; Li, Jingxiang; Bolund, Lars; Kristiansen, Karsten; Wong, Gane Ka-Shu; Olson, Maynard; Zhang, Xiuqing; Li, Songgang; Yang, Huanming; Wang, Jian; Wang, Jun

    2013-01-01

    Using next-generation sequencing technology alone, we have successfully generated and assembled a draft sequence of the giant panda genome. The assembled contigs (2.25 gigabases (Gb)) cover approximately 94% of the whole genome, and the remaining gaps (0.05 Gb) seem to contain carnivore-specific repeats and tandem repeats. Comparisons with the dog and human showed that the panda genome has a lower divergence rate. The assessment of panda genes potentially underlying some of its unique traits indicated that its bamboo diet might be more dependent on its gut microbiome than its own genetic composition. We also identified more than 2.7 million heterozygous single nucleotide polymorphisms in the diploid genome. Our data and analyses provide a foundation for promoting mammalian genetic research, and demonstrate the feasibility for using next-generation sequencing technologies for accurate, cost-effective and rapid de novo assembly of large eukaryotic genomes. PMID:20010809

  5. The NOVO Network: the original scientific basis for its establishment and our R&D vision

    DEFF Research Database (Denmark)

    Winkel, Jørgen; Edwards, Kasper; Dellve, L.

    2017-01-01

    Systems” in the healthcare sector. It was founded in 2006 in Copenhagen and was financially supported by the Nordic Council of Ministers from 2007 to 2015. The motivation to establish the NOVO Network arose when reviewing the literature regarding opportunities to create sustainable production systems....... This work was initiated year 2002 and resultet in a systematic review published 2011 (Westgaard and Winkel 2011). Already in 2006 it was concluded that ergonomic interventions have limited musculoskeletal and mental health effects in a long-range perspective while rationalization has predominant negative...... be challenged due to the frequent negative impact of rationalization on ergonomics and vice versa. This call for dialogue processes between the stakeholders taking more holistic systems perspectives. Dialogue-based change processes may be more common in the Nordic countries compared to other parts of the world...

  6. O novo paradigma da violência The new paradigm of violence

    Directory of Open Access Journals (Sweden)

    Michel Wieviorka

    1997-05-01

    Full Text Available O autor procura redimensionar o conceito de violência dentro do atual estado de globalização mundial. Crise internacional, narcotráfico, derrocada do bloco socialista no leste europeu, políticas assistenciais de organismos internacionais, conceitos de desenvolvimento e de subdesenvolvimento, terrorismo, sectarismo político e religioso, novas conceituações culturais e sociais são temas trabalhados pelo autor com vistas ao estabelecimento de um novo paradigma da violência.The author tries to requalify the concept of violence under the influences of a context of world globalization. International crisis, drug traffic, collapse of the socialist governments, concepts of development and under-development, terrorism, political and religious sectarisms, new culture and social conceptualizations, these are some of the themes which are discussed by the author with the objective to propose a new pardigm for violence.

  7. Case report: Concomitant Chronic Lymphocytic Leukaemia and Cytogenetically Normal de novo Acute Leukaemia in a Patient.

    Science.gov (United States)

    Kajtár, Béla; Rajnics, Péter; Egyed, Miklós; Alizadeh, Hussain

    2015-01-01

    The simultaneous occurrence of acute myeloid leukaemia with untreated chronic lymphocytic leukemia is extremely rare. We report a case of a 74-year-old man who was evaluated for macrocytic anaemia. Based on the morphology and immunophenotyping analysis of peripheral blood, a diagnosis of chronic lymphocytic leukemia was established. Subsequently, the bone marrow examination revealed the presence of two distinct, coexisting CLL and AML clones. Cytogenetic and molecular genetic analysis detected deletion 13q14.3 and unmutated immunoglobulin variable heavy-chain in the CLL clone, only. The AML and CLL clones did not share clonality, and the AML did not involve the peripheral blood. A diagnosis of cytogenetically normal de novo AML occurring concurrently with untreated CLL has not been reported previously in English literature. © 2015 by the Association of Clinical Scientists, Inc.

  8. Paternal Age Explains a Major Portion of De Novo Germline Mutation Rate Variability in Healthy Individuals.

    Directory of Open Access Journals (Sweden)

    Simon L Girard

    Full Text Available De novo mutations (DNM are an important source of rare variants and are increasingly being linked to the development of many diseases. Recently, the paternal age effect has been the focus of a number of studies that attempt to explain the observation that increasing paternal age increases the risk for a number of diseases. Using disease-free familial quartets we show that there is a strong positive correlation between paternal age and germline DNM in healthy subjects. We also observed that germline CNVs do not follow the same trend, suggesting a different mechanism. Finally, we observed that DNM were not evenly distributed across the genome, which adds support to the existence of DNM hotspots.

  9. De novo activating epidermal growth factor mutations (EGFR) in small-cell lung cancer.

    Science.gov (United States)

    Thai, Alesha; Chia, Puey L; Russell, Prudence A; Do, Hongdo; Dobrovic, Alex; Mitchell, Paul; John, Thomas

    2017-09-01

    In Australia, mutations in epidermal growth factor mutations (EGFR) occur in 15% of patients diagnosed with non-small-cell lung cancer and are found with higher frequency in female, non-smokers of Asian ethnicity. Activating mutations in the EGFR gene are rarely described in SCLC. We present two cases of de novo EGFR mutations in patients with SCLC detected in tissue and in plasma cell free DNA, both of whom were of Asian ethnicity and never-smokers. These two cases add to the growing body of evidence suggesting that screening for EGFR mutations in SCLC should be considered in patients with specific clinical features. © 2017 Royal Australasian College of Physicians.

  10. Novos realismos e o risco da ficção

    Directory of Open Access Journals (Sweden)

    Vera Lúcia Follain de Figueiredo

    2010-01-01

    Full Text Available Entre as correntes teóricas contemporâneas, há uma tendência em considerar que a função da imagem midiática já não é imitar, nem sequer fazer-se passar pela realidade, mas substituir o próprio mundo real. Tal pensamento tem aberto caminho para a valorização de narrativas que parecem retratar, espontaneamente, cenas de um “real autêntico”. Partindo desse ponto, o texto discute a crise da ficção e os novos realismos, indagando quais os parâmetros utilizados, em nossos dias, quando se classifica um texto como realista.

  11. A chloroplast pathway for the de novo biosynthesis of triacylglycerol in Chlamydomonas reinhardtii

    Energy Technology Data Exchange (ETDEWEB)

    Fan, J.; Xu, C.; Andre, C.

    2011-06-23

    Neutral lipid metabolism has been extensively studied in yeast, plants and mammals. In contrast, little information is available regarding the biochemical pathway, enzymes and regulatory factors involved in the biosynthesis of triacylglycerol (TAG) in microalgae. In the conventional TAG biosynthetic pathway widely accepted for yeast, plants and mammals, TAG is assembled in the endoplasmic reticulum (ER) from its immediate precursor diacylglycerol (DAG) made by ER-specific acyltransferases, and is deposited exclusively in lipid droplets in the cytosol. Here, we demonstrated that the unicellular microalga Chlamydomonas reinhardtii employs a distinct pathway that uses DAG derived almost exclusively from the chloroplast to produce TAG. This unique TAG biosynthesis pathway is largely dependent on de novo fatty acid synthesis, and the TAG formed in this pathway is stored in lipid droplets in both the chloroplast and the cytosol. These findings have wide implications for understanding TAG biosynthesis and storage and other areas of lipid metabolism in microalgae and other organisms.

  12. De Novo Truncating Variants in SON Cause Intellectual Disability, Congenital Malformations, and Failure to Thrive.

    Science.gov (United States)

    Tokita, Mari J; Braxton, Alicia A; Shao, Yunru; Lewis, Andrea M; Vincent, Marie; Küry, Sébastien; Besnard, Thomas; Isidor, Bertrand; Latypova, Xénia; Bézieau, Stéphane; Liu, Pengfei; Motter, Connie S; Melver, Catherine Ward; Robin, Nathaniel H; Infante, Elena M; McGuire, Marianne; El-Gharbawy, Areeg; Littlejohn, Rebecca O; McLean, Scott D; Bi, Weimin; Bacino, Carlos A; Lalani, Seema R; Scott, Daryl A; Eng, Christine M; Yang, Yaping; Schaaf, Christian P; Walkiewicz, Magdalena A

    2016-09-01

    SON is a key component of the spliceosomal complex and a critical mediator of constitutive and alternative splicing. Additionally, SON has been shown to influence cell-cycle progression, genomic integrity, and maintenance of pluripotency in stem cell populations. The clear functional relevance of SON in coordinating essential cellular processes and its presence in diverse human tissues suggests that intact SON might be crucial for normal growth and development. However, the phenotypic effects of deleterious germline variants in SON have not been clearly defined. Herein, we describe seven unrelated individuals with de novo variants in SON and propose that deleterious variants in SON are associated with a severe multisystem disorder characterized by developmental delay, persistent feeding difficulties, and congenital malformations, including brain anomalies. Copyright © 2016 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  13. De novo 12q22.q23.3 duplication associated with temporal lobe epilepsy.

    Science.gov (United States)

    Vari, Maria Stella; Traverso, Monica; Bellini, Tommaso; Madia, Francesca; Pinto, Francesca; Minetti, Carlo; Striano, Pasquale; Zara, Federico

    2017-08-01

    Temporal lobe epilepsy (TLE) is the most common form of focal epilepsy and may be associated with acquired central nervous system lesions or could be genetic. Various susceptibility genes and environmental factors are believed to be involved in the aetiology of TLE, which is considered to be a heterogeneous, polygenic, and complex disorder. Rare point mutations in LGI1, DEPDC5, and RELN as well as some copy number variations (CNVs) have been reported in families with TLE patients. We perform a genetic analysis by Array-CGH in a patient with dysmorphic features and temporal lobe epilepsy. We report a de novo duplication of the long arm of chromosome 12. We confirm that 12q22-q23.3 is a candidate locus for familial temporal lobe epilepsy with febrile seizures and highlight the role of chromosomal rearrangements in patients with epilepsy and intellectual disability. Copyright © 2017 British Epilepsy Association. Published by Elsevier Ltd. All rights reserved.

  14. Transcriptional regulator-mediated activation of adaptation genes triggers CRISPR de novo spacer acquisition

    DEFF Research Database (Denmark)

    Liu, Tao; Li, Yingjun; Wang, Xiaodi

    2015-01-01

    Acquisition of de novo spacer sequences confers CRISPR-Cas with a memory to defend against invading genetic elements. However, the mechanism of regulation of CRISPR spacer acquisition remains unknown. Here we examine the transcriptional regulation of the conserved spacer acquisition genes in Type I......, it was demonstrated that the transcription level of csa1, cas1, cas2 and cas4 was significantly enhanced in a csa3a-overexpression strain and, moreover, the Csa1 and Cas1 protein levels were increased in this strain. Furthermore, we demonstrated the hyperactive uptake of unique spacers within both CRISPR loci...... in the presence of the csa3a overexpression vector. The spacer acquisition process is dependent on the CCN PAM sequence and protospacer selection is random and non-directional. These results suggested a regulation mechanism of CRISPR spacer acquisition where a single transcriptional regulator senses the presence...

  15. Robust de novo pathway enrichment with KeyPathwayMiner 5 [version 1; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Nicolas Alcaraz

    2016-06-01

    Full Text Available Identifying functional modules or novel active pathways, recently termed de novo pathway enrichment, is a computational systems biology challenge that has gained much attention during the last decade. Given a large biological interaction network, KeyPathwayMiner extracts connected subnetworks that are enriched for differentially active entities from a series of molecular profiles encoded as binary indicator matrices. Since interaction networks constantly evolve, an important question is how robust the extracted results are when the network is modified. We enable users to study this effect through several network perturbation techniques and over a range of perturbation degrees. In addition, users may now provide a gold-standard set to determine how enriched extracted pathways are with relevant genes compared to randomized versions of the original network.

  16. Um novo modelo de previsão de demanda para inovações radicais

    Directory of Open Access Journals (Sweden)

    Donald Neumann

    2014-09-01

    Full Text Available Este trabalho apresenta um novo modelo para a previsão de demanda de inovações radicais baseada em simulação de Dinâmica de Sistemas que combina conceitos do modelo de difusão de Bass e do modelo de escolha discreta. Diferentemente de outras abordagens existentes, esta proposta permite estimar não somente a fatia de mercado do produto, mas também seu comportamento no tempo (timing, a partir das preferências individuais do consumidor e das forças que as influenciam. O modelo proposto pode ser facilmente parametrizado através da Conjoint Analysis e foi testado em escala real no mercado alemão de carros elétricos. Os resultados obtidos colocam em evidência o potencial da abordagem proposta, auxiliando na compreensão dos principais fatores na escolha desse produto.

  17. Marketing de Novos Produtos: Lançamento e Inovação

    Directory of Open Access Journals (Sweden)

    Adriana Conceicao Dutra

    2014-12-01

    Full Text Available Atualmente as empresas lançam um produto com o objetivo de permanecerem por mais tempo no mercado. Embora muitas empresas fracassassem ao lançarem um produto, seria um mito dizer que as maiorias dos novos produtos fracassam ou que seu sucesso vai de acordo com sua atratividade. A modernização traz consigo as premissas, a eficiência, a qualidade e a produtividade, que de certa forma impõem uma carga à sociedade como um todo. Superar as expectativas dos consumidores, por meio de produtos e serviços inovadores, assegura vantagens competitivas e permite às empresas a ocupação de posições de liderança, em mercados altamente competitivos.

  18. Pegylated interferon de novo-induce autoimmune haemolytic anaemia in chronic hepatitis C patient.

    Science.gov (United States)

    Said, Ashraf; Elbahrawy, Ashraf; Alfiomy, Mohamed; Abdellah, Mohamed; Shahat, Khaled; Salah, Mohamed; Mostafa, Sadek; Elwassief, Ahmed; Aboelfotoh, Attef; Abdelhafeez, Hafez; El-Sherif, Assem

    2011-08-11

    A 55-year-old Egyptian woman with chronic hepatitis C undergoing treatment with pegylated interferon (Peg-IFN) alfa-2a plus ribavirin was referred to our hospital on November 2010 with prolonged easy fatigability and an attack of syncope; she had no prior history of autoimmune disorders or allergy. Laboratory investigations documented the presence of Peg-IFN induced autoimmune haemolytic anaemia and autoimmune thyroiditis. Intravenous γ globulin (IVGG) failed to correct the autoimmune process; on the other hand steroid therapy dramatically corrected both haematological and thyroid values, and step down the immune process. Our report indicated that Peg-IFN de novo-induce autoimmune haemolysis, documenting a previous report. IVGG failed to step down the immune process in our case.

  19. ChemTS: an efficient python library for de novo molecular generation

    Science.gov (United States)

    Yang, Xiufeng; Zhang, Jinzhe; Yoshizoe, Kazuki; Terayama, Kei; Tsuda, Koji

    2017-12-01

    Automatic design of organic materials requires black-box optimization in a vast chemical space. In conventional molecular design algorithms, a molecule is built as a combination of predetermined fragments. Recently, deep neural network models such as variational autoencoders and recurrent neural networks (RNNs) are shown to be effective in de novo design of molecules without any predetermined fragments. This paper presents a novel Python library ChemTS that explores the chemical space by combining Monte Carlo tree search and an RNN. In a benchmarking problem of optimizing the octanol-water partition coefficient and synthesizability, our algorithm showed superior efficiency in finding high-scoring molecules. ChemTS is available at https://github.com/tsudalab/ChemTS.

  20. De novo assembly and annotation of the Antarctic copepod (Tigriopus kingsejongensis) transcriptome.

    Science.gov (United States)

    Kim, Hui-Su; Lee, Bo-Young; Han, Jeonghoon; Lee, Young Hwan; Min, Gi-Sik; Kim, Sanghee; Lee, Jae-Seong

    2016-08-01

    The whole transcriptome of the Antarctic copepod (Tigriopus kingsejongensis) was sequenced using Illumina RNA-seq. De novo assembly was performed with 64,785,098 raw reads using Trinity, which assembled into 81,653 contigs. TransDecoder found 38,250 candidate coding contigs which showed homology to other species by BLAST analysis. Functional gene annotation was performed by Gene Ontology (GO), InterProScan, and KEGG pathway analyses. Finally, we identified a number of expressed gene catalog for T. kingsejongensis that is a useful model animal for gene information-based polar research to uncover molecular mechanisms of environmental adaptation on harsh environments. In particular, we observed highly developing lipid metabolism in T. kingsejongensis directly compared to those of the Far East Pacific coast copepod Tigriopus japonicus at the transcriptome level. Copyright © 2016 Elsevier B.V. All rights reserved.

  1. Anterior Abdominal Wall Leiomyoma Arising De Novo in a Perimenopausal Woman

    Directory of Open Access Journals (Sweden)

    Hamed A. Al-Wadaani

    2012-07-01

    Full Text Available Extrauterine or extraintestinal leiomyomas are extremely uncommon especially in the pre-peritoneal area or within the anterior abdominal wall muscles. These tumors have been ascribed to intraoperative seeding during resection of a fibroid or a leiomyoma of gut, to exogenous hormone replacement therapy or a major derangement of glucose and/or lipid metabolism. So far, there is no published report of de novo origin of anterior abdominal wall pure leiomyoma in the literature. The author herein reports a case of perimenopausal multiparous woman without any listing of previous gynecological surgery or hormone therapy who presented with a large pre-peritoneal intramuscular leiomyoma of the anterior abdominal wall. The patient underwent complete primary resection with amelioration of her symptoms.

  2. Prognostic factors in de novo myelodysplastic syndrome in young and middle-aged people

    Directory of Open Access Journals (Sweden)

    Наталья Николаевна Климкович

    2015-01-01

    Full Text Available We spent multivariate analysis of clinical and laboratory parameters for the prediction of de-novo myelodysplastic syndromes (MDS patients aged 18-60 years. The results of clinical application of prognostic systems in MDS show that there is a large variability within individual risk groups, especially at low-risk MDS. So now hematologists conduct research aimed at identifying additional adverse risk MDS. This is done so that patients with low-risk MDS embodiments and unfavorable prognosis could benefit from early therapeutic intervention, and not only be clinician monitored until disease progression. We found that additional adverse risk factors for the development of MDS are the expression of CD95 in bone marrow ≤40 % and FLT3≥60 %. The expression level of CD95 in bone marrow cells≤40 % and FLT3≥60 % can be considered as a prognostic marker progression of MDS and time start specific therapy

  3. De novo acute leukemia with a sole 5q-: morphological, immunological, and clinical correlations.

    Science.gov (United States)

    Duchayne, E; Dastugue, N; Kuhlein, E; Huguet, F; Pris, J

    1993-11-01

    The 5 q deletion is frequently found in myelodysplastic syndromes and acute non lymphoid leukemia, but this anomaly is usually found in secondary diseases and associated with many other chromosomal aberrations. This report describes four cases of "de novo" acute leukemia with a sole 5q- anomaly. They had no cytological, genetic or clinical characteristics of secondary disorders. It is important to note that of the four patients studied, three had proliferation of immature blast cells. One case was classified as a MO AML and two as "undifferentiated" acute leukemia. Furthermore, these four cases of acute leukemia showed a deletion of the same portion of the long arm of chromosome 5: q22q33. On the same part of this chromosome many hematopoietic growth factor genes have been located, like IL3 and GM-CSF which have early undifferentiated hematopoietic stem cells as a their target.

  4. Growth in rice cells requires de novo purine biosynthesis by the blast fungus Magnaporthe oryzae

    Science.gov (United States)

    Fernandez, Jessie; Yang, Kuan Ting; Cornwell, Kathryn M.; Wright, Janet D.; Wilson, Richard A.

    2013-01-01

    Increasing incidences of human disease, crop destruction and ecosystem perturbations are attributable to fungi and threaten socioeconomic progress and food security on a global scale. The blast fungus Magnaporthe oryzae is the most devastating pathogen of cultivated rice, but its metabolic requirements in the host are unclear. Here we report that a purine-requiring mutant of M. oryzae could develop functional appressoria, penetrate host cells and undergo the morphogenetic transition to elaborate bulbous invasive hyphae from primary hyphae, but further in planta growth was aborted. Invasive hyphal growth following rice cell ingress is thus dependent on de novo purine biosynthesis by the pathogen and, moreover, plant sources of purines are neither available to the mutant nor required by the wild type during the early biotrophic phase of infection. This work provides new knowledge about the metabolic interface between fungus and host that might be applicable to other important intracellular fungal pathogens. PMID:23928947

  5. GEODIVERSIDADE, GEOPATRIMÔNIO E GEOTURISMO EM CURRAIS NOVOS, NE DO BRASIL

    Directory of Open Access Journals (Sweden)

    Wendson Dantas de Araújo Medeiros

    2011-01-01

    Full Text Available En este artículo se aborda el asunto de la geodiversidad, geoconservación, geopatrimonio y geoturismo, estudiando el caso de un municipio en el interior del Nordeste brasilero. Se trata de una contribución al debate geográfi co sobre el uso racional y planifi cado de la geodiversidad por el turismo, especialmente el geoturismo. Por lo tanto, se discuten los conceptos de la geodiversidad y geoturismo, tomando como referencia espacial el municipio de Currais Novos/RN, en particular, algunos elementos que se consideran de valor. Por último, se sugieren medidas para uso sostenible de esta geodiversidad, con fi nalidad de obtener una mejor planifi cación e gestión de estas áreas.

  6. Effluents and releases of tritium from Novo-Voronezh-5 reactor

    International Nuclear Information System (INIS)

    Babenko, A.G.; Mekhedov, B.N.; Podporinova, L.E.; Popov, S.V.; Shalin, A.N.

    1990-01-01

    Results of systematic measurements of tritium concentration within technological systems of reactor of Novo-Voronezh NPP conducted to evaluate tritium effluents and releases and radiation doses to population from these effluents and releases are given. It is shown that 68% concerning tritium total amount were disposed into sewerage while 17% - through vent tube and 15% - with water and steam from secondary circuit systems. Standartized tritium effluents from WWER-1000 reactor for 5 year run constitute 15±1.9 GBq/MWxyear and it corresponds to mean value of effluents for foreign NPPs. Tritium concentration in the atmosphere constituted according to calculations (4.1-20)x10 -5 Bq/l. Conclusion is made about insignificant dose to population from tritium gaseous effluents. Detail study is necessary for dose connected with tritium contained in water effluents

  7. Outcomes of de novo and acute decompensated heart failure patients according to ejection fraction.

    Science.gov (United States)

    Choi, Ki Hong; Lee, Ga Yeon; Choi, Jin-Oh; Jeon, Eun-Seok; Lee, Hae-Young; Cho, Hyun-Jai; Lee, Sang Eun; Kim, Min-Seok; Kim, Jae-Joong; Hwang, Kyung-Kuk; Chae, Shung Chull; Baek, Sang Hong; Kang, Seok-Min; Choi, Dong-Ju; Yoo, Byung-Su; Kim, Kye Hun; Park, Hyun-Young; Cho, Myeong-Chan; Oh, Byung-Hee

    2018-03-01

    There are conflicting results among previous studies regarding the prognosis of heart failure with preserved ejection fraction (HFpEF) compared with heart failure with reduced ejection fraction (HFrEF). This study aimed to compare the outcomes of patients with de novo acute heart failure (AHF) or acute decompensated HF (ADHF) according to HFpEF (EF≥50%), or HFrEF (EF<40%) and to define the prognosis of patients with HF with mid-range EF (HFmrEF, 40≤EF<50%). Between March 2011 and February 2014, 5625 consecutive patients with AHF were recruited from 10 university hospitals. A total of 5414 (96.2%) patients with EF data were enrolled, which consisted of 2867 (53.0%) patients with de novo and 2547 (47.0%) with ADHF. Each of the enrolled group was stratified by EF. In de novo, all-cause death rates were not significantly different between HFpEF and HFrEF (HFpEF vs HFrEF, 206/744 (27.7%) vs 438/1631 (26.9%), HR adj 1.15, 95% CI 0.96 to 1.38, p=0.14). However, among patients with ADHF, HFrEF had a significantly higher mortality rate compared with HFpEF (HFpEF vs HFrEF, 245/613 (40.0%) vs 694/1551 (44.7%), HR adj 1.25, 95% CI 1.06 to 1.47, p=0.007). Also, in ADHF, HFmrEF was associated with a significantly lower mortality rate within 1 year compared with HFrEF (HFmrEF vs HFrEF, 88/383 (23.0%) vs 430/1551 (27.7%), HR adj 1.31, 95% CI 1.03 to 1.65, p=0.03), but a significantly higher mortality rate after 1 year compared with HFpEF (HFmrEF vs HFpEF, 83/295 (28.1%) vs 101/469 (21.5%), HR adj 0.70, 95% CI 0.52 to 0.96, p=0.02). HFpEF may indicate a better prognosis compared with HFrEF in ADHF, but not in de novo AHF. For patients with ADHF, the prognosis associated with HFmrEF was similar to that of HFpEF within the first year following hospitalisation and similar to HFrEF 1  year after hospitalisation. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted

  8. Historical outline of 16th century signets: including examples from the Franciscan monastery in Novo mesto

    Directory of Open Access Journals (Sweden)

    Ines Jerele

    2006-01-01

    Full Text Available The library of the Franciscan Monastery in Novo mesto keeps 224 early prints from the 16th century in which 175 printers’ and publishers’ devices were recorded. These were printed between 1501 and 1600 in 88 printers’ workshops across Europe. Printers’ and publishers’ devices, also called signets, were used in the 16th century as trademarks of respective printers and publishers. Spiritual and cultural ideas of the 16th century and intellectual goals of their owners are reflected in the complex humanistic motifs of signets. Most of the 16th century signets can be compared to impresas; they include a symbolic image and a short motto in Latin. This text presents some of the main characteristics of signets registered in Slovenia, such as the meaning, design features and motifs, dating from the early development of print culture in Europe.

  9. De Novo generation of molecular structures using optimization to select graphs on a given lattice

    DEFF Research Database (Denmark)

    Bywater, R.P.; Poulsen, Thomas Agersten; Røgen, Peter

    2004-01-01

    A recurrent problem in organic chemistry is the generation of new molecular structures that conform to some predetermined set of structural constraints that are imposed in an endeavor to build certain required properties into the newly generated structure. An example of this is the pharmacophore...... model, used in medicinal chemistry to guide de novo design or selection of suitable structures from compound databases. We propose here a method that efficiently links up a selected number of required atom positions while at the same time directing the emergent molecular skeleton to avoid forbidden...... positions. The linkage process takes place on a lattice whose unit step length and overall geometry is designed to match typical architectures of organic molecules. We use an optimization method to select from the many different graphs possible. The approach is demonstrated in an example where crystal...

  10. De novo MEIS2 mutation causes syndromic developmental delay with persistent gastro-esophageal reflux.

    Science.gov (United States)

    Fujita, Atsushi; Isidor, Bertrand; Piloquet, Hugues; Corre, Pierre; Okamoto, Nobuhiko; Nakashima, Mitsuko; Tsurusaki, Yoshinori; Saitsu, Hirotomo; Miyake, Noriko; Matsumoto, Naomichi

    2016-09-01

    MEIS2 aberrations are considered to be the cause of intellectual disability, cleft palate and cardiac septal defect, as MEIS2 copy number variation is often observed with these phenotypes. To our knowledge, only one nucleotide-level change-specifically, an in-frame MEIS2 deletion-has so far been reported. Here, we report a female patient with a de novo nonsense mutation (c.611C>G, p.Ser204*) in MEIS2. She showed severe intellectual disability, moderate motor/verbal developmental delay, cleft palate, cardiac septal defect, hypermetropia, severe feeding difficulties with gastro-esophageal reflux and constipation. By reviewing this patient and previous patients with MEIS2 point mutations, we found that feeding difficulty with gastro-esophageal reflux appears to be one of the core clinical features of MEIS2 haploinsufficiency, in addition to intellectual disability, cleft palate and cardiac septal defect.

  11. A de novo SOX10 mutation causing severe type 4 Waardenburg syndrome without Hirschsprung disease.

    Science.gov (United States)

    Sznajer, Yves; Coldéa, Cristina; Meire, Françoise; Delpierre, Isabelle; Sekhara, Tayeb; Touraine, Renaud L

    2008-04-15

    Type 4 Waardenburg syndrome represents a well define entity caused by neural crest derivatives anomalies (melanocytes, intrinsic ganglion cells, central, autonomous and peripheral nervous systems) leading, with variable expressivity, to pigmentary anomalies, deafness, mental retardation, peripheral neuropathy, and Hirschsprung disease. Autosomal dominant mode of inheritance is prevalent when Sox10 gene mutation is identified. We report the natural history of a child who presented with synophrys, vivid blue eye, deafness, bilateral complete semicircular canals agenesis with mental retardation, subtle signs for peripheral neuropathy and lack of Hirschsprung disease. SOX10 gene sequencing identified "de novo" splice site mutation (c.698-2A > C). The present phenotype and the genotype findings underline the wide spectrum of SOX10 gene implication in unusual type 4 Waardenburg syndrome patient. Copyright 2008 Wiley-Liss, Inc.

  12. Globalização: novo paradigma das ciências sociais

    OpenAIRE

    Ianni,Octavio

    1994-01-01

    As ciências sociais estão sendo desafiadas a pensar a globalização do mundo. No fim do século XX, quando se anuncia o XXI, elas se defrontam com os dilemas que se abrem com a globalização das coisas, gentes e idéias. Há processos e estruturas sociais, econômicos, políticos, culturais e outros que apenas começam a ser estudados. Além do que é local, nacional e regional, colocam-se problemas novos e fundamentais com a emergência da sociedade global. As fronteiras geográficas e históricas, cultu...

  13. KeyPathwayMiner - De-novo network enrichment by combining multiple OMICS data and biological networks

    DEFF Research Database (Denmark)

    Baumbach, Jan; Alcaraz, Nicolas; Pauling, Josch K.

    We tackle the problem of de-novo pathway extraction. Given a biological network and a set of case-control studies, KeyPathwayMiner efficiently extracts and visualizes all maximal connected sub-networks that contain mainly genes that are dysregulated, e.g., differentially expressed, in most cases ...

  14. Interstitial deletion 1p as a result of a de novo reciprocal 1p;2p translocation

    DEFF Research Database (Denmark)

    Hertz, Jens Michael; Jensen, P H

    1985-01-01

    A 5-month-old female patient with psychomotor retardation and minor dysmorphisms is described. Cytogenetic analysis using high-resolution banding technique revealed an interstitial deletion of the short arm of one chromosome 1 (p21----p22.2) resulting from a de novo translocation t(1;2)(p22;p25)....

  15. Optic atrophy, cataracts, lipodystrophy/lipoatrophy, and peripheral neuropathy caused by a de novo OPA3 mutation

    OpenAIRE

    Bourne, Stephanie C.; Townsend, Katelin N.; Shyr, Casper; Matthews, Allison; Lear, Scott A.; Attariwala, Raj; Lehman, Anna; Wasserman, Wyeth W.; van Karnebeek, Clara; Sinclair, Graham; Vallance, Hilary; Gibson, William T.

    2017-01-01

    We describe a woman who presented with cataracts, optic atrophy, lipodystrophy/lipoatrophy, and peripheral neuropathy. Exome sequencing identified a c.235C > G p.(Leu79Val) variant in the optic atrophy 3 (OPA3) gene that was confirmed to be de novo. This report expands the severity of the phenotypic spectrum of autosomal dominant OPA3 mutations.

  16. Immobilization of cadmium in soils by UV-mutated Bacillus subtilis 38 bioaugmentation and NovoGro amendment

    International Nuclear Information System (INIS)

    Jiang Chunxiao; Sun Hongwen; Sun Tieheng; Zhang Qingmin; Zhang Yanfeng

    2009-01-01

    Immobilization of cadmium (10 mg Cd per kilogram soil) in soil by bioaugmentation of a UV-mutated microorganism, Bacillus subtilis 38 accompanied with amendment of a bio-fertilizer, NovoGro was investigated using extractable cadmium (E-Cd) by DTPA. B. subtilis 38, the mutant with the strongest resistance against Cd, could bioaccumulate Cd four times greater than the original wild type. Single bioaugmentation of B. subtilis 38 (SB treatment) to soil however did not reduce E-Cd significantly, while the amendment of NovoGro (SN treatment) reduced E-Cd remarkably. Simultaneous application of B. subtilis 38 and NovoGro (SNB treatment) exhibited a synergetic effect compared to the single SB and SN treatment. The immobilization effect was significantly affected by temperature, soil moisture, and pH. It seems that the immobilization on Cd reached the maximum when environmental conditions favored the activity of microorganisms. Under the optimum conditions, after 90 days incubation, E-Cd was 3.34, 3.39, 2.25 and 0.87 mg kg -1 in the control soil, SB, SN and SNB soils, respectively. NovoGro not only showed a great capacity for Cd adsorption, but also promoted the growth of B. subtilis 38. This study provides a potential cost-effective technique for in situ remediation of Cd contaminated soils with bioaugmentation.

  17. Characterization of a de novo duplication of 11p14----p13, using fluorescent in situ hybridization and southern hybridization

    NARCIS (Netherlands)

    Speleman, F.; Mannens, M.; Redeker, B.; Vercruyssen, M.; van Oostveldt, P.; Leroy, J.; Slater, R.

    1991-01-01

    A de novo 11p+ chromosome was found in a child with mild mental retardation but no other remarkable dysmorphic characteristics. Banding studies suggested a duplication of regions 11p13 and 11p14 or regions 11p14 and 11p15. Using fluorescent in situ hybridization and digital imaging microscopy, we

  18. Beroepsdifferentiatie in de tandheelkunde 19 : Het effect van parodontale behandeling op de mate van de novo plaquevorming

    NARCIS (Netherlands)

    Dahan, M; Timmerman, M F; van Winkelhoff, A J; van der Velden, U

    In order to determine whether the quantity of bacteria in saliva and the degree of periodontal infection influence the speed of de novo plaque formation in periodontitis patients, 23 patients rinsed with 10 ml sterile saline. All teeth were then supragingivally and professionally cleaned, after

  19. Integration of CpG-free DNA induces de novo methylation of CpG islands in pluripotent stem cells

    KAUST Repository

    Takahashi, Yuta; Wu, Jun; Suzuki, Keiichiro; Martinez-Redondo, Paloma; Li, Mo; Liao, Hsin-Kai; Wu, Min-Zu; Herná ndez-Bení tez, Reyna; Hishida, Tomoaki; Shokhirev, Maxim Nikolaievich; Esteban, Concepcion Rodriguez; Sancho-Martinez, Ignacio; Belmonte, Juan Carlos Izpisua

    2017-01-01

    that insertion of CpG-free DNA into targeted CGIs induces de novo methylation of the entire CGI in human pluripotent stem cells (PSCs). The methylation status is stably maintained even after CpG-free DNA removal, extensive passaging, and differentiation

  20. Radiotherapy, especially at young age, increases the risk for de novo brain tumors in patients treated for pituitary tumors

    NARCIS (Netherlands)

    Burman, Pia; Van Beek, André P.; Biller, Beverly M.K.; Camacho-Hubner, Cecilia; Mattsson, Anders F.

    Background: Excess mortality due to de novo malignant brain tumors was recently found in a national study of patients with hypopituitarism following treatment of pituitary tumors. Here, we examined a larger multi-national cohort to corroborate and extend this observation. Objective: To investigate

  1. Dysplastic vs. Common Naevus-associated vs. De novo Melanomas: An Observational Retrospective Study of 1,021 Patients

    Directory of Open Access Journals (Sweden)

    Alejandro Martin-Gorgojo

    2018-03-01

    Full Text Available The aim of this case-case study was to determine the differences between dysplastic and common naevus-associated melanomas (NAM and de novo melanomas. A total of 1,021 prospectively collected patients with invasive cutaneous melanoma from an oncology referral centre were included in the study. Of these, 75.51% had de novo melanomas, 12.93% dysplastic NAM, and 11.56% common NAM. Dysplastic NAM, compared with de novo melanomas, were associated with intermittently photo-exposed sites, atypical melanocytic naevi, decreased tumour thickness, and presence of MC1R non-synonymous variants. Common NAM were more frequent on the trunk and of superficial spreading type. Comparison of dysplastic with common NAM showed significant difference only with regard to mitoses. Both subtypes of NAM shared less aggressive traits than de novo melanomas, albeit with no significant differences in survival after multivariate adjustment. In conclusion, NAM present with less aggressive traits, mostly due to a greater awareness among patients of changing moles than due to their intrinsic biological characteristics.

  2. De Novo whole genome sequence of Xylella fastidiosa subsp. multiplex strain BB01 from blueberry in Georgia, USA

    Science.gov (United States)

    This study reports a de novo assembled draft genome sequence of Xylella fastidiosa subsp. multiplex strain BB01 causing blueberry bacterial leaf scorch in Georgia, USA. The BB01 genome is 2,517,579 bp with a G+C content of 51.8% and 2,943 open reading frames (ORFs) and 48 RNA genes....

  3. Effect of Reaction Time on PCDD and PCDF Formation by De novo Synthetic Reactions under Oxygen Deficient and Rich Atmosphere

    Czech Academy of Sciences Publication Activity Database

    Grabic, R.; Pekárek, Vladimír; Ullrich, Jan; Punčochář, Miroslav; Fišerová, Eva; Karban, Jindřich; Šebestová, M.

    2002-01-01

    Roč. 49, č. 7 (2002), s. 691-696 ISSN 0045-6535 R&D Projects: GA ČR GA104/97/S002; GA AV ČR IAA4072901 Keywords : activated carbon * Copper chloride * de novo synthesis Subject RIV: CC - Organic Chemistry Impact factor: 1.461, year: 2002

  4. Trends in presentation, management and survival of patients with de novo metastatic breast cancer in a Southeast Asian setting

    NARCIS (Netherlands)

    Bhoo Pathy, Nirmala; Verkooijen, Helena Marieke; Tan, Ern-Yu; Miao, Hui; Taib, Nur Aishah Mohd; Brand, Judith S.; Dent, Rebecca A.; See, Mee-Hoong; Subramaniam, ShriDevi; Chan, Patrick; Lee, Soo-Chin; Hartman, Mikael; Yip, Cheng-Har

    2015-01-01

    Up to 25% of breast cancer patients in Asia present with de novo metastatic disease. We examined the survival trends of Asian patients with metastatic breast cancer over fifteen years. The impact of changes in patient's demography, tumor characteristics, tumor burden, and treatment on survival trend

  5. Effects of Stress, Reactive Oxygen Species, and the SOS Response on De Novo Acquisition of Antibiotic Resistance in Escherichia coli

    NARCIS (Netherlands)

    Händel, N.; Hoeksema, M.; Freijo Mata, M.; Brul, S.; ter Kuile, B.H.

    2015-01-01

    Strategies to prevent the development of antibiotic resistance in bacteria are needed to reduce the threat of infectious diseases to human health. The de novo acquisition of resistance due to mutations and/or phenotypic adaptation occurs rapidly as a result of interactions of gene expression and

  6. Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly

    DEFF Research Database (Denmark)

    Li, Yingrui; Zheng, Hancheng; Luo, Ruibang

    2011-01-01

    Here we use whole-genome de novo assembly of second-generation sequencing reads to map structural variation (SV) in an Asian genome and an African genome. Our approach identifies small- and intermediate-size homozygous variants (1-50 kb) including insertions, deletions, inversions and their precise...

  7. Batch-processing of imaging or liquid-chromatography mass spectrometry datasets and De Novo sequencing of polyketide siderophores

    Czech Academy of Sciences Publication Activity Database

    Novák, Jiří; Sokolová, Lucie; Lemr, Karel; Pluháček, Tomáš; Palyzová, Andrea; Havlíček, Vladimír

    2017-01-01

    Roč. 1865, č. 7 (2017), s. 768-775 ISSN 1570-9639 R&D Projects: GA ČR(CZ) GA16-20229S; GA MŠk(CZ) LO1509 Institutional support: RVO:61388971 Keywords : Mass spectrometry imaging * De novo sequencing * Siderophores Subject RIV: EE - Microbiology, Virology OBOR OECD: Microbiology Impact factor: 2.773, year: 2016

  8. Improved protein quality in transgenic soybean expressing a de novo synthetic protein, MB-16.

    Science.gov (United States)

    Zhang, Yunfang; Schernthaner, Johann; Labbé, Natalie; Hefford, Mary A; Zhao, Jiping; Simmonds, Daina H

    2014-06-01

    To improve soybean [Glycine max (L.) Merrill] seed nutritional quality, a synthetic gene, MB-16 was introduced into the soybean genome to boost seed methionine content. MB-16, an 11 kDa de novo protein enriched in the essential amino acids (EAAs) methionine, threonine, lysine and leucine, was originally developed for expression in rumen bacteria. For efficient seed expression, constructs were designed using the soybean codon bias, with and without the KDEL ER retention sequence, and β-conglycinin or cruciferin seed specific protein storage promoters. Homozygous lines, with single locus integrations, were identified for several transgenic events. Transgene transmission and MB-16 protein expression were confirmed to the T5 and T7 generations, respectively. Quantitative RT-PCR analysis of developing seed showed that the transcript peaked in growing seed, 5-6 mm long, remained at this peak level to the full-sized green seed and then was significantly reduced in maturing yellow seed. Transformed events carrying constructs with the rumen bacteria codon preference showed the same transcription pattern as those with the soybean codon preference, but the transcript levels were lower at each developmental stage. MB-16 protein levels, as determined by immunoblots, were highest in full-sized green seed but the protein virtually disappeared in mature seed. However, amino acid analysis of mature seed, in the best transgenic line, showed a significant increase of 16.2 and 65.9 % in methionine and cysteine, respectively, as compared to the parent. This indicates that MB-16 elevated the sulfur amino acids, improved the EAA seed profile and confirms that a de novo synthetic gene can enhance the nutritional quality of soybean.

  9. Novo tipo de evaporímetro terrestre A new type of evaporimeter

    Directory of Open Access Journals (Sweden)

    Rino N. Tosello

    1960-01-01

    Full Text Available No presente trabalho descreve-se um novo tipo de evaporímetro, cujo princípio de funcionamento está baseado em leis físicas que regem o fenômeno de tensão superficial. Neste tipo de evaporímetro a medida da evaporação é feita por processo volumétrieo, dispensando o emprego de mecanismos de precisão e dispendiosos. Foi feita uma análise matemática do princípio de funcionamento do novo evaporímetro, demonstrando-se oferecer exatidão plenamente satisfatória para propósitos práticos. São dados suficientes detalhes construtivos, de instalação e operação, a fim de permitir que pessoas e entidades interessadas possam reproduzi-lo e comprovar as vantagens de seu emprêgo.In this paper is described a new type of evaporimeter, the principle of operation of which is based on physical laws governing the surface tension phenomenon. The measurement of evaporation in, the new evaporimeter, described as Evaporimeter IA-58, is made by simple volumetric procedure, thus avoiding the use of precise and expensive mechanisms. A mathematical analysis of the principle of operation is made, and proves that the new evaporimeter can offer satisfactory xeaults for practical use. The operation of the new evaporimeter is very simple, since only volumetric measurements are made, with a graduated cylinder of 1000 ml, both of the added water to restore the water level to the same initial level and the outflown or excess water. It is believed that enough details are given to allow the understanding of the construction, installation and operation of the new evaporimeter, bo that interested persons or organizations could have the model reproduced and verify the advantage of its use.

  10. Categorização de questões de Física do novo ENEM

    Directory of Open Access Journals (Sweden)

    Jesusney Silva Hernandes

    2013-04-01

    Full Text Available http://dx.doi.org/10.5007/2175-7941.2013v30n1p58 Este artigo estuda questões que envolvem Física nas provas de Ciências da Natureza e suas Tecnologias do novo ENEM. Selecionamos itens que evidenciam alguma Física nestas provas. Classificamos as questões por Competência e Habilidade segundo a matriz de referência do Exame e, através da análise de conteúdo de Bardin (2010, propusemos, para cada grupo de itens inseridos em uma dada competência, um agrupamento em categorias. A partir da observação e reflexão das categorias emergentes apresentamos ao longo do texto orientações sobre características das situações-problema que abordam alguma Física no novo ENEM. Além disso, através da análise das categorias emergentes, procuramos avaliar a aproximação das questões selecionadas com as orientações presentes nos Parâmetros Curriculares Nacionais para o Ensino Médio (PCNEM, nas Orientações Complementares aos Parâmetros Curriculares Nacionais (PCN+ e nas Orientações Curriculares para o Ensino Médio (OCEM. Percebemos que muitas orientações que surgiram das categorias emergentes atendem às orientações dos PCN, PCN+ e OCEM. Esperamos que nossa pesquisa possa contribuir para o alinhamento da prática docente com um ensino de Física inovador pautado no desenvolvimento de competências e habilidades, viabilizando melhoria de aprendizado e, consequentemente, de desempenho em Exames como o ENEM.

  11. Algorithm for selection of optimized EPR distance restraints for de novo protein structure determination

    Science.gov (United States)

    Kazmier, Kelli; Alexander, Nathan S.; Meiler, Jens; Mchaourab, Hassane S.

    2010-01-01

    A hybrid protein structure determination approach combining sparse Electron Paramagnetic Resonance (EPR) distance restraints and Rosetta de novo protein folding has been previously demonstrated to yield high quality models (Alexander et al., 2008). However, widespread application of this methodology to proteins of unknown structures is hindered by the lack of a general strategy to place spin label pairs in the primary sequence. In this work, we report the development of an algorithm that optimally selects spin labeling positions for the purpose of distance measurements by EPR. For the α-helical subdomain of T4 lysozyme (T4L), simulated restraints that maximize sequence separation between the two spin labels while simultaneously ensuring pairwise connectivity of secondary structure elements yielded vastly improved models by Rosetta folding. 50% of all these models have the correct fold compared to only 21% and 8% correctly folded models when randomly placed restraints or no restraints are used, respectively. Moreover, the improvements in model quality require a limited number of optimized restraints, the number of which is determined by the pairwise connectivities of T4L α-helices. The predicted improvement in Rosetta model quality was verified by experimental determination of distances between spin labels pairs selected by the algorithm. Overall, our results reinforce the rationale for the combined use of sparse EPR distance restraints and de novo folding. By alleviating the experimental bottleneck associated with restraint selection, this algorithm sets the stage for extending computational structure determination to larger, traditionally elusive protein topologies of critical structural and biochemical importance. PMID:21074624

  12. De Novo Biosynthesis of Vanillin in Fission Yeast (Schizosaccharomyces pombe) and Baker's Yeast (Saccharomyces cerevisiae) ▿

    Science.gov (United States)

    Hansen, Esben H.; Møller, Birger Lindberg; Kock, Gertrud R.; Bünner, Camilla M.; Kristensen, Charlotte; Jensen, Ole R.; Okkels, Finn T.; Olsen, Carl E.; Motawia, Mohammed S.; Hansen, Jørgen

    2009-01-01

    Vanillin is one of the world's most important flavor compounds, with a global market of 180 million dollars. Natural vanillin is derived from the cured seed pods of the vanilla orchid (Vanilla planifolia), but most of the world's vanillin is synthesized from petrochemicals or wood pulp lignins. We have established a true de novo biosynthetic pathway for vanillin production from glucose in Schizosaccharomyces pombe, also known as fission yeast or African beer yeast, as well as in baker's yeast, Saccharomyces cerevisiae. Productivities were 65 and 45 mg/liter, after introduction of three and four heterologous genes, respectively. The engineered pathways involve incorporation of 3-dehydroshikimate dehydratase from the dung mold Podospora pauciseta, an aromatic carboxylic acid reductase (ACAR) from a bacterium of the Nocardia genus, and an O-methyltransferase from Homo sapiens. In S. cerevisiae, the ACAR enzyme required activation by phosphopantetheinylation, and this was achieved by coexpression of a Corynebacterium glutamicum phosphopantetheinyl transferase. Prevention of reduction of vanillin to vanillyl alcohol was achieved by knockout of the host alcohol dehydrogenase ADH6. In S. pombe, the biosynthesis was further improved by introduction of an Arabidopsis thaliana family 1 UDP-glycosyltransferase, converting vanillin into vanillin β-d-glucoside, which is not toxic to the yeast cells and thus may be accumulated in larger amounts. These de novo pathways represent the first examples of one-cell microbial generation of these valuable compounds from glucose. S. pombe yeast has not previously been metabolically engineered to produce any valuable, industrially scalable, white biotech commodity. PMID:19286778

  13. The microaerophilic microbiota of de-novo paediatric inflammatory bowel disease: the BISCUIT study.

    Directory of Open Access Journals (Sweden)

    Richard Hansen

    Full Text Available Children presenting for the first time with inflammatory bowel disease (IBD offer a unique opportunity to study aetiological agents before the confounders of treatment. Microaerophilic bacteria can exploit the ecological niche of the intestinal epithelium; Helicobacter and Campylobacter are previously implicated in IBD pathogenesis. We set out to study these and other microaerophilic bacteria in de-novo paediatric IBD.100 children undergoing colonoscopy were recruited including 44 treatment naïve de-novo IBD patients and 42 with normal colons. Colonic biopsies were subjected to microaerophilic culture with Gram-negative isolates then identified by sequencing. Biopsies were also PCR screened for the specific microaerophilic bacterial groups: Helicobacteraceae, Campylobacteraceae and Sutterella wadsworthensis.129 Gram-negative microaerophilic bacterial isolates were identified from 10 genera. The most frequently cultured was S. wadsworthensis (32 distinct isolates. Unusual Campylobacter were isolated from 8 subjects (including 3 C. concisus, 1 C. curvus, 1 C. lari, 1 C. rectus, 3 C. showae. No Helicobacter were cultured. When comparing IBD vs. normal colon control by PCR the prevalence figures were not significantly different (Helicobacter 11% vs. 12%, p = 1.00; Campylobacter 75% vs. 76%, p = 1.00; S. wadsworthensis 82% vs. 71%, p = 0.312.This study offers a comprehensive overview of the microaerophilic microbiota of the paediatric colon including at IBD onset. Campylobacter appear to be surprisingly common, are not more strongly associated with IBD and can be isolated from around 8% of paediatric colonic biopsies. S. wadsworthensis appears to be a common commensal. Helicobacter species are relatively rare in the paediatric colon.This study is publically registered on the United Kingdom Clinical Research Network Portfolio (9633.

  14. A de novo variant in the ASPRV1 gene in a dog with ichthyosis.

    Science.gov (United States)

    Bauer, Anina; Waluk, Dominik P; Galichet, Arnaud; Timm, Katrin; Jagannathan, Vidhya; Sayar, Beyza S; Wiener, Dominique J; Dietschi, Elisabeth; Müller, Eliane J; Roosje, Petra; Welle, Monika M; Leeb, Tosso

    2017-03-01

    Ichthyoses are a heterogeneous group of inherited cornification disorders characterized by generalized dry skin, scaling and/or hyperkeratosis. Ichthyosis vulgaris is the most common form of ichthyosis in humans and caused by genetic variants in the FLG gene encoding filaggrin. Filaggrin is a key player in the formation of the stratum corneum, the uppermost layer of the epidermis and therefore crucial for barrier function. During terminal differentiation of keratinocytes, the precursor profilaggrin is cleaved by several proteases into filaggrin monomers and eventually processed into free amino acids contributing to the hydration of the cornified layer. We studied a German Shepherd dog with a novel form of ichthyosis. Comparing the genome sequence of the affected dog with 288 genomes from genetically diverse non-affected dogs we identified a private heterozygous variant in the ASPRV1 gene encoding "aspartic peptidase, retroviral-like 1", which is also known as skin aspartic protease (SASPase). The variant was absent in both parents and therefore due to a de novo mutation event. It was a missense variant, c.1052T>C, affecting a conserved residue close to an autoprocessing cleavage site, p.(Leu351Pro). ASPRV1 encodes a retroviral-like protease involved in profilaggrin-to-filaggrin processing. By immunofluorescence staining we showed that the filaggrin expression pattern was altered in the affected dog. Thus, our findings provide strong evidence that the identified de novo variant is causative for the ichthyosis in the affected dog and that ASPRV1 plays an essential role in skin barrier formation. ASPRV1 is thus a novel candidate gene for unexplained human forms of ichthyoses.

  15. A de novo variant in the ASPRV1 gene in a dog with ichthyosis.

    Directory of Open Access Journals (Sweden)

    Anina Bauer

    2017-03-01

    Full Text Available Ichthyoses are a heterogeneous group of inherited cornification disorders characterized by generalized dry skin, scaling and/or hyperkeratosis. Ichthyosis vulgaris is the most common form of ichthyosis in humans and caused by genetic variants in the FLG gene encoding filaggrin. Filaggrin is a key player in the formation of the stratum corneum, the uppermost layer of the epidermis and therefore crucial for barrier function. During terminal differentiation of keratinocytes, the precursor profilaggrin is cleaved by several proteases into filaggrin monomers and eventually processed into free amino acids contributing to the hydration of the cornified layer. We studied a German Shepherd dog with a novel form of ichthyosis. Comparing the genome sequence of the affected dog with 288 genomes from genetically diverse non-affected dogs we identified a private heterozygous variant in the ASPRV1 gene encoding "aspartic peptidase, retroviral-like 1", which is also known as skin aspartic protease (SASPase. The variant was absent in both parents and therefore due to a de novo mutation event. It was a missense variant, c.1052T>C, affecting a conserved residue close to an autoprocessing cleavage site, p.(Leu351Pro. ASPRV1 encodes a retroviral-like protease involved in profilaggrin-to-filaggrin processing. By immunofluorescence staining we showed that the filaggrin expression pattern was altered in the affected dog. Thus, our findings provide strong evidence that the identified de novo variant is causative for the ichthyosis in the affected dog and that ASPRV1 plays an essential role in skin barrier formation. ASPRV1 is thus a novel candidate gene for unexplained human forms of ichthyoses.

  16. The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads.

    Science.gov (United States)

    Wang, Zhiwen; Hobson, Neil; Galindo, Leonardo; Zhu, Shilin; Shi, Daihu; McDill, Joshua; Yang, Linfeng; Hawkins, Simon; Neutelings, Godfrey; Datla, Raju; Lambert, Georgina; Galbraith, David W; Grassa, Christopher J; Geraldes, Armando; Cronk, Quentin C; Cullis, Christopher; Dash, Prasanta K; Kumar, Polumetla A; Cloutier, Sylvie; Sharpe, Andrew G; Wong, Gane K-S; Wang, Jun; Deyholos, Michael K

    2012-11-01

    Flax (Linum usitatissimum) is an ancient crop that is widely cultivated as a source of fiber, oil and medicinally relevant compounds. To accelerate crop improvement, we performed whole-genome shotgun sequencing of the nuclear genome of flax. Seven paired-end libraries ranging in size from 300 bp to 10 kb were sequenced using an Illumina genome analyzer. A de novo assembly, comprised exclusively of deep-coverage (approximately 94× raw, approximately 69× filtered) short-sequence reads (44-100 bp), produced a set of scaffolds with N(50) =694 kb, including contigs with N(50)=20.1 kb. The contig assembly contained 302 Mb of non-redundant sequence representing an estimated 81% genome coverage. Up to 96% of published flax ESTs aligned to the whole-genome shotgun scaffolds. However, comparisons with independently sequenced BACs and fosmids showed some mis-assembly of regions at the genome scale. A total of 43384 protein-coding genes were predicted in the whole-genome shotgun assembly, and up to 93% of published flax ESTs, and 86% of A. thaliana genes aligned to these predicted genes, indicating excellent coverage and accuracy at the gene level. Analysis of the synonymous substitution rates (K(s) ) observed within duplicate gene pairs was consistent with a recent (5-9 MYA) whole-genome duplication in flax. Within the predicted proteome, we observed enrichment of many conserved domains (Pfam-A) that may contribute to the unique properties of this crop, including agglutinin proteins. Together these results show that de novo assembly, based solely on whole-genome shotgun short-sequence reads, is an efficient means of obtaining nearly complete genome sequence information for some plant species. © 2012 The Authors. The Plant Journal © 2012 Blackwell Publishing Ltd.

  17. Characterization and analysis of a de novo transcriptome from the pygmy grasshopper Tetrix japonica.

    Science.gov (United States)

    Qiu, Zhongying; Liu, Fei; Lu, Huimeng; Huang, Yuan

    2017-05-01

    The pygmy grasshopper Tetrix japonica is a common insect distributed throughout the world, and it has the potential for use in studies of body colour polymorphism, genomics and the biology of Tetrigoidea (Insecta: Orthoptera). However, limited biological information is available for this insect. Here, we conducted a de novo transcriptome study of adult and larval T. japonica to provide a better understanding of its gene expression and develop genomic resources for future work. We sequenced and explored the characteristics of the de novo transcriptome of T. japonica using Illumina HiSeq 2000 platform. A total of 107 608 206 paired-end clean reads were assembled into 61 141 unigenes using the trinity software; the mean unigene size was 771 bp, and the N50 length was 1238 bp. A total of 29 225 unigenes were functionally annotated to the NCBI nonredundant protein sequences (Nr), NCBI nonredundant nucleotide sequences (Nt), a manually annotated and reviewed protein sequence database (Swiss-Prot), Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. A large number of putative genes that are potentially involved in pigment pathways, juvenile hormone (JH) metabolism and signalling pathways were identified in the T. japonica transcriptome. Additionally, 165 769 and 156 796 putative single nucleotide polymorphisms occurred in the adult and larvae transcriptomes, respectively, and a total of 3162 simple sequence repeats were detected in this assembly. This comprehensive transcriptomic data for T. japonica will provide a usable resource for gene predictions, signalling pathway investigations and molecular marker development for this species and other pygmy grasshoppers. © 2016 John Wiley & Sons Ltd.

  18. Outcomes of kidney transplant tourism and risk factors for de novo urothelial carcinoma.

    Science.gov (United States)

    Tsai, Hsin-Lin; Chang, Jei-Wen; Wu, Tsai-Hun; King, Kuang-Liang; Yang, Ling-Yu; Chan, Yu-Jiun; Yang, An-Hang; Chang, Fu-Pang; Pan, Chin-Chen; Yang, Wu-Chang; Loong, Che-Chuan

    2014-07-15

    To date, the outcomes of transplant tourism have not been reported extensively. In addition, data about the accuracy of urine cytology for the detection and the role of the BK virus (BKV) in the carcinogenesis of urothelial carcinoma (UC) after renal transplantation are lacking. Three hundred seven patients who received deceased donor kidney transplants between January 2003 and December 2009 were retrospectively studied. The clinical parameters and outcomes between the domestic and tourist groups were compared. We also investigated the risk factors and role of BKV in the carcinogenesis of de novo UC by quantitative real-time polymerase chain reaction. The subjects in the tourist group were older at transplantation and had a shorter dialysis time before transplantation. There were significantly higher incidence rates of BKV viruria, Pneumocystis jiroveci pneumonia, and malignancy in the tourist group. Graft and patient survival were superior in the domestic group. A total of 43 cancers were identified, and the most common type of malignancy was UC (23 patients, 53.5%). The tourist group had a significantly higher incidence of tumors. The sensitivity and specificity of urine cytology for detecting UC were 73.9% and 94.7%, respectively. Independent predictors of UC included female sex, use of Chinese herbal medicine, and transplant tourism. Only two patients (8.7%) with UC had detectable BKV. Transplant tourism was a risk factor for infection and de novo malignancy. Urothelial carcinoma was the most common malignancy after kidney transplantation. Regular screening for the early detection of UC by urine cytology or periodic sonographic surveys is mandatory, especially for those at high risk.

  19. De novo peptide design and experimental validation of histone methyltransferase inhibitors.

    Directory of Open Access Journals (Sweden)

    James Smadbeck

    Full Text Available Histones are small proteins critical to the efficient packaging of DNA in the nucleus. DNA–protein complexes, known as nucleosomes, are formed when the DNA winds itself around the surface of the histones. The methylation of histone residues by enhancer of zeste homolog 2 (EZH2 maintains gene repression over successive cell generations. Overexpression of EZH2 can silence important tumor suppressor genes leading to increased invasiveness of many types of cancers. This makes the inhibition of EZH2 an important target in the development of cancer therapeutics. We employed a three-stage computational de novo peptide design method to design inhibitory peptides of EZH2. The method consists of a sequence selection stage and two validation stages for fold specificity and approximate binding affinity. The sequence selection stage consists of an integer linear optimization model that was solved to produce a rank-ordered list of amino acid sequences with increased stability in the bound peptide-EZH2 structure. These sequences were validated through the calculation of the fold specificity and approximate binding affinity of the designed peptides. Here we report the discovery of novel EZH2 inhibitory peptides using the de novo peptide design method. The computationally discovered peptides were experimentally validated in vitro using dose titrations and mechanism of action enzymatic assays. The peptide with the highest in vitro response, SQ037, was validated in nucleo using quantitative mass spectrometry-based proteomics. This peptide had an IC50 of 13.5 mM, demonstrated greater potency as an inhibitor when compared to the native and K27A mutant control peptides, and demonstrated competitive inhibition versus the peptide substrate. Additionally, this peptide demonstrated high specificity to the EZH2 target in comparison to other histone methyltransferases. The validated peptides are the first computationally designed peptides that directly inhibit EZH2

  20. De novo peptide design and experimental validation of histone methyltransferase inhibitors.

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    James Smadbeck

    Full Text Available Histones are small proteins critical to the efficient packaging of DNA in the nucleus. DNA-protein complexes, known as nucleosomes, are formed when the DNA winds itself around the surface of the histones. The methylation of histone residues by enhancer of zeste homolog 2 (EZH2 maintains gene repression over successive cell generations. Overexpression of EZH2 can silence important tumor suppressor genes leading to increased invasiveness of many types of cancers. This makes the inhibition of EZH2 an important target in the development of cancer therapeutics. We employed a three-stage computational de novo peptide design method to design inhibitory peptides of EZH2. The method consists of a sequence selection stage and two validation stages for fold specificity and approximate binding affinity. The sequence selection stage consists of an integer linear optimization model that was solved to produce a rank-ordered list of amino acid sequences with increased stability in the bound peptide-EZH2 structure. These sequences were validated through the calculation of the fold specificity and approximate binding affinity of the designed peptides. Here we report the discovery of novel EZH2 inhibitory peptides using the de novo peptide design method. The computationally discovered peptides were experimentally validated in vitro using dose titrations and mechanism of action enzymatic assays. The peptide with the highest in vitro response, SQ037, was validated in nucleo using quantitative mass spectrometry-based proteomics. This peptide had an IC50 of 13.5 [Formula: see text]M, demonstrated greater potency as an inhibitor when compared to the native and K27A mutant control peptides, and demonstrated competitive inhibition versus the peptide substrate. Additionally, this peptide demonstrated high specificity to the EZH2 target in comparison to other histone methyltransferases. The validated peptides are the first computationally designed peptides that directly